Design of organic semiconductors: tuning the electronic properties of pi-conjugated oligothiophenes with the 3,4-ethylenedioxythiophene (EDOT) building block

Hybrid oligothiophenes based on a various combinations of thiophene and 3,4-ethylenedioxythiophene (EDOT) groups have been synthesized. UV/Vis absorption spectra show that the number and relative positions of the EDOT groups considerably affect the width of the HOMO-LUMO gap and the rigidity of the conjugated system. Analysis of the crystallographic structure of two hybrid quaterthiophenes confirms that insertion of two adjacent EDOT units in the middle of the molecule leads to a self-rigidification of the conjugated systems by intramolecular SO interactions. Cyclic voltammetry data shows that the first oxidation potential of the oligomers decreases with increasing chain length and increasing number of EDOT groups for a given chain length. Electrochemical studies and theoretical calculations show that the positions of the EDOT units in the conjugated chain control the potential difference (DeltaE(p)) between the first and second oxidation steps. Moving the EDOT groups from the outer to the inner positions of the conjugated system increases DeltaE(p). Theoretical calculations confirm that this phenomenon reflects an increase of the intramolecular coulombic repulsion between positive charges in the dication. A thin-film field-effect transistor was fabricated by vacuum sublimation of a pentamer with alternating thiophene-EDOT structure, and the hole mobility was determined.     

The peripheral benzodiazepine receptor in photodynamic therapy with the phthalocyanine photosensitizer Pc 4

The peripheral benzodiazepine receptor (PBR) is an 18 kDa protein of the outer mitochondrial membrane that interacts with the voltage-dependent anion channel and may participate in formation of the permeability transition pore. The physiological role of PBR is reflected in the high-affinity binding of endogenous ligands that are metabolites of both cholesterol and heme. Certain porphyrin precursors of heme can be photosensitizers for photodynamic therapy (PDT), which depends on visible light activation of porphyrin-related macrocycles. Because the apparent binding affinity of a series of porphyrin analogs for PBR paralleled their ability to photoinactivate cells, PBR has been proposed as the molecular target for porphyrin-derived photocytotoxicity. The phthalocyanine (Pc) photosensitizer Pc 4 accumulates in mitochondria and structurally resembles porphyrins. Therefore, we tested the relevance of PBR binding on Pc 4-PDT. Binding affinity was measured by competition with 3H-PK11195, a high-affinity ligand of PBR, for binding to rat kidney mitochondria (RKM) or intact Chinese hamster ovary (CHO) cells. To assess the binding of the Pc directly, we synthesized 14C-labeled Pc 4 and found that whereas Pc 4 was a competitive inhibitor of 3H-PK11195 binding to the PBR, PK11195 did not inhibit the binding of 14C-Pc 4 to RKM. Further, 14C-Pc 4 binding to RKM showed no evidence of saturation up to 10 microM. Finally, when Pc 4-loaded CHO cells were exposed to activating red light, apoptosis was induced; Pc 4-PDT was less effective in causing apoptosis in a companion cell line overexpressing the antiapoptotic protein Bcl-2. For both cell lines, PK11195 inhibited PDT-induced apoptosis; however, the inhibition was transient and did not extend to overall cell death, as determined by clonogenic assay. The results demonstrate (1) the presence of low-affinity binding sites for Pc 4 on PBR; (2) the presence of multiple binding sites for Pc 4 in RKM and CHO cells other than those that influence PK11195 binding; and (3) the ability of high supersaturating levels of PK11195 to transiently inhibit apoptosis initiated by Pc 4-PDT, with less influence on overall cell killing. We conclude that the binding of Pc 4 to PBR is less relevant to the photocytotoxicity of Pc 4-PDT than are other mitochondrial events, such as photodamage to Bcl-2 and that the observed inhibition of Pc 4-PDT-induced apoptosis by PK11195 likely occurs through a mechanism independent of PBR.     

