Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra

Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as the PRG would require the protein to raise the pK(a) of a hydronium by almost 11 pK(a) units, which is difficult considering known cases of pK(a) shifts in proteins. Our recent quantum mechanics/molecular mechanics (QM/MM) simulations suggested an alternative "intermolecular proton bond" model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pK(a) values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting X-ray structure, and nuclear quantum effects, the "intermolecular proton bond" model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the "intermolecular proton bond" model is likely applicable to the PRG in biomolecular proton pumps in general.     

Advances in high throughput screening of gas sensing materials

The workflow of a high throughput screening setup for the rapid identification of new and improved gas sensor materials is presented. The polyol method was applied to prepare nanoparticulate metal oxides as base materials. These materials have been modified by surface and volume doping. Using multielectrode substrates and high throughput impedance spectroscopy (HT-IS) a wide range of materials could be screened on a short time scale. Selected examples reflect the state of the art for applying HT-IS in search of new selective gas sensing materials.     

Facile Synthesis and Theoretical Conformation Analysis of a Triazine‐Based Double‐Decker Rotor Molecule with Three Anthracene Blades

The facile synthesis of a rotor‐shaped compound with two stacked triazine units, which are symmetrically connected by three anthracene blades through oxygen linkers, is presented. This new double‐decker, which is a potential monomer for two‐dimensional polymerization, was synthesized by using readily available, cheap building blocks, exploiting the known selectivity difference for the nucleophilic substitution of cyanuric chloride. The crystal structure of a C_3h symmetric rotor‐shaped compound with 9,10‐dihydroanthracene blades, which is a direct precursor to the targeted monomer, and the crystal structure of the new double‐decker with the desired C_3h symmetry, are also reported. The synthetic efforts were preceded by a computational analysis, which was triggered by the question of conformational stability of the potential monomer. Two stable conformers could be found, and the barrier for the transition path in the gas phase between these conformers was determined by quantum chemical calculations. Exploratory Born–Oppenheimer molecular‐dynamics simulations revealed a strong influence of solvent–solute interactions on the stability of the conformers, which resulted in an energetic preference of the C_3h symmetric conformation of the double‐decker.     

Teachers’ views on effective mathematics teaching: commentaries from a European perspective

The previous papers of this issue discuss the views teachers from the United States, Australia, Hong Kong SAR, and Mainland China have on effective mathematics teaching and learning. Similarities and differences are found and a differentiation from West to East can be worked out in the order of the regions as listed above. The picture of teachers’ views can, however, be differentiated when they are looked at from a European perspective. On the basis of the analysis of two comparative studies on teaching cultures in three European countries and a questioning of teachers, this commentary therefore locates France, Germany, and England within this framework so that the East–West-contrast is distinguished in more detail.     

Reactivity and properties of [-O-Bi(III...)O=Mo-]n chains

A coordination polymer [Cp(O)2Mo-O-Bi(o-tolyl)2]n, II, containing Mo-O-Bi and Mo=O...Bi moieties was investigated with respect to its behavior in contact with OH- and Cp2MoH2 and as potential single source precursor in the polyol method. It turned out that hydroxide as a base breaks up the polymer to yield CpMoO3- and (o-tolyl)2BiOH. The latter polymerizes to give the coordination polymer [(o-tolyl)2BiOH]n, 1. Alternatively, 1 can be prepared by reacting [(o-tolyl)2Bi(hmpa)2]SO3CF3 with NBu4OH/H2O in thf/water. If, however, NBu4OH/MeOH is used in dichloromethane as the solvent, the (o-tolyl)2BiOH formed intermediately undergoes methanolysis, and finally, [(o-tolyl)2BiOMe]n, 3, is isolated. Although 1 and 3 are very similar compounds, their crystal structures differ significantly: while the structure of 1 is dominated by secondary bonding leading to seesaw-type coordination geometries around the Bi centers, the Bi atoms in 3 are coordinated in a distorted tetrahedral fashion, and secondary bonding plays only a minor role. If 1 is dissolved in a nonpolar, nonprotic solvent, condensation reactions occur immediately leading to [(o-tolyl)2BiOBi(o-tolyl)2], 2, which can be obtained on a preparative scale this way. Compound 3 which can be prepared in good yields may prove to be a useful starting material in bismuth chemistry. Here, it was shown to react with molybdocene dihydrides to provide stable Bi-substituted molybdocene monohydrides [(R)Cp2Mo(H)(Bi(o-tolyl)2)] (R = Me 4, R = H 5); compounds of that type were identified in solution before but had so far eluded isolation. Compound 4, whose crystal structure is discussed, also forms when II is treated with methylated molybdocene dihydride. This obviously leads to the formation of Mo-Bi bonds (--> 4), as well as Mo-OH units, which undergo condensation reactions leading to Mo-O-Mo moieties (i.e., [Cp2Mo2O5] is formed as a byproduct). The use of II as precursor in the polyol method successfully led to bismuthmolybdate nanoparticles (accompanied by crystallites); however, no single phase is obtained, but biphasic materials consisting of Bi(2)Mo2O9 and Bi2MoO6, whose ratio can be determined by the choice of the hydrolyzing reagent, are formed instead. One of these materials proved to be capable of sensing EtOH selectively at elevated temperatures.     

