A novel phosphoramidite method for automated synthesis of oligonucleotides on glass supports for biosensor development

Two protocols for functionalization of glass supports with hexaethylene glycol (HEG)-linked oligonucleotides were developed. The first method (standard amidite protocol) made use of the 2-cyanoethyl-phosphoramidite derivative of 4,4′-dimethoxytrityl-protected HEG. This was first coupled to the support by standard solid-phase phosphoramidite chemistry followed by extension with a thymidylic acid icosanucleotide. Stepwise addition of the linker phosphoramidite graduated at 1% (relative to the total sites available) perstep at 50°C resulted in an optimal yield of immobilized oligonucleotides at a density of 2.24 × 10¹⁰ strands/mm². This observed loading maximum lies well below the theoretical maximum loading owing to nonspecific adsorption of HEG on the glass and subsequent blocking of reactive sites. Surface loadings as high as 3.73 × 10¹⁰/mm² and of excellent sequence quality were achieved with a reverse amidite protocol. The support was first modified into a 2-cyanoethyl-N,N-diisopropylphosphoramidite analog followed by coupling with 4,4′-dimethoxytrityl-protected HEG. This protocol is conveniently available when using a conventional DNA synthesizer. The reverse amidite protocol allowed for control of the surface loading at values suitable for subsequent analytical applications that make use of immobilized oligonucleotides as probes for selective hybridization of sample nucleic acids of unknown sequence and concentration.     

Experimental and Theoretical Conformational Analysis of 5‐Benzylimidazolidin‐4‐one Derivatives – a ‘Playground’ for Studying Dispersion Interactions and a ‘Windshield‐Wiper’ Effect in Organocatalysis

The PF₆ salts of 5‐benzyl‐1‐isopropylidene‐ and 5‐benzyl‐1‐cinnamylidene‐3‐methylimidazolidin‐4‐ones 1 (Scheme) with various substituents in the 2‐position have been prepared, and single crystals suitable for X‐ray structure determination have been obtained of 14 such compounds, i.e., 2 – 10 and 12 – 16 (Figs. 2–5). In nine of the structures, the Ph ring of the benzyl group resides above the heterocycle, in contact with the cis‐substituent at C(2) (staggered conformation A ; Figs. 1–3); in three structures, the Ph ring lies above the iminium π‐plane (staggered conformation B ; Figs. 1 and 4); in two structures, the benzylic C? C bond has an eclipsing conformation ( C ; Figs. 1 and 5) which places the Ph ring simultaneously at a maximum distance with its neighbors, the CO group, the N?C‐π‐system, and the cis‐substituent at C(2) of the heterocycle. It is suggested by a qualitative conformational analysis (Fig. 6) that the three staggered conformations of the benzylic C? C bond are all subject to unfavorable steric interactions, so that the eclipsing conformation may be a kind of ‘escape’. State‐of‐the‐art quantum‐chemical methods, with large AO basic sets (near the limit) for the single‐point calculations, were used to compute the structures of seven of the 14 iminium ions, i.e., 3, 4 / 12, 5 – 7, 13 , and 16 (Table) in the two staggered conformations, A and B , with the benzylic Ph group above the ring and above the iminium π‐system, respectively. In all cases, the more stable computed conformer (‘isolated‐molecule’ structure) corresponds to the one present in the crystal (overlay in Fig. 7). The energy differences are small (≤2 kcal/mol) which, together with the result of a potential‐curve calculation for the rotation around the benzylic C? C bond of one of the structures, 16 (Fig. 8), suggests that the benzyl group is more or less freely rotating at ambident temperatures. The importance of intramolecular London dispersion (benzene ring in ‘contact’ with the cis‐substituent in conformation A ) for DFT and other quantum‐chemical computations is demonstrated; the benzyl‐imidazolidinones 1 appear to be ideal systems for detecting dispersion contributions between a benzene ring and alkyl or aryl CH groups. Enylidene ions of the type studied herein are the reactive intermediates of enantioselective organocatalytic conjugate additions, Diels–Alder reactions, and many other transformations involving α,β‐unsaturated carbonyl compounds. Our experimental and theoretical results are discussed in view of the performance of 5‐benzyl‐imidazolidinones as enantioselective catalysts.     

Predicting the tautomeric equilibrium of acetylacetone in solution. I. The right answer for the wrong reason?