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Solvent extraction of protactinium(v) with bis(2-ethylhexyl)phosphoric acid in toluene

The extraction of Pa(V) from 1M perchloric acid medium with HDEHP in toluene was carried out. The different factors affecting the metal distribution coefficient such as HDEHP concentration in the organic phase, pH of the aqueous phase and the equilibrium temperature were followed. From the data obtained the equilibrium constants of the extraction reaction were calculated. From the temperature variation, the corresponding thermodynamic parameters (G, H and S) were also derived. In the same way, the effect of addition of some N-and 0-containing solvents such as pyridine, 2,2-dipyridyl, n-amyl alcohol, n-decyl alcohol and n-butyl acetate, to the HDEHP organic phase was demonstrated. From the data obtained the suggested mechanisms for the synergistic extraction reactions were discussed together with the corresponding values of the thermodynamic parameters.     

Conformation of DNA modified by monofunctional Ru(II) arene complexes: recognition by DNA binding proteins and repair. Relationship to cytotoxicity

We analyzed DNA duplexes modified at central guanine residues by monofunctional Ru(II) arene complexes [(eta(6)-arene)Ru(II)(en)(Cl)](+) (arene = tetrahydroanthracene or p-cymene, Ru-THA or Ru-CYM, respectively). These two complexes were chosen as representatives of two different classes of Ru(II) arene compounds for which initial studies revealed different binding modes: one that may involve DNA intercalation (tricyclic-ring Ru-THA) and the other (mono-ring Ru-CYM) that may not. Ru-THA is approximately 20 times more toxic to cancer cells than Ru-CYM. The adducts of Ru-THA and Ru-CYM have contrasting effects on the conformation, thermodynamic stability, and polymerization of DNA in vitro. In addition, the adducts of Ru-CYM are removed from DNA more efficiently than those of Ru-THA. Interestingly, the mammalian nucleotide excision repair system has low efficiency for excision of ruthenium adducts compared to cisplatin intrastrand crosslinks.     

Synergistic mechanisms of β-diketone derivatives and zinc-calcium soaps in PVC stabilisation

It has been possible to explain the mechanisms of stabilisation and of the synergistic effects of the β-diketone derivatives claimed in a patent as new stabilisers for improving the efficiency of those recipes based upon zinc and calcium soaps in the prevention of the initial discoloration of poly(vinyl chloride).Using chlorohexene as a model compound for allylic chloride structures and benzoylacetone as a model compound for enolised β-diketone derivatives, it has been shown that the benzoylacetone can substitute allylic chlorine atoms through a C-alkylation reaction which takes place only in the presence of ZnCl₂ as catalyst. This reaction drastically changes the percentage of the enol and causes the appearance of two bands at 1720 cm^?1 and 1680 cm^?1 in the infra-red spectrum due to the ketonic structures During the processing of the PVC on a rolling mill at 180°C in the presence of zinc and calcium stearates and benzoylacetone there is grafting of the ketone derivative through a C-alkylation reaction. There is a closed parallelism between the influence of the benzoylacetone on the dehydrochlorination of the chlorohexene and on the accumulation of chloride ions in the polymer matrix in the presence of zinc and calcium stearate. The synergistic effect of the benzoylacetone in the prevention of the initial discoloration is related to the substitution reaction through a C-alkylation which takes place only in the presence of zinc stearate which generates ZnCl₂ which, in turn, acts as a catalyst for both the C-alkylation and dehydrochlorination.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Cars study of vibrationally excited H2 produced in formaldehyde dissociation

Coherent anti-Stokes Raman scattering (CARS) has been used to observe H₂ from H₂CO + hv H₂ + CO. Photolysis of K = 1 (ortho) lines of the 2¹4¹ S₁ ← S₀ transition produced no para-H₂ (<4% statistical); and demonstrated nuclear spin conservation. H₂ states v = 1, 2 and 3 were comparably populated.     

Synthesis of bipyridine and terpyridine based ruthenium metallosynthons for grafting of multiple pyrene auxiliaries

The synthesis of novel ruthenium(II) bipyridine or terpyridine complexes bearing an increasing number of pyrene or toluyl moieties is described. The ruthenium complexes are constructed in a first step with ligands bearing the required bromine functions, followed in a second step by stepwise grafting of 1-ethynylpyrene or 4-ethynyltoluene promoted by Pd(0). A complex bearing a protected triethylsilylacetylene function was also prepared. In situ deprotection of this function with K₂CO₃ and cross-coupling with 1-bromopyrene afforded a soluble complex in which two pyrene moieties are linearly linked via ethynyl spacers to one of the bipyridine ligands. These highly coloured complexes exhibit well defined absorption and emission properties in solution at both rt and 77 K.