Hydroxylation of sesquiterpenes by enzymes from chicory (Cichorium intybus L.) roots

A microsomal enzyme preparation of chicory roots catalyses the hydroxylation of various sesquiterpene olefins in the presence of NADPH. Most of these hydroxylations take place at an isopropenyl or isopropylidene group. The number of products obtained from any of the substrates is confined to one or, in a few cases, two sesquiterpene alcohols. In addition, the conversion of (+)-valencene into nootkatone through β-nootkatol was observed. The involvement of (+)-germacrene A hydroxylase (a cytochrome P450 enzyme) and other enzymes of sesquiterpene lactone biosynthesis in these reactions is discussed.     

Density-functional theory-based molecular simulation study of liquid methanol

We present a density-functional theory based molecular dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data. We observe that, in line with infrared spectroscopic data, the hydroxyl-stretching mode is significantly redshifted in the liquid, whereas the hydroxyl bending mode shows a blueshift. A substantial enhancement of the molecular dipole moment is accompanied by significant fluctuations due to thermal motion. We compute a value of 32 for the relative permittivity, almost identical to the experimental value of 33. Our results provide valuable data for improvement of empirical potentials.     

Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis

We present the Voronoi Deformation Density (VDD) method for computing atomic charges. The VDD method does not explicitly use the basis functions but calculates the amount of electronic density that flows to or from a certain atom due to bond formation by spatial integration of the deformation density over the atomic Voronoi cell. We compare our method to the well-known Mulliken, Hirshfeld, Bader, and Weinhold [Natural Population Analysis (NPA)] charges for a variety of biological, organic, and inorganic molecules. The Mulliken charges are (again) shown to be useless due to heavy basis set dependency, and the Bader charges (and often also the NPA charges) are not realistic, yielding too extreme values that suggest much ionic character even in the case of covalent bonds. The Hirshfeld and VDD charges, which prove to be numerically very similar, are to be recommended because they yield chemically meaningful charges. We stress the need to use spatial integration over an atomic domain to get rid of basis set dependency, and the need to integrate the deformation density in order to obtain a realistic picture of the charge rearrangement upon bonding. An asset of the VDD charges is the transparency of the approach owing to the simple geometric partitioning of space. The deformation density based charges prove to conform to chemical experience.     

Realistic modeling of ruthenium-catalyzed transfer hydrogenation

We report the first computational study of a fully atomistic model of the ruthenium-catalyzed transfer hydrogenation of formaldehyde and the reverse reaction in an explicit methanol solution. Using ab initio molecular dynamics techniques, we determined the thermodynamics, mechanism, and electronic structure along the reaction path. To assess the effect of the solvent quantitatively, we make a direct comparison with the gas-phase reaction. We find that the energy profile in solution bears little resemblance to the profile in the gas phase and a distinct solvation barrier is found: the activation barriers in both directions are lowered and the concerted hydride and proton transfer in the gas phase are converted into a sequential mechanism in solution with the substrate appearing as methoxide-like intermediate. Our results indicate that besides the metal-ligand bifunctional mechanism, as proposed by Noyori, also a concerted solvent-mediated mechanism is feasible. Our study gives a new perspective of the active role a solvent can have in transition-metal-catalyzed reactions.     

Chiral induction effects in ruthenium(II) amino alcohol catalysed asymmetric transfer hydrogenation of ketones: an experimental and theoretical approach

The enantioselective outcome of transfer hydrogenation reactions that are catalysed by ruthenium(II) amino alcohol complexes was studied by means of a systematically varied series of ligands. It was found that both the substituent at the 1-position in the 2-amino-1-alcohol ligand and the substituent at the amine functionality influence the enantioselectivity of the reaction to a large extent: enantioselectivities (ee values) of up to 95% were obtained for the reduction of acetophenone. The catalytic cycle of ruthenium(II) amino alcohol catalysed transfer hydrogenation was examined at the density functional theory level. The formation of a hydrogen bond between the carbonyl functionality of the substrate and the amine proton of the ligand, as well as the formation of an intramolecular H...H bond and a planar H-Ru-N-H moiety are crucially important for the reaction mechanism. The enantioselective outcome of the reaction can be illustrated with the aid of molecular modelling by the visualisation of the steric interactions between the ketone and the ligand backbone in the ruthenium(II) catalysts.     

