Rational Tuning of the Reactivity of Three-Membered Heterocycle Ring Openings via SN2 Reactions

The development of small-molecule covalent inhibitors and probes continuously pushes the rapidly evolving field of chemical biology forward. A key element in these molecular tool compounds is the “electrophilic trap” that allows a covalent linkage with the target enzyme. The reactivity of this entity needs to be well balanced to effectively trap the desired enzyme, while not being attacked by off-target nucleophiles. Here we investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with a nitrogen (aziridine), phosphorus (phosphirane), oxygen (epoxide) or sulfur atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring opening of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C₆H₁₀Y with Y=NH, PH, O, S). It was revealed that the activation energy of the ring opening does not necessarily follow the trend that is expected from C−Y leaving-group bond strength, but steeply decreases from Y=NH, to PH, to O, to S. We illustrate that the HOMO_Nu–LUMO_Substrate interaction is an all-important factor for the observed reactivity. In addition, we show that the activation energy of aziridines and phosphiranes can be tuned far below that of the corresponding epoxides and thiiranes by the addition of proper electron-withdrawing ring substituents. Our results provide mechanistic insights to rationally tune the reactivity of this class of popular electrophilic traps and can guide the experimental design of covalent inhibitors and probes for enzymatic activity.     

Quantum Chemistry-based Molecular Dynamics Simulations as a Tool for the Assignment of ESI-MS/MS Spectra of Drug Molecules

In organic mass spectrometry, fragment ions provide important information on the analyte as a central part of its structure elucidation. With increasing molecular size and possible protonation sites, the potential energy surface (PES) of the analyte can become very complex, which results in a large number of possible fragmentation patterns. Quantum chemical (QC) calculations can help here, enabling the fast calculation of the PES and thus enhancing the mass spectrometry-based structure elucidation processes. In this work, the previously unknown fragmentation pathways of the two drug molecules Nateglinide (45 atoms) and Zopiclone (51 atoms) were investigated using a combination of generic formalisms and calculations conducted with the Quantum Chemical Mass Spectrometry (QCxMS) program. The computations of the de novo fragment spectra were conducted with the semi-empirical GFNn-xTB (n=1, 2) methods and compared against Orbitrap measured electrospray ionization (ESI) spectra in positive ion mode. It was found that the unbiased QC calculations are particularly suitable to predict non-evident fragment ion structures, sometimes contrasting the accepted generic formulation of fragment ion structures from electron migration rules, where the “true” ion fragment structures are approximated. For the first time, all fragment and intermediate structures of these large-sized molecules could be elucidated completely and routinely using this merger of methods, finding new undocumented mechanisms, that are not considered in common rules published so far. Given the importance of ESI for medicinal chemistry, pharmacokinetics, and metabolomics, this approach can significantly enhance the mass spectrometry-based structure elucidation processes and contribute to the understanding of previously unknown fragmentation pathways.     

On the Stability of Pt-Based Catalysts in HBr/Br2 Solution

Stability studies on supported metal nanoparticles are essential for gaining insight into the design and optimization of high-performance materials. In this work, the dissolutions of Pt-based catalysts in HBr/Br₂ mixture of various concentration regimes were studied and correlated with material structural properties. The dissolution of metal nanoparticles was enhanced by adding Br₂ to the HBr solution. Comparing with commercial Pt/C catalyst, the well-alloyed PtIr/C catalyst was observed to exhibit high resistance towards dissolution. In addition, regulating the accessibility of the metal sites to dissolution-inducing species contributed to the marked stability of the nanoparticles in HBr/Br₂ solutions, as shown for the surface-modified PtIr/C catalysts with organic diamine molecules.     

Using Terpene Synthase Plasticity in Catalysis: On the Enzymatic Conversion of Synthetic Farnesyl Diphosphate Analogues

Four synthetic farnesyl diphosphate analogues were enzymatically converted with three bacterial sesquiterpene synthases, including β-himachalene synthase (HcS) and (Z)-γ-bisabolene synthase (BbS) from Cryptosporangium arvum, and germacrene A synthase (SmTS6) from Streptomyces mobaraensis. These enzyme reactions not only yielded several previously unknown compounds, showing that this approach opened the door to a new chemical space, but substrates with blocked or altered reactivities also gave interesting insights into the cyclisation mechanisms and the potential to catalyse reactions with different initial cyclisation modes.     

A Volatile Lactone of Hymenoscyphus pseudoalbidus,Pathogen of European Ash Dieback,Inhibits Host Germination

The largely unknown secondary metabolism of the plant pathogenic fungus Hymenoscyphus pseudoalbidus was investigated by use of the CLSA method. A set of volatile lactones was identified by GC/MS. The lactones were synthesized and used in bioassays in which one of the compounds was found to be a strong germination inhibitor for ash seeds, causing necroses in the plant tissue.     

Furanosyl Oxocarbenium Ion Stability and Stereoselectivity

Lewis acid mediated substitution reactions using [D]triethylsilane as a nucleophile at the anomeric center of the four pentofuranoses, ribose, arabinose, xylose, and lyxose, all proceed with good to excellent stereoselectivity to provide the 1,2‐cis adducts. To unravel the stereoelectronic effects underlying the striking stereoselectivity in these reactions we have mapped the energy landscapes of the complete conformational space of the oxocarbenium ions of the four pentofuranoses. The potential energy surface maps provide a detailed picture of the influence of the differently oriented substituents and their mutual interactions on the stability of the oxocarbenium ions and the maps can be used to account for the observed stereoselectivities of the addition reactions.     

Pathways of Methane Transformation over Copper-Exchanged Mordenite as Revealed by In Situ NMR and IR Spectroscopy

The reaction of methane with copper-exchanged mordenite with two different Si/Al ratios was studied by means of in situ NMR and infrared spectroscopies. The detection of NMR signals was shown to be possible with high sensitivity and resolution, despite the presence of a considerable number of paramagnetic Cu^II species. Several types of surface-bonded compounds were found after reaction, namely molecular methanol, methoxy species, dimethyl ether, mono- and bidentate formates, Cu^I monocarbonyl as well as carbon monoxide and dioxide, which were present in the gas phase. The relative fractions of these species are strongly influenced by the reaction temperature and the structure of the copper sites and is governed by the Si/Al ratio. While methoxy species bonded to Brønsted acid sites, dimethyl ether and bidentate formate species are the main products over copper-exchange mordenite with a Si/Al ratio of 6; molecular methanol and monodentate formate species were observed mainly over the material with a Si/Al ratio of 46. These observations are important for understanding the methane partial oxidation mechanism and for the rational design of the active materials for this reaction.