Electrospray ionization mass spectrometric studies of nucleophilic carbenes derived from pyrazolium and indazolium carboxylates

Pyrazolium-3-carboxylate and indazolium-3-carboxylate, which belong to the class of pseudo-cross-conjugated mesomeric betaines and which represent the electronically relevant partial structures of the betaine alkaloid Nigellicin, were examined by electrospray ionization mass spectrometry. These compounds decarboxylate to pyrazol-3-ylidene and indazol-3-ylidene. The formation of adducts of these new nucleophilic carbenes under the measurement conditions was examined.     

Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar couplings constants

We apply Bayesian inference to analyze three-bond scalar coupling constants in an objective and consistent way. The Karplus curve and a Gaussian error law are used to model scalar coupling measurements. By applying Bayes' theorem, we obtain a probability distribution for all unknowns, i.e., the torsion angles, the Karplus parameters, and the standard deviation of the Gaussian. We infer all these unknowns from scalar coupling data using Markov chain Monte Carlo sampling and analytically derive a probability distribution that only involves the torsion angles.     

Replica-exchange Monte Carlo scheme for bayesian data analysis

We develop a sampling algorithm to explore the probability densities arising in Bayesian data analysis problems. Our algorithm is a multiparameter generalization of a replica-exchange Monte Carlo scheme. The strategy relies on gradual weighing of experimental data and on Tsallis generalized statistics. We demonstrate the effectiveness of the method on nuclear magnetic resonance data for a folded protein.     

Correction of spin diffusion during iterative automated NOE assignment

Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances. Although several methods for spin diffusion correction have been published, they are often not employed to derive distance restraints. This prompted us to write a user-friendly and CPU-efficient method to correct for spin diffusion that is fully integrated in our program ambiguous restraints for iterative assignment (ARIA). ARIA thus allows automated iterative NOE assignment and structure calculation with spin diffusion corrected distances. The method relies on numerical integration of the coupled differential equations which govern relaxation by matrix squaring and sparse matrix techniques. We derive a correction factor for the distance restraints from calculated NOE volumes and inter-proton distances. To evaluate the impact of our spin diffusion correction, we tested the new calibration process extensively with data from the Pleckstrin homology (PH) domain of Mus musculus beta-spectrin. By comparing structures refined with and without spin diffusion correction, we show that spin diffusion corrected distance restraints give rise to structures of higher quality (notably fewer NOE violations and a more regular Ramachandran map). Furthermore, spin diffusion correction permits the use of tighter error bounds which improves the distinction between signal and noise in an automated NOE assignment scheme.     

New pyrazolium-carboxylates as structural analogues of the pseudo-cross-conjugated betainic alkaloid nigellicine

Pyrazolium-3-carboxylates were examined as relatives of the betainic alkaloid Nigellicine and as new examples of the sparsely populated class 16 of heterocyclic pseudo-cross-conjugated mesomeric betaines (PCCMB). The title compounds were prepared in a 4-step procedure starting from beta-diketo compounds 8 which were cyclized with substituted hydrazines. The resulting isomeric pyrazole esters 9 and 10 were separated and subsequently quaternized with dimethyl sulfate in the presence of nitrobenzene to pyrazolium esters 11 and 12. Saponification was best accomplished in diluted sulfuric acid, which resulted in the formation of the pseudo-cross-conjugated mesomeric betaines 13 and 14 in one step. Protonation to the corresponding carboxylic acids required the treatment of the betaines with tetrafluoroboric acid in dichloromethane. The effect of negative solvatochromism proves the charge separation in the ground state of the molecules. X-ray crystallographic analyses, semiempirical calculations, and ESI mass spectrometric measurements were performed to gain knowledge about the phenomenon of pseudo-cross-conjugation.     

Modeling errors in NOE data with a log-normal distribution improves the quality of NMR structures

The distribution of the deviation of calculated from measured nuclear Overhauser effect (NOE) intensities is a priori unknown. The use of a log-normal distribution to describe these deviations permits the direct calculation of a structure from the measured intensities without first converting them into distance bounds. We show that the log-normal distribution is a natural choice for describing errors in NOE data and that it improves the accuracy, precision, and quality of the calculated structures compared to the usual bounds representation.     

Reductive dechlorination of tetrachloroethylene (PCE) catalyzed by cyanocobalamin

A biomimetic system has been developed for the reductive dechlorination of tetrachloroethylene (PCE). PCE was dechlorinated to trichloroethylene (TCE) and 1,2-dichloroethylene (DCE) in the presence of dithiothreitol or Ti (III) citrate and catalytic amounts of cyanocobalamin in both homogeneous reaction mixtures and packed bed reactor systems. In packed bed reactors with Ti (III) citrate as the reductant, PCE (0.18 mM) conversion averaged 55% at residence times of 1.75 and 3.5 h. The product distribution was 94% TCE and 6% DCE at the lower residence time. DCE formation increased to 45% at the higher residence time. No reduction of PCE was observed in the absence of cyanocobalamin. This system may be useful as a means of pretreatment of halogenated aliphatic hydrocarbons in advance of biological treatment.     

Translation of pseudo-cross-conjugation into chemistry: cycloadditions of mesomeric betaines to the new ring system spiro[indazole-3,3'-pyrrole

Indazolium-3-amidates (X-ray analysis), readily available on trapping the N-heterocyclic carbene indazol-3-ylidene with isocyanates, underwent [3+2]-cycloadditions with activated triple bonds to spiro[indazole-3,3'-pyrroles]. A combination of NMR techniques such as heteronuclear single quantum coherence (HSQC), heteronuclear multiple bond correlation (HMBC), nuclear Overhauser enhancement spectroscopy (NOESY), and 1H/15N correlations were applied to elucidate the structures of the cycloadducts.     

Generation of three-dimensional random rotations in fitting and matching problems

An algorithm is developed to generate random rotations in three-dimensional space that follow a probability distribution arising in fitting and matching problems. The rotation matrices are orthogonally transformed into an optimal basis and then parameterized using Euler angles. The conditional distributions of the three Euler angles have a very simple form: the two azimuthal angles can be decoupled by sampling their sum and difference from a von Mises distribution; the cosine of the polar angle is exponentially distributed and thus straighforward to generate. Simulation results are shown and demonstrate the effectiveness of the method. The algorithm is compared to other methods for generating random rotations such as a random walk Metropolis scheme and a Gibbs sampling algorithm recently introduced by Green and Mardia. Finally, the algorithm is applied to a probabilistic version of the Procrustes problem of fitting two point sets and applied in the context of protein structure superposition.