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PubMed2006

Deactivation of the first excited singlet state of thiophenols.

On the bases of picosecond and nanosecond laser flash photolysis with detection by emission and absorption spectroscopy, a quantitative description is given of all deactivation channels of the first excited singlet state of thiophenols ArSH(S(1)) such as fluorescence, intersystem crossing (ISC), chemical dissociation into radicals, and radiation-less internal conversion (IC). For this purpose, the photolysis of thiophenol and its methyl-, methoxy-, and chloro-substituted derivatives was studied in solvents of increasing polarity: 1-chlorobutane, ethanol, and acetonitrile. The fluorescence lifetime of the thiophenols was found to range from some hundreds of picoseconds up to a few nanoseconds, correlating with fluorescence quantum yields between 0.001-0.040, at room temperature. Depending on the substitution pattern of the aromatic ring, the quantum yield of the S-H bond dissociation was found to be between 0.3-0.5, irrespective of the solvent polarity. In laser photolysis, no triplet formation of the investigated compounds could be observed neither by the direct way nor by subsequent sensitization with beta-carotene. As a difference to the total, the radiation-less internal conversion (Phi(IC)>or= 0.5) was found to be the dominating process.

Antioxidants↗
PubMed1998

The specific variable domain of camel heavy-chain antibodies is encoded in the germline.

The variable domains of the functional heavy-chain antibodies (VHHs) discovered in camels are related to the human VH subgroup III. They are nevertheless clearly distinguishable from the VHs of conventional four-chain immunoglobulins by the presence of important amino acid substitutions, located in the solvent-exposed surface normally covered by the variable domain of the light chain. The analysis of an unrearranged dromedary DNA library revealed that the specific VHH gene with its characteristic amino acid substitutions is encoded in the germline. Therefore, it is concluded that the VHHs do not arise through an ontogenic process of somatic hypermutation. The presence of putative DNA recombination signals that are more prevalent in the camel VHH, compared to the VH germline gene, might play a role in the formation and efficient expansion of the VHH repertoire.

Amino Acid Sequence↗
PubMed2001

Thermodynamic and kinetic studies on the reaction between the vitamin B12 derivative beta-(N-methylimidazolyl)cobalamin and N-methylimidazole: ligand displacement at the alpha axial site of cobalamins.

The equilibria and kinetics of substitution of the 5,6-dimethylbenzimidazole at the alpha site of beta-(N-methylimidazolyl)cobalamin by N-methylimidazole have been investigated, and the product, bis(N-methylimidazolyl)cobalamin, has been characterized by visible and 1H NMR spectroscopies. The equilibrium constant for (N-MeIm)Cbl+ + N-MeIm right harpoon over left harpoon (N-MeIm)2Cbl+ was determined by 1H NMR spectroscopy (9.6 +/- 0.1 M(-1), 25.0 degrees C, I = 1.5 M (NaClO4)). The observed rate constant for this reaction exhibits an unusual inverse dependence on N-methylimidazole concentration, and it is proposed that substitution occurs via a base-off solvent-bound intermediate. Activation parameters typical for a dissociative ligand substitution mechanism are reported at two different N-MeImT concentrations, 5.00 x 10(-3) M (DeltaH++ = 99 +/- 2 kJ x mol(-1), DeltaS++ = 39 +/- 5 J x mol(-1) x K(-1), DeltaV++ = 15.0 +/- 0.7 cm3 x mol(-1), and 1.00 M (DeltaH++ = 109.4 +/- 0.8 kJ x mol(-1), DeltaS++ = 70 +/- 3 J x mol(-1) x K(-1), DeltaV++ = 16.8 +/- 1.1 cm3 x mol(-1)). According to the proposed mechanism, these parameters correspond to the equation of (N-MeIm)2Cbl+ and the ring-opening reaction of the alpha-DMBI of (N-MeIm)Cbl+ to give the solvent-bound intermediate in both cases, respectively.

Acids↗
PubMed1980

Cephalosporanic acids: a new look at reactions at the C-3' position.

Nucleophilic displacement of the acetoxy group of cephalosporanic acids by thiols in aqueous solution at neutral pH provides 3-thiomethyl-substituted compounds with a broad spectrum of antibiotic activity. The aqueous displacement reaction is often destructive of much of the cephalosporanic acid, and products generally require extensive purification. Displacements at a lower pH are complicated by unwanted lactone formation. However, reactions conducted under acid conditions in a variety of anhydrous organic solvents give 3-thiomethyl-substituted compounds in very high yield and quality; no lactone formation is observed. The kinetics of the reaction support an SN1 mechanism. Protonation of the departing acetoxy group appears therefore critical; the more basic solvents, e.g. dimethylsulphoxide and N,N-dimethylformamide, significantly retard the rate of reaction.

