Cooperative hydrogen bonding in trimers involving HCN and HBO

A computational study of the cooperative effect of hydrogen bonding in linear trimers comprised of HCN and HBO molecules was undertaken at the MP2/6-311++G(2d,2p) level of theory. It was found that the third molecule leads to enhancement of the binding relative to that of the dimer species comprising these monomers. HBO is a better proton acceptor and a weaker proton donor than HCN.     

The role of glutathione S-transferase GliG in gliotoxin biosynthesis in Aspergillus fumigatus

Gliotoxin, a redox-active metabolite, is produced by the opportunistic fungal pathogen Aspergillus fumigatus, and its biosynthesis is directed by the gli gene cluster. Knowledge of the biosynthetic pathway to gliotoxin, which contains a disulfide bridge of unknown origin, is limited, although L-Phe and L-Ser are known biosynthetic precursors. Deletion of gliG from the gli cluster, herein functionally confirmed as a glutathione S-transferase, results in abrogation of gliotoxin biosynthesis and accumulation of 6-benzyl-6-hydroxy-1-methoxy-3-methylenepiperazine-2,5-dione. This putative shunt metabolite from the gliotoxin biosynthetic pathway contains an intriguing hydroxyl group at C-6, consistent with a gliotoxin biosynthetic pathway involving thiolation via addition of the glutathione thiol group to a reactive acyl imine intermediate. Complementation of gliG restored gliotoxin production and, unlike gliT, gliG was found not to be involved in fungal self-protection against gliotoxin.     

Intercepting low oxidation state main group hydrides with a nucleophilic N-heterocyclic olefin

The N-heterocyclic olefin, IPr=CH(2) (IPr = [(HCNDipp)(2)C], Dipp = 2,6-(i)Pr(2)C(6)H(3)) has been demonstrated to be of sufficient Lewis basicity to stabilize main group hydrides in unusually low oxidation states.     

Statistical Analysis of Scalar Dissipation Rate Transport in Turbulent Partially Premixed Flames: A Direct Numerical Simulation Study

Statistically planar turbulent premixed and partially premixed flames for different initial turbulence intensities are simulated for global equivalence ratios ??>?=?0.7 and ??>?=?1.0 using three-dimensional Direct Numerical Simulations (DNS) with simplified chemistry. For the simulations of partially premixed flames, a random distribution of equivalence ratio following a bimodal distribution of equivalence ratio is introduced in the unburned reactants ahead of the flame. The simulation parameters in all of the cases were chosen such that the combustion situation belongs to the thin reaction zones regime. The DNS data has been used to analyse the behaviour of the dissipation rate transports of both active and passive scalars (i.e. the fuel mass fraction Y _F and the mixture fraction ξ) in the context of Reynolds Averaged Navier–Stokes (RANS) simulations. The behaviours of the unclosed terms of the Favre averaged scalar dissipation rates of fuel mass fraction and mixture fraction (i.e. \(\widetilde {\varepsilon }_Y =\overline {\rho D\nabla Y_F^{\prime \prime } \cdot \nabla Y_F^{\prime \prime } } /\overline{\rho }\) and \(\widetilde {\varepsilon }_\xi =\overline {\rho D\nabla \xi ^{\prime \prime }\cdot \nabla \xi ^{\prime \prime }} /\overline {\rho })\) transport equations have been analysed in detail. In the case of the \(\widetilde {\varepsilon }_Y \) transport, it has been observed that the turbulent transport term of scalar dissipation rate remains small throughout the flame brush whereas the terms due to density variation, scalar–turbulence interaction, reaction rate and molecular dissipation remain the leading order contributors. The term arising due to density variation remains positive throughout the flame brush and the combined contribution of the reaction and molecular dissipation to the \(\widetilde {\varepsilon }_Y \) transport remains negative throughout the flame brush in all cases. However, the behaviour of scalar–turbulence interaction term of the \(\widetilde {\varepsilon }_Y \) transport equation is significantly affected by the relative strengths of turbulent straining and the straining due to chemical heat release. In the case of the \(\widetilde {\varepsilon }_\xi \) transport, the turbulent transport term remains small throughout the flame brush and the density variation term is found to be negligible in all cases, whilst the reaction rate term is exactly zero. The scalar–turbulence interaction term and molecular dissipation term remain the leading order contributors to the \(\widetilde {\varepsilon }_\xi \) transport throughout the flame brush in all cases that have been analysed in the present study. Performances of existing models for the unclosed terms of the transport equations of \(\widetilde {\varepsilon }_Y \) and \(\widetilde {\varepsilon }_\xi \) are assessed with respect to the corresponding quantities obtained from DNS data. Based on this exercise either suitable models have been identified or new models have been proposed for the accurate closure of the unclosed terms of both \(\widetilde {\varepsilon }_Y \) and \(\widetilde {\varepsilon }_\xi \) transport equations in the context of Reynolds Averaged Navier–Stokes (RANS) simulations.     

