ALKALINE QUENCHING OF BACTERIORHODOPSIN TRYPTOPHANYL FLUORESCENCE: EVIDENCE FOR AQUEOUS ACCESSIBILITY OR A HYDROGEN-BONDED CHAIN

Abstract— Comparison between Trp fluorescence yields of membrane-bound bacteriorhodopsin (BR) and retinylidene-free bacterioopsin (BO) is consistent with a model in which all eight Trp residues are active fiuorophores in the latter, while the emission of all but two residues in the former is lost by energy transfer to retinal. The visible chromophore of BR is progressively bleached with increasing pH. Up to pH 12 this bleaching is reversed on reneutralization; but above this the change is irreversible with the appearance of a new absorption band characteristic of free retinal. Emission yields for both proteins decrease with increasingly alkaline pH in a manner typical of energy transfer to weakly-fluorescent tyrosinate. The limiting yields, reached at a pH corresponding to that producing irreversible bleaching of the visible chromophore, agree with an integral value of one remaining active Trp fluorophore in BR and between one and two in BO and show that the bulk of Trp are within the 11 Å Förster energy-transfer distance of Tyr accessible to OH⁻. Current models of the native protein structure of BR arrange the polypeptide chain primarily in a bundle of seven helical segments with axes perpendicular to the lipid bilayer plane and with buried polar residues, including Trp and Tyr, located at intrahelical surfaces. An interpretation of the observed accessibility of buried Tyr to OH⁻ is that an aqueous region exists within the protein structure. Moreover, this putative aqueous region must be close to the retinylidene chromophore and thus may be associated with the light-driven ion transport system. The results are also compatible with energy transfer to internal Tyr residues which are connected via a chain of phenolate hydrogen bonds to a surface Tyr.     

NMR identification of C11 to C40 branched hydrocarbons derived from the decomposition of polyisobutylene

The composition of nonvolatile fluids obtained from thermally cracking and hydrogenating polyisobutylene was determined by using a combination of gas chromatography and nuclear magnetic resonance spectroscopy (NMR). This work involved the separation and characterization of a homologous series, C₁₁–C₄₀, of sixteen branched hydrocarbon species consisting of repeating isobutylene structures. As a result of this investigation, useful correlations between NMR spectra and molecular structure for highly branched hydrocarbons were developed. The data demonstrate that these hydrocarbons are unique species characterized by “crowded” and sterically hindered geminal methyl and isolated methylene groups. NMR solvent shift studies in benzene solutions indicate that it is possible to differentiate between maximally crowded geminal methyl groups and between maximally crowded methylene groups in these structures. Results of the benzene-induced solvent effects are discussed with respect to the stereochemistry of these molecules and related to existing solvent shift data. These results suggest that these hydrocarbons are polar or nearly polar materials. Successive losses of isobutylene units from stabilized tertiary radicals can account for the formation of the major species identified in these fluids. Higher carbon numbered species have lower refractive indices and densities and higher molal volumes than predicted by calculations.     

A New Silicate Clathrate Hydrate: An X-Ray Diffraction and Nuclear Magnetic Resonance Study of a System with Octameric Silicate Anions and Trivalent Cations

The first crystal structure is reported for a silicate clathrate hydrate involving a triply charged cation [C₁₈H₃₀N₃]³⁺ and an octameric cubic silicate cage. The structure is essentially a host/guest system, with the silicate cages linked into a framework by hydrogen bonding to water molecules. The space group is P with Z = 2, and the asymmetric unit includes a complete cation and half the anion, plus 21 water molecules (4 of which are in disordered positions). Solid-state (CPMAS) ²⁹Si and ¹³CNMR spectra are consistent with the diffraction-determined structure and indicate substantial distortion of the anion from cubic symmetry. Solution-state spectra of precursor solutions and of melted material are also presented and discussed.     

The ionic product of water in concentrated tetramethylammonium chloride solutions

The ionic product of water, pK(w) = - log[H(+)][OH(-)] has been determined in aqueous solutions of tetramethylammonium chloride over the concentration range of 0.1-5.5 M at 25 degrees C using high-precision glass electrode potentiometric titrations. pK(w) data relating to aqueous potassium and sodium chlorides at ionic strengths up to 5 M are markedly lower than the tetramethylammonium chloride results. These differences are almost certainly due to weak associations between potassium and (especially) sodium and hydroxide ions.     

Covalent Schiff base catalysis and turnover by a DNAzyme: a M2+ -independent AP-endonuclease mimic

A DNAzyme, synthetically modified with both primary amines and imidazoles, is found to act as a M2+ -independent AP lyase-endonuclease. In the course of the cleavage reaction, this DNAzyme forms a covalent Schiff base intermediate with an abasic site on a complementary oligodeoxyribonucleotide. This intermediate, which is inferred from NaCNBH3 trapping as well as cyanide inhibition, does not evidently accumulate because the second step, dehydrophosphorylative elimination, is fast compared to Schiff base formation. The 5'-product that remains linked to the catalyst hydrolyzes slowly to regenerate free catalyst. The use of duly modified DNAzymes to perform Schiff base catalysis demonstrates the value of modified nucleotides for enhancing the catalytic repertoire of nucleic acids. This work suggests that DNAzymes will be capable of catalyzing aldol condensation reactions.     

A simple convenient synthesis of trans-1,2,3,4,4a,5,6,10b-octahydrophenanthridines

trans-1,2,3,4,4a,5,6,10b-Octahydrophenanthridine, the 9-methoxy analog, and 5-methyl derivatives ( 6a,6b ) of each have been synthesized from trans-phenylcyclohexylamines ( 2a,2b ) and ethyl chloroformate followed by cyclization and reduction or by cyclization, N-methylation and reduction. The oximes ( la,1b ) of 2-phenylcyclohexanone and the m-methoxy relative, a mixture of the syn and anti isomers, were reduced to 2a and 2b with sodium and ethanol. Hydrogenation (platinum oxide-acetic acid) of 1a gave in addition to 2a , a small yield of 2-cyclohexylcyclohexyl-amine. Similar hydrogenation of 1b gave only this fully reduced compound.     

Dye laser excitation of the fluorosulfate radical. Totally symmetric upper state fundamentals

Upper state vibronic levels associated with totally symmetric fundamentals of the fluorosulfate radical were populated by means of dye laser excitation. The analysis of the resulting fluorescence confirmed the assignment of these levels. Theoretical intensities using the Green's function approach to vibronic coupling were calculated and compared to the experimental values.     

The magnetic susceptibilities of cobaltocene and chromocene

The magnetic susceptibilities of cobaltocene and chromocene have been measured between 83 and 293 K; for cobaltocene the results suggest an appreciable orthorhombic splitting of the ²∏(σ²πδ⁴ ground state, whilst for chromocene the data provide further support for the ³Δ(σδ³) ground state previously deduced.