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PubMed1990

Far-UV CD spectroscopy, IR spectroscopy, and immunological properties of synthetic peptides, including an amphipathic alpha-helical peptide from bovine phospholipase A2.

The immunological properties of bovine phospholipase A2 were investigated in order to locate possible sequential epitopes. Polyvalent antiserum raised against the enzyme was tested for its interaction with synthetic peptides derived from regions adopting hydrogen-bonded secondary structures within the tertiary structure of phospholipase A2. The conformations of each peptide in various solvents were determined by CD and ir spectroscopy in order to relate immunological to structural properties. It was found that sequential epitopes are absent in this enzyme, but that region 90-109 could be a possible T-cell epitope through the formation of an amphipathic alpha-helix.

Amino Acid Sequence↗
PubMed1994

Metabolism of cycloate in radish leaf: metabolite identification by packed capillary flow fast atom bombardment tandem mass spectrometry.

The metabolism of cycloate, a thiocarbamate herbicide, was investigated in mature radish leaf. Twelve new metabolites were identified by liquid chromatographic/mass spectrometric analysis using fast atom bombardment and packed capillary liquid chromatography columns. Full-scan and tandem mass spectrometric methods were employed. Application of the on-column focusing technique resulted in identifications with injections of as little as 15 ng of metabolite (20 ppb in radish). This injection technique allows the practical use of packed capillary liquid chromatography/mass spectrometry in sample-limited applications. Cycloate is oxidized to several ring-hydroxylated isomers that are subsequently glucosylated and esterified with malonic acid. Cycloate is also conjugated with glutathione. Metabolic hydrolysis of the glutathione conjugate formed a cysteine conjugate that is further metabolized by amidation with either malonic or acetic acid. Transamination of the cysteine conjugate gave a thiolactic acid derivative. Metabolites were also identified that were the result of both ring-hydroxylation and conjugation with glutathione. One of these, an N-acetylcysteine conjugate, is the first report of a mercapturic acid in plants. The structures of two of the new metabolites were confirmed by chemical synthesis.

Biotransformation↗
PubMed2006

DNA-binding studies of mixed-ligand (ethylenediamine)ruthenium(II) complexes.

A series of mixed-ligand ruthenium(II) complexes of the type [Ru(en)(2)bpy](2+) (bpy=2,2-bipyridine; 1), [Ru(en)(2)phen](2+) (phen=1,10-phenantroline; 2), [Ru(en)(2)IP](2+) (IP=imidazo[4,5-f][1,10]phenanthroline; 3), and [Ru(en)(2)PIP](2+) (PIP=2-phenylimidazo[4,5-f][1,10]phenanthroline; 4) have been isolated and characterized by UV/VIS, IR, and (1)H-NMR spectral methods. The binding of the complexes with calf thymus DNA has been investigated by absorption, emission spectroscopy, viscosity measurements, DNA melting, and DNA photo-cleavage. The spectroscopic studies together with viscosity measurements and DNA melting studies support that complexes 1 and 2 bind to CT DNA (=calf thymus DNA) by groove mode. Complex 2 binds more avidly to CT DNA than complex 1, complexes 3 and 4 bind to CT DNA by intercalation mode, 4 binds more avidly to CT DNA than 3. Noticeably, the four complexes have been found to be efficient photosensitisers for strand scissions in plasmid DNA.

Animals↗
PubMed2005

Synthesis of N-heteroaryl retinals and their artificial bacteriorhodopsins.

N-Heteroaryl retinals derived from indole, 1-indolizine and 3-indolizine (10 a-c) have been synthesized after their UV/Vis red-shifted absorption properties had been predicted by time-dependent density functional theory (TD-DFT) computations. The three new analogues form artificial pigments upon recombination with bacterioopsin: indolyl retinal 10 a undergoes fast and efficient reconstitution to form a species with a UV/Vis absorbance maximum similar to that of wild-type bacteriorhodopsin, whilst the indolizinyl retinals 10 b and 10 c also reconstitute in significant proportion to give noticeably red-shifted, although unstable, pigments. Significant changes in the pK(a) values of these artificial bacteriorhodopsins are interpreted as arising from nonoptimal binding-site occupancy by the chromophore due to steric constraints.

Algorithms↗
PubMed2004

Peralkynylated buta-1,2,3-trienes: exceptionally low rotational barriers of cumulenic C=C bonds in the range of those of peptide C--N bonds.

A variety of 1,1,4,4-tetraal kynylbutatrienes and 1,4-dialkynylbutatrienes was synthezized by dimerization of the corresponding gem-dibromoolefins. Both (1)H and (13)C NMR spectroscopy indicated that the di- and tetraalkynylated butatrienes are formed as a mixture of cis and trans isomers. Variable temperature NMR studies evidenced a facile cis-trans isomerization, thus preventing the separation of these isomers by gravity or high-performance liquid chromatography (HPLC). For 1,1,4,4-tetraalkynylbutatrienes, the activation barrier deltaG( not equal ) was measured by magnetization transfer to be around 20 kcal mol(-1), in the range of the barrier for internal rotation about a peptide bond. Unlike the tetraalkynylated [3]cumulenes, 1,4-dialkynylbutatrienes are more difficult to isomerize and could, in one case, be obtained isomerically pure. Based on experimental data, the rotational barrier DeltaG( not equal ) for 1,4-dialkynylbutatrienes is estimated to be around 25 kcal mol(-1). The hypothesis of a stabilizing effect of the four alkynyl substituents on the proposed but-2-yne-1,4-diyl singlet diradical transition state of this cis-trans isomerization is further supported by a computational study.

