Normalization procedures and reference material selection in stable HCNOS isotope analyses: an overview

The uncertainties of stable isotope results depend not only on the technical aspects of measurements, but also on how raw data are normalized to one of the international isotope scales. The inconsistency in the normalization methods used and in the selection of standards may lead to substantial differences in the results obtained. Therefore, unification of the data processing protocols employed is highly desirable. The best performing methods are two-point or multipoint normalization methods based on linear regression. Linear regression is most robust when based on standards that cover the entire range of δ values typically observed in nature, regardless of the δ values of the samples analysed. The uncertainty can be reduced by 50 % if measurements of two different standards are performed four times, or measurements of four standards are performed twice, with each batch of samples. Chemical matrix matching between standards and samples seems to be critical for δ ¹⁸O of nitrate or δ ²H of hair samples (thermal conversion/elemental analyser), for example; however, it is not necessarily always critical for all types of samples and techniques (e.g. not for most δ ¹⁵N and δ ¹³C elemental analyser analyses). To ensure that all published data can be recalculated, if δ values of standards or the isotope scales are to be updated, the details of the normalization technique and the δ values of the standards used should always be clearly reported.     

Prosthetic heme modification during halide ion oxidation. Demonstration of chloride oxidation by horseradish peroxidase

Myeloperoxidase (MPO), eosinophil peroxidase (EPO), and chloroperoxidase can oxidize iodide, bromide, and chloride, but most peroxidases, including the prototypical horseradish peroxidase (HRP), reportedly only oxidize iodide and, in some cases, bromide. We report here that incubation of HRP with Br(-) and H(2)O(2) at acidic pH results in both bromination of monochlorodimedone and modification of the heme group. Mass spectrometry indicates that the heme 2- and 4-vinyl groups are modified by either replacement of a vinyl hydrogen by a bromide or addition of HOBr to give a bromohydrin. These reactions do not occur if protein-free heme and Br(-) are co-incubated with H(2)O(2) or if the HRP reaction is carried out at pH 7. Surprisingly, similar prosthetic heme modifications occur in incubations of HRP with H(2)O(2) and Cl(-). A mechanism is proposed involving oxidation of Br(-) or Cl(-) to give HOBr or HOCl, respectively, followed by addition to a vinyl group. In the reaction with Cl(-), a meso-chloro heme adduct is also formed. This first demonstration of Cl(-) oxidation by HRP, and the finding that prosthetic heme modification occurs when Br(-) or Cl(-) is oxidized in the absence of a cosubstrate, show that only modest tuning is required to achieve the unique chloride oxidation activity of MPO and EPO. The results raise the question of how the prosthetic hemes of MPO and EPO, whose function is to produce oxidized halide species, escape modification.     

Thio Analogues of Pyrimidine Bases: Syntheses and Spectral Study of New Potentially Biologically Active 2,4-Di-Ortho-(Meta- and Para-)Bromo- (Chloro and Nitro)-Benzylthio-5-Bromouracils (and 6-Methyluracils)

Eighteen new 2,4-di-ortho- (meta- and para-) bromo-(chloro- and nitro-)benzylthio-5-bromouracils (and 6-methyluracils) have been prepared. The structures of these compounds were confirmed by spectral (IR, UV/vis, ¹H NMR) and elemental analyses. Estimation of pharmacotherapeutic potential has been made for synthesized compounds on the basis of prediction of activity spectra for substances (PASS).     

Stability of Ibuprofen in its Inclusion Complex with β-Cyclodextrin

The ibuprofen--cyclodextrin inclusion complex was prepared by theco-precipitation method. The identity of the obtained product was verified by X-ray and thermogravimetric techniques. The effect of -cyclodextrin on the stability of ibuprofen was analysed.     

Model studies of the optical rotation,and theoretical determination of its sign for β‐pinene and trans‐pinane

We have carried out extensive studies on the basis set dependence of the calculated specific optical rotation (OR) in molecules at the level of the time–dependent Hartree–Fock and density functional approximations. To reach the limits of the basis set saturation, we have devised an artificial model, the asymmetrically deformed (chiral) methane (CM) molecule. This small system permits to use basis sets which are prohibitively large for real chiral molecules and yet shows all the important features of the basis set dependence of the OR values. The convergence of the OR has been studied with n‐aug‐cc‐pVXZ basis sets of Dunning up to the 6–ζ. In a parallel series of calculations, we have used the recently developed large polarized (LPolX) basis sets. The relatively small LPolX sets have been shown to be competitive to very large n‐aug‐cc‐pVXZ basis sets. The conclusions reached in calculations of OR in CM concerning the usefulness of LPolX basis sets have been further tested on (S)‐methyloxirane and (S)‐fluoro‐oxirane. The smallest set of the LPolX family (LPol–ds) has been found to yield OR values of similar quality as those obtained with much larger Dunning's aug‐cc‐pVQZ basis set. These results have encouraged us to carry out the OR calculations with LPol–ds basis sets for systems as large as β‐pinene and trans‐pinane. In both cases, our calculations have lead to the correct sign of the OR value in these molecules. This makes the relatively small LPol–ds basis sets likely to be useful in OR calculations for large molecules. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Circular logic: nonribosomal peptide-like macrocyclization with a ribosomal peptide catalyst

A protease from ribosomal peptide biosynthesis macrocyclizes diverse substrates, including those resembling nonribosomal peptide and hybrid polyketide-peptide products. The proposed mechanism is analogous to thioesterase-catalyzed chemistry, but the substrates are amide bonds rather than thioesters.     

