Formation of Highly Ordered Molecular Porous 2D Networks from Cyano-Functionalized Porphyrins on Cu(111)

We investigated the adsorption of three related cyano-functionalized tetraphenyl porphyrin derivatives on Cu(111) by scanning tunneling microscopy (STM) in ultra-high vacuum (UHV) with the goal to identify the role of the cyano group and the central Cu atom for the intermolecular and supramolecular arrangement. The porphyrin derivatives studied were Cu-TCNPP, Cu-cisDCNPP, and 2H-cisDCNPP, that is, Cu-5,10,15,20-tetrakis-(p-cyano)-phenylporphyrin, Cu-meso-cis-di(p-cyano)-phenylporphyrin and 2H-meso-cis-di(p-cyano)-phenylporphyrin, respectively. Starting from different structures obtained after deposition at room temperature, all three molecules form the same long-range ordered hexagonal honeycomb-type structure with triangular pores and three molecules per unit cell. For the metal-free 2H-cisDCNPP, this occurs only after self-metalation upon heating. The structure-forming elements are pores with a distance of 3.1 nm, formed by triangles of porphyrins fused together by cyano-Cu-cyano interactions with Cu adatoms. This finding leads us to suggest that two cyano-phenyl groups in the “cis” position is the minimum prerequisite to form a highly ordered 2D porous molecular pattern. The experimental findings are supported by detailed density functional theory calculations to analyze the driving forces that lead to the formation of the porous hexagonal honeycomb-type structure.     

Studying protein–protein affinity and immobilized ligand–protein affinity interactions using MS-based methods

This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein–protein and protein–immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein–protein and protein–immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS.     

What every chemist should know about plant names

Chemists screen plants for their constituents on a daily basis, and the data gathered is of importance to a wide range of fields such as medicine, evolutionary biology and ecology. However, the use of this data is sometimes impeded by incorrect citation of the species names. In this Viewpoint, I explain why chemists should be aware of the essentials of plant naming, and describe some easy quality checks that can be performed to avoid errors being perpetuated.     

Optimization of information content in a mass spectrometry based flow-chemistry system by investigating different ionization approaches

Current development in catalyst discovery includes combinatorial synthesis methods for the rapid generation of compound libraries combined with high-throughput performance-screening methods to determine the associated activities. Of these novel methodologies, mass spectrometry (MS) based flow chemistry methods are especially attractive due to the ability to combine sensitive detection of the formed reaction product with identification of introduced catalyst complexes. Recently, such a mass spectrometry based continuous-flow reaction detection system was utilized to screen silver-adducted ferrocenyl bidentate catalyst complexes for activity in a multicomponent synthesis of a substituted 2-imidazoline. Here, we determine the merits of different ionization approaches by studying the combination of sensitive detection of product formation in the continuous-flow system with the ability to simultaneous characterize the introduced [ferrocenyl bidentate+Ag]⁺ catalyst complexes. To this end, we study the ionization characteristics of electrospray ionization (ESI), atmospheric-pressure chemical ionization (APCI), no-discharge APCI, dual ESI/APCI, and dual APCI/no-discharge APCI. Finally, we investigated the application potential of the different ionization approaches by the investigation of ferrocenyl bidentate catalyst complex responses in different solvents.     

Generation of clean iron nanocrystals on an ultra-thin SiO(x) film on Si(001)

Upon exposure to Fe(CO)(5), the formation of pure cubic Fe nanocrystals with dimensions up to ~75 nm is reported on ultra-thin SiO(x) films (thickness ≈ 0.5 nm) on Si(001), which have been prepared in situ under UHV conditions. The active centers for initial decomposition of Fe(CO)(5) resulting in the growth of the Fe clusters are proposed to be SiO sites. After nucleation at these sites, further crystal growth is observed due to autocatalytic dissociation of Fe(CO)(5) at room temperature. The density of the Fe clusters can be increased by irradiating the surface with a focused electron beam (15 keV) prior to gas exposure. The formation of the active SiO sites upon electron irradiation is attributed to oxygen desorption via the Knotek-Feibelman mechanism.     

