Deuterium NMR studies of inositol liquid crystals [1]

Deuterium NMR investigations are presented on members of two new mesogenic series derived from the naturally occurring stereoisomers myo- and scW/o-inositol. Tetraethers of these two series exhibit thermotropic columnar phases in which the columns are apparently formed by stacked hydrogen bonded dimers of these molecules which chemically are vicinal diols. Deuterium NMR measurements were performed on the tetraoctyl homologues 2e (a cis diol) and 3e (a trans diol) of these series. We have investigated mixtures of these diols with small amounts of benzene-d₆ as probe molecules as well as samples of the neat diol compounds deuteriated at their hydroxyl groups. The results obtained show that the mesophases of both compounds are uniaxial and align partially in a magnetic field upon slow cooling from their isotropic liquids. The alignment is with the director parallel to the field direction indicating that the anisotropic magnetic susceptibility of this mesophase is positive. The deuterium quadrupole splitting of the benzene-d₆ probe in both systems is temperature dependent and in the trans diol 3e it even changes sign. This is interpreted in terms of a model in which the benzene-d₆ probe equilibrates rapidly between two (or more) solvation sites with quadrupole splittings of opposite signs The deuterium spectra of the neat deuterium labelled cis diol 2e exhibit two different signals due to the two deuterons which are located at the axial and equatorial hydroxyl groups. This indicates that there is no fast intra- or intermolecular exchange of the hydroxyl hydrogens. The overall quadrupole splittings of the hydroxyl deuterons in this compound are highly reduced compared to their static values and this is interpreted in terms of motional modes involving both reorientation of the hydroxyl deuterons about their C-O axis and overall reorientation of the molecules (or pairs of molecules) around the columnar axes. The corresponding spectra of the neat deuteriated trans diol 3e exhibit a single spectrum indicating that both hydroxyl deuterons in this compound are equivalent, or very nearly so. Within the mesophase region the spectrum undergoes gradual changes due to the increase in the molecular mobility, but the overall motional narrowing is less than in the cis isomer 2e. Apparently due to stronger hydrogen bonding in the trans isomer 3e the precession of the hydroxyl groups is hindered and a fast molecular reorientation is only possible at high temperatures.     

New applications of atomic physics to the study of nuclear properties

The hyperfine interaction couples the atomic electrons and the nucleus, and because of this interaction, there is a fundamental link between the fields of atomic physics and nuclear physics. Of course, information flows in both directions through this link. This paper reviews in broad terms the previous applications of atomic physics methods to the study of nuclear properties and fundamental interactions, and then focuses on the possible applications of atom trapping methods to nuclear physics problems.Supported in part by the National Science Foundation.     

Determination of thickness, dielectric constant of thiol films, and kinetics of adsorption using surface plasmon resonance

This paper describes the formation of a self-assembled monolayer of 11-mercaptoundecanoic acid (MUA) under different concentrations on a gold sensor disk, monitoring in situ and in real time using surface plasmon resonance spectroscopy (SPR). The film thickness and dielectric constant were determined for a fully formed monolayer using one-color approach SPR. The kinetic studies of the film formation in ethanol solution indicated that the self-assembled monolayer is formed in a two-step adsorption process. In this sense, this unpublished route was applied on the basis of a model where many molecules are adsorbed at an initial step and then can be desorbed and/or rearranged to form a perfect monolayer.     

Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment

Quantum mechanical and quantum mechanical/molecular mechanical calculations in conjunction with continuum solvation models have been used to analyze CH-pi interactions in model systems of aryl- and alkyl-aromatic interactions, as well as in a model folding system designed to study those interactions. High level calculations reproduced accurately the interaction of CH-pi interactions in both alkyl- and aryl-based model systems. Dispersion effects dominate the interaction, but the electrostatics term is also relevant for aryl CH-pi interactions. Theoretical calculations were also used to examine the influence of CH-pi interactions in determining the conformational flexibility of folding models. Finally, a critical comparison of the results obtained from high level calculations on model systems and the experimental data derived for folding models in apolar solvents was carried out, which allowed us to reconcile the apparent discrepancy found between both data.     