Solid state NMR spectroscopy as a precise tool for assigning the tautomeric form and proton position in the intramolecular bridges of o-hydroxy Schiff bases

Two analogous Schiff bases, (S,E)-2-((1-hydroxy-3-methyl-1,1-diphenylbutan-2-ylimino)methyl)phenol (1) and (S,Z)-2-hydroxy-6-((1-hydroxy-3-methyl-1,1-diphenylbutan-2-ylamino)methylene)cyclohexa-2,4-dienone (2), exist in the solid state as phenol-imine and keto-amine tautomers, respectively. Their crystal structures were solved using the X-ray diffraction method. Sample 1 forms orthorhombic crystals of space group P2(1)2(1)2(1), while 2 forms monoclinic crystals of space group P2(1). In each sample, one molecule is in the asymmetric unit of the crystal structure. One-dimensional and two-dimensional solid state NMR techniques were used for structure assignment and for inspection of the (13)C and (15)N δ(ii) of the chemical shift tensor (CST) values. NMR study indicates that the span (Ω = δ(11)-δ(33)) and the skew (κ = 3(δ(22)-δ(iso)/Ω) are extremely sensitive to change in the tautomeric form of the Schiff bases. Theoretical calculations of NMR shielding parameters for 1 and 2 and a model compound with reduced aliphatic residue were performed using the GIAO method with B3LYP functional and 6-311++g(d,p) basis sets. From comparative analysis of the experimental and theoretical parameters, it was concluded that the position of hydrogen in the intramolecular bridge has tremendous influence on (13)C and (15)N CST parameters. Inspection of Ω and κ parameters allowed for the establishment of the nature of the hydrogen bonding and the assignment of the equilibrium proton position in the intramolecular bridges in the solid state.     

Synthesis of β-amino-α-trifluoromethyl alcohols and their applications in organic synthesis

A comprehensive overview on methods applied for syntheses of β-amino-α-trifluoromethyl alcohols, including stereocontrolled variants, is presented. In addition, reported cases of the exploration of β-amino-α-trifluoromethyl alcohols for the preparation of trifluoromethylated peptidomimetics and other biologically active, fluorinated compounds are discussed. Attractive opportunities for their applications as organocatalysts are also presented.     

Structure and atropisomerisation of new diastereomeric gossypol Schiff bases with (R)-(+)-2-amino-3-benzyloxy-1-propanol studied by NMR,ECD and DFT methods

Gossypol Schiff base with (R)-(+)-2-amino-3-benzyloxy-1-propanol 1 was synthesised and resolved by HPLC method into diastereomers to study their atropisomerisation process. The spectroscopic analysis performed by one- and two-dimensional NMR, UV–vis and FT-IR methods indicated that the compound exists in solution as an enamine-oxo tautomer. The ECD measurements and TD-DFT calculations allowed us to unambiguously determine the configuration about the axially chiral biaryl moiety of 1. The conditions of the atropisomerisation processes of diastereopure gossypol Schiff bases (S_AX,R)-1 and (R_AX,R)-1 were determined on the basis of ECD and NMR measurements. Exposure of the diastereomers of 1 to sunlight and to the light at λ = 254 nm significantly accelerated the atropisomerisation when compared to its rate in the dark.     

Determination of selenomethionine, selenocysteine, and inorganic selenium in eggs by HPLC–inductively coupled plasma mass spectrometry

A method for the simultaneous determination of selenomethionine (SeMet), selenocysteine (SeCys), and selenite [Se(IV)] in chicken eggs was developed. A sample preparation protocol including defatting, protein denaturation, and carbamidomethylation was optimized in order to achieve complete protein digestion and to avoid SeCys losses. Quantification was carried out by reversed-phase HPLC–inductively coupled plasma mass spectrometry (ICP MS) after quantitative isolation of the selenium-containing fraction by size-exclusion liquid chromatography. The detection limits were 0.06, 0.003, and 0.01 μg g⁻¹ (dry weight) for SeCys, Se(IV) and SeMet, respectively, and the precision was 5–10%. The end products of carbamidomethylation of the different selenium species were identified for the first time by electrospray QTOF MS after custom-designed 2D HPLC purification. Differences in selenium speciation in egg yolk and white were highlighted, the yolk containing more SeCys and the white more SeMet. An insight into selenium bioaccessibility in eggs was obtained by digestion with simulated gastric and gastrointestinal juices and size-exclusion HPLC-ICP MS.