Characterisation and proposed origin of mass spectrometric ions observed 30 Th above the ionised molecules of per-O-methylated carbohydrates

Derivatisation of carbohydrates by permethylation significantly improves the mass spectrometric intensity of carbohydrate-derived ions and allows more readily interpretable fragmentation; in addition, samples are conveniently separated from salts, and larger oligosaccharides are more readily ionised. It has previously been recognised that, in the mass spectra of permethylated carbohydrates, a series of ions indicating species 30 Da larger than the fully methylated carbohydrate molecules are also observed. These species have not been characterised in the literature despite their apparently ubiquitous occurrence in the mass spectra of permethylated carbohydrates. Tandem mass spectrometry (MS/MS) experiments were performed on permethylated carbohydrates and reduced permethylated carbohydrates that exhibit the artefact, demonstrating that the artefact is not reducing terminal specific, and that the artefact can be introduced at any hydroxyl residue. It was further demonstrated through the use of different alkylation reagents that the origin of this artefact group is the alkylating reagent itself. It is proposed that side reactions that occur between the permethylation reagents allow the production of small amounts of iodomethyl methyl ether. This reagent can then compete with methyl iodide for reaction with the carbohydrate -OH groups. The result is partial incorporation of a methoxymethyl moiety instead of a methyl group, detected as '+30' artefact ions.     

Interference between the hydrogen bonds to the two rings of nicotine

The biochemical transport and binding of nicotine depends on the hydrogen bonding between water and binding site residues to the pyridine ring and the protonated pyrrolidinium ring. To test the independence of these two moderately separated hydrogen-bonding sites, we have calculated the structures of clusters of protonated nicotine with water and a bicarbonate anion, benzene, indole, or a second water molecule. Unprotonated nicotine-water clusters have also been studied for contrast. The potential energy surfaces are first explored with an intermolecular anisotropic atom-atom model potential. Full geometry optimizations are then carried out using density functional theory to include nonadditive terms in the interaction energies. The presence of the charge on the pyrrolidine nitrogen removes the conventional hydrogen-bonding site on the pyridine ring. The hydrogen-bond ability of this site is nearly recovered when the protonated pyrrolidinium ring is bound to a bicarbonate anion, whereas its interaction with benzene shows a much smaller effect. Indole appears to partially restore the hydrogen-bond ability of the pyridine nitrogen, although indole and benzene both pi-bond to the pyrrolidinium ring. A second hydrogen-bonding water produces a significant conformational distortion of the nicotine. This demonstrates the limitations of the conventional qualitative predictions of hydrogen bonding based on the independence of molecular fragments. It also provides benchmarks for the development of atomistic modeling of biochemical systems.     

Strong solute-solute dispersive interactions in a protein-ligand complex

The contributions of solute-solute dispersion interactions to binding thermodynamics have generally been thought to be small, due to the surmised equality between solute-solvent dispersion interactions prior to the interaction versus solute-solute dispersion interactions following the interaction. The thermodynamics of binding of primary alcohols to the major urinary protein (MUP-I) indicate that this general assumption is not justified. The enthalpy of binding becomes more favorable with increasing chain length, whereas the entropy of binding becomes less favorable, both parameters showing a linear dependence. Despite the hydrophobicity of the interacting species, these data show that binding is not dominated by the classical hydrophobic effect, but can be attributed to favorable ligand-protein dispersion interactions.     

Dipole-bound anions of highly polar molecules: ethylene carbonate and vinylene carbonate

Results of experimental and theoretical studies of dipole-bound negative ions of the highly polar molecules ethylene carbonate (EC, C3H4O3, mu=5.35 D) and vinylene carbonate (VC, C3H2O3, mu=4.55 D) are presented. These negative ions are prepared in Rydberg electron transfer (RET) reactions in which rubidium (Rb) atoms, excited to ns or nd Rydberg states, collide with EC or VC molecules to produce EC- or VC- ions. In both cases ions are produced only when the Rb atoms are excited to states described by a relatively narrow range of effective principal quantum numbers, n*; the greatest yields of EC- and VC- are obtained for n*(max)=9.0+/-0.5 and 11.6+/-0.5, respectively. Charge transfer from low-lying Rydberg states of Rb is characteristic of a large excess electron binding energy (Eb) of the neutral parent; employing the previously derived empirical relationship Eb=23/n*(max)(2.8) eV, the electron binding energies are estimated to be 49+/-8 meV for EC and 24+/-3 meV for VC. Electron photodetachment studies of EC- show that the excess electron is bound by 49+/-5 meV, in excellent agreement with the RET results, lending credibility to the empirical relationship between Eb and n*(max). Vertical electron affinities for EC and VC are computed employing aug-cc-pVDZ atom-centered basis sets supplemented with a (5s5p) set of diffuse Gaussian primitives to support the dipole-bound electron; at the CCSD(T) level of theory the computed electron affinities are 40.9 and 20.1 meV for EC and VC, respectively.     