Multiresidue determination of fluoroquinolones in shrimp by liquid chromatography-fluorescence-mass spectrometry

An efficient multiresidue method for analysis of fluoroquinolones in shrimp has been developed in which quantitation by fluorescence and confirmation by Multiple Stage Mass Spectrometry (MS) is achieved simultaneously. In this method, shrimp tissue is extracted with ammoniacal acetonitrile and the extract is defatted and then evaporated. After dissolution in basic phosphate buffer, fluoroquinolones in the extract are separated by liquid chromatography and quantitated, taking advantage of their intense fluorescence. Eluate from the fluorescence detector enters the MS, which allows for confirmation by monitoring ratios of 2 prominent product ions in the MS3 or MS2 spectrum. Using this method, 8 fluoroquinolones have been analyzed in shrimp samples fortified at 10, 25, 50, or 100 ppb levels. Recoveries for desethyleneciprofloxacin, norfloxacin, ciprofloxacin, danofloxacin, enrofloxacin, orbifloxacin, sarafloxacin, and difloxacin ranged from 75 to 92%, with relative standard deviation values of <6%. The limits of quantitation ranged from 0.1 to 1 ng/g. Enrofloxacin and ciprofloxacin were also successfully determined in enrofloxacin-incurred shrimp using this method.     

Tautomeric conjugate acids of 2-aminopyrroles: effect of substituents, solvation and cosolute

The tautomeric preferences of the conjugated acids of 2-aminopyrrole derivatives have been examined both in the gas phase and in aqueous solution by using a combination of quantum mechanical, self-consistent reaction field and Monte Carlo–free-energy perturbation methods. The results show that the nature of substituents, the solvent and the presence of cosolute are relevant factors in modulating the relative stability between the tautomeric conjugate acids protonated at the heterocyclic ring and at the exocyclic amino nitrogen. Thus, attachment of electron-withdrawing groups to the ring, solvation in polar solvents, and the presence of negatively charged cosolutes tend to favor protonation at the exocyclic amino nitrogen. Nevertheless, none of these factors alone suffice to change the tautomeric preference for the ring-protonated forms. The results point out that the concerted occurrence of the three factors is necessary to shift the tautomeric preference towards the conjugated species protonated at the exocyclic nitrogen.Contribution to the Jacopo Tomasi Honorary Issue     

Theoretical study of the mechanisms of substrate recognition by catalase

A variety of theoretical methods including classical molecular interaction potentials, classical molecular dynamics, and activated molecular dynamics have been used to analyze the substrate recognition mechanisms of peroxisomal catalase from Saccharomyces cerevisiae. Special attention is paid to the existence of channels connecting the heme group with the exterior of the protein. On the basis of these calculations a rationale is given for the unique catalytic properties of this enzyme, as well as for the change in enzyme efficiency related to key mutations. According to our calculations the water is expected to be a competitive inhibitor of the enzyme, blocking the access of hydrogen peroxide to the active site. The main channel is the preferred route for substrate access to the enzyme and shows a cooperative binding to hydrogen peroxide. However, the overall affinity of the main channel for H(2)O(2) is only slightly larger than that for H(2)O. Alternative channels connecting the heme group with the monomer interface and the NADP(H) binding site are detected. These secondary channels might be important for product release.     

