Thermodynamic trans-Effects of the Nucleotide Base in the B12 Coenzymes

The thermodynamic effects of the nucleotide coordination on the Co-C bond strengths in the B ₁₂ coenzymes were analyzed. Methyl group transfer reactions from methylcob( III )inamides to cob( II )inamides and cob( I )inamides in neutral aqueous solution were used in equilibration experiments to determine the effect fo the intramolecular coordination of the nucleotide function on the Co-C bond dissociation energies of methylcob( III )alamin ( 4 ). In the equilibrium between 4 , cob( I )inamide ( 11 ), cob( I )alamin ( 10 ) and methylcob( III )inamide 6 (Scheme 2), 4 and 11 were found to predominate ( 4 + 11 ? 10 + 6 , equilibrium constant K_I/III≈0.004), while the equilibrium between 4 , cob( II )inamide 9 , cob( II )alamin ( 5 ), and 6 (Scheme 1) proved to be well balanced ( 4 + 9 ? 5 + 6 , equilibrium constant K_II/III=0.60). These equilibrium values indicate the nucleotide coordination to stabilize the Co–C bond in 4 both against homolysis (slight effect) and against nucleophilic heterolysis (considerable effect). They reflect a stabilization of the complete corrins 4 and 5 by the nucleotide coordination, which is also indicated for 4 and 5 by their (nucleotide) basicity. The latter information, where available for other organocobalamins, allows the analysis of the thermodynamicnucleotide trans effect there as well: e.g. in coenzyme B ₁₂ ( 1 ), the nucleotide coordination is found this way to weaken the Co–C bond towards homolysis by ca. 0.7 kcal/mol.     

Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry

The topic of this article is the development and the present state of the art of computer chemistry, the computer-assisted solution of chemical problems. Initially the problems in computer chemistry were confined to structure elucidation on the basis of spectroscopic data, then programs for synthesis design based on libraries of reaction data for relatively narrow classes of target compounds were developed, and now computer programs for the solution of a great variety of chemical problems are available or are under development. Previously it was an achievement when any solution of a chemical problem could be generated by computer assistance. Today, the main task is the efficient, transparent, and non-arbitrary selection of meaningful results from the immense set of potential solutions—that also may contain innovative proposals. Chemistry has two aspects, constitutional chemistry and stereochemistry, which are interrelated, but still require different approaches. As a result, about twenty years ago, an algebraic model of the logical structure of chemistry was presented that consisted of two parts: the constitution-oriented algebra of be- and r-matrices, and the theory of the stereochemistry of the chemical identity group. New chemical definitions, concepts, and perspectives are characteristic of this logic-oriented model, as well as the direct mathematical representation of chemical processes. This model enables the implementation of formal reaction generators that can produce conceivable solutions to chemical problems—including unprecedented solutions—without detailed empirical chemical information. New formal selection procedures for computer-generated chemical information are also possible through the above model. It is expedient to combine these with interactive methods of selection. In this review, the Munich project is presented and discussed in detail. It encompasses the further development and implementation of the mathematical model of the logical structure of chemistry as well as the experimental verification of the computer-generated results. The article concludes with a review of new reactions, reagents, and reaction mechanisms that have been found with the PC-programs IGOR and RAIN.     

Multidimensional nano-HPLC coupled with tandem mass spectrometry for analyzing biotinylated proteins

Multidimensional high-performance liquid chromatography (HPLC) is a key method in shotgun proteomics approaches for analyzing highly complex protein mixtures by complementary chromatographic separation principles. Here, we describe an integrated 3D-nano-HPLC/nano-electrospray ionization quadrupole time-of-flight mass spectrometry system that allows an enzymatic digestion of proteins followed by an enrichment and subsequent separation of the created peptide mixtures. The online 3D-nano-HPLC system is composed of a monolithic trypsin reactor in the first dimension, a monolithic affinity column with immobilized monomeric avidin in the second dimension, and a reversed phase C18 HPLC-Chip in the third dimension that is coupled to a nano-ESI-Q-TOF mass spectrometer. The 3D-LC/MS setup is exemplified for the identification of biotinylated proteins from a simple protein mixture. Additionally, we describe an online 2D-nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS setup for the enrichment, separation, and identification of cross-linked, biotinylated species from chemical cross-linking of cytochrome c and a calmodulin/peptide complex using a novel trifunctional cross-linker with two amine-reactive groups and a biotin label.

Synthesis of 2,2,5,5‐Tetrasubstituted 1,4‐Dioxa‐2,5‐disilacyclohexanes via Organotin(IV)‐Catalyzed Transesterification of (Acetoxymethyl)alkoxysilanes

(Acetoxymethyl)silanes 2 , 7 a – c , and 10 a – c with at least one alkoxy group, of the general formula (AcOCH₂)Si(OR)_3?n(CH₃)_n (R: Me, Et, iPr; n=0, 1, 2), were synthesized from the corresponding (chloromethyl)silanes 1 , 6 a – c , and 9 a – c by treatment with potassium acetate under phase‐transfer‐catalysis conditions. These compounds were found to provide 2,2,5,5‐organo‐substituted 1,4‐dioxa‐2,5‐disilacyclohexanes 3 , 8 a – c , and 11 a – c if treated with organotin(IV) catalysts such as dioctyltin oxide. The reaction proceeds through transesterification of the acetoxy and alkoxy units followed by ring‐closure to form a dimeric six‐membered ring. The corresponding alkyl acetates are formed as the reaction by‐products. With these mild conditions, the method overcomes the drawbacks of previously reported synthetic routes to furnish 2,2,5,5‐tetramethyl‐1,4‐dioxa‐2,5‐disilacyclohexane ( 3 ) and even allows the synthesis of 1,4‐dioxa‐2,5‐disilacyclohexanes bearing hydrolytically labile alkoxy substituents at the silicon atom in good yields and high purity. These new materials were fully characterized by NMR spectroscopy, elemental analysis, mass spectrometry, and X‐ray analysis (trans‐ 8 a ).     

