The Broad Aryl Acid Specificity of the Amide Bond Synthetase McbA Suggests Potential for the Biocatalytic Synthesis of Amides

Amide bond formation is one of the most important reactions in pharmaceutical synthetic chemistry. The development of sustainable methods for amide bond formation, including those that are catalyzed by enzymes, is therefore of significant interest. The ATP‐dependent amide bond synthetase (ABS) enzyme McbA, from Marinactinospora thermotolerans, catalyzes the formation of amides as part of the biosynthetic pathway towards the marinacarboline secondary metabolites. The reaction proceeds via an adenylate intermediate, with both adenylation and amidation steps catalyzed within one active site. In this study, McbA was applied to the synthesis of pharmaceutical‐type amides from a range of aryl carboxylic acids with partner amines provided at 1–5 molar equivalents. The structure of McbA revealed the structural determinants of aryl acid substrate tolerance and differences in conformation associated with the two half reactions catalyzed. The catalytic performance of McbA, coupled with the structure, suggest that this and other ABS enzymes may be engineered for applications in the sustainable synthesis of pharmaceutically relevant (chiral) amides.     

Dissipative mechanism of a semilinear higher order parabolic equation in RN

It is known that the concept of dissipativeness is fundamental for understanding the asymptotic behavior of solutions to evolutionary problems. In this paper we investigate the dissipative mechanism for some semilinear fourth-order parabolic equations in the spaces of Bessel potentials and discuss some weak conditions that lead to the existence of a compact global attractor. While for second-order reaction–diffusion equations the dissipativeness mechanism has already been satisfactorily understood (see Arrieta et al. (2004), doi:10.1142/S0218202504003234 [7]), for higher order problems in unbounded domains it has not yet been fully developed. As shown throughout the paper, one of the main differences from the case of reaction–diffusion equations stems from the lack of a maximum principle. Thus we have to rely here on suitable energy estimates for the solutions. As in the case of second-order reaction–diffusion equations, we show here that both linear and nonlinear terms have to collaborate in order to produce dissipativeness. Thus, the dissipative mechanisms in second-order and fourth-order equations are similar, although the lack of a maximum principle makes the proofs more difficult and the results not as complete.Finally, we make essential use of the sharp results of Cholewa and Rodriguez-Bernal (2012), doi:10.1016/j.na.2011.08.022 [12], on linear fourth-order equations with a very large class of linear potentials.     

Radiation induced microstructural evolution and amorphization of intermetallic compounds

Abstract

A theoretical model is developed to study the influence of radiation-induced microstructural evolution on the amorphization kinetics of intermetallic compounds. The amorphization mechanism is assumed to be the buildup to a critical level of defect complexes. A complex consists of a coupled interstitial-vacancy pair. It is shown that the process of amorphization under particle bombardment is obstructed in alloy systems in which interstitials exhibit a tendency to cluster. In these systems, interstitial clustering delays the buildup of complexes. Under electron irradiation, the complex concentration attains a very low level after high doses, and the crystalline-to-amorphous transition is inhibited down to fairly low temperatures. During heavy ion bombardment, cascade damage produces an enhancement of complex formation and the transition takes place. It is shown that the kinetics of amorphization under ion bombardment depends on temperature at low temperatures, where amorphization is mostly due to complex accumulation. On the other hand, the present analyses indicate that direct in-cascade amorphization becomes more important as the bombardment temperature increases. Zr₃Al is used as a model system. The theoretical calculations yield good agreement with experimental results.     

Thin silica films on Ru(0001): monolayer, bilayer and three-dimensional networks of [SiO4] tetrahedra

The atomic structure of thin silica films grown over a Ru(0001) substrate was studied by X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, low energy electron diffraction, helium ion scattering spectroscopy, CO temperature programmed desorption, and scanning tunneling microscopy in combination with density functional theory calculations. The films were prepared by Si vapor deposition and subsequent oxidation at high temperatures. The silica film first grows as a monolayer of corner-sharing [SiO(4)] tetrahedra strongly bonded to the Ru(0001) surface through the Si-O-Ru linkages. At increasing amounts of Si, the film forms a bilayer of corner-sharing [SiO(4)] tetrahedra which is weakly bonded to Ru(0001). The bilayer film can be grown in either the crystalline or vitreous state, or both coexisting. Further increasing the film thickness leads to the formation of vitreous silica exhibiting a three-dimensional network of [SiO(4)]. The principal structure of the films can be monitored by infrared spectroscopy, as each structure shows a characteristic vibrational band, i.e., ～1135 cm(-1) for a monolayer film, ～1300 cm(-1) for the bilayer structures, and ～1250 cm(-1) for the bulk-like vitreous silica.     

Distinct hepatic lipid profile of hypertriglyceridemic mice determined by easy ambient sonic-spray ionization mass spectrometry

Easy ambient sonic-spray ionization mass spectrometry (EASI-MS) was used to interrogate the hepatic lipid profiles of hypertriglyceridemic and control normotriglyceridemic mice. The analyses of ex vivo complex lipid mixtures were made directly with EASI-MS without accompanying separation steps. Intense ions for phosphatidylcholines and triacylglycerols were observed in the positive ion mode whereas the spectra in the negative ion mode provided profiles of phosphatidylethanolamines and phosphatidylinositol. EASI-MS was coupled to high-performance thin-layer chromatography for analysis of free fatty acids. Fourier transform–ion cyclotron resonance–mass spectrometry was also employed to confirm the identity of the detected lipids. We demonstrated higher incorporation of oleic acid in phosphatidylcholine and triacylglycerol composition, higher relative abundance of arachidonic acid containing phosphatidylinositol, and overall distinct free fatty acid profile in the livers of genetic hypertriglyceridemic mice. We propose that these alterations in liver lipid composition are related to the higher tissue and body metabolic rates described in these hypertriglyceridemic mice.     

Entropy in the cusp and phase transitions for geodesic flows

In this paper we study the geodesic flow for a particular class of Riemannian non-compact manifolds with variable pinched negative sectional curvature. For a sequence of invariant measures we are able to prove results relating the loss of mass and bounds on the measure entropies. We compute the entropy contribution of the cusps. We develop and study the corresponding thermodynamic formalism. We obtain certain regularity results for the pressure of a class of potentials. We prove that the pressure is real analytic until it undergoes a phase transition, after which it becomes constant. Our techniques are based on the one hand on symbolic methods and Markov partitions, and on the other on geometric techniques and approximation properties at the level of groups.     

Efficient transport of gold atoms with a scanning tunneling microscopy tip and a linker molecule

A thiophene-containing molecule attached to a scanning tunneling microscopy (STM) tip is used to transport gold atoms on a Au(111) surface. The molecule contains eight thiophene rings and therefore has sulfur atoms that are known to bind to gold atoms. Using a gold-coated tip, the molecules previously deposited on the surface bind to the lower-coordination gold atoms of the tip. When that tip is used to scan the surface, the still free thiophene rings (not all of the sulfur atoms bind to the tip) can attach to gold atoms from the surface and drag them along the scanning direction, depositing them either at the position where the tip changes its scanning direction or where the tip encounters an "up step", whichever event occurs first.