NMR conformational analysis of biosynthetic precursor-type lipid A: monomolecular state and supramolecular assembly

The detailed conformational analysis of a single molecule of the tetraacyl biosynthetic precursor-type lipid A and its characteristic supramolecular assembly in aqueous SDS-micelles are described. Regular molecular arrangements were observed by detailed analysis of the NMR spectra of synthetically pure specimens, including regiospecifically 13C-labeled ones. NMR analysis of a biologically inactive precursor-type analogue with four shorter acyl chains demonstrated its conformational flexibility, indicating the importance of hydrophobic interactions for maintaining the conformation of such molecules.     

Partial pressure dependency of 17O/16O and 18O/16O of molecular oxygen in the mass spectrometer

A method to determine both (17)O/(16)O and (18)O/(16)O ratios for molecular oxygen with high precision by direct introduction into the mass spectrometer without gas separation is presented. Because both (17)O/(16)O and (18)O/(16)O in mixed gases have good linear correlations with their mixing ratios, these isotopic compositions can be determined without a gas-separation procedure by calibration using prepared standard gases with variable mixed ratios and by monitoring the amounts of fragment ions. Analytical precision for delta(17)O and delta(18)O of 45 and 7 per meg, respectively, were obtained. The observed partial pressure dependency of isotopic composition may be caused by isotope fractionation during admission from the ionization chamber into the flight tube of the mass spectrometer.     

Insight on Structural Change in Sol–Gel-Derived Silica Gel with Aging under Basic Conditions for Mesopore Control

Structural rearrangement of sol–gel-derived silica gel by aging under basic conditions was investigated using small angle X-ray scattering (SAXS) and ²⁹Si nuclear magnetic resonance (NMR). A wet silica gel prepared under acidic conditions had a fractal nature, and many unreacted silanols remained on the surface. During aging of the gel in ammonia solution, additional Si—O—Si bonds rapidly formed, whereas the change in mesoscale structure gradually proceeded. This result was compared with that of simulation modeling the Ostwald ripening, i.e. dissolution from positive curvature and reprecipitation on negative curvature. In the simulation, structural change in a cluster from fractal nature to particle aggregates was well visualized in 2-dimmensional square lattice. Both scattering profiles calculated from the model clusters and the change in average coordination number of monomers in the cluster well agreed with the experimental SAXS and NMR results, respectively. This agreement strongly ensures us that structural change by aging under basic conditions proceeds through the Ostwald ripening. The mesopore size as well as mesopore volume in calcined silica gel is determined by the shrinkage degree during drying and calcination. The sample aged in basic solution restrains the shrinkage because of the growth of particulate structure, and retains large size and volume of pores.     

Chiral sensing for amino acid derivative based on a [2]rotaxane composed of an asymmetric rotor and an asymmetric axle

A racemic [2]rotaxane, composed of an asymmetric rotor and an asymmetric axle, formed a diastereomer with an amino acid derivative, and showed an optical response for the chiral recognition.     

Adsorption Equilibrium Equation of Carboxylic Acids on Anion-Exchange Resins in Water

The adsorption of propionic acid and benzoic acid on anion-exchange resins was analyzed, and an adsorption equilibrium equation of carboxylic acids was proposed. The adsorption of carboxylic acids on the anion-exchange resins was considered to be the sum of the physical adsorption of the molecule and the ion-exchange adsorption of the ion, which were independent of each other. For the physical adsorption of carboxylic acids, it was conformed to the Freundlich equation. For the ion-exchange adsorption of carboxylate ions, the equilibrium equation corresponded well with the experimental results for wide ranges of concentration and pH. The equation contains a selectivity coefficient S(A)(Cl) for the chloride ion versus the carboxylate ion, which was considered essentially a constant. The influent of the bicarbonate ion from carbon dioxide in air could also be expressed by the additional equilibrium equation with the selectivity coefficient S(HCO(3))(Cl) for the chloride ion versus the bicarbonate ion. Consequently, an adsorption equilibrium equation can estimate the equilibrium adsorption amounts. Even the effect of a coexisting bicarbonate ion is inconsequential when the parameters of the Freundlich isotherm equation and the selectivity coefficients of the carboxylate ion and the bicarbonate ion in each resin are determined in advance. Copyright 2001 Academic Press.     

Prediction of CB[8] host–guest binding free energies in SAMPL6 using the double-decoupling method

This study reports the results of binding free energy calculations for CB[8] host–guest systems in the SAMPL6 blind challenge (receipt ID 3z83m). Force-field parameters were developed specific for each of host and guest molecules to improve configurational sampling. We used quantum mechanical (QM) implicit solvent calculations and QM force matching to determine non-bonded (partial atomic charges) and bonded terms, respectively. Free energy calculations were carried out using the double-decoupling method (DDM) combined with Hamiltonian replica exchange method (HREM) and Bennett acceptance ratio (BAR) method. The root mean square error (RMSE) of the predicted values using DDM with respect to the experimental results was 4.32 kcal/mol. The coefficient of determination (R²) and Kendall rank coefficient (τ) were 0.49 and 0.52, respectively, highest of all submissions. In addition, these were compared to the results obtained by umbrella sampling (US) and weighted histogram analysis method (WHAM). Overall, DDM achieved a higher prediction accuracy than the US method. Results are discussed in terms of parameterization and free energy simulations.