Optical sensors based on hybrid DNA/conjugated polymer complexes

Single-stranded DNA (ss-DNA) can specifically bind to various targets, including a complementary ss-DNA, ions, proteins, drugs, and so forth. When binding takes place, the oligonucleotide probe often undergoes a conformational transition. This conformational change of the negatively charged ss-DNA can be detected by using a water-soluble, cationic polythiophene derivative, which transduces the complex formation into an optical (colorimetric or fluorometric) signal without any labeling of the probe or the target. This simple and rapid methodology has enabled the specific and sensitive detection of nucleic acids and human thrombin. This new biophotonic tool can easily be applied to the detection of various other biomolecules and is also useful in the high-throughput screening of new drugs.     

A molecular modelling study of the interaction of noradrenaline with theβ 2-adrenergic receptor

Summary A model of the ₂-adrenergic receptor binding site is built from the primary structure of the receptor, experimental evidence for key binding residues and analogy with a homologous protein of partially determined structure. It is suggested that residues Trp-109, Thr-110 and Asp-113 are involved in ligand binding. Noradrenaline is successfully docked into this model, and the results of an INDO molecular orbital calculation on the complex indicate that a charge transfer interaction between Trp-109 and noradrenaline is possible.     

Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations

An additive procedure (SIBFA) is developed for the rapid computation of conformational energy variations in very large molecules. The macromolecule is built out of constitutive molecular fragments and the intramolecular energy is computed as a sum of interaction energies between the fragments. The electrostatic and the polarization components are calculated using multicenter multipole expansions of theab initio SCF electron density of the fragments. The repulsion component is obtained as a sum of bond and lone pair interactions.Tests of the procedure on a series of model compounds containing ether oxygens and pyridine-like nitrogens are reported and compared with the results of correspondingab initio SCF calculations. The resulting methodology is compatible with the simultaneous computation of intermolecular interactions.     

Intrazeolite photooxygenation of chiral alkenes. Control of facial selectivity by confinement and cation-π interactions

Depending on the nature of the substituents on the stereogenic carbon atom, the ene reaction of singlet oxygen with several chiral alkenes by confinement within thionin-supported zeolite NaY, may exhibit significant changes on facial selectivity by comparison to their photooxygenation reaction in solution. It is proposed that, apart from the conformational consequences as a result of the alkene confinement within the zeolite cavities, a synergism between Na⁺-π interactions and singlet oxygen-Na⁺ interactions plays a significant role in the transition states of ene hydroperoxidation. Within NaY, the diastereoselectivity may significantly depend on the site selectivity, as probed through specific deuterium labelling of trisubstituted alkenes bearing a gem-dimethyl group. In certain cases, a remote stereogenic centre relative to the reacting double bond may induce enhanced diastereoselection and regioselectivity.     

COCl2…NH3和COCl2…H2S体系的理论研究

在MP2水平上,用aug-cc-pVTZ基组对COC l2…NH3和COC l2…H2S体系进行几何优化和频率计算,同时使用Counterpoise技术进行BSSE校正,分别得到4个COC l2…NH3和2个COC l2…H2S无虚频的稳定结构:N(S)…C连接的构型(Ⅰ,Ⅱ,Ⅴ)和N(S)…C—lC直线型连接的构型(Ⅲ,Ⅳ,Ⅵ).第一类构型比第二类构型相互作用能更大、更稳定.在得到的6个稳定络合物中,络合物Ⅰ是最稳定的.     

On the choice of active space orbitals in MCSCF calculations

We describe a procedure which may be used to aid selection of the active space in multiconfigurational self-consistent field (MCSCF) calculations for general chemical systems. Starting from a restricted Hartree-Fock calculation, we define a hierarchy of interacting virtual orbitals for every occupied orbital. The most strongly interacting orbitals are then taken to constitute the active space in a configuration interaction (CI) calculation. The natural orbital occupation numbers obtained from the CI calculation are then used to choose the active space to be used in a subsequent MCSCF calculation. We illustrate our method on a number of systems (Li₂, B₂, C₂, carbonyl oxide and the transition state for oxidation of H₂S by dioxirane). In all these cases, ‘intuitive’ active spaces are inadequate, as are active spaces derived from the natural orbitals of unrestricted Hartree-Fock calculations.     

Electric polarizabilities,magnetic susceptibilities and dispersion coefficients for hydrocarbons

Using wavefunctions given in the companion paper bond properties and interactions are computed. Results are in agreement with other theoretical estimates and provide good molecular results. Differences between similar bonds can be accounted for by change in bond length. Simple formulae can be used to normalize bond contributions according to bond length. Parameters should be applicable to macromolecules.     

Volumetric properties of H2O, D2O, and methanol in acetonitrile at 278.15—318.15 K

The densities of H₂O, D₂O, and MeOH solutions in acetonitrile with the solute concentrations up to 0.07 molar fractions at 278.15, 288.15, 298.15, 308.15, and 318.15 K were measured using vibrating-tube densimetry with an error 8·10^–6 g cm^–3. The limiting partial molar volumes for the H/D isotopomers of water and IaII in acetonitrile (V^– ₂ ) and the isotope effects in V^– ₂ and in excess molar volumes of acetonitrile—water mixtures were calculated. Molecules of H₂O, D₂O, and IaII form associates with acetonitrile molecules via hydrogen bonds. The associates have the packing volumes close to those in the individual solute. The water and methanol molecules were assumed to be incorporated into the acetonitrile structure without substantial changes in the latter. However, this process results in some compression of the system with a simultaneous increase in its expansibility.     

The nature of the AuI ... AuI Interactions between Cationic [AuL2]+ Complexes in the Solid State

The interaction energy of a [Au{C(NHMe)₂}₂]⁺ ... [Au{C(NHMe)₂}₂]⁺ dimer is investigated using the MP2 method and the LANL2DZ basis set when isolated or embedded in ionic an [Au{C(NHMe)₂}₂]₂anion₂ aggregate, a good model for the environment that these dimers feel in ionic crystals. A repulsive interaction energy is obtained when the dimer is isolated. However, it is possible to find short Au^I ... Au^I separations in [Au{C(NHMe)₂}₂]₂anion₂ aggregates, because in these aggregates the sum of the cation ... anion interactions overweight the sum of the cation ... cation plus anion...anion interactions. This explains why short Au^I ... Au^I separations are found in ionic crystals. The Au^I ... Au^I interaction found in [Au{C(NHMe)₂}₂]₂ anion₂ aggregates shows the same features observed in energetically stable dimers presenting Au^I... Au^I bonds. This makes appropriate to use the name counterion-mediated bonds for the Au^I... Au^I interactions found in [Au{C(NHMe)₂}₂]₂ anion₂ aggregates and ionic crystals.     

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Summary An extensive crystal survey of the Cambridge Structural Database has been carried out to provide hydrogen-bond data for use in drug-design strategies. Previous crystal surveys have generated 1D frequency distributions of hydrogen-bond distances and angles, which are not sufficient to model the hydrogen bond as a ligand-receptor interaction. For each hydrogen-bonding group of interest to the drug designer, geometric hydrogen-bond criteria have been derived. The 3D distribution of complementary atoms about each hydrogen-bonding group has been ascertained by dividing the space about each group into bins of equal volume and counting the number of observed hydrogen-bonding contacts in each bin. Finally, the propensity of each group to form a hydrogen bond has been calculated. Together, these data can be used to predict the potential site points with which a ligand could interact and there-fore could be used in molecular-similarity studies, pharmacophore query searching of databases, or de novo design algorithms.