Base modified peptidic nucleic acids: synthesis and crystallographic analysis of intermediates

Peptidic Nucleic Acids (PNAs) are achiral, uncharged nucleic add mimetics, with a novel backbone composed of N-(2-aminoethyl)glycine units attached to the DNA bases through carboxymethylene linkers. With the aim of extending and improving upon the molecular recognition properties of PNAs, the aim of this work was to synthesjse PNA building block intermediates containing a series of substituted purine bases for subsequent use in automated PNA synthesis. Four purine bases: 2,6~diaminopurine (D), isoGuanine (isoG), xanthine (X) and hypoxanthine (H) were identified for incorporation into PNAs targeted to DNA, with the promise of increased hybrid stability over extended pH ranges together with improvements over the use of adenine (A) in duplex formation, and cytosine (C) in triplex formation. A reliable, high-yielding synthesis of the PNA backbone component N -('2- butyloxycarbonyl-aminoethyl)glycinate ethyl ester was establishecl. The precursor N~(2-butyloxycarbonyl)amino acetonitrile was crystallised and analysed by X-ray crystallography for the first time. An excellent refinement (R = 0.0276) was attained for this structure, allowing comparisons with known analogues. Although chemical synthesis of pure, fully-characterised PNA monomers was not achieved, chemical synthesis of PNA building blocks composed of diaminopurine, xanthine and hypoxanthine was completely successful. In parallel, a second objective of this work was to characterise and evaluate novel crystalline intermediates, which formed a new series of substituted purine bases, generated by attaching alkyl substituents at the N9 or N7 sites of purine bases. Crystallographic analysis was undertaken to probe the regiochemistry of isomers, and to reveal interesting structural features of the new series of similarly-substituted purine bases. The attainment of the versatile synthetic intermediate 2,6-dichloro~9- (carboxymethyl)purine ethyl ester, and its homologous regioisomers 6-chloro~9- (carboxymethyl)purine ethyl ester and 6-chloro-7-(carboxymethyl)purine ethyl ester, necessitated the use of X-ray crystallographic analysis for unambiguous structural assignment. Successful refinement of the disordered 2,6-diamino-9-(carboxymethyl) purine ethyl ester allowed comparison with the reported structure of the adenine analogue, ethyl adenin-9-yl acetate. Replacement of the chloro moieties with amino, azido and methoxy groups expanded the internal angles at their point of attachment to the purine ring. Crystallographic analysis played a pivotal role towards confirming the identity of the peralkylated hypoxanthine derivative diethyl 6-oxo-6,7-dihydro-3H-purlne~3,7~djacetate, where two ethyl side chains were found to attach at N3 and N7,

The structural and electrochemical consequences of hydrogenating Copper N2S2 Schiff base macrocycles

A series of cis and trans tetradentate copper macrocyclic complexes, of ring size fourteen - sixteen, which employ amine and thioether donor groups are reported. Apart from 5,6,15,16-bisbenzo-8,13-diaza-1,4-dithia-cyclohexadecane copper(I) (cis-[Cu(H4NbuSen)]+) all of the complexes are obtained in the copper(II) form. Crystallographic analysis shows that the copper(II) complexes all adopt a distorted planar geometry around the copper. In contrast, cis-[Cu(H4NbuSen)]+ is found to adopt a distorted tetrahedral geometry. The complexes were subjected to electrochemical analysis in water and acetonitrile. The effect of the solvent, positions of the donor atoms (cis/trans) on E1/2 is discussed as is the comparison of the electrochemical behaviour of these complexes with their parent Schiff base macrocycles.

June Sutor and the C-H…O hydrogen bonding controversy

In 1962, D. June Sutor published the first crystallographic analysis of C–H…O hydrogen bonding based on a selection of structures then known. Her follow-up paper the next year cited more structures and provided more details, but her ideas met with formidable opposition. This review begins by describing knowledge of C-H…O hydrogen bonding available at the time from physico-chemical and spectroscopic studies. By comparison of structures cited by Sutor with modern redeterminations, the soundness of her basic data set is assessed. The plausibility of the counter-arguments against her is evaluated. Finally, her biographical details are presented along with consideration of factors that might have impeded the acceptance of her work. © 2012 Taylor & Francis.

