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Atomic force microscopy, AFM, is a powerful tool that can produce detailed topographical images of individual nano-structures with a high signal-to-noise ratio without the need for ensemble averaging. However, the application of AFM in structural biology has been hampered by the tip-sample convolution effect, which distorts images of nano-structures, particularly those that are of similar dimensions to the cantilever probe tips used in AFM. Here we show that the tip-sample convolution results in a feature-dependent and non-uniform distribution of image resolution on AFM topographs. We show how this effect can be utilised in structural studies of nano-sized upward convex objects such as spherical or filamentous molecular assemblies deposited on a flat surface, because it causes ‘magnification’ of such objects in AFM topographs. Subsequently, this enhancement effect is harnessed through contact-point based deconvolution of AFM topographs. Here, the application of this approach is demonstrated through the 3D reconstruction of the surface envelope of individual helical amyloid filaments without the need of cross-particle averaging using the contact-deconvoluted AFM topographs. Resolving the structural variations of individual macromolecular assemblies within inherently heterogeneous populations is paramount for mechanistic understanding of many biological phenomena such as amyloid toxicity and prion strains. The approach presented here will also facilitate the use of AFM for high-resolution structural studies and integrative structural biology analysis of single molecular assemblies.

In this work we present new concepts of VANESA, a tool for modeling and simulation in systems biology. We provide a convenient way to handle mathematical expressions and take physical units into account. Simulation and result management has been improved, and syntax and consistency checks, based on physical units, reduce modeling errors. As a proof of concept, essential components of the aerobic carbon metabolism of the green microalga Chlamydomonas reinhardtii are modeled and simulated. The modeling process is based on xHPN Petri net formalism and simulation is performed with OpenModelica, a powerful environment and compiler for Modelica. VANESA, as well as OpenModelica, is open source, free-of-charge for non-commercial use, and is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.

The syntheses and structures of tert-butylaminomethyl(mesityl)phosphinic acid ethyl ester 2 and its zinc dichloride complex 3 are reported. In the solid state, both compounds are dimeric via hydrogen bridges. In the complex 3, the phosphinic acid ester 2 coordinates the zinc dichloride diastereoselectively.

The synthesis of the 2,8-dioxa-5-aza-1-stanna-bicyclo[3.3.01.5]octane [PhN(CH2CH2O)2Sn]n (3) by a combined ligand exchange/redox reaction and independently by the reaction of tin(II)butoxide with N-phenyldiethanolamine is reported. Compound 3 was characterized by elemental analysis and single crystal X-ray diffraction analysis. In the solid state, it is a coordination polymer via intermolecular O→Sn interactions at O-Sn distances of 2.325 (3) and 2.379 (3) Å. The intramolecular N→Sn interactions at distances of 2.818 (3) and 3.096 (3) Å are rather weak.

The reaction of the silanes X2SiCl2 (X=H, Cl) with the dilithium salts of N-phenyldiethanolamine (1) and N-4-fluorophenyl-di-(2-dimethylpropan-2-ol)amine (2), respectively, gave the novel 5-aza-2,8-dioxasilabicyclo[3.3.01.5]octanes RN(CH2CR′2O)2SiX2 (3, R=Ph, R′=X=H; 4, R=Ph, R′=H, X=Cl; 5, R=4-FC6H4, R′=Me, X=H). These compounds were characterized by multinuclear NMR spectroscopy and single crystal X-ray diffraction analysis (1–4). The molecular structures of the dialkanolamines 1 and 2 are characterized by intra- and intermolecular O-H ··· O(H) hydrogen bridges giving rise to formation of eight-membered O4H4 rings (1) and polymeric chains (2). The 5-aza-2,8-dioxasilabicyclo[3.3.01.5]octanes show intramolecular N→Si interactions at distances of 2.961(2) (3) and 2.970(2) (4) Å, respectively. Also reported is the molecular structure of the hexachloridostannate salt [Ph(H)N(CH2CH2OH)2]2SnCl6 (6a) that was serendipitously obtained from the reaction of compound 3 with Ph3CSnCl5 under non-inert reaction conditions. Furthermore, DFT calculations on 3 and 4 as well as cyclovoltammetric studies were performed.