Chemical ionization of phenyl n-propyl ether and methyl substituted analogs: Propene loss initiated by competing proton transfer to the oxygen atom and the aromatic ring

The mechanism of propene loss from protonated phenyl n-propyl ether and a series of mono-, di-, and trimethylphenyl n-propyl ethers has been examined by chemical ionization (CI) mass spectrometry in combination with tandem mass spectrometry experiments. The role of initial proton transfer to the oxygen atom and the aromatic ring, respectively, has been probed with the use of deuterated CI reagents, D₂O, CD₃OD, and CD₃CN (given in order of increasing proton affinity), in combination with deuterium labeling of the β position of the n-propyl group or the phenyl ring. The metastable [M + D]⁺ ions of phenyl n-propyl ether—formed with D₂O as the CI reagent—eliminate C₃H₅D and C₃H₆ in a ratio of 10:90, which indicates that the added deuteron is incorporated to a minor extent in the expelled neutral species. In the experiments with CD₃OD as the CI reagent, the ratio between the losses of C₃H₅D and C₃H₆ from the metastable [M + D]⁺ ions of phenyl n-propyl ether is 18:82, whereas the ratio becomes 27:73 with CD₃CN as the reagent. A similar trend in the tendency to expel a propene molecule that contains the added deuteron is observed for the metastable [M + D]⁺ ions of phenyl n-propyl ether labeled at the β position of the alkyl group. Incorporation of a hydrogen atom that originates from the aromatic ring in the expelled propene molecule is of negligible importance as revealed by the minor loss of C₃H₅D from the metastable [M + H]⁺ ions of C₆D₅OCH₂CH₂CH₃ irrespective of whether H₂O, CH₃OH, or CH₃CN is the CI reagent. The combined results for the [M + D]⁺ ions of phenyl n-propyl ether and deuterium-labeled analogs are suggested to be in line with a model that assumes that propene loss occurs not only from species formed by deuteron transfer to the oxygen atom, but also from ions generated by deuteron transfer to the ring. This is substantiated by the results for the methyl-substituted ethers, which reveal that the position as well as the number of methyl groups bonded to the ring exert a marked effect on the relative importances of the losses of C₃H₅D and C₃H₆ from the metastable [M + D]⁺ ions of the unlabeled methyl-substituted species.     

Partial Oxidation as a Rational Approach to Kinetic Control in Bioinspired Magnetite Synthesis

Biological systems show impressive control over the shape, size and organization of mineral structures, which often leads to advanced physical properties that are tuned to the function of these materials. Such control is also found in magnetotactic bacteria, which produce—in aqueous medium and at room temperature—magnetite nanoparticles with precisely controlled morphologies and sizes that are generally only accessible in synthetic systems with the use of organic solvents and/or the use of high‐temperature methods. The synthesis of magnetite under biomimetic conditions, that is, in water and at room temperature and using polymeric additives as control agents, is of interest as a green production method for magnetic nanoparticles. Inspired by the process of magnetite biomineralization, a rational approach is taken by the use of a solid precursor for the synthesis of magnetite nanoparticles. The conversion of a ferrous hydroxide precursor, which we demonstrate with cryo‐TEM and low‐dose electron diffraction, is used to achieve control over the solution supersaturation such that crystal growth can be regulated through the interaction with poly‐(α,β)‐dl ‐aspartic acid, a soluble, negatively charged polymer. In this way, stable suspensions of nanocrystals are achieved that show remanence and coercivity at the size limit of superparamagnetism, and which are able to align their magnetic moments forming strings in solution as is demonstrated by cryo‐electron tomography.     

Decoding the components of dynamics in three‐domain proteins

In this study, we examine the feasibility and limitations of describing the motional behavior of three‐domain proteins in which the domains are linearly connected. In addition to attempting the determination of the internal and overall reorientational correlation times, we investigate the existence of correlations in the motions between the three domains. Since in linearly arranged three‐domain proteins, there are typically no experimental data that can directly report on motional correlation between the first and the third domain, we address this question by dynamics simulations. Two limiting cases occur: (1) for weak repulsive potentials and (2) when strong repulsive potentials are applied between sequential domains. The motions of the terminal domains become correlated in the case of strong interdomain repulsive potentials when these potentials do not allow the angle between the sequential domains to be smaller than about 60°. Using the model‐free (MF) and extended MF formalisms of Lipari and Szabo, we find that the motional behavior can be separated into two components; the first component represents the concerted overall motion of the three domains, and the second describes the independent component of the motion of each individual domain. We find that this division of the motional behavior of the protein is maintained only when their timescales are distinct and can be made when the angles between sequential domains remain between 60° and 160°. In this work, we identify and quantify interdomain motional correlations. © 2013 Wiley Periodicals, Inc.     

