Determination of formates by oxidation with iodine

A selective determination of formates based on oxidation with iodine at 100° in presence of potassium hydrogen tartrate, and final titration with thiosulphate solution, is described. The error is below 0.5% for 25–90 mg of formic acid. Few other organic acids interfere.     

Separation and characterization of underivatized oligosaccharides using liquid chromatography and liquid chromatography-electrospray ionization mass spectrometry

Native cyclodextrin-based columns are particularly useful for the analysis of oligosaccharides because the retention of these carbohydrates is based mainly on the hydrogen bonding interactions of oligosaccharide hydroxyl groups with the stationary phase. Thus, the retention time predictably increases with the number of analyte hydroxyl groups, which corresponds to the elongation of the oligosaccharide chain. High-performance liquid chromatography (HPLC) coupled to electrospray ionization (ESI) mass spectrometry (MS) was used for the separation and characterization of underivatized oligosaccharide mixtures. With the limits of detection as low as 50 pg, all individual components of oligosaccharide mixtures (up to 11 glucose units long) were baseline resolved on a Cyclobond I 2000 column and detected using ESI-MS. Low flow rates and narrow I.D. columns increase the ESI-MS sensitivity significantly. The method showed potential usefulness for the sensitive and quick analysis of hydrolysis products of polysaccharides, and for trace levels of individual oligosaccharide or oligosaccharide isomers from biological systems.     

Bound states of a more general exponential screened Coulomb potential

An alternative approximation scheme has been used in solving the Schr?dinger equation to the more general case of exponential screened Coulomb potential, V(r) = −(a/r)[1 + (1 + br)e ^−2br ]. The bound state energies of the 1s, 2s and 3s-states, together with the ground state wave function are obtained analytically upto the second perturbation term.      

Pd2(dba)3/P(i-BuNCH2CH2)3N-catalyzed Stille cross-coupling of aryl chlorides

[reaction: see text] The Pd(2)(dba)(3)/P(i-BuNCH(2)CH(2))(3)N (1d) catalyst system is highly effective for the Stille cross-coupling of aryl chlorides with organotin compounds. This method represents only the second general method for the coupling of aryl chlorides. Other proazaphosphatranes possessing benzyl substituents also generate very active catalysts for Stille reactions. Noteworthy features of the method are: (a) commercial availability of ligand 1d, (b) the wide array of aryl chlorides that can be coupled, and (c) applicability to aryl, vinyl, and allyl tin reagents.     

From Valleys to Ridges: Exploring the Dynamic Energy Landscape of Single Membrane Proteins

Membrane proteins are involved in essential biological processes such as energy conversion, signal transduction, solute transport and secretion. All biological processes, also those involving membrane proteins, are steered by molecular interactions. Molecular interactions guide the folding and stability of membrane proteins, determine their assembly, switch their functional states or mediate signal transduction. The sequential steps of molecular interactions driving these processes can be described by dynamic energy landscapes. The conceptual energy landscape allows to follow the complex reaction pathways of membrane proteins while its modifications describe why and how pathways are changed. Single‐molecule force spectroscopy (SMFS) detects, quantifies and locates interactions within and between membrane proteins. SMFS helps to determine how these interactions change with temperature, point mutations, oligomerization and the functional states of membrane proteins. Applied in different modes, SMFS explores the co‐existence and population of reaction pathways in the energy landscape of the protein and thus reveals detailed insights into local mechanisms, determining its structural and functional relationships. Here we review how SMFS extracts the defining parameters of an energy landscape such as the barrier position, reaction kinetics and roughness with high precision.     

Mechanical properties of bovine rhodopsin and bacteriorhodopsin: possible roles in folding and function

Molecular interactions and mechanical properties that contribute to the stability and function of proteins are complex and of fundamental importance. In this study, we used single-molecule dynamic force spectroscopy (DFS) to explore the interactions and the unfolding energy landscape of bovine rhodopsin and bacteriorhodopsin. An analysis of the experimental data enabled the extraction of parameters that provided insights into the kinetic stability and mechanical properties of these membrane proteins. Individual structural segments of rhodopsin and bacteriorhodopsin have different properties. A core of rigid structural segments was observed in rhodopsin but not in bacteriorhodopsin. This core may reflect differences in mechanisms of protein folding between the two membrane proteins. The different structural rigidity of the two proteins may also reflect their adaptation to differing functions.     

Structural transitions in ion coordination driven by changes in competition for ligand binding

Transferring Na(+) and K(+) ions from their preferred coordination states in water to states having different coordination numbers incurs a free energy cost. In several examples in nature, however, these ions readily partition from aqueous-phase coordination states into spatial regions having much higher coordination numbers. Here we utilize statistical theory of solutions, quantum chemical simulations, classical mechanics simulations, and structural informatics to understand this aspect of ion partitioning. Our studies lead to the identification of a specific role of the solvation environment in driving transitions in ion coordination structures. Although ion solvation in liquid media is an exergonic reaction overall, we find it is also associated with considerable free energy penalties for extracting ligands from their solvation environments to form coordinated ion complexes. Reducing these penalties increases the stabilities of higher-order coordinations and brings down the energetic cost to partition ions from water into overcoordinated binding sites in biomolecules. These penalties can be lowered via a reduction in direct favorable interactions of the coordinating ligands with all atoms other than the ions themselves. A significant reduction in these penalties can, in fact, also drive up ion coordination preferences. Similarly, an increase in these penalties can lower ion coordination preferences, akin to a Hofmeister effect. Since such structural transitions are effected by the properties of the solvation phase, we anticipate that they will also occur for other ions. The influence of other factors, including ligand density, ligand chemistry, and temperature, on the stabilities of ion coordination structures are also explored.     

Theoretical investigation of intramolecular magnetic interaction through an ethylenic coupler

We show that an ethylenic coupler provides a very strong intramolecular magnetic interaction. A recently synthesized nitronyl nitroxide derivative, D-NIT2, is investigated by ab initio quantum chemical methods. The broken symmetry approach yields a coupling constant -541 K that is in good agreement with the observed value in solid state.     

Heavy-quark bound states in potentials with the Bethe-Salpeter equation

The spinless Bethe—Salpeter equation is solved for three attractive static quark-antiquark potentials of the form V(r)=–ar^–+br+c, 01, and the effective non-Coulombic power-law potential of the formV(r)=ar ^0.1+c to obtain the spin-averaged energy levels in bottomonium (b ) and charmonium (c ) families. The shifted 1/N expansion technique is used. Calculations of the energy eigenvalues are carried out up to third order and parameters of each potential are adjusted to obtain the best agreement with the experimental spin-averaged data (SAD). Flavor-dependent and flavor-independent cases are considered in this work.