Multiple polypeptide forms observed in two-dimensional gels of Methylococcus capsulatus (Bath) polypeptides are generated during the separation procedure

We have examined two-dimensional electrophoresis (2-DE) gel maps of polypeptides from the Gram-negative bacterium Methylococcus capsulatus (Bath) and found the same widespread trains of spots as often reported in 2-DE gels of polypeptides of other Gram-negative bacteria. Some of the trains of polypeptides, both from the outer membrane and soluble protein fraction, were shown to be generated during the separation procedure of 2-DE, and not by covalent post-translational modifications. The trains were found to be regenerated when rerunning individual polypeptide spots. The polypeptides analysed giving this type of trains were all found to be classified as stable polypeptides according to the instability index of Guruprasad et al. (Protein Eng. 1990, 4, 155-161). The phenomenon most likely reflects conformational equilibria of polypeptides arising from the experimental conditions used, and is a clear drawback of the standard 2-DE procedure, making the gel picture unnecessarily complex to analyse.     

Ion Association in Lanthanide Chloride Solutions

A better understanding of the solution chemistry of the lanthanide (Ln) salts in water would have wide ranging implications in materials processing, waste management, element tracing, medicine and many more fields. This is particularly true for minerals processing, given governmental concerns about lanthanide security of supply and the drive to identify environmentally sustainable processing routes. Despite much effort, even in simple systems, the mechanisms and thermodynamics of Ln^III association with small anions remain unclear. In the present study, molecular dynamics (MD), using a newly developed force field, provide new insights into LnCl₃(aq) solutions. The force field accurately reproduces the structure and dynamics of Nd³⁺, Gd³⁺ and Er³⁺ in water when compared to calculations using density functional theory (DFT). Adaptive-bias MD simulations show that the mechanisms for ion pairing change from dissociative to associative exchange depending upon cation size. Thermodynamics of association reveal that whereas ion pairing is favourable, the equilibrium distribution of species at low concentration is dominated by weakly bound solvent-shared and solvent-separated ion pairs, rather than contact ion pairs, reconciling a number of contrasting observations of Ln^III–Cl association in the literature. In addition, we show that the thermodynamic stabilities of a range of inner sphere and outer sphere coordination complexes are comparable and that the kinetics of anion binding to cations may control solution speciation distributions beyond ion pairs. The techniques adopted in this work provide a framework with which to investigate more complex solution chemistries of cations in water.     

Termolecular ion-molecule reactions in Titan’s atmosphere. II: The structure of the association adducts of HCNH+ with C2H2 and C2H4

The ion-molecule reactivity of the products formed in the association reactions of HCNH+ with C2H2 (C3H4N+) and C2H4 (C3H6N+) has been investigated to provide information on the structures of the adducts thus formed. The C3H4N+ and C3H6N+ adducts were formed in the reaction flow tube of a flowing afterglow sourced-selected ion flow tube (FA-SIFT) and their reactivity with a neutral molecular "probe" examined. The reactivity of possible known structural isomers for the C3H4N+ and C3H6N+ ions was investigated in both the FA-SIFT and an ion cyclotron resonance spectrometer (ICR). Ab initio investigations of the potential energy surfaces for both structures at the G2(MP2) level have also been performed and structures corresponding to local minima on both surfaces have been identified and evaluated. The results of these experimental and theoretical studies show that at room temperature, the C3H4N+ adduct ion contains two isomers; a less reactive one that is likely to be a four-membered cyclic covalent isomer (approximately 70%) and a faster reacting component that is probably an electrostatic complex (approximately 30%). The C3H6N+ adduct ion formed from HCNH+ + C2H4 at room temperature is a single isomer that is likely to be the four-membered covalently bound cyclic CH2CH2CHNH+ species.     

Electronic structure of unstable intermediates

The geometry of the linear molecule HBO, has been investigated within the restricted Hartree-Fock LCAO-MO-SCF approximation. The calculated bond lengths for the near Hartree-Fock calculation were R(H-B)=2.1913 bohr, R(B-O)=2.2284 bohr. Several one electron properties have been calculated for the minimum energy configuration.     

