Intramolecular interactions of L‐phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules

Intramolecular interactions between fragments of L ‐phenylalanine, i.e., phenyl and alaninyl, have been investigated using dual space analysis (DSA) quantum mechanically. Valence space photoelectron spectra (PES), orbital energy topology and correlation diagram, as well as orbital momentum distributions (MDs) of L ‐phenylalanine, benzene and L ‐alanine are studied using density functional theory methods. While fully resolved experimental PES of L ‐phenylalanine is not yet available, our simulated PES reproduces major features of the experimental measurement. For benzene, the simulated orbital MDs for 1e_1g and 1a_2u orbitals also agree well with those measured using electron momentum spectra. Our theoretical models are then applied to reveal intramolecular interactions of the species on an orbital base, using DSA. Valence orbitals of L ‐phenylalanine can be essentially deduced into contributions from its fragments such as phenyl and alaninyl as well as their interactions. The fragment orbitals inherit properties of their parent species in energy and shape (ie., MDs). Phenylalanine orbitals show strong bonding in the energy range of 14‐20 eV, rather than outside of this region. This study presents a competent orbital based fragments‐in‐molecules picture in the valence space, which supports the fragment molecular orbital picture and building block principle in valence space. The optimized structures of the molecules are represented using the recently developed interactive 3D‐PDF technique. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

45- and 70-base DNA supramolecular polymerizations on quartz crystal microbalance biosensor

Supramolecular polymerizations of 45- and 70- base DNAs on the surface of an in-situ time-resolved 27 MHz quartz crystal microbalance biosensor.     

Electrochemical detection of Arachis hypogaea (peanut) agglutinin binding to monovalent and clustered lactosyl motifs immobilized on a polypyrrole film

Direct detection of peanut agglutinin/lactose interactions was realized by an electrochemical approach based on a polypyrrole coated electrode displaying pendant carbohydrates.     

Radicals masquerading as electrophiles: a computational study of the intramolecular addition reactions of acyl radicals to imines

Ab initio calculations using 6-311G**, cc-pVDZ, and aug-cc-pVDZ, with (MP2, QCISD, CCSD(T)) and without (UHF) electron correlation, and density functional methods (BHandHLYP and B3LYP) predict that cyclization of the 5-aza-5-hexenoyl and (E)-6-aza-5-hexenoyl radicals proceed to afford the 5-exo products. At the CCSD(T)/cc-pVDZ//BHandHLYP/cc-pVDZ level of theory, energy barriers (deltaE(double dagger)) of 36.1 and 47.0 kJ mol(-1) were calculated for the 5-exo and 6-endo pathways for the cyclization of the 5-aza-5-hexenoyl radical. On the other hand, at the same level of theory, deltaE(double dagger) of 38.9 and 45.4 kJ mol(-1) were obtained for the 5-exo and 6-endo cyclization modes of (E)-6-aza-5-hexenoyl radical, with exothermicities of about 27 and 110 kJ mol(-1) calculated for the exo and endo modes, respectively. Under suitable experimental conditions, the 6-endo cyclization product is likely to dominate. Analysis of the molecular orbitals involved in these ring-closure reactions indicate that both reactions at nitrogen are assisted by dual orbital interactions involving simultaneous SOMO-pi* and LP-pi* overlap in the transitions states. Interestingly, the (Z)-6-aza-5-hexenoyl radical, that cannot benefit from these dual orbital effects is predicted to ring-close exclusively in the 5-exo fashion.     

Crystal structure of aquo (hydroxo) (ethylenediaminetetraacetato) sodium(I) tin(IV), NaSn(OH)(edta)(H2O)

NaSn(OH)(edta)(H₂O) is monoclinic, space groupP2₁/c, witha=9.747(3)Å,b=9.121(3)Å,c=16.430(6)Å, =98.69(4)°, ų, andZ=4. The coordination environment of Sn(IV) is a capped octahedron. Sn–O distances range from 1.990(6)Å to 2.351(7)Å. Na(I) is five coordinated to three different edta molecules. Na–O distances range from 2.283(9)Å to 2.414(7)Å. The edta ligand presents the E, G/R conformation. The crystal structure is composed of sheets parallel to (001): inside a sheet Sn(OH)(edta) molecules are connected to each other by the Na(I) interactions.     

