The structural characteristics of organozinc complexes incorporating N,N'-bidentate ligands

Dimethylzinc reacts with an excess of N-2-pyridylaniline 6 to give the homoleptic species, Zn[PhN(2-C(5)H(4)N)](2) 8. Single crystal X-ray diffraction reveals a solid-state dimer based on an 8-membered (NCNZn)(2) core motif. Zn[CyN(2-C(5)H(4)N)]Me (Cy =c-C(6)H(11)) 10, prepared by the combination of ZnMe(2) with the corresponding cyclohexyl-substituted pyridylamine, is also dimeric in the solid state but reveals a central (ZnN)(2) metallacycle. Employment of (p-Tol)NH(2-C(5)H(4)N)(p-Tol = 4-MeC(6)H(4)) 11 yielded the tris(zinc) adduct Zn(3)[(p-Tol)N(2-C(5)H(4)N)](4)Me(2) 12, which incorporates a central chiral molecule of 'Zn[(p-Tol)N(2-C(5)H(4)N)](2)' 12a, that bridges two 'Zn[(p-Tol)N(2-C(5)H(4)N)]Me' 12b units. A similar trimetallic structure is noted when the pyridylaniline substrate 11 is replaced with the bicyclic guanidine 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine (hppH), affording Zn(3)(hpp)(4)Me(2) 13. Spectroscopic studies point to retention of the solid-state structure of in hydrocarbon solution. Reaction of 13 with dimesityl borinic acid, Mes(2)BOH (Mes = mesityl), affords Zn(3)(hpp)(4)(OBMes(2))(2) 14 in which the trimetallic core is retained. This reactivity is in contrast to the closely related reaction of dimeric Zn[Me(2)NC[N(i)Pr](2)]Me 15 with Mes(2)BOH, which yielded Zn[Me(2)NC[N(i)Pr](2)][OBMes(2)].Me(2)NC[N(i)Pr][NH(i)Pr] 16 as a result of protonation at the guanidine ligand in addition to the Zn-Me bond.     

On-line LC-GC-AED and LC-GC-MS – multidimensional methods for the analysis of PAC in fuels,combustion emissions and atmospheric samples

The composition and concentration of polycyclic aromatic compounds (PAC) in fuels. Theier combustion products and in the atmosphere remains a topic of considerable interest. Despite the wealth of literature on the identification of PAC, speciation at low concentrations remains difficult due to instrument limitation and the complexity of fuel and environmental samples. Consequently on line sample preparation procedures (SPE, SFE, LC, etc.) are becomeing an increasingly important step in the analysis procedure particularly where sample clean-up and fractionation are essential for improving analytical resolution. In this study a normal phase high pressure analytical resolution. In this study a normal phase high pressure liquid chromatography-gas chromatography (LC-GC) system has been developed to provide quantitative analysis of samples, as diverse as coal liquids, petroleum fuels, diesel exhaust particulates, and urban air particulates. Separation and identification of parent and alkylated PAH, hetercycline nitro-and oxy-PAC can be achieved by direct coupling to an atomic emission detector and a bech top mass spectrometer. For both systems the primary LC separation combined with the large sample volume transferred to GC vastly improves detection limits. Furthermore the complimentary nature of the two detectors used enables the positive indentification of many unknowns.     

The alpha-helix folds more rapidly at the C-terminus than at the N-terminus

The helix-coil dynamics of different sections of an alpha-helical model peptide were observed separately by nanosecond temperature jump experiments with IR detection on a series of isotopically labeled peptides. The results show that the helix-coil dynamics of the alpha-helical C-terminus are faster than those of the N-terminus.     

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.     

Comment: 2004's fastest organic and biomolecular chemistry!

In January 2004, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC) - a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?     

Experimental studies of the dynamics of the bond-forming reactions of CF2(2+) with H2O using position-sensitive coincidence spectroscopy

The dynamics of the product channels forming OCF(+)+H(+)+HF and HCF(2) (+)+H(+)+O following the collisions of CF(2) (2+) with H(2)O have been investigated with a new position-sensitive coincidence experiment at a center-of-mass collision energy of 5.6 eV. The results show the formation of OCF(+) occurs via the formation of a doubly charged collision complex [H(2)O-CF(2)](2+) which subsequently undergoes a charge separating dissociation to form H(+) and HOCF(2) (+). The HOCF(2) (+) monocation subsequently fragments to form HF+OCF(+). The lifetimes of the collision complex and the HOCF(2) (+) ion are at least of the order of their rotational period. The kinetic energy release in this reaction indicates that it involves the ground state of CF(2) (2+) and forms the ground electronic states of OCF(+) and HF. The mechanism for forming HCF(2) (+) involves the direct and rapid abstraction of a hydride ion from H(2)O by CF(2) (2+). The resulting OH(+) ion subsequently fragments to H(+)+O, on a time scale at least comparable with its rotational period.     

