The ultrafast dynamics of hydrogen-bonded liquids: molecular structure-dependent occurrence of normal arrhenius or fractional Stokes-Einstein-Debye rotational diffusive relaxation

The ultrafast rotational-diffusive dynamics of the peptide linkage model compounds N-methylacetamide (NMA), acetamide (Ac), and N,N-dimethylacetamide (DMA) have been studied as a function of temperature using optically heterodyne-detected optical Kerr effect (OHD-OKE) spectroscopy. Both NMA and Ac exhibit a non-Arrhenius temperature dependence of the rotational diffusive relaxation time. By contrast, the non-hydrogen-bonding DMA exhibits normal hydrodynamic behavior. The unusual dynamics of NMA and Ac are attributed to the decoupling of single-molecule rotational diffusive relaxation from the shear viscosity via a transition between stick and slip boundary conditions, which arises from local heterogeneity in the liquid due to the formation of hydrogen-bonded chains or clusters. This provides new insight into the structure and dynamics of an important peptide model compound and the first instance of such a phenomenon in a room-temperature liquid. The OHD-OKE responses of carboxylic acids acetic acid (AcOH) and dichloroacetic acid (DCA) are also reported. These, along with the terahertz Raman spectra, show no evidence of the effects observed in amide systems, but display trends consistent with the presence of an equilibrium between the linear and cyclic dimer structures at all temperatures and moderate-to-high mole fractions in aqueous solution. This equilibrium manifests itself as hydrodynamic behavior in the liquid phase.     

Donor-acceptor distance-dependence of photoinduced electron-transfer rate in flavoproteins

Ultrafast fluorescence quenching of flavin in flavodoxin from Megasphaera elsdenii was investigated by means of a fluorescence up-conversion method. Fluorescence lifetimes of flavodoxin from M. elsdenii were estimated to be tau(1) approximately 165 fs (0.97%) and tau(2) approximately 10 ps (0.03%). Correlation of photoinduced electron-transfer rates (k(ET)) with averaged distances (D(av)) between isoalloxazine and nearby tryptophan or tyrosine was examined and obtained an empirical equation of ln k(ET) vs D(av) by means of a nonlinear least-squares method using reported data together with flavodoxin from M. elsdenii. The values of D(av) were calculated from X-ray structures of the flavoproteins. The ln k(ET) was approximately linear at D(av) shorter than 7 A. The model free empirical equation was expressed as ln k(ET) = 29.7 + (-0.327 D(av) + 2.84 x 10(-5))/(0.698 - D(av)(2)). We also analyzed the observed values of ln k(ET) with Marcus theory, but could not obtain reasonable results. Our analysis suggests that the average distance, rather than the shortest (edge to edge) distance or interplanar angles between the aromatics rings, is the key factor in the process of the photoinduced electron transfer in these flavoproteins.     

Enantioselective addition of terminal alkynes to aldehydes catalyzed by a Cu(I)-TRAP complex

The addition of terminal alkynes to aromatic aldehydes was carried out under mild conditions in the presence of a Cu-phosphine complex, which was prepared in situ from Cu(O-t-Bu) and TRAP chiral bisphosphine, to yield enantiomerically enriched propargyl alcohols with moderate enantioselectivities. Furthermore, according to stoichiometric reactions, the reaction presumably involves the addition of a TRAP-coordinated Cu(I) acetylide to an aldehyde.     

Toward a rational design of the assembly structure of polymetallic asymmetric catalysts: design, synthesis, and evaluation of new chiral ligands for catalytic asymmetric cyanation reactions

New chiral ligands (4 and 5) for polymetallic asymmetric catalysts were designed based on the hypothesis that the assembled structure should be stable when made from a stable module 8. A metal-ligand=5:6+μ-oxo+OH complex was generated from Gd(OⁱPr)₃ and 4 or 5, and this complex was an improved asymmetric catalyst for the desymmetrization of meso-aziridines with TMSCN and conjugate addition of TMSCN to α,β-unsaturated N-acylpyrroles, compared to the previously reported catalysts derived from 1-3. These two groups of catalysts produced opposing enantioselectivity even though the ligands had the same chirality. The functional difference in the asymmetric catalysts is derived from differences in the higher-order structure of the polymetallic catalysts.     

