Feasibility of probing boundary morphology of structured materials by 2D NMR q-space imaging

It is well known that one-dimensional (1D) q-space imaging allows retrieval of structural information at cellular resolution. Here we demonstrate by simulation that boundary morphology of structured materials can be derived from 2D q-space mapping. Based on a finite-difference model for restricted diffusion, 2D q-space maps obtained from water diffusion inside apertures at various levels of asperity were simulated. The results indicate that the observed ring patterns (diffraction minima) reveal the boundary profiles of the apertures but become blurred in the case of significant variation in aperture size. For uniform size distribution of apertures, a quantitative measure of surface roughness can be established by means of spatial autocorrelation analysis. The results suggest that 2D q-space imaging may allow probing of the boundary morphology of structured materials and possibly biological cells.     

Epoxide-opening and group-transfer reactions mediated by monomeric zirconium imido complexes

N-tert-Butylimidozirconocene (Cp2Zr=Nt-Bu) and its analogue (ebthi)Zr=NAr (ebthi = ethylenebis(tetrahydroindenyl), Ar = 2,6-dimethylphenyl) undergo overall cycloaddition reactions at ambient temperature with epoxides that lack accessible beta-hydrogens. The process results in addition of the Zr=N bond to an epoxide C-O bond, leading to azazirconacyclopentanes. The regio- and stereochemistry of the products implicate a stepwise mechanism, with the intermediacy of zwitterions having substantial carbocation character at the substituted carbon of the ring-opened epoxide-derived fragment. The azametallacycles undergo facile cleavage to beta-amino alcohols upon addition of mild acid.     

Rigid pyridyl substituted NHC ligands,their Pd(0) complexes and their application in selective transfer semihydrogenation of alkynes

The synthesis of an air‐stable series of Pd⁰ complexes with unsymmetric bidentate N‐pyridine N‐heterocyclic carbene ligands has been described. The carbenes were generated by synthesis of the silver(I) complexes from the imidazolium salts, followed by transmetallation of the C‐N ligands to obtain the target electron‐rich zerovalent palladium compounds. The bidentate coordination behaviour of the ligands was confirmed by ¹H, ¹³C NMR and X‐ray spectroscopy. The complexes are active precatalysts for the selective transfer semihydrogenation of alkynes to Z‐alkenes, with selectivities up to 99%. Copyright © 2011 John Wiley & Sons, Ltd.     

Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides

The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography–electrospray ionization–tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.     

Thermal‐ and Light‐Induced Spin Crossover in a Guest‐Dependent Dinuclear Iron(II) System

We previously reported the dinuclear material [Fe^II₂(ddpp)₂(NCS)₄] ? 4 CH₂Cl₂ ( 1? 4 CH₂Cl₂; ddpp=2,5‐di(2′,2′′‐dipyridylamino)pyridine) and its partially desolvated analogue ( 1? CH₂Cl₂), which undergo two‐ and one‐step spin‐crossover (SCO) transitions, respectively. Here, we manipulate the type and degree of solvation in this system and find that either a one‐ or two‐step spin transition can be specifically targeted. The chloroform clathrate 1? 4 CHCl₃ undergoes a relatively abrupt one‐step SCO, in which the two equivalent Fe^II sites within the dinuclear molecule crossover simultaneously. Partial desolvation of 1? 4 CHCl₃ to form 1? 3 CHCl₃ and 1? CHCl₃ occurs through single‐crystal‐to‐single‐crystal processes (monoclinic C2/c to P2₁/n to P2₁/n) in which the two equivalent Fe^II sites become inequivalent sites within the dinuclear molecule of each phase. Both 1? 3 CHCl₃ and 1? CHCl₃ undergo one‐step spin transitions, with the former having a significantly higher SCO temperature than 1? 4 CHCl₃ and the latter, and each has a broader SCO transition than 1? 4 CHCl₃, attributable to the overlap of two SCO steps in each case. Further magnetic manipulation can be carried out on these materials through reversibly resolvating the partially desolvated material with chloroform to produce the original one‐step SCO, or with dichloromethane to produce a two‐step SCO reminiscent of that seen for 1? 4 CH₂Cl₂. Furthermore, we investigate the light‐induced excited spin state trapping (LIESST) effect on 1? 4 CH₂Cl₂ and 1? CH₂Cl₂ and observe partial LIESST activity for the former and no activity for the latter.     

Age-dependent transient shear banding in soft glasses

We study numerically the formation of long-lived transient shear bands during shear startup within two models of soft glasses (a simple fluidity model and an adapted "soft glassy rheology" model). The degree and duration of banding depends strongly on the applied shear rate, and on sample age before shearing. In both models the ultimate steady flow state is homogeneous at all shear rates, consistent with the underlying constitutive curve being monotonic. However, particularly in the soft glassy rheology case, the transient bands can be extremely long lived. The banding instability is neither "purely viscous" nor "purely elastic" in origin, but is closely associated with stress overshoot in startup flow.     

Criterion for extensional necking instability in polymeric fluids

We study the linear instability with respect to necking of a filament of polymeric fluid undergoing uniaxial extension. Contrary to the widely discussed Considère criterion, we find the onset of instability to relate closely to the onset of downward curvature in the time (and so strain) evolution of the zz component of the molecular strain, for extension along the z axis. In establishing this result numerically across five of the most widely used models of polymer rheology, and by analytical calculation, we argue it to apply generically. Particularly emphasized is the importance of polymer chain stretching in partially mitigating necking. We comment finally on the relationship between necking and the shape of the underlying steady state constitutive curve for homogeneous extension.     

A new lot sizing and scheduling heuristic for multi-site biopharmaceutical production

Biopharmaceutical manufacturing requires high investments and long-term production planning. For large biopharmaceutical companies, planning typically involves multiple products and several production facilities. Production is usually done in batches with a substantial set-up cost and time for switching between products. The goal is to satisfy demand while minimising manufacturing, set-up and inventory costs. The resulting production planning problem is thus a variant of the capacitated lot-sizing and scheduling problem, and a complex combinatorial optimisation problem. Inspired by genetic algorithm approaches to job shop scheduling, this paper proposes a tailored construction heuristic that schedules demands of multiple products sequentially across several facilities to build a multi-year production plan (solution). The sequence in which the construction heuristic schedules the different demands is optimised by a genetic algorithm. We demonstrate the effectiveness of the approach on a biopharmaceutical lot sizing problem and compare it with a mathematical programming model from the literature. We show that the genetic algorithm can outperform the mathematical programming model for certain scenarios because the discretisation of time in mathematical programming artificially restricts the solution space.     

Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan

The β-lactams are the most important class of antibiotics in clinical use. Their lethal targets are the transpeptidase domains of penicillin binding proteins (PBPs), which catalyze the cross-linking of bacterial peptidoglycan (PG) during cell wall synthesis. The transpeptidation reaction occurs in two steps, the first being formation of a covalent enzyme intermediate and the second involving attack of an amine on this intermediate. Here we use defined PG substrates to dissect the individual steps catalyzed by a purified E. coli transpeptidase. We demonstrate that this transpeptidase accepts a set of structurally diverse D-amino acid substrates and incorporates them into PG fragments. These results provide new information on donor and acceptor requirements as well as a mechanistic basis for previous observations that noncanonical D-amino acids can be introduced into the bacterial cell wall.