Dithiolene transfer from nickel to a dimolybdenum centre: the first dithiolene alkyne complex

Transfer of dithiolene ligands from [Ni(S₂C₂Ph₂)₂] to the dimolybdenum complex [Mo₂(μ-C₂R₂)(CO)₄Cp₂] (R=CO₂Me, Cp=η-C₅H₅) affords the first example of a dithiolene alkyne complex, [Mo₂(μ-C₂R₂)(μ-S₂C₂Ph₂)₂Cp₂], together with [Mo₂(μ-SCRCR)(μ-SCPhCPh)Cp₂] in which sulfur transfer from dithiolene to alkyne has occurred.     

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.     

Automated linkage of proteins and payloads producing monodisperse conjugates

Controlled protein functionalization holds great promise for a wide variety of applications. However, despite intensive research, the stoichiometry of the functionalization reaction remains difficult to control due to the inherent stochasticity of the conjugation process. Classical approaches that exploit peculiar structural features of specific protein substrates, or introduce reactive handles via mutagenesis, are by essence limited in scope or require substantial protein reengineering. We herein present equimolar native chemical tagging (ENACT), which precisely controls the stoichiometry of inherently random conjugation reactions by combining iterative low-conversion chemical modification, process automation, and bioorthogonal trans-tagging. We discuss the broad applicability of this conjugation process to a variety of protein substrates and payloads.

Controlled protein functionalization holds great promise for a wide variety of applications.

Applications of protein conjugates are limitless, including imaging, diagnostics, drug delivery, and sensing.^1–4 In many of these applications, it is crucial that the conjugates are homogeneous.⁵ The site-selectivity of the conjugation process and the number of functional labels per biomolecule, known as the degree of conjugation (DoC), are crucial parameters that define the composition of the obtained products and are often the limiting factors to achieving adequate performance of the conjugates. For instance, immuno-PCR, an extremely sensitive detection technique, requires rigorous control of the average number of oligonucleotide labels per biomolecule (its DoC) in order to achieve high sensitivity.⁶ In optical imaging, the performance of many super-resolution microscopy techniques is directly defined by the DoC of fluorescent tags.⁷ For therapeutics, an even more striking example is provided by antibody–drug conjugates, which are prescribed for the treatment of an increasing range of cancer indications.⁸ A growing body of evidence from clinical trials indicates that bioconjugation parameters, DoC and DoC distribution, directly influence the therapeutic index of these targeted agents and hence must be tightly controlled.⁹Standard bioconjugation techniques, which rely on nucleophile–electrophile reactions, result in a broad distribution of different DoC species (Fig. 1a), which have different biophysical parameters, and consequently different functional properties.¹⁰Open in a separate windowFig. 1Schematic representation of the types of protein conjugates.To address this key issue and achieve better DoC selectivity, a number of site-specific conjugation approaches have been developed (Fig. 1b). These techniques rely on protein engineering for the introduction of specific motifs (e.g., free cysteines,¹¹ selenocysteines,¹² non-natural amino acids,^13,14 peptide tags recognized by specific enzymes^15,16) with distinct reactivity compared to the reactivity of the amino acids present in the native protein. These motifs are used to simultaneously control the DoC (via chemo-selective reactions) and the site of payload attachment. Both parameters are known to influence the biological and biophysical parameters of the conjugates,¹¹ but so far there has been no way of evaluating their impact separately.The influence of DoC is more straightforward, with a lower DoC allowing the minimization of the influence of payload conjugation on the properties of the protein substrate. The lowest DoC that can be achieved for an individual conjugate is 1 (corresponding to one payload attached per biomolecule). It is noteworthy that DoC 1 is often difficult to achieve through site-specific conjugation techniques due to the symmetry of many protein substrates (e.g., antibodies). Site selection is a more intricate process, which usually relies on a systematic screening of conjugation sites for some specific criteria, such as stability or reactivity.¹⁷Herein, we introduce a method of accessing an entirely new class of protein conjugates with multiple conjugation sites but strictly homogenous DoCs (Fig. 1c). To achieve this, we combined (a) iterative low conversion chemical modification, (b) process automation, and (c) bioorthogonal trans-tagging in one workflow.The method has been exemplified for protein substrates, but it is applicable to virtually any native bio-macromolecule and payload. Importantly, this method allows for the first time the disentangling of the effects of homogeneous DoC and site-specificity on conjugate properties, which is especially intriguing in the light of recent publications revealing the complexity of the interplay between payload conjugation sites and DoC for in vivo efficacy of therapeutic bioconjugates.¹⁸ Finally, it is noteworthy that this method can be readily combined with an emerging class of site-selective bioconjugation reagents to produce site-specific DoC 1 conjugates, thus further expanding their potential for biotechnology applications.¹⁹