Tandem ring-closing metathesis and hydrogenation towards cyclic dinucleotides

Cyclic dinucleotides containing a butylene nucleobase-phophotriester connection are synthesised by a tandem ring-closing metathesis and hydrogenation reaction.     

13C,13C coupling constants from a mixture of isotopomers (13C) of substituted aromatic compounds; 1-nitronaphthalenes

¹³C Homonuclear decoupling experiments led to the assignment of the carbon-carbon coupling constants of ¹³C-enriched 1-nitronaphthalene obtained by nitration of [1-¹³C]naphthalene. The effects of substituents on coupling constants can be explained on the basis of the electronegativity of the first atom of the substituent, and the observed substituent effects are shown to be parallel to previous data for oxygen containing substituents.     

General biorthogonal projected bases as applied to second-order Møller-Plesset perturbation theory

With low-order scaling correlated wave function theories in mind, we present second quantization formalism as well as biorthonormalization procedures for general--singular or nonsingular--bases. Of particular interest are the so-called projected atomic orbital bases, which are obtained from a set of atom-centered functions and feature a separation of occupied and virtual spaces. We demonstrate the formalism by deriving and implementing second-order M?ller-Plesset perturbation theory in it, and discuss the convergence and preconditioning of the iterative amplitude equations in detail.     

The synthesis of double-headed nucleosides by the CuAAC reaction and their effect in secondary nucleic acid structures

Four double-headed nucleosides were prepared by the CuAAC reaction. Hereby, a triazole-containing linker connects an additional thymine or adenine to the 2'-position of 2'-deoxyuridine, a thymine to the 5'-position of thymidine and a thymine to the 6'-position of an LNA-thymidine monomer. Whereas no conclusive recognition effects of the additional thymines were found when introduced in LNA or at the 5'-position, both thymine and adenine in the 2'-position were found to stabilise three-way junctions in both dsDNA and DNA?:?RNA contexts and to give cross-strand interactions in a DNA-duplex, when specifically introduced in a so-called (+1)-zipper motif.     

Electrochemically Driven Cup‐and‐Ball CuI and CuII Complexes

The conformation of copper “funnel” complexes that contains a coordinating appended arm can be electrochemically switched between endo, which corresponds to the self‐coordination of the arm through the cavity, and exo positions. This process, which is reminiscent of a cup‐and‐ball device, is activated by an exogenous ligand for complexes that contain a hydroxy‐terminated arm. The exchange is electrochemically triggered and is operated in either Cu^I or Cu^II redox states, depending on the exogenous ligand, that is, CO or n‐butylamine, respectively.     

Pipek–Mezey localization of occupied and virtual orbitals

Recent advances in orbital localization algorithms are used to minimize the Pipek–Mezey localization function for both occupied and virtual Hartree–Fock orbitals. Virtual Pipek–Mezey orbitals for large molecular systems have previously not been considered in the literature. For this work, the Pipek–Mezey (PM) localization function is implemented for both the Mulliken and a Löwdin population analysis. The results show that the standard PM localization function (using either Mulliken or Löwdin population analyses) may yield local occupied orbitals, although for some systems the occupied orbitals are only semilocal as compared to state‐of‐the‐art localized occupied orbitals. For the virtual orbitals, a Löwdin population analysis shows improvement in locality compared to a Mulliken population analysis, but for both Mulliken and Löwdin population analyses, the virtual orbitals are seen to be considerably less local compared to state‐of‐the‐art localized orbitals. © 2013 Wiley Periodicals, Inc.     

High-affinity DNA targeting using readily accessible mimics of N2'-functionalized 2'-amino-α-L-LNA

N2'-Pyrene-functionalized 2'-amino-α-L-LNAs (locked nucleic acids) display extraordinary affinity toward complementary DNA targets due to favorable preorganization of the pyrene moieties for hybridization-induced intercalation. Unfortunately, the synthesis of these monomers is challenging (~20 steps, <3% overall yield), which has precluded full characterization of DNA-targeting applications based on these materials. Access to more readily accessible functional mimics would be highly desirable. Here we describe short synthetic routes to a series of O2'-intercalator-functionalized uridine and N2'-intercalator-functionalized 2'-N-methyl-2'-aminouridine monomers and demonstrate, via thermal denaturation, UV-vis absorption and fluorescence spectroscopy experiments, that several of them mimic the DNA-hybridization properties of N2'-pyrene-functionalized 2'-amino-α-L-LNAs. For example, oligodeoxyribonucleotides (ONs) modified with 2'-O-(coronen-1-yl)methyluridine monomer Z, 2'-O-(pyren-1-yl)methyluridine monomer Y, or 2'-N-(pyren-1-ylmethyl)-2'-N-methylaminouridine monomer Q display prominent increases in thermal affinity toward complementary DNA relative to reference strands (average ΔT(m)/mod up to +12 °C), pronounced DNA-selectivity, and higher target specificity than 2'-amino-α-L-LNA benchmark probes. In contrast, ONs modified with 2'-O-(2-napthyl)uridine monomer W, 2'-O-(pyren-1-yl)uridine monomer X or 2'-N-(pyren-1-ylcarbonyl)-2'-N-methylaminouridine monomer S display very low affinity toward DNA targets. This demonstrates that even conservative alterations in linker chemistry, linker length, and surface area of the appended intercalators have marked impact on DNA-hybridization characteristics. Straightforward access to high-affinity building blocks such as Q, Y, and Z is likely to accelerate their use in DNA-targeting applications within nucleic acid based diagnostics, therapeutics, and material science.     

Duplex and triplex formation of mixed pyrimidine oligonucleotides with stacking of phenyl-triazole moieties in the major groove

5-(1-Phenyl-1,2,3-triazol-4-yl)-2'-deoxycytidine was synthesized from a modified CuAAC protocol and incorporated into mixed pyrimidine oligonucleotide sequences together with the corresponding 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine. With consecutive incorporations of the two modified nucleosides, improved duplex formation with a complementary RNA and improved triplex formation with a complementary DNA duplex were observed. The improvement is due to π-π stacking of the phenyl-triazole moieties in the major groove. The strongest stacking and most pronounced positive influence on thermal stability was found in between the uridine analogues or with the cytidine analogue placed in the 3' direction to the uridine analogue. Modeling indicated a different orientation of the phenyl-triazole moieties in the major groove to account for the difference between the two nucleotides. The modified oligonucleotides were all found to be significantly stabilized toward nucleolytic degration.