An implicit edge‐based ALE method for the incompressible Navier–Stokes equations

A new finite volume method for the incompressible Navier–Stokes equations, expressed in arbitrary Lagrangian–Eulerian (ALE) form, is presented. The method uses a staggered storage arrangement for the pressure and velocity variables and adopts an edge‐based data structure and assembly procedure which is valid for arbitrary n‐sided polygonal meshes. Edge formulas are presented for assembling the ALE form of the momentum and pressure equations. An implicit multi‐stage time integrator is constructed that is geometrically conservative to the precision of the arithmetic used in the computation. The method is shown to be second‐order‐accurate in time and space for general time‐dependent polygonal meshes. The method is first evaluated using several well‐known unsteady incompressible Navier–Stokes problems before being applied to a periodically forced aeroelastic problem and a transient free surface problem. Published in 2003 by John Wiley & Sons, Ltd.     

Ionization-enhanced decomposition of 2,4,6-trinitrotoluene (TNT) molecules

The unimolecular decomposition reaction of TNT can in principle be used to design ways to either detect or remove TNT from the environment. Here, we report the results of a density functional theory study of possible ways to lower the reaction barrier for this decomposition process by ionization, so that decomposition and/or detection can occur at room temperature. We find that ionizing TNT lowers the reaction barrier for the initial step of this decomposition. We further show that a similar effect can occur if a positive moiety is bound to the TNT molecule. The positive charge produces a pronounced electron redistribution and dipole formation in TNT with minimal charge transfer from TNT to the positive moiety.     

Oxidative dehydrocoupling of N-H bonds using a redox-active main group superbase

Reaction of the redox-active base Sn(NMe(2))(2)/(n)BuLi with o-phenylene diamine leads to oxidative dehydrocoupling and rearrangement into the triazolyl anion.     

A quadruply-bonded [Cr2(guanidinate)4]4- tetraanion

The reaction of chromocene, Cp(2)Cr, with dilithiated 2,3-diphenylguanidine [(PhNH)(2)C=NH = L(2)H(3)] gives the novel, quadruply-bonded tetraanion [Cr(2)(L(2)H)(4)](4-).     

Transition metal catalysed ammonia-borane dehydrogenation in ionic liquids

Significant advantages result from combining the disparate hydrogen release pathways for ammonia-borane (AB) dehydrogenation using ionic liquids (ILs) and transition metal catalysts. With the RuCl(2)(PMe(3))(4) catalyst precursor, AB dehydrogenation selectivity and extent are maximized in an IL with a moderately coordinating ethylsulfate anion.     

The role of CN and CO ligands in the vibrational relaxation dynamics of model compounds of the [FeFe]-hydrogenase enzyme

The vibrational dynamics of (μ-propanedithiolate)Fe(2)(CO)(4)(CN)(2)(2-), a model compound of the active site of the [FeFe]-hydrogenase enzyme, have been examined via ultrafast 2D-IR spectroscopy. The results indicate that the vibrational coupling between the stretching modes of the CO and CN ligands is small and restricted to certain modes but the slow growth of off-diagonal peaks is assigned to population transfer processes occurring between these modes on timescales of 30-40 ps. Analysis of the dynamics in concert with anharmonic density functional theory simulations shows that the presence of CN ligands alters the vibrational relaxation dynamics of the CO modes in comparison to all-carbonyl model systems and suggests that the presence of these ligands in the enzyme may be an important feature in terms of directing the vibrational relaxation mechanism.     

Gas-phase ion-molecule reactions using regioselectively generated radical cations to model oxidative damage and probe radical sites in peptides

Collision induced dissociation (CID) of sodiated peptide derivatives containing a nitrate ester functionality was used to regiospecifically generate three isomeric radicals of the model peptide Bz-Ala-Gly-OMe corresponding to radicals formed at: C(α) of the alanine residue [4+Na](+); C(α) of the glycine residue [5+Na](+); and the side chain of alanine [6+Na](+). The ion-molecule reactions of these peptide radicals were examined to model oxidative damage to peptides and to probe whether the radical sites maintain their integrity or whether they isomerise via intramolecular hydrogen atom transfer (HAT). Only [6+Na](+) is reactive towards O(2), forming the peroxyl radical [7+Na](+), which loses O(2), HO˙ and HO(2)˙ under CID. The radical ion [7 + Na](+) abstracts a hydrogen atom from 4-fluorothiophenol to form the hydroperoxide [8+Na](+), which upon CID fragments via the combined loss of HO˙ and CH(2)O. In contrast, all three of the isomeric sodiated radicals react with NO˙ and NO(2)˙ to form adducts. CID of the NO adducts only regenerates the radicals via NO˙ loss, thus providing no structural information. In contrast, CID of the NO(2) adducts gives rise to a range of product ions and the spectra are different for each of the three adducts, suggesting that the isomeric radicals [4+Na](+), [5+Na](+) and [6+Na](+) are produced as discrete species. Finally, CID of the NO(2) adducts was used to probe the rearrangement of the radicals [4+Na](+), [5+Na](+) and [6+Na](+) prior to their reaction with NO(2)˙: [6 + Na](+) rearranges to a mixture of [4+Na](+) and [5+Na](+) while [5+Na](+) rearranges to [4+Na](+).     

Highly substituted oxabicyclic derivatives from furan: synthesis of (±)-platensimycin

A stereocontrolled approach to a key platensimycin intermediate was achieved from a commercially available furylcarboxylate. Key to our approach is the highly efficient formal [4 + 3] cyclocondensation of a substituted furan with tetrabromocyclopropene along with an intramolecular γ-alkylation to construct the final ring of the caged intermediate.     

Resolution of discordant HIV-1 protease resistance rankings using molecular dynamics simulations

The emergence of drug resistance is a major challenge for the effective treatment of HIV. In this article, we explore the application of atomistic molecular dynamics simulations to quantify the level of resistance of a patient-derived HIV-1 protease sequence to the inhibitor lopinavir. A comparative drug ranking methodology was developed to compare drug resistance rankings produced by the Stanford HIVdb, ANRS, and RegaDB clinical decision support systems. The methodology was used to identify a patient sequence for which the three rival online tools produced differing resistance rankings. Mutations at only three positions ( L10I , A71IV, and L90M ) influenced the resistance level assigned to the sequence. We use ensemble molecular dynamics simulations to elucidate the origin of these discrepancies and the mechanism of resistance. By simulating not only the full patient sequences but also systems containing the constituent mutations, we gain insight into why resistance estimates vary and the interactions between the various mutations. In the same way, we also gain valuable knowledge of the mechanistic causes of resistance. In particular, we identify changes in the relative conformation of the two beta sheets that form the protease dimer interface which suggest an explanation of the relative frequency of different amino acids observed in patients at residue 71.