An average-of-configuration method for using Kohn-Sham density functional theory in modeling ligand-field theory

The Amsterdam Density Functional (ADF) package has been used to constrain Kohn-Sham DFT in such a fashion that a transition from KS-DFT to ligand-field theory in the form of the parametrical d(q)() model is completely well-defined. A relationship is established between the strong-field approximation of the parametrical d(2) model for the tetrahedral complexes VCl(4)(-) and VBr(4)(-) and certain fixed-orbital ADF-computed energies. In this way values for all the parameters of the d(2)() model may be computed, thus allowing the ADF results to be expressed in terms of a KS-DFT energy matrix that can be diagonalized. This means that the KS-DFT deficiency with regard to computation of nondiagonal elements has been overcome and the KS-DFT eigenenergies have become available through the KS-DFT mimicking of the ligand-field plus repulsion model. By using mutually orthogonal strong-field energy matrices, the mimicking has been further elucidated. The computed values for the empirical parameters of VCl(4)(-) and VBr(4)(-) are in good agreement with experimental data. The spectrochemical and the nephelauxetic series have been computed by including the remaining halide complexes and the quantitatively special position of F(-)() among the halides corroborated for both series.     

UV absorption spectra of HO2, CH3O2, C2H5O2, and CH3C(O)CH2O2 radicals and mechanism of the reactions of F and Cl atoms with CH3C(O)CH3

Pulse radiolysis techniques were used to measure the gas phase UV absorption spectra of the title peroxy radicals over the range 215–340 nm. By scaling to σ(CH₃O₂)_{240 nm} = (4.24 ± 0.27) × 10^?18, the following absorption cross sections were determined: σ(HO₂)_{240 nm} = 1.29 ± 0.16, σ(C₂H₅O₂)_{240 nm} = 4.71 ± 0.45, σ(CH₃C(O)CH₂O₂)_{240 nm} = 2.03 ± 0.22, σ(CH₃C(O)CH₂O₂)_{230 nm} = 2.94 ± 0.29, and σ(CH₃C(O)CH₂O₂)_{310 nm} = 1.31 ± 0.15 (base e, units of 10^?18 cm² molecule^?1). To support the UV measurements, FTIR‐smog chamber techniques were employed to investigate the reaction of F and Cl atoms with acetone. The F atom reaction proceeds via two channels: the major channel (92% ± 3%) gives CH₃C(O)CH₂ radicals and HF, while the minor channel (8% ± 1%) gives CH₃ radicals and CH₃C(O)F. The majority (>97%) of the Cl atom reaction proceeds via H atom abstraction to give CH₃C(O)CH₂ radicals. The results are discussed with respect to the literature data concerning the UV absorption spectra of CH₃C(O)CH₂O₂ and other peroxy radicals. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 283–291, 2002     

Copper-mediated cross-coupling reactions of N-unsubstituted sulfoximines and aryl halides

[reaction: see text] Copper-mediated cross-coupling reactions of sulfoximines with aryl iodides and aryl bromides provide N-arylated sulfoximines in high yields. The method is complementary to the known palladium-catalyzed N-arylation and allows the preparation of N-arylated sulfoximines, which have previously been inaccessible.     

Hydrophobicity and counterion effects on the binding of ionic surfactants to uncharged polymeric hydrogels

Gel swelling experiments have been used to study the binding of ionic surfactants to a series of nonionic alkylacrylamide hydrogels of increasing hydrophobicity. The binding of hexadecyl trimethylammonium (C16TA+) to uncharged gels is sensitive to both the hydrophobicity of the gel and the counterion to the surfactant. There is a minimum hydrophobicity threshold below which binding of the surfactant does not occur, and this is influenced by the counterion to the surfactant. The surfactant concentration at the onset of binding, the critical association concentration (cac), decreases with increasing gel hydrophobicity. The maximum swelling of the gel (at intermediate network hydrophobicity) increases in the order of the Hofmeister series of anions, bromide (Br-) < chloride (Cl-) < acetate (Ac-). At higher gel hydrophobicity, differences in swelling are no longer observed on changing the counterion. A minimum hydrophobicity threshold was also found for the binding of the anionic surfactants sodium dodecyl sulfate (SDS) and sodium dodecyl-di(ethylene oxide)-sulfate (SD-(EO)2-S). Differences in the swelling behavior with network hydrophobicity are explained in terms of the degree of saturation of the gel with surfactant at the cmc.     

Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids

Locked nucleic acids (LNAs) containing one or more 2'-O,4'-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. unprecedented helical thermostability when hybridized with cognate RNA and DNA. To acquire a detailed understanding of the structural features of LNA giving rise to its remarkable properties, we have conducted structural studies by use of NMR spectroscopy and now report high-resolution structures of two LNA:RNA hybrids, the LNA strands being d(5'-CTGAT(L)ATGC-3') and d(5'-CT(L)GAT(L)AT(L)GC-3'), respectively, T(L) denoting a modified LNA monomer with a thymine base, along with the unmodified DNA:RNA hybrid. In the structures, the LNA nucleotides are positioned as to partake in base stacking and Watson-Crick base pairing, and with the inclusion of LNA nucleotides, we observe a progressive change in duplex geometry toward an A-like duplex structure. As such, with the inclusion of three LNA nucleotides, the hybrid adopts an almost canonical A-type duplex geometry, and thus it appears that the number of modifications has reached a saturation level with respect to structural changes, and that further incorporations would furnish only minute changes in the duplex structure. We attempt to rationalize the conformational steering induced by the LNA nucleotides by suggesting that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.     

Ortho lithiation-in situ borylation of substituted morpholine benzamides

Morpholine amides are cheap and safe alternative to Weinreb amides as acylating agents of organometallic species. Herein, the in-situ lithiation/borylation of 18 ortho- meta- and para-substituted morpholine benzamides has been investigated. 10 of the 18 substrates provided the desired boronic esters as the major isomer (>90% regioselectivity) in crude isolated yields ranging from 68 to 93%. The synthetic usability of such building blocks was subsequently illustrated via the synthesis of a kinase inhibitor.     

Modification of σ‐Donor Properties of Terminal Carbide Ligands Investigated Through Carbide–Iodine Adduct Formation

The terminal carbide ligands in [(Cy₃P)₂X₂Ru≡C] complexes (X=halide or pseudohalide) coordinate molecular iodine, affording charge‐transfer complexes rather than oxidation products. Crystallographic and vibrational spectroscopic data show the perturbations of iodine to vary with the auxiliary ligand sphere on ruthenium, demonstrating the σ‐donor properties of carbide complexes to be tunable.     

Interfacing Click Chemistry with Automated Oligonucleotide Synthesis for the Preparation of Fluorescent DNA Probes Containing Internal Xanthene and Cyanine Dyes

Double‐labeled oligonucleotide probes containing fluorophores interacting by energy‐transfer mechanisms are essential for modern bioanalysis, molecular diagnostics, and in vivo imaging techniques. Although bright xanthene and cyanine dyes are gaining increased prominence within these fields, little attention has thus far been paid to probes containing these dyes internally attached, a fact which is mainly due to the quite challenging synthesis of such oligonucleotide probes. Herein, by using 2′‐O‐propargyl uridine phosphoramidite and a series of xanthenes and cyanine azide derivatives, we have for the first time performed solid‐phase copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC) click labeling during the automated phosphoramidite oligonucleotide synthesis followed by postsynthetic click reactions in solution. We demonstrate that our novel strategy is rapid and efficient for the preparation of novel oligonucleotide probes containing internally positioned xanthene and cyanine dye pairs and thus represents a significant step forward for the preparation of advanced fluorescent oligonucleotide probes. Furthermore, we demonstrate that the novel xanthene and cyanine labeled probes display unusual and very promising photophysical properties resulting from energy‐transfer interactions between the fluorophores controlled by nucleic acid assembly. Potential benefits of using these novel fluorescent probes within, for example, molecular diagnostics and fluorescence microscopy include: Considerable Stokes shifts (40–110 nm), quenched fluorescence of single‐stranded probes accompanied by up to 7.7‐fold light‐up effect of emission upon target DNA/RNA binding, remarkable sensitivity to single‐nucleotide mismatches, generally high fluorescence brightness values (FB up to 26), and hence low limit of target detection values (LOD down to <5 nM ).     

Eigenvalue amplitudes of the Potts model on a torus

We consider the Q-state Potts model in the random-cluster formulation, defined on finite   two-dimensional lattices of size L×N$L\times N$ with toroidal boundary conditions. Due to the non-locality of the clusters, the partition function Z(L,N)$Z(L,N)$ cannot be written simply as a trace of the transfer matrix TL${\mathrm{T}}_L$. Using a combinatorial method, we establish the decomposition Z(L,N)=_∑l,Dkb(l,Dk)K_l,Dk$Z(L,N)={\sum }_{l,D_k}{b}^{(l,D_k)}{K}_{l,D_k}$, where the characters K_l,Dk=i_∑N(λi)$K_{l,D_k}={\sum }_i{({\lambda }_i)}^N$ are simple traces. In this decomposition, the amplitudes b(l,Dk)$b^{(l,D_k)}$ of the eigenvalues λi${\lambda }_i$ of TL${\mathrm{T}}_L$ are labelled by the number l=0,1,…,L$l=0,1,\dots ,L$ of clusters which are non-contractible with respect to the transfer (N  ) direction, and a representation Dk$D_k$ of the cyclic group Cl$C_l$. We obtain rigorously a general expression for b(l,Dk)$b^{(l,D_k)}$ in terms of the characters of Cl$C_l$, and, using number theoretic results, show that it coincides with an expression previously obtained in the continuum limit by Read and Saleur.