Double-quantum 13C nuclear magnetic resonance of bathorhodopsin, the first photointermediate in mammalian vision

The 13C chemical shifts of the primary visual photointermediate bathorhodopsin have been observed by performing double-quantum magic-angle-spinning NMR at low temperature in the presence of illumination. Strong isomerization shifts have been observed upon the conversion of rhodopsin into bathorhodopsin.     

Finite-difference solution of the Poisson–Boltzmann equation: Complete elimination of self-energy

A new procedure to solve the Poisson–Boltzmann equation is proposed and shown to be efficient. The electrostatic potential due to the reaction field is calculated directly. Self-interactions among the charges are completely eliminated. Therefore, the reference calculation to cancel out the self-energy is not needed. © 1996 by John Wiley & Sons, Inc.     

Bootstrap classification and point-based feature selection from age-staged mouse cerebellum tissues of matrix assisted laser desorption/ionization mass spectra using a fuzzy rule-building expert system

A bootstrap method for point-based detection of candidate biomarker peaks has been developed from pattern classifiers. Point-based detection methods are advantageous in comparison to peak-based methods. Peak determination and selection are problematic when spectral peaks are not baseline resolved or on a varying baseline. The benefit of point-based detection is that peaks can be globally determined from the characteristic features of the entire data set (i.e., subsets of candidate points) as opposed to the traditional method of selecting peaks from individual spectra and then combining the peak list into a data set. The point-based method is demonstrated to be more effective and efficient using a synthetic data set when compared to using Mahalanobis distance for feature selection. In addition, probabilities that characterize the uniqueness of the peaks are determined.This method was applied for detecting peaks that characterize age-specific patterns of protein expression of developing and adult mouse cerebella from matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) data. The mice comprised three age groups: 42 adults, 19 14-day-old pups, and 16 7-day-old pups. Three sequential spectra were obtained from each tissue section to yield 126, 57 and 48 spectra for adult, 14-day-old pup, and 7-day-old pup spectra, respectively. Each spectrum comprised 71,879 mass measurements in a range of 3.5-50 kDa. A previous study revealed that 846 unique peaks were detected that were consistent for 50% of the mice in each age group (C. Laurent, D.F. Levinson, S.A. Schwartz, P.B. Harrington, S.P. Markey, R.M. Caprioli, P. Levitt, Direct profiling of the cerebellum by MALDI MS: a methodological study in postnatal and adult mouse, J. Neurosci. Res. 81 (2005) 613-621.).A fuzzy rule-building expert system (FuRES) was applied to investigate the correlation of age with features in the MS data. FuRES detected two outlier pup-14 spectra. Prediction was evaluated using 100 bootstrap samples of 2 Latin-partitions (i.e., 50:50 split between training and prediction set) of the mice. The spectra without the outliers yielded classification rates of 99.1 ± 0.1%, 90.1 ± 0.8%, and 97.0 ± 0.6% for adults, 14-day-old pups, and 7-day-old pups, respectively. At a 95% level of significance, 100 bootstrap samples disclosed 35 adult and 21 pup distinguishing peaks for separating adults from pups; and 8 14-day-old and 15 7-day-old predictive peaks for separating 14-day-old pup from 7-day-old pup spectra. A compressed matrix comprising 40,393 points that were outside the 95% confidence intervals of one of the two FuRES discriminants was evaluated and the classification improved significantly for all classes. When peaks that satisfied a quality criterion were integrated, the 55 integrated peak areas furnished significantly improved classification for all classes: the selected peak areas furnished classification rates of 100%, 97.3 ± 0.6%, and 97.4 ± 0.3% for adult, 14-day-old pups, and 7-day-old pups using 100 bootstrap Latin partitions evaluations with the predictions averaged. When the bootstrap size was increased to 1000 samples, the results were not significantly affected. The FuRES predictions were consistent with those obtained by discriminant partial least squares (DPLS) classifications.     