Tear and skin phospholipids:analysis and hydrogel analogues

This thesis is concerned with the analysis of phospholipids in the tear film and with the synthesis of phospholipids analogous to hydrogels. The work consists of two areas. The first area is the study of the phospholipids in the tear film, their nature and fate. The use of liquid chromatography mass spectrometry determined that the concentration of phospholipids in the tear film was less than previously thought. The analysis of the tear film phospholipids continued with thin layer chromatography. This showed the presence of diacylglycerides (DAGs) in the tear film at relatively high concentrations. The activity of an enzyme, phospholipase C, was found in the tear film. It was hypothesised that the low concentration of phospholipids and high concentrations of DAG in the tear film was due to the action of this enzyme. The second area of study was the synthesis of phospholipids analogous materials for use in ocular and dermal applications for use in ocular and dermal applications.For ocular applications the synthesis involved the use of the monomer N,N-dimethyl-N-(2-acryloylethyl)-N-(3-sulfopropyl) ammonium betaine (SPDA) in combination with 2-hdyroxyethyl methacrylate (HEMA). Charge-balanced membranes were also synthesised using potentially anionic monomers in conjunction with cationic monomers in stoichiometrically equivalent ratios also with HEMA as a commoner. Membranes of SPDA copolymers and charge-balanced copolymers proved to have some properties suitable for ocular applications. The dermal materials consisted of one family of partially hydrated hydrogels synthesised from SPDA in combination with ionic monomers: sodium 2-(acrylamido)-2-methyl propane sulfonate and acrylic acid-bis(3-sulfopropyl)-ester, potassium salt. A second family of partially hydrated hydrogels was synthesised from N-vinyl pyrrolidone in combination with the same ionic monomers. Both of the partially hydrated hydrogels synthesised proved to have some properties suitable for use as adhesives for the skin.

Tear analysis and lens-tear interactions:part II. Ocular lipids-nature and fate of meibomian gland phospholipids

Purpose: Published data indicate that the polar lipid content of human meibomian gland secretions (MGS) could be anything between 0.5% and 13% of the total lipid. The tear film phospholipid composition has not been studied in great detail and it has been understood that the relative proportions of lipids in MGS would be maintained in the tear film. The purpose of this work was to determine the concentration of phospholipids in the human tear film. Methods: Liquid chromatography mass spectrometry (LCMS) and thin layer chromatography (TLC) were used to determine the concentration of phospholipid in the tear film. Additionally, an Amplex Red phosphatidylcholine-specific phospholipase C (PLC) assay kit was used for determination of the activity of PLC in the tear film. Results: Phospholipids were not detected in any of the tested human tear samples with the low limit of detection being 1.3 µg/mL for TLC and 4 µg/mL for liquid chromatography mass spectrometry. TLC indicated that diacylglycerol (DAG) may be present in the tear film. PLC was in the tear film with an activity determined at approximately 15 mU/mL, equivalent to the removal of head groups from phosphatidylcholine at a rate of approximately 15 µM/min. Conclusions: This work shows that phospholipid was not detected in any of the tested human tear samples (above the lower limits of detection as described) and suggests the presence of DAG in the tear film. DAG is known to be at low concentrations in MGS. These observations indicate that PLC may play a role in modulating the tear film phospholipid concentration.

Synthetic, crystallographic, and computational study of copper(II) complexes of ethylenediaminetetracarboxylate ligands

Copper(II) complexes of hexadentate ethylenediaminetetracarboxylic acid type ligands Heda3p and Heddadp (Heda3p = ethylenediamine-N-acetic-N,N',N'-tri-3-propionic acid; H eddadp = ethylenediamine-N,N'-diacetic-N,N'-di-3- propionic acid) have been prepared. An octahedral trans(O) geometry (two propionate ligands coordinated in axial positions) has been established crystallographically for the Ba[Cu(eda3p)]·8HO compound, while Ba[Cu(eddadp)]·8HO is proposed to adopt a trans(O ) geometry (two axial acetates) on the basis of density functional theory calculations and comparisons of IR and UV-vis spectral data. Experimental and computed structural data correlating similar copper(II) chelate complexes have been used to better understand the isomerism and departure from regular octahedral geometry within the series. The in-plane O-Cu-N chelate angles show the smallest deviation from the ideal octahedral value of 90°, and hence the lowest strain, for the eddadp complex with two equatorial ß-propionate rings. A linear dependence between tetragonality and the number of five-membered rings has been established. A natural bonding orbital analysis of the series of complexes is also presented.