Flame atomic absorption spectrometric determination of cadmium and copper in biological reference materials using on-line sorbent extraction preconcentration

Summary Cadmium and copper at the g/g to ng/g level in plant and animal tissue reference materials, and at the g/l level in urine were determined by flame atomic absorption spectrometry using on-line sorbent extraction preconcentration based on flow injection techniques. Bonded silica reversed phase sorbent with octadecyl functional groups (RP-C 18), packed in a 100 l column, was used to collect the diethylammonium-N,N-diethyldithiocarbamate (DDTC) complex formed on-line in the sample digests at low pH. Methanol was used to elute the analyte chelates directly into the nebulizer-burner system of the spectrometer. Small air segments introduced before and after elution prevented the eluent from mixing with the sample solution and increased the sensitivity. A sampling frequency of 85/h could be obtained with a sample loading time of 30 s at a flow rate of 4.0 ml/min. The enrichment factor for both elements was 20 and the enhancement factors, including the effect of the organic solvent and with the flow spoiler removed, were 126 and 114 for cadmium and copper, respectively. The detection limits (3) were 0.15 g/l for cadmium and 0.2 g/l for copper. The precision was 2.3% and 1.4% r.s.d. for 10 g/l Cd and 45 g/l Cu, respectively (n=11). Results for the determination of cadmium and copper in various biological reference materials were typically in good agreement with certified values. Low recoveries were observed, however, for cadmium in samples containing high levels of copper and/or iron, such as bovine liver.On leave from Flow Injection Analysis Research Center, Institute of Applied Ecology, Academia Sinica, Shenyang, China     

Optimisation of extraction procedures for metallothionein-isoforms and superoxide dismutase from liver samples using spiking experiments

The speciation of trace element species in solid matrices like liver samples is still problematic due to two reasons. On the one hand direct methods with sufficient selectivity and sensitivity are currently not available. Therefore extraction procedures have to be applied which are often problematic in respect to species stability. On the other hand there are no reference materials with known amounts of metal proteins like metallothionein-isoforms (MT) and superoxide dismutase (SOD) for quality control. So the aim of this study was to develop and optimise procedures for the species-preserving extraction of the model compounds MT and SOD from liver samples. Spiking experiments were performed to overcome the lack of appropriate reference materials. In a first step the stability of the model species without liver matrix was investigated by the variation of several extraction parameters. The extractant and exposure to ultrasonic energy especially had a great influence on the recovery of the species while temperature, buffer concentration and atmospheric conditions were less critical. In a second step spiked liver samples were extracted with a selection of procedures taken from the literature. Most of these methods provided recoveries between 70% and 100%. Additionally the buffer concentration and the extractant-to-liver ratio were varied for optimisation. The metal balance of an extraction showed recoveries of 81% for Cd, 94% for Cu and 87% for Zn.     

Resolution enhancement in multidimensional solid-state NMR spectroscopy of proteins using spin-state selection

We show that the resolution of homonuclear multidimensional solid-state NMR correlation experiments can be significantly improved using transition selection and spin-state-selective polarization transfer techniques. The selection and transfer of single states allow the removal of the J-coupling contribution from the line width in both the direct and indirect spectral dimensions. This is demonstrated with a new spin-state-selective CO-Calpha correlation experiment, applied to a microcrystalline 85-residue protein. With this new sequence, all four components of the CO-Calpha cross-peaks are separated into different spectra, obtained by linear combination of four recorded data sets. Line narrowing of up to 44% was obtained on the protein sample for the spin-state-selective CO-Calpha spectrum compared to a standard spin-diffusion experiment. The new technique also allows an easy distinction between "direct" and "relayed" transfer cross-peaks.     

Pentopyranosyl Oligonucleotide Systems. 9th Communication

Pyranosyl‐RNA (‘p‐RNA’ ) is an oligonucleotide system isomeric to natural RNA and composed of the very same building blocks as RNA. Its generational, chemical, and informational properties are deemed to be those of an alternative nucleic acid system that could have been a candidate in Nature's evolutionary choice of the molecular basis of genetic function. We consider the study of the chemistry of p‐RNA as etiologically relevant in the sense that knowledge of its structural, chemical, and informational properties on the chemical level offers both a perspective and reference points for the recognition of specific structural assets of the RNA structure that made it the (supposedly) superior system among possible alternatives and, therefore, the system that became part of biology as we know it today. The paper describes the chemical synthesis of β‐d‐ (and L )‐ribopyranosyl‐(4′→2′)‐oligonucleotide sequences, presents a resume of their structural and chemical properties, and cautiously discusses what we may and may not have learned from the pyranosyl isomer of RNA with respect to the conundrum of RNA's origin.