This study investigates how the various components (method, basis set, and treatment of solvent effects) of a theoretical approach influence the relative energies between keto and enol forms of acetylacetone, which is an important model system to study the solvent effects on chemical equilibria from experiment and theory. The computations show that the most popular density functional theory (DFT) approaches, such as B3LYP overestimate the stability of the enol form with respect to the keto form by ～10 kJ mol^?1, whereas the very promising SCS‐MP2 approach is underestimating it. MP2 calculations indicate that in particular the basis set size is crucial. The Dunning Huzinaga double ζ basis (D95z(d,p)) used in previous studies overestimates the stability of the keto form considerably as does the popular split‐valence plus polarization (SVP) basis. Bulk properties of the solvent included by continuum approaches strongly stabilize the keto form, but they are not sufficient to reproduce the reversal in stabilities measured by low‐temperature nuclear magnetic resonance experiments in freonic solvents. Enthalpic and entropic effects further stabilize the keto form, however, the reversal is only obtained if also molecular effects are taken into account. Such molecular effects seem to influence only the energy difference between the keto and the enol forms. Trends arising due to variation in the dielectric constant of the solvent result from bulk properties of the solvent, i.e., are already nicely described by continuum approaches. As such this study delivers a deep insight into the abilities of various approaches to describe solvent effects on chemical equilibria. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Temperature dependence of structure and dynamics of the hydrated Ca2+ ion according to ab initio quantum mechanical charge field and classical molecular dynamics

Simulations using ab initio quantum mechanical charge field molecular dynamics (QMCF MD) and classical molecular dynamics using two‐body and three‐body potentials were performed to investigate the hydration of the Ca²⁺ ion at different temperatures. Results from the simulations demonstrate significant effects of temperature on solution dynamics and the corresponding composition and structure of hydrated Ca²⁺. Substantial increase in ligand exchange events was observed in going from 273.15 K to 368.15 K, resulting in a redistribution of coordination numbers to lower values. The effect of temperature is also visible in a red‐shift of the ion‐oxygen stretching frequencies, reflecting weakened ligand binding. Even the moderate increase from ambient to body temperature leads to significant changes in the properties of Ca²⁺ in aqueous environment. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Compressed Corannulene in a Molecular Cage

Self‐assembled coordination cages can be employed as a molecular press, where the bowl‐shaped guest corannulene (C₂₀H₁₀) is significantly flattened upon inclusion within the hydrophobic cavity. This is demonstrated by the pairwise inclusion of corannulene with naphthalene diimide as well as by the dimer inclusion of bromocorannulene inside the box‐like host. The compressed corannulene structures are unambiguously revealed by single‐crystal X‐ray analysis.     

Iron‐Catalyzed Intramolecular C(sp2)−H Amination

The nucleophilic iron complex Bu₄N[Fe(CO)₃(NO)] (TBA[Fe]) catalyzes the direct intramolecular C?H amination of α‐azidobiaryls and (azidoaryl)alkenes into the corresponding carbazoles and indoles, respectively, under mild conditions and with low catalyst loadings. These features and the broad functional‐group tolerance render this method a particularly attractive alternative to established noble‐metal‐based procedures.     

Interface Engineering of MoS2/Ni3S2 Heterostructures for Highly Enhanced Electrochemical Overall‐Water‐Splitting Activity

To achieve sustainable production of H₂ fuel through water splitting, low‐cost electrocatalysts for the hydrogen‐evolution reaction (HER) and the oxygen‐evolution reaction (OER) are required to replace Pt and IrO₂ catalysts. Herein, for the first time, we present the interface engineering of novel MoS₂/Ni₃S₂ heterostructures, in which abundant interfaces are formed. For OER, such MoS₂/Ni₃S₂ heterostructures show an extremely low overpotential of ca. 218 mV at 10 mA cm^?2, which is superior to that of the state‐of‐the‐art OER electrocatalysts. Using MoS₂/Ni₃S₂ heterostructures as bifunctional electrocatalysts, an alkali electrolyzer delivers a current density of 10 mA cm^?2 at a very low cell voltage of ca. 1.56 V. In combination with DFT calculations, this study demonstrates that the constructed interfaces synergistically favor the chemisorption of hydrogen and oxygen‐containing intermediates, thus accelerating the overall electrochemical water splitting.     

Picosecond dynamics and microheterogenity of water+dioxane mixtures

Dielectric spectra from 200 MHz up to 3 THz were determined to study the fast dynamics of dilute water+1,4-dioxane. epsilon(nu) could be fitted by a collision induced oscillator at high frequencies plus two Debye relaxations in the microwave region. Isotope substitution was used to assign water and dioxane modes. The presence of the cooperative hydrogen-bond network relaxation down to a water mole fraction of 0.005 suggests a microheterogeneous structure of the mixtures even at low water content. The collision mode of dioxane at approximately 2 THz grows upon water addition, revealing the presence of H2O molecules in dioxane-rich domains.