NIFTy 3 – Numerical Information Field Theory: A Python Framework for Multicomponent Signal Inference on HPC Clusters

NIFTy , “Numerical Information Field Theory,” is a software framework designed to ease the development and implementation of field inference algorithms. Field equations are formulated independently of the underlying spatial geometry allowing the user to focus on the algorithmic design. Under the hood, NIFTy ensures that the discretization of the implemented equations is consistent. This enables the user to prototype an algorithm rapidly in 1D and then apply it to high‐dimensional real‐world problems. This paper introduces NIFTy  3, a major upgrade to the original NIFTy  framework. NIFTy  3 allows the user to run inference algorithms on massively parallel high performance computing clusters without changing the implementation of the field equations. It supports n‐dimensional Cartesian spaces, spherical spaces, power spaces, and product spaces as well as transforms to their harmonic counterparts. Furthermore, NIFTy  3 is able to handle non‐scalar fields, such as vector or tensor fields. The functionality and performance of the software package is demonstrated with example code, which implements a mock inference inspired by a real‐world algorithm from the realm of information field theory. NIFTy  3 is open‐source software available under the GNU General Public License v3 (GPL‐3) at https://gitlab.mpcdf.mpg.de/ift/NIFTy/tree/NIFTy_3 .     

Synthesis of μ2-Oxo-Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations

Iron(III) porphyrins have the propensity to form μ₂-oxo-dimers, the structures of which resemble two wheels on an axle. Whereas their crystal structure is known, their solution structure and internal dynamics is not. In the present work, the structure and dynamics of such dimers were studied by means of electron paramagnetic resonance (EPR) spectroscopy and quantum chemistry based molecular dynamics (MD) simulations by using the semiempirical tight-binding method (GFN-xTB). To enable EPR investigation of the dimers, a nitroxide was attached to each of the tetraphenylporphyrin cores through a linear and a bent linker. The inter-nitroxide distance distributions within the dimers were determined by continuous-wave (cw)-EPR and pulsed electron–electron double resonance (PELDOR or DEER) experiments and, with the help of MD, interpreted in terms of the rotation of the porphyrin planes with respect to each other around the Fe–O–Fe axis. It was found that such rotation is restricted to the four registers defined by the phenyl substituents. Within the registers, the rotation angle swings between 30° and 60° in the proximal and between 125° and 145° in the distal register. With EPR, all four angles were found to be equally populated, whereas the 30° and 145° angles are strongly favored to the expense of the 60° and 125° angles in the MD simulation. In either case, the internal dynamics of these dimers thus resemble the motion of a step motor.     

Synthesis of Highly Functionalized N,N-Diarylamides by an Anodic C,N-Coupling Reaction

We report an innovative, sustainable and straightforward protocol for the synthesis of N,N-diarylamides equipped with nonprotected hydroxyl groups by using electrosynthesis. The concept allows the application of various substrates furnishing diarylamides with yields up to 57 % within a single and direct electrolytic protocol. The method is thereby easy to conduct in an undivided cell with constant current conditions offering a versatile and short-cut alternative to conventional pathways.     

Self-similar asymptotic behavior for the solutions of a linear coagulation equation

In this paper we consider the long-time asymptotics of a linear version of the Smoluchowski equation which describes the evolution of a tagged particle moving in a random distribution of fixed particles. The volumes v of these particles are independently distributed according to a probability distribution which decays asymptotically as a power law $v^{?\sigma }$. The validity of the equation has been rigorously proved in [22] taking as a starting point a particle model and for values of the exponent $\sigma >3$, but the model can be expected to be valid, on heuristic grounds, for $\sigma >\frac{5}{3}$. The resulting equation is a non-local linear degenerate parabolic equation. The solutions of this equation display a rich structure of different asymptotic behaviors according to the different values of the exponent σ. Here we show that for $\frac{5}{3}<\sigma <2$ the linear Smoluchowski equation is well-posed and that there exists a unique self-similar profile which is asymptotically stable.     

Electron transfer at different electrode materials: Metals,semiconductors, and graphene

Electron transfer reactions are the most important processes at electrochemical interfaces. They are determined by the interplay between the interaction of the reactant with the solvent and the electronic levels of the electrode surface. Theoretical treatments only based on Density Functional Theory calculations are not sufficient. This review emphasizes mainly the effect of the electronic structure of the electrode material on electron transfer under different kinetic regimes. Our goal is to understand experimental results in the framework of a theory valid for arbitrary strengths of electronic coupling.     

From Binuclear Complexes to Molecular Necklaces: Incorporating Flexible Ligands into Rotaxanes

The conversion of binuclear complexes into larger molecular necklaces can be achieved through rigidifying flexible ligands by threading them through a crown ether to form either an interpenetrated [2]pseudorotaxane or a permanently interlocked [2]rotaxane. The resulting complexes and assemblies are characterized by ¹H and DOSY NMR in solution and single‐crystal X‐ray diffraction in the solid‐state.     

Columnar Liquid‐Crystalline Dinaphthoperylenetetracarboxdiimides

Although the double Friedel–Crafts acylation of arenes with ethyl chloroglyoxylate is hindered by the strongly deactivating effect of the first‐entering glyoxylic substituent, the double reaction is successful with the reactive arene perylene under long reaction times and with concomitant ester hydrolysis. The reaction is regiospecific, giving the 3,9‐regioisomer exclusively. This perylenylenediglyoxylic acid is condensed first with o‐bromophenylacetic acid and then with α‐branched alkylamines to yield the title compounds. Whilst the corresponding tetraalkyl esters only show monotropic mesophases, these diimides show enantiotropic columnar mesophases that can be maintained at room temperature if racemically branched alkyl chains of moderate size are used. A palladium‐induced C?C bond migration during the build‐up of the arene system leads to an isomeric side product of reduced symmetry that can be isolated by aggregation‐controlled chromatographic separation. The HOMO and LUMO energies of the title compounds are considerably higher than those of established perylenetetracarboxdiimides.