ZIBgridfree: efficient conformational analysis by partition-of-unity coupling

Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely $n$ -pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.     

Ring Enlargement of Three-Membered Heterocycles by Treatment with In Situ Formed Tricyanomethane

Although the chemistry of elusive tricyanomethane (cyanoform) has been studied during a period of more than 150 years, this compound has very rarely been utilized in the synthesis or modification of heterocycles. Three-membered heterocycles, such as epoxides, thiirane, aziridines, or 2H-azirines, are now treated with tricyanomethane, which is generated in situ by heating azidomethylidene-malonodinitrile in tetrahydrofuran at 45 °C or by adding sulfuric acid to potassium tricyanomethanide. This leads to ring expansion with formation of 2-(dicyanomethylidene)oxazolidine derivatives or creation of the corresponding thiazolidine, imidazolidine, or imidazoline compounds and opens up a new access to these push–pull-substituted olefinic products. The regio- and stereochemistry of the ring-enlargement processes are discussed, and the proposed reaction mechanisms were confirmed by using ¹⁵N-labeled substrates. It turns out that different mechanisms are operating; however, tricyanomethanide is always acting as a nitrogen-centered nucleophile, which is quite unusual if compared to other reactions of this species.     

Host-Guest Chemistry of Truncated Tetrahedral Imine Cages with Ammonium Ions

Three shape-persistent [4+4] imine cages with truncated tetrahedral geometry with different window sizes were studied as hosts for the encapsulation of tetra-n-alkylammonium salts of various bulkiness. In various solvents the cages behave differently. For instance, in dichloromethane the cage with smallest window size takes up NEt₄⁺ but not NMe₄ ^{+ ,} which is in contrast to the two cages with larger windows hosting both ions. To find out the reason for this, kinetic experiments were carried out to determine the velocity of uptake but also to deduce the activation barriers for these processes. To support the experimental results, calculations for the guest uptakes have been performed by molecular mechanics’ simulations. Finally, the complexation of pharmaceutical interested compounds, such as acetylcholine, muscarine or denatonium have been determined by NMR experiments.     

Spatially Resolved Bottom‐Side Fluorination of Graphene by Two‐Dimensional Substrate Patterning

Patterned functionalization can, on the one hand, open the band gap of graphene and, on the other hand, program demanding designs on graphene. The functionalization technique is essential for graphene‐based nanoarchitectures. A new and highly efficient method was applied to obtain patterned functionalization on graphene by mild fluorination with spatially arranged AgF arrays on the structured substrate. Scanning Raman spectroscopy (SRS) and scanning electron microscopy coupled with energy‐dispersive X‐ray spectroscopy (SEM‐EDS) were used to characterize the functionalized materials. For the first time, chemical patterning on the bottom side of graphene was realized. The chemical nature of the patterned functionalization was determined to be the ditopic scenario with fluorine atoms occupying the bottom side and moieties, such as oxygen‐containing groups or hydrogen atoms, binding on the top side, which provides information about the mechanism of the fluorination process. Our strategy can be conceptually extended to pattern other functionalities by using other reactants. Bottom‐side patterned functionalization enables utilization of the top side of a material, thereby opening up the possibilities for applications in graphene‐based devices.     

An Arylazopyrazole‐Based N‐Heterocyclic Carbene as a Photoswitch on Gold Surfaces: Light‐Switchable Wettability,Work Function,and Conductance

A novel photoresponsive and fully conjugated N‐heterocyclic carbene (NHC) has been synthesized that combines the excellent photophysical properties of arylazopyrazoles (AAPs) with an NHC that acts as a robust surface anchor (AAP‐BIMe). The formation of self‐assembled monolayers (SAMs) on gold was proven by ToF‐SIMS and XPS, and the organic film displayed a very high stability at elevated temperatures. This stability was also reflected in a high desorption energy, which was determined by temperature‐programmed SIMS measurements. E‐/Z‐AAP‐BIMe@Au photoisomerization resulted in reversible alterations of the surface energy (i.e. wettability), the surface potential (i.e. work function), and the conductance (i.e. resistance). The effects could be explained by the difference in the dipole moment of the isomers. Furthermore, sequential application of a dummy ligand by microcontact printing and subsequent backfilling with AAP‐BIMe allowed its patterning on gold. To the best of our knowledge, this is the first example of a photoswitchable NHC on a gold surface. These properties of AAP‐BIMe@Au illustrate its suitability as a molecular switch for electronic devices.     

Site‐Selective Oxidation of Monolayered Liquid‐Exfoliated WS2 by Shielding the Basal Plane through Adsorption of a Facial Amphiphile

In recent years, various functionalization strategies for transition‐metal dichalcogenides have been explored to tailor the properties of materials and to provide anchor points for the fabrication of hybrid structures. Herein, new insights into the role of the surfactant in functionalization reactions are described. Using the spontaneous reaction of WS₂ with chloroauric acid as a model reaction, the regioselective formation of gold nanoparticles on WS₂ is shown to be heavily dependent on the surfactant employed. A simple model is developed to explain the role of the chosen surfactant in this heterogeneous functionalization reaction. The surfactant coverage is identified as the crucial element that governs the dominant reaction pathway and therefore can severely alter the reaction outcome. This study shows the general importance of the surfactant choice and how detrimental or beneficial a certain surfactant can be to the desired functionalization.     

Allylic rearrangement of trans-pinocarveol esters

The allylic rearrangement of trans-pinocarveol esters ( I ) to myrtenol esters ( II ), a reaction of interest in the chemistry of terpenes and cannabinoids, has been theoretically investigated. The intramolecular, cyclization-induced rearrangement results in equilibrium mixtures of the starting compounds and the products with the ratio of I vs. II in the equilibrium mixture being determined by their thermodynamic stabilities. The relative thermodynamic stabilities as reflected by calculated AM1 heats of formations (ΔHf) were determined for various I-II ester pairs. The study, in agreement with available experimental evidence, indicates that generally I , which contain an endocyclic double bond, are more stable and thus predominantly form following rearrangements. In two cases (acetate and pivalate) the stability is reversed. Calculations performed for similar structures, esters of 2-methylene cyclohexane-1-ol ( IV ) and 1-cyclohexene-1-methanol ( V ) gave similar results. Structural and electronic factors which might influence the stability of these compounds were examined. Interestingly, a correlation between thermodynamic stability and dipole moments was observed. © 1996 John Wiley & Sons, Inc.