Lamellar structure in poly(ala-gly) determined by solid-state NMR and statistical mechanical calculations

Lamellar structure of poly(Ala-Gly) or (AG)n in the solid was examined using 13C solid-state NMR and statistical mechanical approaches. Two doubly labeled versions, [1-13C]Gly14[1-13C]Ala15- and [1-13C]Gly18[1-13C]Ala19 of (AG)15 were examined by two-dimensional (2D) 13C spin diffusion NMR in the solid state. In addition five doubly labeled [15N,13C]-versions of the same peptide, (AG) 15 and 15 versions labeled [3-13C] in each of the successive Ala residues were utilized for REDOR and 13C CP/MAS NMR measurements, respectively. The observed spin diffusion NMR spectra were consistent with a structure containing a combination of distorted beta-turns with a large distribution of the torsion angles and antiparallel beta-sheets. The relative proportion of the distorted beta-turn form was evaluated by examination of 13C CP/MAS NMR spectra of [3-13C]Ala-(AG)15. In addition, REDOR determinations showed five kinds of atomic distances between doubly labeled 13C and 15N nuclei which were also interpreted in terms of a combination of beta-sheets and beta-turns. Our statistical mechanical analysis is in excellent agreement with our Ala Cbeta 13C CP/MAS NMR data strongly suggesting that (AG)15 has a lamellar structure.     

Polyproline-rod approach to isolating protein targets of bioactive small molecules: isolation of a new target of indomethacin

Identification of protein targets of bioactive small molecules has been a technical hurdle of chemical genetics. Here we report a polyproline-rod approach to isolating protein targets of small molecules from cell lysates. The results indicate that insertion of a long, rigid polyproline helix between a small-molecule bait and a biotin tag boosts the capacity of affinity purification and thereby permits isolation of low-abundance or low-affinity proteins. In the course of the proof-of-concept experiments, we isolated glyoxalase 1 (GLO1) as a new target of indomethacin, a widely used antiinflammatory drug. Molecular biological experiments suggest that inhibition of GLO1 enzyme activity is related to the clinically recognized beneficial side effects of the indomethacin family of nonsteroidal antiinflammatory drugs.     

Unexpected preference of the E. coli translation system for the ester bond during incorporation of backbone-elongated substrates

There have been recent advances in the ribosomal synthesis of various molecules composed of nonnatural ribosomal substrates. However, the ribosome has strict limitations on substrates with elongated backbones. Here, we show an unexpected loophole in the E. coli translation system, based on a remarkable disparity in its selectivity for beta-amino/hydroxy acids. We challenged beta-hydroxypropionic acid (beta-HPA), which is less nucleophilic than beta-amino acids but free from protonation, to produce a new repertoire of ribosome-compatible but main-chain-elongated substrates. PAGE analysis and mass-coupled S-tag assays of amber suppression experiments using yeast suppressor tRNAPheCUA confirmed the actual incorporation of beta-HPA into proteins/oligopeptides. We investigated the side-chain effects of beta-HPA and found that the side chain at position alpha and R stereochemistry of the beta-substrate is preferred and even notably enhances the efficiency of incorporation as compared to the parent substrate. These results indicate that the E. coli translation machinery can utilize main-chain-elongated substrates if the pKa of the substrate is appropriately chosen.     

Host-guest effect on chirality transfer from a binaphthyl derivative to a host nematic liquid crystal

A novel dichiral compound possessing both an asymmetric axis and a chiral centre induces opposite twist senses and distinct helical pitches in different host nematic liquid crystals; the host-guest effect on chirality transfer is discussed in terms of molecular recognition.     

Oxidation of allylic alcohols to alpha,beta-unsaturated carbonyl compounds with aqueous hydrogen peroxide under organic solvent-free conditions

Allylic alcohols are chemoselectively oxidized to alpha,beta-unsaturated carbonyl compounds in high yield with aqueous H(2)O(2) in the presence of Pt black catalyst under organic solvent-free conditions. The catalyst is easily recyclable and effective for at least 7 cycles.