On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

Hyperpolarized 13C Magnetic Resonance Imaging of Fumarate Metabolism by Parahydrogen-induced Polarization: A Proof-of-Concept in vivo Study

Hyperpolarized [1-¹³C]fumarate is a promising magnetic resonance imaging (MRI) biomarker for cellular necrosis, which plays an important role in various disease and cancerous pathological processes. To demonstrate the feasibility of MRI of [1-¹³C]fumarate metabolism using parahydrogen-induced polarization (PHIP), a low-cost alternative to dissolution dynamic nuclear polarization (dDNP), a cost-effective and high-yield synthetic pathway of hydrogenation precursor [1-¹³C]acetylenedicarboxylate (ADC) was developed. The trans-selectivity of the hydrogenation reaction of ADC using a ruthenium-based catalyst was elucidated employing density functional theory (DFT) simulations. A simple PHIP set-up was used to generate hyperpolarized [1-¹³C]fumarate at sufficient ¹³C polarization for ex vivo detection of hyperpolarized ¹³C malate metabolized from fumarate in murine liver tissue homogenates, and in vivo ¹³C MR spectroscopy and imaging in a murine model of acetaminophen-induced hepatitis.     

Dynamical study of femtosecond-laser-ablated liquid-aluminum nanoparticles using spatiotemporally resolved x-ray-absorption fine-structure spectroscopy

We study the temperature evolution of aluminum nanoparticles generated by femtosecond laser ablation with spatiotemporally resolved x-ray-absorption fine-structure spectroscopy. We successfully identify the nanoparticles based on the L-edge absorption fine structure of the ablation plume in combination with the dependence of the edge structure on the irradiation intensity and the expansion velocity of the plume. In particular, we show that the lattice temperature of the nanoparticles is estimated from the L-edge slope, and that its spatial dependence reflects the cooling of the nanoparticles during plume expansion. The results reveal that the emitted nanoparticles travel in a vacuum as a condensed liquid phase with a lattice temperature of about 2500 to 4200 K in the early stage of plume expansion.     

Dephasing of a superconducting flux qubit

In order to gain a better understanding of the origin of decoherence in superconducting flux qubits, we have measured the magnetic field dependence of the characteristic energy relaxation time (T(1)) and echo phase relaxation time (T(2)(echo)) near the optimal operating point of a flux qubit. We have measured T(2)(echo) by means of the phase cycling method. At the optimal point, we found the relation T(2)(echo) approximately 2T(1). This means that the echo decay time is limited by the energy relaxation (T(1) process). Moving away from the optimal point, we observe a linear increase of the phase relaxation rate (1/T(2)(echo)) with the applied external magnetic flux. This behavior can be well explained by the influence of magnetic flux noise with a 1/f spectrum on the qubit.     

Tailoring D‐Amino Acid Oxidase from the Pig Kidney to R‐Stereoselective Amine Oxidase and its Use in the Deracemization of α‐Methylbenzylamine

The deracemization of racemic amines to yield enantioenriched amines using S‐stereoselective amine oxidases (AOx) has recently been attracting attention. However, R‐stereoselective AOx that are suitable for deracemization have not yet been identified. An R‐stereoselective AOx was now evolved from porcine kidney D ‐amino acid oxidase (pkDAO) and subsequently use for the deracemization of racemic amines. The engineered pkDAO, which was obtained by directed evolution, displayed a markedly changed substrate specificity towards R amines. The mutant enzyme exhibited a high preference towards the substrate α‐methylbenzylamine and was used to synthesize the S amine through deracemization. The findings of this study indicate that further investigations on the structure–activity relationship of AOx are warranted and also provide a new method for biotransformations in organic synthesis.     

Synthesis of CF2H‐Containing Oxime Ethers Derivatives from ClCF2H,tert‐Butyl Nitrile and Indoles

Summaryof main observation and conclusion A new and intriguing methodology to access various O-difluoromethylation oxime compounds from CICF2H,TBN and indoles is developed under mild reaction conditions.This strategy can suppress N-difluoromethylation of indoles successfully,in which there are two different active species(:CF2and·NO)while indoles are unprotected,featuringsimple operation and radical involvement.     

Dehydration‐fragmentation mechanism of cathinones and their metabolites in ESI‐CID

Various cathinone‐derived designer drugs (CATs) have recently appeared on the drug market. This study examined the mechanism for the generation of dehydrated ions for CATs during electrospray ionization collision‐induced dissociation (ESI‐CID). The generation mechanism of dehydrated ions is dependent on the amine classification in the cathinone skeleton, which is used in the identification of CATs. The two hydrogen atoms eliminated during the dehydration of cathinone (primary amine) and methcathinone (secondary amine) were determined, and the reaction mechanism was elucidated through the deuterium labeling experiments. The hydrogen atom bonded to the amine nitrogen was eliminated with the proton added during ESI, in both of the tested compounds. This provided evidence that CATs with tertiary amine structures (such as dimethylcathinone and α‐pyrrolidinophenones [α‐PPs]) do not undergo dehydration. However, it was shown that the two major tertiary amine metabolites (1‐OH and 2″‐oxo) of CATs generate dehydrated ions in ESI‐CID. The dehydration mechanisms of the metabolites of α‐pyrrolidinobutiophenone (α‐PBP) belongs to α‐PPs were also investigated. Stable‐isotope labeling showed the dehydration of the 1‐OH metabolite following a simple mechanism where the hydroxy group was eliminated together with the proton added during ESI. In contrast, the dehydration mechanism of the 2″‐oxo metabolite involved hydrogen atoms in three or more locations along with the carbonyl group oxygen, indicating that dehydration occurred via multiple mechanisms likely including the rearrangement reaction of hydrogen atoms. These findings presented herein indicate that the dehydrated ions in ESI‐CID can be used for the structural identification of CATs.     

Effects of Al concentration and resulting long-period superstructures on the plastic properties at room temperature of Al-rich TiAl single crystals

The role of Al₅Ti₃ and h-Al₂Ti long-period superstructures on the plastic properties of TiAl at room temperature is investigated on five single crystals with aluminium content comprised between 54.7 at.%, and 62.5 at.%. After annealing at 1200°C for 1?h, the Al₅Ti₃ superstructure develops in the L1₀ (γ) matrix upon increasing Al concentration except for Ti–62.5 at.%Al where h-Al₂Ti substitutes for Al₅Ti₃. The CRSS for <110]{111} first increases abruptly with the development of the Al₅Ti₃-type ordering. Then, the CRSS reaches a plateau at which dislocations assemble in groups of four to prevent extra anti-phase boundary (APB) from being engendered during glide throughout the Al₅Ti₃ phase. In Ti–62.5 at.%Al, the CRSS for ordinary slip further increases upon the precipitation of h-Al₂Ti in the L1₀ phase, whereas it decreases when the crystal is fully transformed into single-phased Al₅Ti₃. <101] superlattice dislocations are primarily activated under both the [210] and [1?1?8.6] load orientations irrespective of the Al concentration, but the dislocation microstructure strongly depends on orientation as well as on the degree of Al₅Ti₃ ordering. In the [210] orientation, the frequency of the decomposition of <101] dislocations into 1/2<110] and 1/2<112] dislocations decreases abruptly with the development of Al₅Ti₃. This is interpreted in terms of the increased difficulty to move ordinary dislocations. Under the [1?1?8.6] orientation, the density of faulted dipoles diminishes remarkably with the development of Al₅Ti₃. This is consistent with the transformation of the low energy extrinsic stacking fault of the L1₀ phase into a higher energy complex extrinsic stacking fault.