Statistical Analysis of Cross Scalar Dissipation Rate Transport in Turbulent Partially Premixed Flames: A Direct Numerical Simulation Study

Statistically planar turbulent partially premixed flames for different initial intensities of decaying turbulence have been simulated for global equivalence ratios <????> = 0.7 and <????> = 1.0 using three-dimensional simplified chemistry based Direct Numerical Simulations (DNS). The simulation parameters are chosen such that the combustion situation belongs to the thin reaction zones regime and a random bi-modal distribution of equivalence ratio ?? is introduced in the unburned gas ahead of the flame to account for mixture inhomogeneity. The DNS data has been used to analyse the statistical behaviour of the transport of the cross-scalar dissipation rate based on the fuel mass fraction Y _F and the mixture fraction ?? fluctuations $\,\tilde{\varepsilon}_{Y\xi}={\overline{\rho D\nabla Y_{F}^{\prime\prime}.\nabla \xi^{\prime\prime}} } \big/ {\bar {\rho }}$ (where $\bar{q}$ , $\tilde{q}={\overline{\rho q} } \big/ {\bar {\rho }}$ and $q^{\prime\prime} =q-\tilde {q}$ are Reynolds average, Favre mean and Favre fluctuation of a general quantity q) in the context of Reynolds Averaged Navier?CStokes simulations where ?? is the gas density and D is the gas diffusivity. The statistical behaviours of the unclosed terms in the $\tilde{\varepsilon }_{Y\xi } $ transport equation originating from turbulent transport T ₁, density variation T ₂, scalar?Cturbulence interaction T ₃, chemical reaction rate T ₄ and the molecular dissipation rate D ₂ have been analysed in detail. It has been observed that the contributions of T ₂, T ₃, T ₄ and D ₂ play important roles in the $\tilde{\varepsilon }_{Y\xi } $ transport for the globally stoichiometric cases, but in the globally fuel-lean cases the contributions of T ₂ and T ₄ become relatively weaker in comparison to the contributions of T ₃ and D ₂. The term T ₁ remains small in comparison to the leading order contributions of T ₃ and D ₂ for all cases, but the contribution of T ₁ plays a more important role in the low Damköhler combustion cases. The term T ₂ behaves as a sink term towards the unburned gas side but becomes a source term towards the burned gas side. The scalar?Cturbulence interaction term T ₃ has been found to be generally positive throughout the flame brush, but in globally stoichiometric cases the contribution of T ₃ becomes negative in regions of intense heat release. The combined contribution of (T ₄ ?C D ₂) remains mostly as a sink in all cases studied here. Models are proposed for the unclosed terms of the $\tilde{\varepsilon }_{Y\xi } $ transport equation in the context of Reynolds Averaged Navier?CStokes simulations, which are shown to satisfactorily predict the corresponding quantities extracted from the DNS data for all cases.     

Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: a nonequilibrium molecular dynamics study

Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V ?(-1). A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-á-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.     

Determination of the potassium content of explosive residues using miniaturised isotachophoresis

A new method has been developed to allow the determination of potassium in post-explosion residues to be made using miniaturised isotachophoresis. The method is based on the use of a caesium leading ion with 4.5 mM 18-crown-6 ether added to retard the potassium to allow reliable determinations to be made. With the conditions selected no interference was noted from other small inorganic cations, such as ammonium, barium, calcium, magnesium, sodium or strontium. The method was successfully applied to the analysis of seven samples containing explosive residues obtained from the unconfined burning of several flash powders. The procedure was found to offer good linearity for potassium determinations over the concentration range of 1.25-150 μg/mL with a coefficient of determination of 0.999 achieved.     

Tailoring enzyme-rich environmental DNA clones: a source of enzymes for generating libraries of unnatural natural products

A detailed bioinformatics analysis of six glycopeptide biosynthetic gene clusters isolated from soil environmental DNA (eDNA) megalibraries indicates that a subset of these gene clusters contains collections of tailoring enzymes that are predicted to result in the production of new glycopeptide congeners. In particular, sulfotransferases appear in eDNA-derived gene clusters at a much higher frequency than would be predicted from the characterization of glycopeptides from cultured Actinomycetes . Enzymes found on tailoring-enzyme-rich eDNA clones associated with these six gene clusters were used to produce a series of new sulfated glycopeptide derivatives in both in vitro and in vivo derivatization studies. The derivatization of known natural products with eDNA-derived tailoring enzymes is likely to be a broadly applicable strategy for generating libraries of new natural product variants.     

A Stream Function Approach to Optical Flow with Applications to Fluid Transport Dynamics

Optical flow is one of the classical problems in computer vision, but it has recently also been adapted to applications from other fields, such as fluid mechanics and dynamical systems. If the goal is to analyze the dynamics of system whose evolution is governed by a flow field that is the gradient of a potential function – which describes many flows in fluid dynamics – it is natural to approach the optical flow problem by reconstructing the potential function, also called the stream function, rather than reconstructing the components of the flow directly. This alternate approach allows one to impose scientific priors, via regularization, directly on the flow itself rather than on its components independently. We demonstrate the stream function formulation of optical flow and its application to reconstructing an oceanic fluid flow driven by satellite measurements. It is also shown how these flow fields can be used to analyze mixing and mass transport in the fluid system being imaged. (© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)