Detection of carbohydrate-binding proteins by oligosaccharide-modified polypyrrole interfaces using electrochemical surface plasmon resonance

This paper reports on the use of electrochemical surface plasmon resonance (E-SPR) for the detection of carbohydrate-binding proteins. The generation of an SPR sensor specific to lectins Arachis hypogaea (PNA) and Maackia amurensis (MAA) is based on the electrochemical polymerization of oligosaccharide derivatives functionalized by pyrrole groups. The resulting thin conducting polymer films were characterized using E-SPR and atomic force microscopy (AFM). The specific binding of PNA to polypyrrole-lactosyl and of MAA to polypyrrole-3'-sialyllactosyl films was investigated using SPR. The detection limit was 41 nM for PNA and 83 nM for MAA. Through Scatchard analysis and linear transformation of the SPR sensorgram data, association (k(ass)) and dissociation rate constants (k(diss)) could be determined.     

A coupled cluster study of the electronic spectroscopy and photochemistry of Cr(CO)6

The transition energies to the low-lying singlet and triplet excited states of Cr(CO)(6) are computed by equation-of-motion coupled cluster singles and doubles (EOM-CCSD) and similarity transformed equation-of-motion coupled cluster singles and doubles (STEOM-CCSD) methods with all-electrons basis sets. Both experimental and optimized geometries are used for the calculations. Calculations with various basis sets, among them one of the largest calculations performed at the EOM-CCSD level, based on atomic natural orbitals with 627 functions, were used to evaluate the basis set influence on computed transition energies. The presence of a shoulder at 3.9 eV in the experimental absorption spectrum, assigned to the (1)A(1g)-->(1)T(2u) transition, which was not reproduced by recent density functional theory (DFT) or multi-state complete active space perturbation theory (MS-CASPT2) is supported by the present STEOM-CCSD calculations with a theoretical value of 3.92 eV. In addition to this weak (1)A(1g)--> a (1)T(2u) absorption, we observe two strong absorptions corresponding to (1)A(1g)--> a (1)T(1u) at 4.37 eV (vs. an experimental value of 4.46 eV) and (1)A(1g)--> b (1)T(1u) at 5.20 eV (vs. an experimental value of 5.53 eV). Both are characterized as metal-to-ligand charge-transfer (MLCT) allowed transitions. The first metal-centered (MC) absorption at 4.37 eV in our best calculation is degenerate with the lowest MLCT absorbing state. The one-dimensional potential energy curves associated to the low-lying singlet MLCT and MC states as a function of the chromium axial carbonyl bond distance q(a) = [Cr-CO(axial)] show that an avoided crossing exists between the a (1)T(1g) (MC) and a (1)T(1u) (MLCT) states near 1.92 A, which is very close to the equilibrium Cr-CO distance. Moreover, the MC state seems to be dissociative for the CO loss. These two important features could explain the ultra-fast dissociation of CO (100 fs) observed in recent low intensity laser probed gas phase experiments.     

Luminescence of Eu3+ and Tb3+ Complexes of Two Macrobicyclic Ligands Derived from a Tetralactam Ring and a Chromophoric Antenna

Two macrobicyclic ligands derived from an 18‐membered tetralactam ring and 2,2′‐bipyridine or 2,6‐bis(pyrazol‐1‐yl)pyridine moieties, 1 and 2 , respectively, form stable complexes with Gd^III, Eu^III, and Tb^III ions in aqueous solution. The ligand‐based luminescence is retained in the Gd^III cryptates, whereas this radiative deactivation is quenched in the Eu^III and Tb^III cryptates by ligand‐to‐metal energy transfer, resulting in the usual metal‐centered emission spectra. Singlet‐ and triplet‐state energies, emission‐decay lifetimes, and luminescence yields were measured. [Tb⊂ 1 ]³⁺ cryptate shows a long luminescence lifetime (τ=1.12 ms) and a very high metal luminescence quantum yield (Φ=0.25) in comparison with those reported in the literature for Tb³⁺ complexes sensitized by a bipyridine chromophore. By comparison to [Ln⊂ 1 ]³⁺, [Ln⊂ 2 ]³⁺ presents markedly lower luminescence properties, due to worse interaction between the 2,6‐bis(pyrazol‐1‐yl)pyridine unit and the metal ion. Moreover, the luminescent metal and the triplet ligand energy levels of [Eu⊂ 2 ]³⁺ do not match. The effects of H₂O molecules coordinated to the metal centre and of thermally activated decay processes on nonradiative deactivation to the ground‐state are also reported.