Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions

Predicting the fragmentation patterns of proteins would be beneficial for the reliable identification of intact proteins by mass spectrometry. However, the ability to accurately make such predictions remains elusive. An approach to predict the specific cleavage sites in whole proteins resulting from collision-induced dissociation by use of an improved electrostatic model for calculating the proton configurations of highly-charged protein ions is reported. Using ubiquitin, cytochrome c, lysozyme and β-lactoglobulin as prototypical proteins, this approach can be used to predict the fragmentation patterns of intact proteins. For sufficiently highly charged proteins, specific cleavages occur near the first low-basicity amino acid residues that are protonated with increasing charge state. Hybrid QM/QM′ (QM=quantum mechanics) and molecular dynamics (MD) simulations and energy-resolved collision-induced dissociation measurements indicated that the barrier to the specific dissociation of the protonated amide backbone bond is significantly lower than competitive charge remote fragmentation. Unlike highly charged peptides, the protons at low-basicity sites in highly charged protein ions can be confined to a limited sequence of low-basicity amino acid residues by electrostatic repulsion, which results in highly specific fragmentation near the site of protonation. This research suggests that the optimal charge states to form specific sequence ions of intact proteins in higher abundances than the use of less specific ion dissociation methods can be predicted a priori.     

A Promiscuous De Novo Retro‐Aldolase Catalyzes Asymmetric Michael Additions via Schiff Base Intermediates

Recent advances in computational design have enabled the development of primitive enzymes for a range of mechanistically distinct reactions. Here we show that the rudimentary active sites of these catalysts can give rise to useful chemical promiscuity. Specifically, RA95.5‐8, designed and evolved as a retro‐aldolase, also promotes asymmetric Michael additions of carbanions to unsaturated ketones with high rates and selectivities. The reactions proceed by amine catalysis, as indicated by mutagenesis and X‐ray data. The inherent flexibility and tunability of this catalyst should make it a versatile platform for further optimization and/or mechanistic diversification by directed evolution.     

Impact of the Oxygen Defects and the Hydrogen Concentration on the Surface of Tetragonal and Monoclinic ZrO2 on the Reduction Rates of Stearic Acid on Ni/ZrO2

The role of the specific physicochemical properties of ZrO₂ phases on Ni/ZrO₂ has been explored with respect to the reduction of stearic acid. Conversion on pure m‐ZrO₂ is 1.3 times more active than on t‐ZrO₂, whereas Ni/m‐ZrO₂ is three times more active than Ni/t‐ZrO₂. Although the hydrodeoxygenation of stearic acid can be catalyzed solely by Ni, the synergistic interaction between Ni and the ZrO₂ support causes the variations in the reaction rates. Adsorption of the carboxylic acid group on an oxygen vacancy of ZrO₂ and the abstraction of the α‐hydrogen atom with the elimination of the oxygen atom to produce a ketene is the key to enhance the overall rate. The hydrogenated intermediate 1‐octadecanol is in turn decarbonylated to heptadecane with identical rates on all catalysts. Decarbonylation of 1‐octadecanol is concluded to be limited by the competitive adsorption of reactants and intermediate. The substantially higher adsorption of propionic acid demonstrated by IR spectroscopy and the higher reactivity to O₂ exchange reactions with the more active catalyst indicate that the higher concentration of active oxygen defects on m‐ZrO₂ compared to t‐ZrO₂ causes the higher activity of Ni/m‐ZrO₂.     

Copper‐Catalyzed Amidation of Primary and Secondary Alkyl Boronic Esters

The oxidative copper‐catalyzed cross‐coupling of functionalized alkyl boronic esters with primary amides is reported. Through the identification of appropriate diketimine ligands, conditions for efficient coupling of both primary and secondary alkyl boronic esters with diverse primary amides, including acetamide, have been developed.     

A study of the effect of step excrescences and free‐stream disturbances on boundary layer stability

In this work, a study of the mechanism by which free‐stream acoustic and vorticity disturbances interact with a boundary layer flow developing over a flat plate featuring a step excrescence located at a certain distance from a blunt leading edge is included. The numerical tool is a high‐fidelity implicit numerical algorithm solving for the unsteady, compressible form of the Navier–Stokes equations in a body‐fitted curvilinear coordinates and employing high‐accurate compact differencing schemes with Pade‐type filters. Acoustic and vorticity waves are generated using a source term in the momentum and energy equations, as opposed to using inflow boundary conditions, to avoid spurious waves that may propagate from boundaries. The results show that the receptivity to surface step excrescences is largely the result of an overall adverse pressure gradient posed by the step, and that the free‐stream disturbances accelerate the generation of instabilities in the downstream. As expected, it is found that the acoustic disturbance interacting with the surface imperfection is more efficient in exciting the Tollmien–Schlichting waves than the vorticity disturbance. The latter generates Tollmien–Schlichting waves that are grouped in wave packets consistent with the wavelength of the free‐stream disturbance. Copyright © 2015 John Wiley & Sons, Ltd.     

Copper‐Catalyzed Formation of α‐Alkoxycycloalkenones from N‐Tosylhydrazones

The combination of 20 mol % of copper iodide and lithium tert‐butoxide triggers the formation of a broad range of substituted, functionalized α‐alkoxy 2H‐naphthalenones from readily available N‐tosylhydrazones. The data suggests that this transformation occurs through cycloaddition of a copper carbenoid with an ester, followed by a Lewis acid‐catalyzed [1,2] alkyl shift of the in situ generated alkoxyepoxide intermediate.     

Semiclassical Trajectory Studies of Reactive and Nonreactive Scattering of OH(A 2Σ+) by H2 Based on an Improved Full-Dimensional Ab Initio Diabatic Potential Energy Matrix

We present a new full-dimensional diabatic potential energy matrix (DPEM) for electronically nonadiabatic collisions of OH(A ²Σ⁺) with H₂, and we calculate the probabilities of electronically adiabatic inelastic collisions, nonreactive quenching, and reactive quenching to form H₂O+H. The DPEM was fitted using a many-body expansion with permutationally invariant polynomials in bond-order functions to represent the many-body part. The dynamics calculations were carried out with the fewest-switches with time uncertainty and stochastic decoherence (FSTU/SD) semiclassical trajectory method. We present results both for head-on collisions (impact parameter b equal to zero) and for a full range of impact parameters. The results are compared to experiment and to earlier FSTU/SD and quantum dynamics calculations with a previously published DPEM. The various theoretical results all agree that nonreactive quenching dominates reactive quenching, but there are quantitative differences between the two DPEMs and between the b=0 results and the all-b results, especially for the probability of reactive quenching.