Acids↗
PubMed1982

The lipid solubility of fixative, staining and embedding media, and the introduction of LX-112 and poly/bed-812 as dehydrants for epoxy resin embedment.

The manufacture of Shell, Epon-812 (E-812) resin has recently been discontinued. E-812 and two newly introduced E-812 substitutes, and Ladd-112 (LX-112) and the Polysciences, Poly/bed-812 (PB-812) resins, were studied biochemically and morphologically for their effectiveness as polar dehydrants. Their technical properties as general E-812 replacements were also explored. In the biochemical studies, acetone was more effective in retaining lung phospholipid components than ethanol, the resin dehydration was more effective than either acetone or ethanol. There was no appreciable difference in lipid solubility among the three resins. Acetone and uranyl magnesium acetate each had a loosening effect on previously fixed phospholipids. The PB-812 and E-812 resin dehydrated blocks of dense animal tissues, demonstrated serious technical difficulties during sectioning. The L-112 resin substitute, due to its low viscosity and improved infiltration, was found to be technically as effective a dehydrant as ethanol or acetone. None of the three resins was successful as dehydrating agents for the plant tissue. With organic solvent dehydration, both epoxy resin substitutes demonstrated excellent embedment properties with both animal and plant tissues.

Animals↗
PubMed1991

The potential of cryofixation and freeze substitution: observations and theoretical considerations.

The theoretical and experimental evidence in favour of cryofixation and freeze-substitution are critically reviewed. The solubility of macromolecules in water is due to the hydration shells. Their behaviour at different temperatures and the consequences of their removal during the processing for embedding are explained. Gelation prior to the transfer into solvents prevents macromolecules aggregating. During substitution at low temperatures, DNA is gelled, justifying the use of the term cryofixation. It is proposed that the preservation of hydration shells at the lowest temperature, and their transformation into minute gaps after a rise of temperature, facilitates the exhibition of epitopes.

Animals↗
PubMed2004

Temperature and solvent control of the stereoselectivity in the reactions of singlet oxygen with oxazolidinone-substituted enecarbamates.

Oxazolidinone-functionalized enecarbamates react stereoselectively with singlet oxygen to give methyldesoxybenzoin (MDB) in moderate to high enantiomeric excess. The stereochemical outcome depends on the E/Z substrate geometry, temperature, and solvent variables. The analysis of the differential activation parameters suggests a large contribution from the entropy term in determining the enantioselectivity. We demonstrate the utility of the temperature and solvent variables in determining the degree of the photochemical kinetic resolution of the enecarbamates; for example, in the photooxygenation at -70 degrees C in methanol, MDB may be obtained in methanol.

Benzoin↗
PubMed1985

Biological monitoring of workers exposed to organic solvents--past and present.

The development of biological monitoring for persons exposed to organic solvents is described. The advantages of this supervision strategy, as well as the reservation against it, are discussed. With the target organs of organic solvents, matrices and parameters for biological monitoring taken into consideration, the following recommendations can be given: the determination of solvent level in blood or alveolar air as a substitute is obligatory for the biological monitoring of organic solvents (the toxic stress of the target organ--the brain--is reflected this way); metabolites have to be determined also when they or their predecessors impair other organs. The discussion of chemical analysis, interference and influencing factors, as well as biological limit values, leads to suggestions of how to interpret the results of biological monitoring. Beyond the estimation of the health risk of the individual worker, the results also have to be interpreted on a group basis. Only in this way can all information on biological monitoring be used to the advantage of prevention. In summary, today biological monitoring is possible for most of the organic solvents. Estimation of health risk in the case of simultaneous exposure to several solvents is still not possible. Parameters measuring toxic strain must be established. The various social groups have to be convinced of the advantages of biological monitoring.

Environmental Monitoring↗
PubMed2001

Freeze-substitution: origins and applications.