Accessing N‐Stereogenicity through a Double Aza‐Michael Reaction: Mechanistic Insights

Further development of the chemistry and applications of chiral compounds that possess configurationally stable stereogenic nitrogen atoms is hampered by the lack of efficient strategies to access such compounds in an enantiomerically pure form. Esters of propiolic acid and chiral alcohols were evaluated as cheap and readily available Michael acceptors in a diastereoselective synthesis of N‐stereogenic compounds by means of a double aza‐Michael conjugate addition. Diastereomeric ratios of up to 74:26 and high yields were achieved with (?)‐menthyl propiolate as a substrate. Furthermore, a detailed mechanistic investigation was undertaken to shed some light on the course of this domino transformation. Kinetic studies revealed that the protic‐solvent additive acts as a Brønsted acid and activates the ester toward the initial attack of the tetrahydrodiazocine partner. Conversely, acidic conditions proved unfavorable during the final cyclization step that provides the product.     

A Reduced SNARE Model for Membrane Fusion

Let's get together : A minimal model system was developed to mimic the SNARE‐protein‐mediated fusion of biological membranes (see picture). Fusion between two populations of liposomes is controlled by a pair of complementary lipidated oligopeptides that form noncovalent coiled‐coil complexes and thereby force the membranes into close proximity to promote fusion. The model system displays the key characteristics of in vivo fusion events.

     

Osmotic coefficients of atomistic NaCl (aq) force fields

Solvated ions are becoming increasingly important for (bio)molecular simulations. But there are not much suitable data to validate the intermediate-range solution structure that ion-water force fields produce. We compare six selected combinations of four biomolecular Na-Cl force fields and four popular water models by means of effective ion-ion potentials. First we derive an effective potential at high dilution from simulations of two ions in explicit water. At higher ionic concentration multibody effects will become important. We propose to capture those by employing a concentration dependent dielectric permittivity. With the so obtained effective potentials we then perform implicit solvent simulations. We demonstrate that our effective potentials accurately reproduce ion-ion coordination numbers and the local structure. They allow us furthermore to calculate osmotic coefficients that can be directly compared with experimental data. We show that the osmotic coefficient is a sensitive and accurate measure for the effective ion-ion interactions and the intermediate-range structure of the solution. It is therefore a suitable and useful quantity for validating and parametrizing atomistic ion-water force fields.     

Fringed sound fields and their interaction with liquid-solid interfaces

On the one hand, it is well known that Gaussian beams possess the ability to stimulate Rayleigh waves, resulting in the Schoch effect, a lateral beam displacement. This effect, often characterized by a reflected sound pattern consisting of two anti-phase beams, is due to the re-radiation of sound because of the stimulation of leaky Rayleigh waves. On the other hand, fringed sound beams are characterized by the fact that they consist of a number of neighboring anti-phase narrow beams. They are a first approximation of a sound field originating from a phased array of harmonic vibrating crystals in which each crystal vibrates in anti-phase compared to its neighbor. The individual lobes within the fringed sound pattern diverge much less than standard Gaussian beams of the same size. The current study investigates the interaction of fringed beams with a liquid-solid interface. It is found that under certain conditions, a fringed beam, incident at the Rayleigh angle, produces a reflected sound pattern that contains a wide lobe that is not fringed. It is also shown that under other conditions, contrary to the famous forward displacement of the reflected sound for incident Gaussian beams, a strong backward displacement occurs for fringed beams.     

On the accurate measurement of amide one-bond 15N-1H couplings in proteins: effects of cross-correlated relaxation, selective pulses and dynamic frequency shifts

Amide one-bond 15N-1H scalar couplings of 15N- and [15N,2H]-isotopically enriched ubiquitin have been measured with the Quantitative J approach by monitoring NMR signal intensity modulation. Scalar couplings of the non-deuterated protein are in average approximately 0.6 Hz larger than values of deuterated ubiquitin. This deviation is 30 times the error derived from experiment reproducibility. Refocusing dipole/dipole cross-correlated relaxation decreases the discrepancy to approximately 0.1 Hz, suggesting that it likely originates from relaxation interference. Alternatively, the subtraction of J values obtained at different magnetic fields largely reduces the relaxation effects. In contrast, the dynamic frequency shift whose main contribution to 1J(15N-1H) arises from 15N chemical shielding anisotropy/NH dipole cross-correlation, is not eliminated by refocusing spin evolution under this interaction. Furthermore, the average difference of 1J(15N-1H) values at two magnetic fields closely agrees with the theoretical expected difference in the dynamic frequency shift.