Mesomorphism,isomerization, and dynamics in a new series of pyramidic liquid crystals

Nona-alkanoyloxy tribenzocyclononene (CTV-n, where n is the number of carbons in the side chains) were prepared for n = 2 to 14. The homologues of this series appear in two stable isomeric forms, rigid crown and flexible saddle. We report on their isomerization equilibria and dynamics in solution and on their mesomorphic properties in the neat state. The crown-saddle equilibrium and interconversion kinetics of the CTV-8 isomers were studied in dimethyl formamide solutions using high-resolution (1)H NMR in the temperature range from 50 to 130 degrees C. At lower temperatures, the isomerization is too slow to measure. In this range the equilibrium saddle fraction increases from approximately 0.40 to approximately 0.65, whereas the isomerization rate increases from approximately 10(-)(4) to approximately 1 s(-)(1). The saddle isomer undergoes fast pseudorotation at room temperature, but below about -50 degrees C, it becomes slow enough to affect the NMR line width. The rate parameters for this process were estimated from the carbon-13 spectra in methylene chloride solutions to be, k(p)(-100 degrees C) approximately 1.7 x 10(3) s(-)(1) and E(a) approximately 9.6 kJ/mol. The slow crown-saddle isomerization at room temperature (half-life of about one year) allows quantitative separation (by chromatography) of the two isomers and their separate investigation. When the alkanoyloxy side chains are sufficiently long both isomers are mesogenic (n >or= 4 for the saddle and n >or= 5 for the crown), exhibiting hexagonal columnar mesophases. The structure, dynamics, and mesomorphic properties of these mesophase were investigated by X-ray diffraction, optical polarizing microscopy, differential scanning calorimetry, and NMR. The lattice parameters of the crown and saddle mesophases of corresponding homologues are almost identical and increase monotonically with increasing length of the side chains. The clearing temperatures of the saddle isomers are consistently lower than those of the corresponding crowns. Within each series, the clearing temperatures are almost independent of the length of the side chains (156 to 170 degrees C for the crown and 115 to 148 degrees C for the saddle). The thermal and kinetic properties of the neat compounds lead to peculiar phase sequences, as observed in the polarizing microscope and in the DSC thermogram, involving repeated, back and forth, interconversion between the two isomers. Carbon-13 MAS NMR measurements of the crown and saddle mesophases of several homologues were carried out. The spectra of the crown mesophase exhibit dynamic features consistent with planar 3-fold molecular jumps about the column axes. A quantitative analysis for the CTV-8 crown homologue yielded the following Arrhenius parameters, A = 3.1 x 10(22)s(-)(1) and E(a) = 130.1kJ/mol. These unusually high values suggest that the barrier to the jump process is temperature dependent, decreasing with increasing temperature. The rate of this 3-fold jump process is slower for the lower homologues and faster for the higher ones. In contrast, the saddle isomers in the mesophase do not show dynamic effects in their carbon-13 MAS spectra. They do not undergo pseudorotation, and it appears that the molecules remain locked within the columns in a saddle conformation, up to the clearing temperature. However, on (super-)cooling to room temperature and below, selective line broadening is observed in their carbon-13 MAS spectra. This suggests that the saddle conformation is twisted in the mesophase and undergoes fast high-amplitude jumps between the twisted forms. On cooling, these high-amplitude librations freeze out to give an orientationally disordered state. On a very long time scale (of the order of days at 100 degrees C), the saddle mesophase transforms into that of the crown, apparently by sublimation.     

Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives

The structural, dynamical, and recognition properties of antiparallel DNA triplexes formed by the antiparallel d(G#G.C), d(A#A.T), and d(T#A.T) motifs (the pound sign and dot mean reverse-Hoogsteen and Watson-Crick hydrogen bonds, respectively) are studied by means of "state of the art" molecular dynamics simulations. Once the characteristics of the helix are defined, molecular dynamics and thermodynamic integration calculations are used to determine the expected stabilization of the antiparallel triplex caused by the introduction of 8-aminopurines. Finally, oligonucleotides containing 8-aminopurine derivatives are synthesized and tested experimentally using several approaches in a variety of systems. A very large stabilization of the triplex is found experimentally, as predicted by simulations. These results open the possibility for the use of oligonucleotides carrying 8-aminopurines to bind single-stranded nucleic acids by formation of antiparallel triplexes.