Encapsulation dehydration colligative cryoprotective strategies and amplified fragment length polymorphism markers to verify the identity and genetic stability of euglenoids following cryopreservation

An encapsulation/dehydration procedure was developed for Euglena gracilis Klebs as a 'model alga' to examine various cryoprotective regimes combined with controlled rate cooling to cryopreserve other Euglenoid taxa. Cryoprotective variables were optimised to enable reproducible growth following a combination of alginate encapsulation, sucrose osmotic dehydration, air desiccation, methanol treatment, cooling to -40 degrees C and plunging into liquid nitrogen (LN). Amplified Fragment Length Polymorphism (AFLP) analysis was adapted to: (i) verify algal identity by discriminating between different Euglenoids and (ii) examine the genetic stability of algal cultures prior to various stages of cryoprotective treatments and following exposure to LN. AFLPs were highly reproducible (> 99%) as reliable diagnostic markers, where a single DNA fragment change accounted for -0.4% of the detectable variation in an AFLP pattern. AFLP changes were detected in cryoprotective treatments following LN exposure. Successive stages of the dehydration and desiccation treatments did not accumulate AFLP changes indicating these are random events.     

Formation and manipulation of discrete supramolecular azobenzene assemblies

Azobenzene derivatives were deposited onto a Au(111) surface and studied by scanning tunneling microscopy. The symmetry of the parent azobenzene was broken by introducing tert-butyl groups which are known to decouple the molecular core from the substrate, on the one end, and carboxylic acid groups which direct and stabilize the supramolecular assembly structure on the surface by intermolecular hydrogen bonding, on the other end. As a consequence of the interacting COOH groups, the molecules assemble on the surface either in extended, polymeric chains and/or in discrete, hexameric rosettes. The high stability of the rosette structure is proven experimentally by controlled lateral displacement on the surface without breaking the non-covalent interactions. Although switching attempts were not successful, the approach herein should facilitate the construction of well-defined multi-switch arrays. Electronic Supplementary Material  The online version of this article () contains supplementary material, which is available to authorized users.     

Kinetic analysis of the photochemically and thermally induced isomerization of an azobenzene derivative on Au(111) probed by two-photon photoemission

Two-photon photoemission (2PPE) spectroscopy is employed to quantify the photochemically and thermally induced trans ⇌ cis isomerization of the molecular switch tetra-tert-butyl-azobenzene (TBA) adsorbed on an Au(111) surface. The isomerization of TBA is accompanied by significant changes in the electronic structure, namely different energetic positions of the lowest unoccupied molecular orbital of both isomers and the appearance of an unoccupied final state for cis-TBA. A quantitative analysis of these effects allows the calculation of cross sections for the reversible isomerization and determination of the ratio between both isomers in the photostationary state, where 55±5% of the molecules are switched to cis-TBA. The cross section for the photoinduced trans → cis isomerization is 3.3±0.5×10⁻²² cm², while for the back reaction, a value of 2.7±0.5×10⁻²² cm² is obtained. Furthermore a pronounced reduction of the activation energy by a factor of four compared to the free molecule is found for the thermally activated cis → trans isomerization of the surface-adsorbed TBA. This demonstrates that the potential energy landscape of the adsorbed TBA is remarkably different from the liquid phase.