Bead-bead interaction parameters in dissipative particle dynamics: relation to bead-size, solubility parameter, and surface tension

Dissipative particle dynamics (DPD) is a mesoscale modeling method for simulating equilibrium and dynamical properties of polymers in solution. The basic idea has been around for several decades in the form of bead-spring models. A few years ago, Groot and Warren established an important link between DPD and the Flory-Huggins chi-parameter theory for polymer solutions. We revisit the Groot-Warren theory and investigate the DPD interaction parameters as a function of bead size. In particular, we show a consistent scheme of computing the interfacial tension in a segregated binary mixture. Results for three systems chosen for illustration are in excellent agreement with experimental results. This opens the door for determining DPD interactions using interfacial tension as a fitting parameter.     

Automated molecular design: A new fragment-joining algorithm

Summary A popular first step in the problem of structure-based, de novo molecule design is to identify regions where specific functional groups or chemical entities would be expected to interact strongly. When the three-dimensional structure of the receptor is not available, it may be possible to derive a pharmacophore giving the three-dimensional relationships between such chemical groups. The task then is to design synthetically feasible molecules which not only contain the required groups, but which can also position them in the desired relative orientation. One way to do this is to first link the groups using an acyclic chain. We have investigated the application of the tweak algorithm [Shenkin, P.S. et al., Biopolymers, 26 (1987) 2053] for generating families of acyclic linkers. These linking structures can subsequently be braced using a ring-joining algorithm [Leach, A.R. and Lewis, R.A., J. Comput. Chem., 15 (1994) 233], giving rise to an even wider variety of molecular skeletons for further studies.     

Direct electron transfer from modified glassy carbon electrodes carrying covalently immobilised mediators to a dissolved viologen accepting pyridine nucleotide oxidoreductase and dihydrolipoamide dehydrogenase

N,N′-Diaminopropyl-4,4′-bipyridinium dication (DAPV) and cobalt diaminosarcophagine (Co—diamsar) were covalently bound on functionalised glassy carbon electrodes. The electron transfer from the modified electrodes to dissolved dihydrolipoamide dehydrogenase (Lip-DH) or viologen accepting pyridine nucleotide oxidoreductase (VAPOR) was tested by NADH formation in potentiostatically controlled electrochemical cells. The NADH formed was used to reduce pyruvate to -lactate catalysed by -lactate dehydrogenase ( -LDH). The reaction kinetics between the modified electrodes and the dissolved enzymes have been examined.     

Ruthenium dihydride complexes: NMR studies of intramolecular isomerization and fluxionality including the detection of minor isomers by parahydrogen-induced polarization

NMR studies reveal that complexes Ru(CO)(2)(H)(2)L(2) (L = PMe(3), PMe(2)Ph, and AsMe(2)Ph) can have three geometries, ccc, cct-L, and cct-CO, with equilibrium ratios that are highly dependent on the electronic properties of L; the cct-L form is favored, because the sigma-only hydride donor is located trans to CO rather than L. When L = PMe(3), the ccc form is only visible when p-H(2) is used to amplify its spectral features. In contrast, when L = AsMe(2)Ph, the ccc and cct-L forms are present in similar quantities and, hence, must have similar free energies; for this complex, however, the cct-CO isomer is also detectable. These complexes undergo a number of dynamic processes. For L(2) = dppe, an interchange of the hydride positions within the ccc form is shown to be accompanied by synchronized CO exchange and interchange of the two phosphorus atoms. This process is believed to involve the formation of a trigonal bipyramidal transition state containing an eta(2)-H(2) ligand; in view of the fact that k(HH)/k(DD) is 1.04 and the synchronized rotation when L(2) = dppe, this transition state must contain little H-H bonding character. Pathways leading to isomer interconversion are suggested to involve related structures containing eta(2)-H(2) ligands. The inverse kinetic isotope effect, k(HH)/k(DD) = 0.5, observed for the reductive elimination of dihydrogen from Ru(CO)(2)(H)(2)dppe suggests that substantial H-H bond formation occurs before the H(2) is actually released from the complex. Evidence for a substantial steric influence on the entropy of activation explains why Ru(CO)(2)(H)(2)dppe undergoes the most rapid hydride exchange. Our studies also indicate that the species [Ru(CO)(2)L(2)], involved in the addition of H(2) to form Ru(CO)(2)(H)(2)L(2), must have singlet electron configurations.     

