Compressive advection and multi‐component methods for interface‐capturing

This paper develops methods for interface‐capturing in multiphase flows. The main novelties of these methods are as follows: (a) multi‐component modelling that embeds interface structures into the continuity equation; (b) a new family of triangle/tetrahedron finite elements, in particular, the P₁DG‐P₂(linear discontinuous between elements velocity and quadratic continuous pressure); (c) an interface‐capturing scheme based on compressive control volume advection methods and high‐order finite element interpolation methods; (d) a time stepping method that allows use of relatively large time step sizes; and (e) application of anisotropic mesh adaptivity to focus the numerical resolution around the interfaces and other areas of important dynamics. This modelling approach is applied to a series of pure advection problems with interfaces as well as to the simulation of the standard computational fluid dynamics benchmark test cases of a collapsing water column under gravitational forces (in two and three dimensions) and sloshing water in a tank. Two more test cases are undertaken in order to demonstrate the many‐material and compressibility modelling capabilities of the approach. Numerical simulations are performed on coarse unstructured meshes to demonstrate the potential of the methods described here to capture complex dynamics in multiphase flows. Copyright © 2015 John Wiley & Sons, Ltd.     

The configurational dependence of binding free energies: A Poisson–Boltzmann study of Neuraminidase inhibitors

The linear finite difference Poisson-Boltzmann (FDPB) equation is applied to the calculation of the electrostatic binding free energies of a group of inhibitors to the Neuraminidase enzyme. An ensemble of enzyme-inhibitor complex conformations was generated using Monte Carlo simulations and the electrostatic binding free energies of subtly different configurations of the enzyme-inhibitor complexes were calculated. It was seen that the binding free energies calculated using FDPB depend strongly on the configuration of the complex taken from the ensemble. This configurational dependence was investigated in detail in the electrostatic hydration free energies of the inhibitors. Differences in hydration energies of up to 7 kcal mol^–1 were obtained for root mean square (RMS) structural deviations of only 0.5 Å. To verify the result, the grid size and parameter dependence of the calculated hydration free energies were systematically investigated. This showed that the absolute hydration free energies calculated using the FDPB equation were very sensitive to the values of key parameters, but that the configurational dependence of the free energies was independent of the parameters chosen. Thus just as molecular mechanics energies are very sensitive to configuration, and single-structure values are not typically used to score binding free energies, single FDPB energies should be treated with the same caution.     

An Immobilized‐Dirhodium Hollow‐Fiber Flow Reactor for Scalable and Sustainable C−H Functionalization in Continuous Flow

A scalable flow reactor is demonstrated for enantioselective and regioselective rhodium carbene reactions (cyclopropanation and C?H functionalization) by developing cascade reaction methods employing a microfluidic flow reactor system containing immobilized dirhodium catalysts in conjunction with the flow synthesis of diazo compounds. This allows the utilization of the energetic diazo compounds in a safe manner and the recycling of the dirhodium catalysts multiple times. This approach is amenable to application in a bulk‐scale synthesis employing asymmetric C?H functionalization by stacking multiple fibers in one reactor module. The products from this sequential flow–flow reactor are compared with a conventional batch reactor or flow–batch reactor in terms of yield, regioselectivity, and enantioselectivity.     

Controlling Proton and Electron Transfer Rates to Enhance the Activity of an Oxygen Reduction Electrocatalyst

An electrochemical approach is developed that allows for the control of both proton and electron transfer rates in the O₂ reduction reaction (ORR). A dinuclear Cu ORR catalyst was prepared that can be covalently attached to thiol‐based self‐assembled monolayers (SAMs) on Au electrodes using azide–alkyne click chemistry. Using this architecture, the electron transfer rate to the catalyst is modulated by changing the length of the SAM, and the proton transfer rate to the catalyst is controlled with an appended lipid membrane modified with proton carriers. By tuning the relative rates of proton and electron transfer, the current density of the lipid‐covered catalyst is enhanced without altering its core molecular structure. This electrochemical platform will help identify optimal thermodynamic and kinetic parameters for ORR catalysts and catalysts of other reactions that involve the transfer of both protons and electrons.     

