Towards a black‐box for biological EXAFS data analysis. II. Automatic BioXAS Refinement and Analysis (ABRA)

In biological systems, X‐ray absorption spectroscopy (XAS) can determine structural details of metal binding sites with high resolution. Here a method enabling an automated analysis of the corresponding EXAFS data is presented, utilizing in addition to least‐squares refinement the prior knowledge about structural details and important fit parameters. A metal binding motif is characterized by the type of donor atoms and their bond lengths. These fit results are compared by bond valance sum analysis and target distances with established structures of metal binding sites. Other parameters such as the Debye–Waller factor and shift of the Fermi energy provide further insights into the quality of a fit. The introduction of mathematical criteria, their combination and calibration allows an automated analysis of XAS data as demonstrated for a number of examples. This presents a starting point for future applications to all kinds of systems studied by XAS and allows the algorithm to be transferred to data analysis in other fields.     

Elimination of autofluorescence background from fluorescence tissue images by use of time-gated detection and the AzaDiOxaTriAngulenium (ADOTA) fluorophore

Sample autofluorescence (fluorescence of inherent components of tissue and fixative-induced fluorescence) is a significant problem in direct imaging of molecular processes in biological samples. A large variety of naturally occurring fluorescent components in tissue results in broad emission that overlaps the emission of typical fluorescent dyes used for tissue labeling. In addition, autofluorescence is characterized by complex fluorescence intensity decay composed of multiple components whose lifetimes range from sub-nanoseconds to a few nanoseconds. For these reasons, the real fluorescence signal of the probe is difficult to separate from the unwanted autofluorescence. Here we present a method for reducing the autofluorescence problem by utilizing an azadioxatriangulenium (ADOTA) dye with a fluorescence lifetime of approximately 15 ns, much longer than those of most of the components of autofluorescence. A probe with such a long lifetime enables us to use time-gated intensity imaging to separate the signal of the targeting dye from the autofluorescence. We have shown experimentally that by discarding photons detected within the first 20 ns of the excitation pulse, the signal-to-background ratio is improved fivefold. This time-gating eliminates over 96 % of autofluorescence. Analysis using a variable time-gate may enable quantitative determination of the bound probe without the contributions from the background.     

Synthesis and fluorescence properties of DMCX+—a stable oxygen-bridged [4]helicenium dye

A one-step synthesis of the stable [4]helicenium dye, 1,13-dimethoxy-chromeno[2,3,4-kl]xanthenium hexafluorophosphate (DMCX⁺) from the readily available tris(2,6-dimethoxyphenyl)carbenium ion is reported. The crystal structure, the chemical stability, and dye properties of the DMCX⁺ helicenium system are described.     

Improved growth of solution‐deposited thin films on polycrystalline Cu(In,Ga)Se2

CdS and Zn(O,S) grown by chemical bath deposition (CBD) are well established buffer materials for Cu(In,Ga)Se₂ (CIGS) solar cells. As recently reported, a non‐contiguous coverage of CBD buffers on CIGS grains with {112} surfaces can be detected, which was explained in terms of low surface energies of the {112} facets, leading to deteriorated wetting of the chemical solution on the CIGS surface. In the present contribution, we report on the effect of air annealing of CIGS thin films prior to the CBD of CdS and Zn(O,S) layers. In contrast to the growth on the as‐grown CIGS layers, these buffer lay‐ ers grow densely on the annealed CIGS layer, even on grains with {112} surfaces. We explain the different growth behavior by increased surface energies of CIGS grains due to the annealing step, i.e., due to oxidation of the CIGS surface. Reference solar cells were processed and completed by i‐ZnO/ZnO:Al layers for CdS and by (Zn,Mg)O/ZnO:Al for Zn(O,S) buffers. For solar cells with both, CdS and Zn(O,S) buffers, air‐annealed CIGS films with improved buffer coverage resulted in higher power‐conversion efficiencies, as compared with the devices containing as‐grown CIGS layers. (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Toeplitz Operators with Uniformly Continuous Symbols

Let T _f be a Toeplitz operator on the Segal–Bargmann space or the standard weighted Bergman space over a bounded symmetric domain \({\Omega \subset {\bf C}^n}\) with possibly unbounded symbol f. Combining recent results in Bauer et al. (J. Funct. Anal. 259:57–78, 2010), Bauer et al. (J. reine angew. Math. doi: 10.1515/crelle-2015-0016), Issa (Integr. Equ. Oper. Theory 70:569–582, 2011) we show that in the case of uniformly continuous symbols f with respect to the Euclidean metric on C ⁿ and the Bergman metric on \({\Omega}\), respectively, the operator T _f is bounded if and only if f is bounded. Moreover, T _f is compact if and only if f vanishes at the boundary of \({\Omega.}\) This observation substantially extends a result in Coburn (Indiana Univ. Math. J. 23:433–439, 1973).     

The Benzylperoxyl Radical as a Source of Hydroxyl and Phenyl Radicals

The benzyl radical ( 1 ) is a key intermediate in the combustion and tropospheric oxidation of toluene. Because of its relevance, the reaction of 1 with molecular oxygen was investigated by matrix‐isolation IR and EPR spectroscopy as well as computational methods. The primary reaction product of 1 and O₂ is the benzylperoxyl radical ( 2 ), which exists in several conformers that can easily interconvert even at cryogenic temperatures. Photolysis of radical 2 at 365 nm results in a formal [1,3]‐H migration and subsequent cleavage of the O?O bond to produce a hydrogen‐bonded complex between the hydroxyl radical and benzaldehyde ( 4 ). Prolonged photolysis produces the benzoyl radical ( 5 ) and water, which finally yield the phenyl radical ( 7 ), CO, and H₂O. Thus, via a sequence of exothermic reactions 1 is transformed into radicals of even higher reactivity, such as OH and 7 . Our results have implications for the development of models for the highly complicated process of combustion of aromatic compounds.