Freeze-substitution is a physicochemical process in which biological specimens are immobilized and stabilized for microscopy. Water frozen within cells is replaced by organic solvents at subzero temperatures. Freeze-substitution is widely used for ultrastructural and immunocytochemical analyses of cells by transmission and scanning electron microscopy. Less well recognized is its superiority over conventional chemical fixation in preserving labile and rare tissue antigens for immunocytochemistry by light microscopy. In the postgenome era, the focus of molecular genetics will shift from analyzing DNA sequence structure to elucidating the function of gene networks, the intercellular effects of polygenetic diseases, and the conformational rearrangements of proteins in situ. Novel strategies will be needed to integrate knowledge of chemical structures of normal and abnormal macromolecules with the physiology and developmental biology of cells and tissues from whole organisms. This review summarizes the progress and future prospects of freeze-substitution for such explorations.

Animals↗
PubMed1994

The prediction and orientation of alpha-helices from sequence alignments: the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules.

Amino acid substitution tables are used to estimate the extent to which amino acids in families of homologous proteins are exposed to the solvent. The approach depends on the comparison of difference environment-dependent tables for solvent accessible/inaccessible residues with amino acid substitutions at each position in an aligned set of sequences. The periodicity in the predicted accessible/inaccessible residues is calculated using a Fourier transform procedure modified from that used to calculate hydrophobic moments. alpha-Helices are identified from the characteristic periodicities and the solvent accessible face of the helix is defined. The initial helix predictions are refined using rules for identifying the N- and C-termini of helices from sequence alignments. These rules have been defined from a study of protein structures. The combined method correctly predicts 79% of the residues in helices and incorrectly predicts only 12% of the nonhelical residues as helical. In addition, since the method is reliable at predicting the correct number of helices in the correct position in the sequence and since it also predicts the internal face of each helix, the results can be used to postulate 3-D arrangements of the secondary structure elements.

Amino Acid Sequence↗
PubMed2003

Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures.

Occurrence and accommodation of charged amino acid residues in proteins that are structurally equivalent to buried non-polar residues in homologues have been investigated. Using a dataset of 1,852 homologous pairs of crystal structures of proteins available at 2A or better resolution, 14,024 examples of apolar residues in the structurally conserved regions replaced by charged residues in homologues have been identified. Out of 2,530 cases of buried apolar residues, 1,677 of the equivalent charged residues in homologues are exposed and the rest of the charged residues are buried. These drastic substitutions are most often observed in homologous protein pairs with low sequence identity (<30%) and in large protein domains (>300 residues). Such buried charged residues in the large proteins are often located in the interface of sub-domains or in the interface of structural repeats, Beyond 7A of residue depth of buried apolar residues, or less than 4% of solvent accessibility, almost all the substituting charged residues are buried. It is also observed that acidic sidechains have higher preference to get buried than the positively charged residues. There is a preference for buried charged residues to get accommodated in the interior by forming hydrogen bonds with another sidechain than the main chain. The sidechains interacting with a buried charged residue are most often located in the structurally conserved regions of the alignment. About 50% of the observations involving hydrogen bond between buried charged sidechain and another sidechain correspond to salt bridges. Among the buried charged residues interacting with the main chain, positively charged sidechains form hydrogen bonds commonly with main chain carbonyls while the negatively charged residues are accommodated by hydrogen bonding with the main chain amides. These carbonyls and amides are usually located in the loops that are structurally variable among homologous proteins.

Amino Acid Substitution↗
PubMed2003

Synthesis and characterization of tricyanovinyl-capped oligothiophenes as low-band-gap organic materials.

Tricyanovinyl-capped oligothiophenes of up to six rings have been synthesized and characterized. The substituted oligomers display dramatic reductions in both their optical and electrochemical band gaps in comparison to unsubstituted oligomers. The solvatochromic behavior of the terthiophene-substituted molecule was investigated in a variety of solvents. Stable oxidations and reductions were exhibited by the sexithiophene-substituted molecule on the CV time scale. [structure: see text]

Journal Article↗
PubMedDate not supplied

[A study of the effect of solvent composition and viscosity on the molecular dynamics of human serum albumin using Rayleigh scattering of Mössbauer radiation].

By means of RSMR changes of human serum albumen intramolecular mobility by addition of 1.5% and 7.5% of glutar dialdehyde (GD) in concentrated protein solution, heat denaturation of a protein or substitution of water by water-glycerol solvent with amount of water to glycerol: 1 to 2 were studied. It is shown that the elastic fraction for HSA is changed much less addition of GD or by heat denaturation than by substitution of water solution by water-glycerol. It seems that the observed strong influence of glycerol on intramolecular mobility of HSA is connected mostly with effective dehydration of protein (by substitution of the part of a water solvent by glycerol) and with a small volume decrease of protein (due to preference hydration effect) rather than with the increase of the solvent viscosity.