Two‐Color Valence‐to‐Core X‐ray Emission Spectroscopy Tracks Cofactor Protonation State in a Class I Ribonucleotide Reductase

Proton transfer reactions are of central importance to a wide variety of biochemical processes, though determining proton location and monitoring proton transfers in biological systems is often extremely challenging. Herein, we use two‐color valence‐to‐core X‐ray emission spectroscopy (VtC XES) to identify protonation events across three oxidation states of the O₂‐activating, radical‐initiating manganese–iron heterodinuclear cofactor in a class I‐c ribonucleotide reductase. This is the first application of VtC XES to an enzyme intermediate and the first simultaneous measurement of two‐color VtC spectra. In contrast to more conventional methods of assessing protonation state, VtC XES is a more direct probe applicable to a wide range of metalloenzyme systems. These data, coupled to insight provided by DFT calculations, allow the inorganic cores of the Mn^IVFe^IV and Mn^IVFe^III states of the enzyme to be assigned as Mn^IV(μ‐O)₂Fe^IV and Mn^IV(μ‐O)(μ‐OH)Fe^III, respectively.     

Total Synthesis of (6R,10R,13R,14R,16R,17R,19S,20R,21R,24S, 25S,28S,30S,32R,33R,34R,36S,37S,39R)‐Azaspiracid‐3 Reveals Non‐Identity with the Natural Product

A convergent and stereoselective total synthesis of the previously assigned structure of azaspiracid‐3 has been achieved by a late‐stage Nozaki–Hiyama–Kishi coupling to form the C21?C22 bond with the C20 configuration unambiguously established from l ‐(+)‐tartaric acid. Postcoupling steps involved oxidation to an ynone, modified Stryker reduction of the alkyne, global deprotection, and oxidation of the resulting C1 primary alcohol to the carboxylic acid. The synthetic product matched naturally occurring azaspiracid‐3 by mass spectrometry, but differed both chromatographically and spectroscopically.     

A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors

As of mid-2017, only one structure of the human immunodeficiency virus (HIV) integrase core domain co-crystallised with an active site inhibitor was reported. In this structure (1QS4), integrase is complexed with a diketo-acid based strand-transfer inhibitor (INSTI). This structure has been a preferred platform for the structure-based design of INSTIs despite concerns relating to structural irregularities arising from crystallographic packing effects. A survey of the current pool of 297 reported integrase catalytic core structures indicated that the anatomy of the active site in the complex structure 1QS4 exhibits subtle variations relative to all other structures examined. Consequently, the 1QS4 structure was employed for docking studies. From the docking of twenty-seven allyltyrosine analogues, a 3-point inhibitor binding motif required for activity was established and successfully utilised in the development of a tripeptide displaying an EC₅₀ value of 10 ± 5 μM in HIV infected human T-cells. Additional docking of “in-house” compound libraries unearthed a methyl ester based nitrile derivative displaying an IC₅₀ value of 0.5 μM in a combined 3′-processing and strand-transfer assay.     

Comparison of chiral NMR solvating agents for the enantiodifferentiation of amines

Chiral, enantiomerically pure organic-soluble acids are often used as NMR chiral solvating agents (CSAs) for analyzing the enantiopurity of amines. However, the reports that describe CSAs for amines provide limited comparisons to other previously reported reagents. As such, it is difficult to know which among the many CSAs to pick when studying a new amine. We report a comparison of thirteen commercially available CSAs for the analysis of primary, secondary and tertiary amines in chloroform-d. (R)-α-methoxyphenylacetic acid, (R)-(-)-O-acetylmandelic acid, (R)-2-methoxy-2-(1-naphthyl)propionic acid and (R)-(-)-1,1′-binaphthyl-2,2′-diylhydrogenphosphate are identified as the best four to use as a starting point for the analysis of a new amine.     

A practical microwave method for the synthesis of fluoromethy 4-methylbenzenesulfonate in tert-amyl alcohol

Fluorine substitution is an established tool in medicinal chemistry to favourably alter the molecular properties of a lead compound of interest. However, gaps still exist in the library of synthetic methods for accessing certain fluorine-substituted motifs. One such area is the fluoromethyl group, particularly when required in a fluoroalkylating capacity. The cold fluorination of methylene ditosylate is under evaluated in the literature, often proceeding with low yields or harsh conditions. This report describes a novel microwave method for the rapid nucleophilic fluorination of methylene ditosylate using inexpensive reagents in good isolated yield (65%).     

Fast Exfoliation and Functionalisation of Two‐Dimensional Crystalline Carbon Nitride by Framework Charging

Two‐dimensional (2D) layered graphitic carbon nitride (gCN) nanosheets offer intriguing electronic and chemical properties. However, the exfoliation and functionalisation of gCN for specific applications remain challenging. We report a scalable one‐pot reductive method to produce solutions of single‐ and few‐layer 2D gCN nanosheets with excellent stability in a high mass yield (35 %) from polytriazine imide. High‐resolution imaging confirmed the intact crystalline structure and identified an AB stacking for gCN layers. The charge allows deliberate organic functionalisation of dissolved gCN, providing a general route to adjust their properties.