Glycosidic bond formation in aqueous solution: on the oxocarbenium intermediate

The mechanism of specific acid-catalyzed glycosidic bond formation between methanol and alpha-d-glucopyranoside in aqueous solution at 300 K was studied using Car-Parrinello molecular dynamics. The reaction was found to proceed through a non-solvent equilibrated oxocarbenium cation intermediate characterized by the loss of a hydrogen-bonding interaction between the ring oxygen and solvating water. The mechanism, which was found to be D(N)A(N) in nature, is discussed in detail.     

The ion sensitivity of surface conductive single crystalline diamond

Charge build-up at the solid/aqueous interface is a ubiquitous phenomenon that determines the properties of interfacial electrical double layers. Due to its unique properties, the surface of diamond offers an attractive platform to investigate charging mechanisms in aqueous solutions. We investigate the surface charge by studying the ion sensitivity of H-terminated single crystalline diamond surface conductive layers. The effect of monovalent and divalent salts has been probed at different pH values. For a pH above 3.5, increasing the ionic strength results in a decrease of the surface conductivity, in contrast to the results obtained for pH below 3.5. Electrokinetic experiments are in good agreement with the surface conductivity measurements, showing an isoelectric point at pH 3.5 for the H-terminated diamond surface. We discuss the results in terms of the Coulombic screening by electrolyte ions of the surface potential, which is induced by a pH-dependent surface charge. The origin of this surface charge is discussed in terms of charge regulation by amphoteric hydroxyl surface groups and unsymmetrical adsorption of hydroxide and hydronium ions induced by the hydrophobic nature of the H-terminated diamond surface. This surface charge can have important consequences for processes governed by the diamond/aqueous interface, such as electron transfer to charged redox molecules, adsorption of charged molecules and proteins, and ion sensitivity.     

Isochorismate pyruvate lyase: a pericyclic reaction mechanism?

Isochorismate pyruvate lyase (IPL) catalyzes the cleavage of isochorismate to give salicylate and pyruvate, a key step in bacterial siderophore biosynthesis. We investigated the enzyme from Pseudomonas aeruginosa using isochorismate selectively deuterated at C2 as a substrate. Monitoring the reaction by 2H NMR spectroscopy revealed that the label is quantitatively transferred from C2 to C9, producing stoichiometric amounts of [3-2H]pyruvate as product. Moreover, the deuterium kinetic isotope effect of 2.34 +/- 0.08 on kcat indicates that C-H cleavage is significantly rate limiting. Consistent with these data, hybrid density functional theory (HDFT) calculations at the Becke3LYP/DZ+(2d,p) level of theory predict a concerted but highly asynchronous pericyclic transition structure, in which carbon-oxygen bond cleavage is more advanced than hydrogen atom transfer from C2 to C9; the calculated 2H isotope effect of 2.22 at C2 is in excellent accord with the experimental value. Together, these findings indicate that IPL should be added to the small set of proteins that are known to catalyze pericyclic reactions. They also raise the possibility that enzymes, such as chorismate pyruvate lyase, salicylate synthase, 4-amino-4-deoxychorismate lyase, and anthranilate synthase, which accelerate formally similar reaction steps, may also exploit pericyclic mechanisms.     

Why is polonium simple cubic and so highly anisotropic?

Using the state-of-the-art ab initio electronic structure calculations, we explain why alpha-Po prefers the simple cubic structure (it is due to the relativistic mass-velocity and Darwin terms), elucidate its extreme elastic anisotropy (this is an intrinsic property of the simple cubic crystal structure), and predict a transformation to a mixture of two trigonal structures at pressures of 1-3 GPa.     

Synthesis of a highly enantiomerically enriched silyllithium compound

The highly enantiomerically enriched silyllithium compound lithiomethylphenyl(1-piperidinylmethyl)silane (4) reacts stereospecifically with chlorosilanes, but over a period of several hours slow racemization in solution at room temperature occurs, which can be suppressed by a transmetalation reaction with MgBr2(thf)4.     

Inverse temperature transition of a biomimetic elastin model: reactive flux analysis of folding/unfolding and its coupling to solvent dielectric relaxation

The inverse temperature transition (ITT) of a biomimetic model for elastin, capped GVG(VPGVG) in liquid water, is investigated by a comprehensive classical molecular dynamics study. The temperature dependence of the solvation structure and dynamics of the octapeptide are compared using three common force fields, CHARMM, GROMOS, and OPLS. While these force fields differ in quantitative detail, they all predict this octapeptide to undergo a "folding transition" to closed conformations upon heating and a subsequent "unfolding transition" to open conformations at still higher temperatures, thus reproducing the ITT scenario. The peptide kinetics is analyzed within the reactive flux formalism applied to the largest-amplitude mode extracted from principal component analysis, and the solvent's dielectric fluctuations are obtained from the total water dipole autocorrelations. Most importantly, preliminary evidence for an intimate coupling of peptide folding/unfolding dynamics, and thus the ITT, and dielectric relaxation of bulk water is given, possibly being consistent with a "slave mode" picture.     

On the significance of the anchoring group in the design of antenna materials based on phthalocyanine stopcocks and zeolite L

The synthesis of stopcocks based on zinc phthalocyanine for selective adsorption at the channel entrances of zeolite L is reported. The introduction of either an inert SiMe? moiety, an imidazolium cation or a reactive isothiocyanate (NCS) group allows attachment to the channel entrances of zeolite L through van der Waals interactions, electrostatic interactions, or covalent binding, respectively. Stopcocks that rely on van-der-Waals-driven adsorption require careful selection of the solvent used for the deposition onto the zeolite surface to avoid a nonspecific distribution of the molecules. Regarding the design of photonic antenna systems, a stopcock with a cationic tail was found to be the most convenient, based on the observation that efficient energy transfer from molecules located in the zeolite nanochannels is more readily obtained than in the other cases.     

Self-organization of 1-methylnaphthalene on the surface of artificial snow grains: a combined experimental-computational approach

A combined experimental-computational approach was used to study the self-organization and microenvironment of 1-methylnaphthalene (1MN) deposited on the surface of artificial snow grains from vapors at 238 K. The specific surface area of this snow (1.1 × 10(4) cm(2) g(-1)), produced by spraying very fine droplets of pure water from a nebulizer into liquid nitrogen, was determined using valerophenone photochemistry to estimate the surface coverage by 1MN. Fluorescence spectroscopy at 77 K, in combination with molecular dynamics simulations, and density functional theory (DFT) and second-order coupled cluster (CC2) calculations, provided evidence for the occurrence of ground- and excited-state complexes (excimers) and other associates of 1MN on the snow grains' surface. Only weak excimer fluorescence was observed for a loading of 5 × 10(-6) mol kg(-1), which is ～2-3 orders of magnitude below monolayer coverage. However, the results indicate that the formation of excimers is favored at higher surface loadings (>5 × 10(-5) mol kg(-1)), albeit still being below monolayer coverage. The calculations of excited states of monomer and associated moieties suggested that a parallel-displaced arrangement is responsible for the excimer emission observed experimentally, although some other associations, such as T-shape dimer structures, which do not provide excimer emission, can still be relatively abundant at this surface concentration. The hydrophobic 1MN molecules, deposited on the ice surface, which is covered by a relatively flexible quasi-liquid layer at 238 K, are then assumed to be capable of dynamic motion resulting in the formation of energetically preferred associations to some extent. The environmental implications of organic compounds' deposition on snow grains and ice are discussed.