Gas chromatographic/mass spectrometric determination of 3-methoxy-1,2-propanediol and cyclic diglycerols, by-products of technical glycerol, in wine: interlaboratory study

The aim of the present study was to provide the official wine control authorities with an internationally validated method for the determination of 3-methoxy-1,2-propanediol (3-MPD) and cyclic diglycerols (CycDs)-both of which are recognized as impurities of technical glycerol-in different types of wine. Because glycerol gives a sweet flavor to wine and contributes to its full-body taste, an economic incentive is to add glycerol to a wine to mask its poor quality. Furthermore, it is known that glycerol, depending on whether it is produced from triglycerides or petrochemicals, may contain considerable amounts of 3-MPD in the first case or CycDs in the second. However, because these compounds are not natural wine components, it is possible to detect glycerol added to wine illegally by determining the above-mentioned by-products. To this end, one of the published methods was adopted, modified, and tested in a collaborative study. The method is based on gas chromatographic/mass spectrometric analysis of diethyl ether extracts after salting out with potassium carbonate. The interlaboratory study for the determination of 3-MPD and CycDs in wine was performed in 11 laboratories in 4 countries. Wine samples were prepared and sent to participants as 5 blind duplicate test materials and 1 single test material. The concentrations covered ranges of 0.1-0.8 mg/L for 3-MPD and 0.5-1.5 mg/L for CycDs. The precision of the method was within the range predicted by the Horwitz equation. HORRAT values obtained for 3-MPD ranged from 0.8 to 1.7, and those obtained for CycDs ranged from 0.9 to 1.3. Average recoveries were 104 and 109%, respectively.     

Reductive activation of nitrate reductases

Protein film voltammetry of Paracoccus pantotrophus respiratory nitrate reductase (NarGH) and Synechococcus elongatus assimilatory nitrate reductase (NarB) shows that reductive activation of these enzymes may be required before steady state catalysis is observed. For NarGH complementary spectroscopic studies suggest a structural context for the activation. Catalytic protein film voltammetry at a range of temperatures has allowed quantitation of the activation energies for nitrate reduction. For NarGH with an operating potential of ca. 0.05 V the activation energy of ca. 35 kJ mol-1 is over twice that measured for NarB whose operating potential is ca. -0.35 V.     

Bi(III) halides as efficient catalysts for the O-acylative cleavage of tetrahydrofurans: an expeditious entry to tetralins

The mild (DCM/20 °C), quantitative, regioselective, O-acylative cleavage of tetrahydrofurans using organic acid halides with catalytic Bi(III) halides is reported. X-ray crystallography is used to rationalise the failure of the reaction in the case of certain crowded acid chlorides, and a useful aspect of chemoselectivity is revealed. The synthetic potential of this reaction is illustrated with a highly efficient O-acylative cleavage/intramolecular alkylation approach to tetralins.     

Nonadiabatic alignment of asymmetric top molecules: rotational revivals

The rotational revival structure of asymmetric top molecules, following irradiation by an intense picosecond laser pulse, is explored theoretically and experimentally. Numerically we solve nonperturbatively for the rotational dynamics of a general asymmetric top subject to a linearly polarized intense pulse, and analyze the dependence of the dynamical alignment on the field and system parameters. Experimentally we use time-resolved photofragment imaging to measure the alignment of two molecules with different asymmetry, iodobenzene, and iodopentafluorobenzene. Our numerical results explain the experimental observations and generalize them to other molecules. The rotational revival structure of asymmetric tops differs qualitatively from the intensively studied linear top case. Potentially it provides valuable structural information about molecules.     

Model studies for the synthesis of galbonolide B

The construction of the fourteen membered ring present in galbonolide B 1 is reported. The 10,11-diene system present in the southern portion of has been constructed using an ester enolate rearrangement/silicon mediated fragmentation cascade, whilst the macrocycle has been synthesised following a Johnson rearrangement/mercury assisted ring closure protocol.