Synthesis of 2-aryl-3-hydroxymethyl-5,5-difluoropiperidines

A strategy toward the synthesis of functionalized 5,5-difluoropiperidines, a class of compounds with potential as building block in medicinal chemistry, was developed. In a three-step procedure 2,2-difluoroglutaric anhydride was synthesized starting from ethyl bromodifluoroacetate. This key intermediate reacts fluently with various imines to yield 5,5-difluoropiperidinone carboxylic acids. Subsequent esterification of the obtained carboxylic acids enabled the isolation of trans-substituted 5,5-difluoro-2-arylpiperidinone-3-carboxylates as the major isomers. Reduction of the difluorinated piperidinonecarboxylates using borane gave rise to new trans-2-aryl-1-benzyl-5,5-difluoro-3-hydroxymethylpiperidines in excellent yields.     

Two-dimensional ordered beta-sheet lipopeptide monolayers

A series of amphiphilic lipopeptides, ALPs, consisting of an alternating hydrophilic and hydrophobic amino acid residue sequence coupled to a phospholipid tail, was designed to form supramolecular assemblies composed of beta-sheet monolayers decorated by lipid tails at the air-water interface. A straightforward synthetic approach based on solid-phase synthesis, followed by an efficient purification protocol was used to prepare the lipid-peptide conjugates. Structural insight into the organization of monolayers was provided by surface pressure versus area isotherms, circular dichroism, Fourier transform infrared spectroscopy, and Brewster angle microscopy. In situ grazing-incidence X-ray diffraction (GIXD) revealed that lipopeptides six to eight amino acids in length form a new type of 2D self-organized monolayers that exhibit beta-sheet ribbons segregated by lipid tails. The conclusions drawn from the experimental findings were supported by a representative model based on molecular dynamics simulations of amphiphilic lipopeptides at the vacuum-water interface.     

Core precession and global modes in granular bulk flow

We report a novel transition to core precession for granular flows in a split-bottomed shear cell. This transition is related to a qualitative change in the 3D flow structure: For shallow layers of granular material, the shear zones emanating from the split reach the free surface, while for deep layers the shear zones meet below the surface, causing precession. The surface velocities reflect this transition by a change of symmetry. As a function of layer depth, we find that three qualitatively different smooth and robust granular flows can be created in this simple shearing geometry.     

Real-Time Reconstruction of Arbitrary Slices for Quantitative and In Situ 3D Characterization of Nanoparticles

A detailed 3D investigation of nanoparticles at a local scale is of great importance to connect their structure and composition to their properties. Electron tomography has therefore become an important tool for the 3D characterization of nanomaterials. 3D investigations typically comprise multiple steps, including acquisition, reconstruction, and analysis/quantification. Usually, the latter two steps are performed offline, at a dedicated workstation. This sequential workflow prevents on-the-fly control of experimental parameters to improve the quality of the 3D reconstruction, to select a relevant nanoparticle for further characterization, or to steer an in situ tomography experiment. Here, an efficient approach to overcome these limitations is presented, based on the real-time reconstruction of arbitrary 2D reconstructed slices through a 3D object. Implementation of this method may lead to generalized implementation of electron tomography for routine nanoparticle characterization in 3D.     

Formation of a liquid crystalline phase from phosphatidylcholine at the oil-aqueous interface

Adsorption of phospholipid (1,2-dioleoyl-sn-glycero-3-phosphatidylcholine) and formation of a surface phase at the oil-water interface has been followed by using ellipsometry. The properties of the interfacial phase were found to depend strongly on whether phospholipid was added to the oil phase or to the aqueous phase as liposomal structures. In the latter case a monolayer formed, while if the phospholipid was supplied from the oil phase a lamellar phase appeared at the interface. The effect on the stabilizing surface phase of a surface-active protein (beta-lactoglobulin) was also investigated. The observations are important for understanding stabilizing properties of surface-active compounds commonly used to stabilize emulsions. In addition it has been demonstrated that ellipsometry can be used to study the initial process when a two-phase system consisting of a water and an oil phase is transformed into a three phase system or eventually to a one-phase system.