Dynamics of Bacteriorhodopsin in the Dark-Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy

To achieve efficient proton pumping in the light-driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark-adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays only 10 % residual proton pumping activity, are less well ordered, suggesting a link between side-chain dynamics on the cytosolic side of the bR cavity and proton pumping activity. In addition, slow conformational exchange, attributed to low frequency motions of aromatic rings, was indirectly observed for residues on the extracellular side of the bR cavity. This may be related to reorganization of the water network. These observations provide a detailed picture of previously undescribed equilibrium dynamics on different time scales for ground-state bR.     

A General Catalyst Based on Cobalt Core–Shell Nanoparticles for the Hydrogenation of N-Heteroarenes Including Pyridines

Herein, we report the synthesis of specific silica-supported Co/Co₃O₄ core–shell based nanoparticles prepared by template synthesis of cobalt-pyromellitic acid on silica and subsequent pyrolysis. The optimal catalyst material allows for general and selective hydrogenation of pyridines, quinolines, and other heteroarenes including acridine, phenanthroline, naphthyridine, quinoxaline, imidazo[1,2-a]pyridine, and indole under comparably mild reaction conditions. In addition, recycling of these Co nanoparticles and their ability for dehydrogenation catalysis are showcased.     

Synthesis of Highly Substituted γ‐Butyrolactones by a Gold‐Catalyzed Cascade Reaction of Benzyl Esters

Easily accessible benzylic esters of 3‐butynoic acids in a gold‐catalyzed cyclization/rearrangement cascade reaction provided 3‐propargyl γ‐butyrolactones with the alkene and the carbonyl group not being conjugated. Crossover experiments showed that the formation of the new C?C bond is an intermolecular process. Initially propargylic–benzylic esters were used, but alkyl‐substituted benzylic esters worked equally well. In the case of the propargylic–benzylic products, a simple treatment of the products with aluminum oxide initiated a twofold tautomerization to the allenyl‐substituted γ‐butyrolactones with conjugation of the carbonyl group, the olefin, and the allene. The synthetic sequence can be conducted stepwise or as a one‐pot cascade reaction with similar yields. Even in the presence of the gold catalyst the new allene remains intact.     

Comprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry: A New Tool Complementing Metabolomic Analyses of Polar Metabolites

Mass spectrometry (MS) driven metabolomics is a frequently used tool in various areas of life sciences; however, the analysis of polar metabolites is less commonly included. In general, metabolomic analyses lead to the detection of the total amount of all covered metabolites. This is currently a major limitation with respect to metabolites showing high turnover rates, but no changes in their concentration. Such metabolites and pathways could be crucial metabolic nodes (e.g., potential drug targets in cancer metabolism). A stable-isotope tracing capillary electrophoresis–mass spectrometry (CE-MS) metabolomic approach was developed to cover both polar metabolites and isotopologues in a non-targeted way. An in-house developed software enables high throughput processing of complex multidimensional data. The practicability is demonstrated analyzing [U-¹³C]-glucose exposed prostate cancer and non-cancer cells. This CE-MS-driven analytical strategy complements polar metabolite profiles through isotopologue labeling patterns, thereby improving not only the metabolomic coverage, but also the understanding of metabolism.     

Diffusion of Gold Nanoparticles in Inverse Opals Probed by Heterodyne Dynamic Light Scattering

The diffusive behavior of nanoparticles inside porous materials is attracting a lot of interest in the context of understanding, modeling, and optimization of many technical processes. A very powerful technique for characterizing the diffusive behavior of particles in free media is dynamic light scattering (DLS). The applicability of the method in porous media is considered, however, to be rather difficult due to the presence of multiple sources of scattering. In contrast to most of the previous approaches, the DLS method was applied without ensuring matching refractive indices of solvent and porous matrix in the present study. To test the capabilities of the method, the diffusion of spherical gold nanoparticles within the interconnected, periodic nanopores of inverse opals was analyzed. Despite the complexity of this system, which involves many interfaces and different refractive indices, a clear signal related to the motion of particles inside the porous media was obtained. As expected, the diffusive process inside the porous sample slowed down compared to the particle diffusion in free media. The obtained effective diffusion coefficients were found to be wave vector-dependent. They increased linearly with increasing spatial extension of the probed particle concentration fluctuations. On average, the slowing-down factor measured in this work agrees within combined uncertainties with literature data.

     

Quadrilateral surface meshes without self-intersecting dual cycles for hexahedral mesh generation

Several promising approaches for hexahedral mesh generation work as follows: Given a prescribed quadrilateral surface mesh they first build the combinatorial dual of the hexahedral mesh. This dual mesh is converted into the primal hexahedral mesh, and finally embedded and smoothed into the given domain. Two such approaches, the modified whisker weaving algorithm by Folwell and Mitchell, as well as a method proposed by the author, rely on an iterative elimination of certain dual cycles in the surface mesh. An intuitive interpretation of the latter method is that cycle eliminations correspond to complete sheets of hexahedra in the volume mesh.

Although these methods can be shown to work in principle, the quality of the generated meshes heavily relies on the dual cycle structure of the given surface mesh. In particular, it seems that difficulties in the hexahedral meshing process and poor mesh qualities are often due to self-intersecting dual cycles. Unfortunately, all previous work on quadrilateral surface mesh generation has focused on quality issues of the surface mesh alone but has disregarded its suitability for a high-quality extension to a three-dimensional mesh.

In this paper, we develop a new method to generate quadrilateral surface meshes without self-intersecting dual cycles. This method reuses previous b-matching problem formulations of the quadrilateral mesh refinement problem. The key insight is that the b-matching solution can be decomposed into a collection of simple cycles and paths of multiplicity two, and that these cycles and paths can be consistently embedded into the dual surface mesh.

A second tool uses recursive splitting of components into simpler subcomponents by insertion of internal two-manifolds. We show that such a two-manifold can be meshed with quadrilaterals such that the induced dual cycle structure of each subcomponent is free of self-intersections if the original component satisfies this property. Experiments show that we can achieve hexahedral meshes with a good quality.