The matching of electrostatic extrema: A useful method in drug design? A study of phosphodiesterase III inhibitors

Summary Ligands which bind to a specific protein binding site are often expected to have a similar electrostatic environment which complements that of the binding site. One method of assessing molecular electrostatic similarity is to examine the possible overlay of the maxima and minima in the electrostatic potential outside the molecules and thereby match the regions where strong electrostatic interactions, including hydrogen bonds, with the residues of the binding site may be possible. This approach is validated with accurate calculations of the electrostatic potential, derived from a distributed multipole analysis of an ab initio charge density of the molecule, so that the effects of lone pair and -electron density are correctly included. We have applied this method to the phosphodiesterase (PDE) III substrate adenosine-3,5-cyclic monophosphate (cAMP) and a range of nonspecific and specific PDE III inhibitors. Despite the structural variation between cAMP and the inhibitors, it is possible to match three or four extrema to produce relative orientations in which the inhibitors are sufficiently sterically and electrostatically similar to the natural substrate to account for their affinity for PDE III. This matching of extrema is more apparent using the accurate electrostatic models than it was when this approach was first applied, using semiempirical point charge models. These results reinforce the hypothesis of electrostatic similarity and give weight to the technique of extrema matching as a useful tool in drug design.     

A Product Formed from Glycylglycine in the Presence of Vanadate and Hydrogen Peroxide: The (Glycylde-N-hydroglycinato-kappa(3)N(2),N(N)(),O(1))oxoperoxovanadate(V) Anion

A crystalline glycylglycine complex of monoperoxovanadate has been obtained and its X-ray structure determined. The coordination is pentagonal bipyramidal with the peroxo group and a tridentate glycylglycine occupying the equatorial positions. The axial positions of the anion are occupied by the oxo ligand and by one oxygen of the peroxo group of the adjacent anion. The latter interaction establishes the seventh bond and produces a dimeric structure in the crystalline material. NMR studies of its dissolution in water combined with previously reported results from equilibrium measurements show that the dimer dissociates in water to the monomeric precursor. It is proposed that this monomer corresponds to the complex responsible for the inhibition of the vanadium-catalyzed decomposition of hydrogen peroxide by glycylglycine. Crystal structure of [NEt(4)][VO(O(2))(GlyGly)].1.58H(2)O: monoclinic, space group P2(1); Z = 4; a = 10.618(2) ?; b = 14.803(2) ?; c = 11.809(2) ?; beta = 101.37(2) degrees; V = 1819.7 ?(3); T = 198 K; R(F)() = 0.029 for 2664 data (I(o) >/= 2.5sigma(I(o))) and 431 variables.     

Mononuclear nitrogen/sulfur-ligated zinc methoxide and hydroxide complexes: investigating ligand effects on the hydrolytic stability of zinc alkoxide species

The synthesis and properties of mononuclear zinc methoxide ([(ebnpa)Zn-OCH3]ClO4) (1) and hydroxide ([(ebnpa)Zn-OH]ClO4) (2) complexes of a new mixed nitrogen/sulfur ligand (ebnpa = N-2-(ethylthio)ethyl-N,N-bis(6-neopentylamino-2-pyridylmethyl)amine) are reported. The structures of 1 and 2 were determined by X-ray diffraction. Each possesses a single zinc-coordinated anion (methoxide or hydroxide) and exhibits an overall trigonal bipyramidal geometry. Structural and spectroscopic studies indicate the presence of two hydrogen-bonding interactions involving the oxygen atom of the zinc-bound anion in each complex. Treatment of [(ebnpa)Zn-OH]ClO4 with CH3OH results in the formation of an equilibrium mixture of 1 and 2. 1H NMR spectroscopic methods were used to examine the equilibrium as a function of temperature, yielding KMe (304 K) = 0.30(8), DeltaHMe = -0.9(1) kcal/mol, and DeltaSMe = -5(1) eu. The negative enthalpy indicates that spontaneous zinc alkoxide formation from a hydroxide precursor occurs in this system at low temperature. Using the experimentally determined DeltaHMe value, we found the homolytic Zn-O bond dissociation energy (BDE) in the Zn-OCH3 unit to be approximately -14 kcal/mol relative to the Zn-O BDE in the Zn-OH unit.     