First Synthesis and Characterization of CH4@C60

The endohedral fullerene CH₄@C₆₀, in which each C₆₀ fullerene cage encapsulates a single methane molecule, has been synthesized for the first time. Methane is the first organic molecule, as well as the largest, to have been encapsulated in C₆₀ to date. The key orifice contraction step, a photochemical desulfinylation of an open fullerene, was completed, even though it is inhibited by the endohedral molecule. The crystal structure of the nickel(II) octaethylporphyrin/ benzene solvate shows no significant distortion of the carbon cage, relative to the C₆₀ analogue, and shows the methane hydrogens as a shell of electron density around the central carbon, indicative of the quantum nature of the methane. The ¹H spin‐lattice relaxation times (T₁) for endohedral methane are similar to those observed in the gas phase, indicating that methane is freely rotating inside the C₆₀ cage. The synthesis of CH₄@C₆₀ opens a route to endofullerenes incorporating large guest molecules and atoms.     

Solid-state NMR spectroscopy of molecular hydrogen trapped inside an open-cage fullerene

Solid-state 1H experiments were performed an open-cage fullerene hosting molecular hydrogen. The anisotropy of the molecular hydrogen rotation was studied by double-quantum magic-angle-spinning NMR. The time scale of the molecular hydrogen rotation was estimated by spin-lattice relaxation measurements as a function of temperature.     

Determination of the dissociation constant and limiting equivalent conductance of a weak electrolyte from conductance measurements on the weak electrolyte

A method is described for computing the dissociation constant and equivalent conductance at infinite dilution, A_o , for a weak electrolyte from as few as two conductance measurements at different concentrations. The iterative procedure applied to acetic acid data yielded a dissociation constant of 1.80 X 10-⁵ and an average value (n = 4) of A_o of 389.5 compared with an expected value of 390.7.     

Protein-induced bonding perturbation of the rhodopsin chromophore detected by double-quantum solid-state NMR

We have obtained carbon-carbon bond length data for the functional retinylidene chromophore of rhodopsin, with a spatial resolution of 3 pm. The very high resolution was obtained by performing double-quantum solid-state NMR on a set of noncrystalline isotopically labelled bovine rhodopsin samples. We detected localized perturbations of the carbon-carbon bond lengths of the retinylidene chromophore. The observations are consistent with a model in which the positive charge of the protonated Schiff base penetrates into the polyene chain and partially concentrates around the C13 position. This coincides with the proximity of a water molecule located between the glutamate-181 and serine-186 residues of the second extracellular loop, which is folded back into the transmembrane region. These measurements support the hypothesis that the polar residues of the second extracellular loop and the associated water molecule assist the rapid selective photoisomerization of the retinylidene chromophore by stabilizing a partial positive charge in the center of the polyene chain.     

Heterogeneous chemistry of butanol and decanol with sulfuric acid: implications for secondary organic aerosol formation

Recent environmental chamber studies suggest that acid-catalyzed reactions between alcohols and aldehydes in the condensed phase lead to the formation of hemiacetals and acetals, enhancing secondary organic aerosol (SOA) growth. We report measurements of heterogeneous uptake of butanol and decanol on liquid H2SO4 in the range of 62-84 wt % and between 273 and 296 K. Both alcohols exhibit two distinct types of uptake behaviors (partially irreversible vs totally irreversible uptake), depending on the acid concentration and temperature. For the partially irreversible uptake, a fraction of the alcohol was physically absorbed while the other fraction underwent irreversible reaction. For the totally irreversible uptake, the alcohols were completely lost onto the sulfuric acid. The Henry's law solubility constant (H*) was determined from the time-dependent uptake, while the reactive uptake coefficients were calculated from the time-independent irreversible loss. Coexistence of butanol or decanol with octanal or decanal did not show enhanced uptake of the aldehydes in the sulfuric acid. Protonation and dissolution likely account for the reversible uptake, while formation of alkyl sulfate or dialkyl sulfate explains irreversible uptake of the alcohols. The results suggest that heterogeneous uptake of larger alcohols is unlikely of significant importance in the lower atmosphere except in the case of freshly nucleated aerosols that may have high acid concentrations.