A practical synthesis of (+/-)-alpha-isosparteine from a tetraoxobispidine core

[reaction: see text] The title alkaloid was synthesized in racemic form from 3,7-diallyl-2,4,6,8-tetraoxo-3,7-diazabicyclo[3.3.1]nonane (7) by a regioselective diallylation reaction followed by double ring-closing olefin metathesis and exhaustive reduction. Tetraoxobispidine 7 was itself prepared in three simple operations from dimethyl malonate. The entire sequence to alpha-isosparteine was conducted on a multigram scale and proceeded without recourse to chromatography.     

Synthesis of the branched-chain sugar aceric acid: a unique component of the pectic polysaccharide rhamnogalacturonan-II

Described herein is the synthesis of 3-C-carboxy-5-deoxy-L-xylose (aceric acid), a rare branched-chain sugar found in the complex pectic polysaccharide rhamnogalacturonan-II. The key synthetic step in the construction of aceric acid was the stereoselective addition of 2-trimethylsilyl thiazole to 5-deoxy-1,2-O-isopropylidene-alpha-L-erythro-pentofuran-3-ulose (2), which was prepared from L-xylose. The thiazole group was efficiently converted into the required carboxyl group via conventional transformations. Aceric acid was also synthesized by dihydroxylation of a 3-C-methylene derivative of 2 followed by oxidation of the resulting hydroxylmethyl group. The C-2 epimer of aceric acid was also synthesized using thiazole addition chemistry, starting from L-arabinose.     

1,3-Migration of a phenyl group in the conversion of (Me3Si)2(PhMe2Si)CSiMePhX into (Me3Si)2(Ph2MeSi)CSiMe2Y species

The finding that compounds of the type (Me₃Si)₂(PhMe₂Si)CSiMePhX react with electrophiles to give very predominantly rearranged products (Me₃Si)₂(Ph₂MeSi)CSiMe₂Y, which would be expected to be thermodynamically disfavoured, can be rationalized in terms of a mechanism in which the anchimerically-assisted departure of X⁻ gives the Ph-bridged cation [(Me₃Si)₂

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MePh]⁺ which is attacked by the nucleophile at the less hindered centre bearing two Me groups rather than that bearing one Me and one Ph group, with the outcome determined by kinetic rather than thermodynamic factors. Both (Me₃Si)₂(Ph₂MeSi)CSiMe₂Br and its isomer (Me₃Si)₂(PhMe₂Si)CSiMePhBr react with AgBF₄ in CH₂Cl₂ or Et₂O to give >95% of the fluoride (Me₃Si)₂(Ph₂MeSi)CSiMe₂F. Reaction of the bromide (Me₃Si)₂(PhMe₂Si)CSiMePhBr with AgO₂CCF₃ in Et₂O, and that of the hydride (Me₃Si)₂(PhMe₂Si)CSiMePhH with ICl in CCl₄, likewise give >95% of the rearranged (Me₃Si)₂(Ph₂MeSi)CSiMe₂O₂CCF₃ and (Me₃Si)₂(Ph₂MeSi)CSiMe₂Cl, respectively.     

Capillary zone electrophoresis of alpha-helical diastereomeric peptide pairs with anionic ion-pairing reagents

The present study uses an unique capillary electrophoresis (CE) approach, that we have termed ion-interaction capillary zone electrophoresis (II-CZE), for the separation of diastereomeric peptide pairs where a single site in the centre of the non-polar face of an 18-residue amphipathic alpha-helical peptide is substituted by the 19 L- or D-amino acids. Through the addition of perfluorinated acids at very high concentrations (up to 400 mM), such concentration levels not having been used previously in chromatography or CE, to the background electrolyte (pH 2.0), we have been able to achieve baseline resolution of all 19 diastereomeric peptide pairs with an uncoated capillary. Since each diastereomeric peptide pair has the same sequence, identical mass-to-charge ratio and identical intrinsic hydrophobicity, such a separation by CZE has previously been considered theoretically impossible. Excellent resolution was achieved due to maximum advantage being taken of even subtle disruption of peptide structure/conformation (due to the presence of D-amino acids) of the non-polar face of the amphipathic alpha-helix and its interaction with the hydrophobic anionic ion-pairing reagents. In addition, due to the excellent resolution of diastereomeric peptide pairs by this novel CZE approach, we have also been able to separate a mixture of these closely-related alpha-helical peptides.