Alkenes↗
PubMed2005

On the electronic structure of ethidium.

The electronic structure of the common intercalating agent ethidium bromide (3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide) is dominated by an interplay of electron donating and withdrawing effects mediated by its nitrogen atoms. X-ray crystallography, UV/Vis and IR absorption, fluorescence emission, and NMR spectroscopy are used to probe the electronic properties of the phenanthridinium "core" of ethidium as well as its exocyclic amines and 6-phenyl groups. Interestingly, despite its positive charge, most of ethidium's aromatic carbon and hydrogen atoms have high electron densities (compared to both 6-phenylphenanthridine and benzene). The data suggest that electron donation by ethidium's exocyclic amines dominates over the electron withdrawing effects of its endocyclic iminium in their combined influence on the electron densities of these atoms. Ethidium's nitrogen atoms are, conversely, electron deficient where the 5-position is the most electropositive, followed by the 3-amino, and lastly the 8-amino group. These results have been used to generate an empirically-based pi-electron density map of ethidium that may prove useful to understanding its nucleic acid binding specificity.

Crystallography, X-Ray↗
PubMed2005

Experimental and computational studies of hydrogen bonding and proton transfer to [Cp*Fe(dppe)H].

The present contribution reports experimental and computational investigations of the interaction between [Cp*Fe(dppe)H] and different proton donors (HA). The focus is on the structure of the proton transfer intermediates and on the potential energy surface of the proton transfer leading to the dihydrogen complex [Cp*Fe(dppe)(H2)]+. With p-nitrophenol (PNP) a UV/Visible study provides evidence of the formation of the ion-pair stabilized by a hydrogen bond between the nonclassical cation [Cp*Fe(dppe)(H2)]+ and the homoconjugated anion ([AHA]-). With trifluoroacetic acid (TFA), the hydrogen-bonded ion pair containing the simple conjugate base (A-) in equilibrium with the free ions is observed by IR spectroscopy when using a deficit of the proton donor. An excess leads to the formation of the homoconjugated anion. The interaction with hexafluoroisopropanol (HFIP) was investigated quantitatively by IR spectroscopy and by 1H and 31P NMR spectroscopy at low temperatures (200-260 K) and by stopped-flow kinetics at about room temperature (288-308 K). The hydrogen bond formation to give [Cp*Fe(dppe)H]HA is characterized by DeltaH degrees =-6.5+/-0.4 kcal mol(-1) and DeltaS degrees = -18.6+/-1.7 cal mol(-1) K(-1). The activation barrier for the proton transfer step, which occurs only upon intervention of a second HFIP molecule, is DeltaH(not equal) = 2.6+/-0.3 kcal mol(-1) and DeltaS(not equal) = -44.5+/-1.1 cal mol(-1) K(-1). The computational investigation (at the DFT/B3 LYP level with inclusion of solvent effects by the polarizable continuum model) reproduces all the qualitative findings, provided the correct number of proton donor molecules are used in the model. The proton transfer process is, however, computed to be less exothermic than observed in the experiment.

Computer Simulation↗
PubMed2005

Heteroditopic ligand accommodating a fused phenanthroline and a schiff base cavity as molecular spacer in the study of electron and energy transfer.

The synthesis and characterisation of the heteroditopic ligand N,N'-bis(3,5-di-tert-butylsalicylidene)-5,6-(1,10-phenanthroline)diamine (DPSalH(2)) bearing a phenanthroline and a bis(salicylidene)diimine cavity are reported. This versatile ligand combines two of the most widely used ligands in coordination chemistry. Sequential metallation of the phenanthroline end with Ru(II) and the salophenic cavity with Cu(II) is described. Electrochemical behaviour of the supramolecular complexes [Ru(bpy)(2)(DPSalH(2))](2+) and [Ru(bpy)(2)(DPSalCu)](2+) are analysed in connection with UV/Vis and EPR spectroscopy. The data for the one-electron-reduced species and the singly oxidised species of the binuclear Ru(II)-Cu(II) complex confirmed the formation of metalloradical complexes. Density functional calculations on the free ligand and the copper-only complex indicate in both cases that the HOMOs and LUMOs are developed on the Schiff base cavity with minor contributions on the bipyridine end. These findings support a bichromophoric character for our ruthenium complexes in the ground state, a necessary condition in the design of supramolecular systems for the study of electron transfer. Photophysical studies indicate fast quenching of the triplet excited state in both complexes, which suggests strong intercomponent excited-state interactions. Evidence is presented that this quenching is due to intramolecular electron transfer, at least in the case of [Ru(bpy)(2)(DPSalH(2))](2+), for which a charge-separated state with a remarkable lifetime of about 30 mus was observed.

Copper↗