Size control of dendrimer-templated silica

One of the most significant challenges facing the biomimetic synthesis of materials is achieving the requisite level of dimensional and spatial control. Typical reaction conditions for biomimetic silica synthesis allow for continued growth and ripening leading to the formation of larger nanospheres on the order of 200-600 nm in diameter. Herein, we have used polyamidoamine and polypropylenimine dendrimers as templates to expand the reaction conditions of biogenic silica production to produce a more robust synthesis leading to size-selective precipitation of silica nanospheres. Through the use of defined concentrations of phosphate buffer and main group metal chloride salts, we have shown that the biomimetic silica growth process is controlled by cationic neutralization of the anionic silica nanosphere surface. Neutralization minimizes electrostatic repulsions, allowing for agglomerization and continued growth of nanospheres. By controlling these concentrations, we can selectively produce silica nanospheres of desired dimensions between 30 and 300 nm without adversely affecting the template's activity.     

Development of a gas chromatography/ion trap mass spectrometry based method for the quantification of polybrominated diphenyl ethers and polychlorinated biphenyls in adipose tissue

A combined gas chromatographic mass spectrometric (GC/MS/MS) method for the determination of seven polybrominated diphenyl ethers (PBDEs) and seven marker polychlorinated biphenyls (PCBs) in adipose tissue has been developed. Adipose tissue was melted and filtered through anhydrous sodium sulphate to obtain pure fat. Clean-up was performed using a glass column containing acidified silica, deactivated alumina and anhydrous sodium sulphate. Polybrominated biphenyl (PBB) 155 and Mirex were added as internal standards for PBDEs and PCBs, respectively. Injection standards, PBB 103 and PCB 143, for PBDEs and PCBs, respectively, were added before analysis with GC/MS/MS. The developed GC/MS/MS method has the advantage of being more selective than single MS methods because matrix effects are largely eliminated. Validation of this method was conducted according to Commission Decision 2002/657/EC. Decision limits for PBDEs and PCBs ranged from 0.06-0.15 ng g(-1) and from 0.35-1.22 ng g(-1), respectively. Detection capabilities were all between 0.23-0.55 ng g(-1) for PBDEs and between 0.98-2.29 ng g(-1) for PCBs. Precision, recovery, bias and selectivity were tested, with satisfactory results.     

Examining the role of surfactant packing in phase transformations of periodic templated silica/surfactant composites

In this work, we examine the role of curvature and surfactant packing in controlling the structure of periodic silica/surfactant composites by driving such materials through a transformation from a hexagonal to a lamellar phase. We focus on how the interplay of desired packing and volume constraints dictates the resulting structures. In general, surfactants expand in a complex way upon heating, and this can cause a change in the optimal packing geometry. However, the presence of a rigid silica framework may prevent surfactants from reaching this preferred volume and/or curvature. Real-time in situ X-ray diffraction is used to monitor the structural evolution of these materials heated under hydrothermal treatments. Because the thermal-driven disorder of the surfactant tails drives the phase transition, we examine four types of composites with varying tail density. Ordinarily, composites consist of surfactants with one 20-carbon tail and one positively charged ammonium headgroup. Tail density is varied by replacing a small amount (0-16%) of these single-tail, single-head surfactants with single-tail, double-head 'gemini' surfactants. A greater head--tail ratio indeed produces different results, causing the phase transition to occur at higher temperatures. Using simple geometric models to gain better understanding of our experimental results, we find that, while both unfavorable curvature and limited volume may exist for the surfactants in these composites, the constrained curvature appears to be the dominant effect in driving structural rearrangement.