Defects in oxygen-depleted titanate nanostructures

The identification of defects and their controlled generation in titanate nanostructures is a key to their successful application in photoelectronic devices. We comprehensively explored the effect of vacuum annealing on morphology and composition of Na(2)Ti(3)O(7) nanowires and protonated H(2)Ti(3)O(7) nanoscrolls using a combination of scanning electron microscopy, Auger and Fourier-transform infrared (FT-IR) spectroscopy, as well as ab initio density functional theory (DFT) calculations. The observation that H(2)Ti(3)O(7) nanoscrolls are more susceptible to electronic reduction and annealing-induced n-type doping than Na(2)Ti(3)O(7) nanowires is attributed to the position of the conduction band minimum. It is close to the vacuum level and, thus, favors the Fermi level-induced compensation of donor states by cation vacancies. In agreement with theoretical predictions that suggest similar formation energies for oxygen and sodium vacancies, we experimentally observed the annealing induced depletion of sodium from the surface of the nanowires.     

Representation of Hydrogen Atoms in Molecular Dynamics Simulations: The Influence on the Computed Properties of Thin Polystyrene Films

The united atoms (UA) and dummy hydrogen atom (DHA) approaches for molecular dynamics simulations of the interface between oxidized atactic polystyrene (aPS) thin films and water are compared. For both oxidized and non‐oxidized aPS films the polymer density profile decays steepest when using the UA model. The surface roughness of the aPS film and the ordering of the phenyl rings near the surface decrease upon changing from vacuum to water for the UA, but not for the DHA model. This also supports the fact that the non‐oxidized aPS films modeled in DHA representation become less hydrophobic. The water structure close to the interface also suggests that the aPS films modeled using UA are more hydrophobic compared to the aPS films modeled with DHA in the phenyl rings.

     

A New Approach to Cycling in a 2-locus 2-allele Genetic Model

In the reproductive process new genetic types arise due to crossing over and recombination at the meiotic stage. A simplified biological model will be developed which incorporates this effect and the effect of selection. Although a chromosome may contain thousands of genes we will consider a simplified model consisting of two genetic loci, each containing two alleles of some gene.

The model will be then turned into a difference equation or mapping model x* = G(x,r) where x represents the frequency distribution of genotypes in a certain infinite population, x* is this distribution one generation later and r is the recombination parameter. For a certain choice of fitness and recombination parameters the mapping exhibits several fixed points. As r is varied one of the fixed points of the mapping loses its stability due to a conjugate pair of eigenvalues of the linearized mapping leaving the unit disk. It is shown that the required non-resonance conditions and “nonlinear damping” condition are satisfied and thus the fixed point undergoes a Neimark–Sacker bifurcation to a cycling or oscillatory state.

Once a cycling orbit is established one can conclude that genetic variation (over time) of the population can be maintained. This work reformulates and proves earlier observations of Alan Hastings in a way that makes the treatment of chromosomes with more genetic loci more straightforward.     

Stresses in alumina scales on NiCrAlY-alloys determined by XSE and LRS

The effect of silicon and titanium on the spallation resistance of alumina scales grown on NiCrAlY-type alloys has been investigated. For this purpose cyclic oxidation experiments on model alloys with different additions of silicon or titanium were carried out at temperatures between 950 and 1100 °C. Selected samples were analysed by X-ray stress evaluation (XSE) after various times of oxidation. It was found that the compressive stresses measured at ambient temperature increase with increasing time and are affected by the presence of silicon. The XSE results were used to calibrate laser Raman spectroscopy (LRS) for strain measurement. Then, the suitability of Raman spectroscopy for stress measurement at higher temperatures was evaluated.Dedicated to Professor Dr. rer. nat. Dr. h.c. Hubertus Nickel on to occasion of his 65th birthday