Humans↗
PubMed2001

Thermodynamic quantitative structure-activity relationship analysis for enzyme-ligand interactions in aqueous phosphate buffer and organic solvent.

Thermodynamic quantitative structure-activity relationships (QSAR) for chymotrypsin-ligand binding is developed, and the results are compared for the effects of organic solvent on the substrate specificity of the enzymes to those in aqueous phosphate buffer. This is the first of such analysis utilizing thermodynamic QSAR. A possible explanation for the difference describing the effects of organic solvent for the binding of substituted phenyl esters of N-benzoyl L-alanine analogues [PhCONHCH(Me)COOC(6)H(4)-p-X, I] observed in both the classical and the thermodynamic QSAR is presented.

Alanine↗
PubMed2007

Reactivity of dehydrometallophthalocyanines and -porphyrazines.

The zinc dehydrophthalocyanine 2 and zinc dehydrobenzoporhyrazine 8 a were generated from the 1N-aminobenzotriazole-annulated zinc phtalocyanine 1 and zinc benzoporhyrazine 8, respectively, by oxidation with Pb(OAc)(4) in different solvents, for example, diethyl ether, tetrahydrofuran, acetic acid, and benzene. The reactivity of 2 and 8 a was studied in detail. These species not only easily undergo Diels-Alder additions with dienes, but also the used solvents can be added. Among the addition products with solvents ethoxy-, acetoxy-, acetoxybutyloxy-substituted and barrelen-fused phthalocyanines and benzoporpyrazines were isolated. No products resulting from the dimerization of two dehydro species were observed either for 2 or 8 a. Analysis of the reaction products in comparison with those obtained by oxidation of 1-aminobenzotriazole 15 under similar conditions proves a higher reactivity (electrophilicity) of the dehydro-PcZn 2 and dehydro-PzZn 8 a in comparison with unsubstituted benzyne towards the solvents used, such as diethyl ether and benzene.

Catalysis↗
PubMed2004

Fine tuning of the electronic coupling between metal centers in cyano-bridged mixed-valent trinuclear complexes.

We report the synthesis, characterization, and spectroscopic properties of a family of trinuclear cyano-bridged mixed-valent compounds, trans-[Ru(II)L(4)[NCFe(III)(CN)(5)](2)](4-), trans-[Ru(II)L(4)[CNFe(III)(CN)(5)](2)](4-), and cis-[Ru(II)(bpy)(2)[NCFe(III)(CN)(5)](2)](4-) (L = pyridine, 4-tert-butylpyridine, and 4-methoxypyridine). Tetraphenylphosphonium salts of complexes trans-[Ru(II)L(4)[NCFe(III)(CN)(5)](2)](4-) (L = pyridine and 4-tert-butylpyridine) crystallize in the space groups C2 and P2(1)/c, respectively, and show a linear arrangement of the metal units and an almost completely eclipsed configuration of the equatorial ligands. An intense band (epsilon approximately 2000-9000 M(-1) cm(-1)) is observed for all of the compounds in the NIR region of the spectrum, not present in the separated building blocks, and strongly solvent dependent. We assign it as a metal-to-metal charge transfer (MMCT) from the Ru(II) to the terminal Fe(III) moieties in the context of a simplified three-center model. The electrochemistry measurements reveal a splitting of the redox waves for the reduction of the iron centers for some of the complexes with a trans configuration between the metal units, ranging from 100 to 260 mV, depending on the substituting pyridine ligand and the solvent, suggesting long-range metal-metal interactions. These interactions are rationalized in terms of the energy matching between the pi-symmetry orbitals of the metals and the cyanide bridge. The one- and two-electron reduced species derived from compounds trans-[Ru(II)L(4)[NCFe(III)(CN)(5)](2)](4-,5-,6-) were characterized in methanolic solution. The mixed-valent Fe(II)-Ru(II)-Fe(III) system exhibits an intense red shifted band in the NIR region of the spectrum, arising from the superposition of MMCT bands from the central Ru(II) to the terminal Fe(III) fragments and from the 1 nm distant Fe(II) to Fe(III) centers.

Journal Article↗