Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.     

Ultrasound-assisted oxidative desulfurization of liquid fuels and its industrial application

Latest environmental regulations require a very deep desulfurization to meet the ultra-low sulfur diesel (ULSD, 15 ppm sulfur) specifications. Due to the disadvantages of hydrotreating technology on the slashing production conditions, costs and safety as well as environmental protection, the ultrasound-assisted oxidative desulfurization (UAOD) as an alternative technology has been developed. UAOD process selectively oxidizes sulfur in common thiophenes in diesel to sulfoxides and sulfones which can be removed via selective adsorption or extractant. SulphCo has successfully used a 5000 barrel/day mobile “Sonocracking” unit to duplicate on a commercial scale its proprietary process that applies ultrasonics at relatively low temperatures and pressures. The UAOD technology estimate capital costs less than half the cost of a new high-pressure hydrotreater. The physical and chemical mechanisms of UAOD process are illustrated, and the effective factors, such as ultrasonic frequency and power, oxidants, catalysts, phase-transfer agent, extractant and adsorbent, on reaction kinetics and product recovery are discussed in this review.     

Luminescent N-isopropylacrylamide–surfmer copolymer hydrogels prepared upon electrostatic self-assembly of 1-pyrenesulfonate

The preparation of luminescent hydrogels based on the electrostatic self-assembly of 1-pyrenesulfonate (PyS) anions in a positively charged N-isopropylacrylamide (NiPAAm)/surfmer copolymer gel is described. The hydrogels were prepared from a micellar aqueous solution of 11-acryloyloxyundecyltrimethylammonium bromide and NiPAAm upon ⁶⁰Co-gamma irradiation. For assembly of PyS, the gel was shrunken at 50 °C and re-swollen at 20 °C in an aqueous solution of sodium 1-pyrenesulfonate. Re-swelling was accompanied by electrostatic assembly of PyS anions within the gel. Subsequently, the excess non-bound PyS ions were removed by repeatedly swelling and shrinking the gel in pure water at 20 °C and 50 °C, respectively. Incorporation of PyS ions in the hydrogel was studied using UV/Vis spectroscopy and energy dispersive x-ray (EDX) measurements. The amount of electrostatically adsorbed PyS was found to be proportional to the amount of copolymerized surfmer. EDX studies indicated that 20% of the bromide counterions were replaced for PyS. The PyS counterions could be released again if the functionalized hydrogel was immersed in acidified water. At a pH of 1, an almost complete release of PyS was found after 250 h. The preparation method can be used to introduce a variety of functional properties in thermoresponsive charged copolymer gels.     

Synthesis and reactivity of some diselenasila cycles containing an annelated dicarba‐closo‐dodecaborane(12) unit

The use of 1,2‐diselenolato‐1,2‐dicarba‐closo‐dodecaborane(12) dianions [1,2‐(1,2‐C₂B₁₀H₁₀)Se₂]^2? prepared in situ as the dilithium salt may lead to irreproducible results. This is shown by the straightforward synthesis of silanes using the purified and isolated dianions, in contrast with previous less successful attempts. Thus, the reactions of the dianions with dichlorosilanes afford the five‐membered diselenasila cycles containing the SiMe₂ or the SiPh₂ units, and with 1,2‐dichloro‐tetramethyldisilane the six‐membered cycle containing the Si₂Me₄ unit. The latter was studied by X‐ray diffraction, and all products were characterized by multinuclear magnetic resonance (¹H, ¹³C, ²⁹Si, ⁷⁷Se NMR) in solution. Novel isotope effects were detected in ¹³C and ⁷⁷Se NMR spectra. Exchange reactions of the five‐ and six‐membered diselanasila cycles with chlorosilanes were studied. Copyright © 2009 John Wiley & Sons, Ltd.     

Advances towards Cell-Specific Gene Transfection: A Small-Molecule Approach Allows Order-of-Magnitude Selectivity

A transfection vector that can home in on tumors is reported. Whereas previous vectors that allow moderately cell selective gene transfection used larger systems, this small-molecule approach paved the way for precise structure-activity relationship optimization. For this, biotin, which mediates cell selectivity, was combined with the potent DNA-binding motif tetralysine-guanidinocarbonypyrrol via a hydrophilic linker, thus enabling SAR-based optimization. The new vector mediated biotin receptor (BR)-selective transfection of cell lines with different BR expression levels. Computer-based analyses of microscopy images revealed a preference of one order of magnitude for the BR-positive cell lines over the BR-negative controls.     

Die chemie der schweren carben-analogen R2M,M = Si,Ge, Sn: IX. Eigenschaften und thermolyse von neuen 7-silabicyclo[2.2.1]heptadienen

Factors governing the ease and mechanism of 7-silabicyclo[2.2.1]heptadienes thermolysis in order to generate free silylenes and the corresponding benzene derivatives are investigated. For this purpose, 29 new compounds of the types VII–X have been prepared. No indications for a polar mechanism or an intermediate biradical could be found. The degradation is exactly of first order in all cases investigated sofar, and is enhanced by phenyl groups at the bridgehead C atoms, if a conformation coplanar with the basic ring is allowed by the neighbouring substituents, but is not enhanced by phenyl groups at the Si. The X-ray structure of two typical derivatives is discussed with this respect. A special mechanism is operating in the easy thermolysis of carbomethoxy-substituted compounds leading to cyclic sila enolether intermediates.