Energy Read-out as a Probe of Kinetically Hidden Transition States

Predicting Collision-Induced-Dissociation Tandem Mass Spectra (CID-MS/MS) Using Ab Initio Molecular Dynamics

Compound identification is at the center of metabolomics, usually by comparing experimental mass spectra against library spectra. However, most compounds are not commercially available to generate library spectra. Hence, for such compounds, MS/MS spectra need to be predicted. Machine learning and heuristic models have largely failed except for lipids. Here, quantum chemistry software can be used to predict mass spectra. However, quantum chemistry predictions for collision induced dissociation (CID) mass spectra in LC-MS/MS are rare. We present the CIDMD (Collision-Induced Dissociation via Molecular Dynamics) framework to model CID-based MS/MS spectra. It uses first-principles molecular dynamics (MD) to simulate the physical process of molecular collisions in CID tandem mass spectrometry. First, molecular ions are constructed at specific protonation sites. Using density functional theory, these protonated ions are targeted by argon collider gas atoms at user-specified velocities. Subsequent bond breakages are simulated over time for at least 1,000 fs. Each simulation is repeated multiple times from various collisional directions. Fragmentations are accumulated over those repeated collisions to generate CIDMD in silico mass spectra. Twelve small metabolites (<205 Da) were selected to test the accuracy of this framework in comparison to experimental MS/MS spectra. When testing different protomers, collider velocities, number of simulations, simulation time and impact factor b cutoffs, we yielded 261 predicted mass spectra. These in silico spectra resulted in entropy similarity scores of an average 624 ± 189 for all 261 spectra compared to their corresponding experimental spectra, which improved to 828 ± 77 when using optimal parameters of the most probable protomers for 12 molecules. With increasing molecular mass, higher velocities achieved better results. Similarly, different protomers showed large differences in fragmentation; hence, with increasing numbers of protomers and tautomers, the average CIDMD prediction accuracy decreased. Mechanistic details showed that specific fragment ions can be produced from different protomers via multiple fragmentation pathways. We propose that CIDMD is a suitable tool to predict mass spectra of small metabolites like produced by the gut microbiome.

Revealing the nature of covalently tethered distonic radical anions in the generation of heteroatom-centered radicals: evidence for the polarity-matching PCET pathway

Recognition of the intermediacy and regulation of reactivity patterns of radical intermediates in radical chemistry have profound impacts on harnessing and developing the full potential of open-shell species in synthetic settings. In this work, the possibility of in situ formation of O/N-X intermediates from Brønsted base covalently tethered carbonyl hypohalites (BCTCs) for the generation of heteroatom-centered radicals has certainly been excluded by NMR experiments and density functional theory calculations. Instead, the spectroscopic analyses reveal that the BCTCs serve as precursors of tether-tunable distonic radical anions (TDRAs) which have been unequivocally substantiated to be involved in the direct cleavage of O/N-H bonds to generate the corresponding heteroatom-centered radicals. Meanwhile, a deep insight into the properties and reactivities of the resulting TDRAs indicates that the introduction of a tethered Brønsted base on the parent open-shell species reinforces their stabilities and leads to a reversal of electrophilicity. Moreover, the dual descriptor values and electrophilicity indices are calculated based on eleven reported radical reactions involving various electrophilic/nucleophilic radical species, further confirming their validity in the prediction of the polar effect and the polarity-matching consistency between nucleophilic TDRAs and protic O/N-H bonds. The additional halogen-free experiments mediated by the combination of phthaloyl peroxide and TEMPO also prove the feasibility of the TDRA-assisted philicity-regulation approach. Lastly, detailed intrinsic bond orbital (IBO) and Hirschfeld spin population analyses are employed to elucidate that the H-atom abstraction processes are the polarity-matching proton-coupled electron transfer (PCET) pathways, with a degree of oxidative asynchronicity.

Synthetic Doping of Diamondoids through Skeletal Editing

We present a strategy for the skeletal editing of diamondoid structures to selectively displace methylene for heteroatom moieties in the carbon framework. This constitutes a synthetic approach to doping diamond-like structures with electron donor dopants (O, N, and S). The key steps involve two subsequent retro-Barbier fragmentations followed by cage reconstruction in the presence of a dopant. Remarkably, the incorporation of n-dopants reduces the strain of the diamondoid cage as shown through homodesmotic equations.

Heavy-Atom Kinetic Isotope Effects: Primary Interest or Zero Point?

Chemists have many options for elucidating reaction mechanisms. Global kinetic analysis and classic transition-state probes (e.g., LFERs, Eyring) inevitably form the cornerstone of any strategy, yet their application to increasingly sophisticated synthetic methodologies often leads to a wide range of indistinguishable mechanistic proposals. Computational chemistry provides powerful tools for narrowing the field in such cases, yet wholly simulated mechanisms must be interpreted with great caution. Heavy-atom kinetic isotope effects (KIEs) offer an exquisite but underutilized method for reconciling the two approaches, anchoring the theoretician in the world of calculable observables and providing the experimentalist with atomistic insights. This Perspective provides a personal outlook on this synergy. It surveys the computation of heavy-atom KIEs and their measurement by NMR spectroscopy, discusses recent case studies, highlights the intellectual reward that lies in alignment of experiment and theory, and reflects on the changes required in chemical education in the area.

Alkoxy Radicals See the Light: New Paradigms of Photochemical Synthesis

Alkoxy radicals are highly reactive species that have long been recognized as versatile intermediates in organic synthesis. However, their development has long been impeded due to a lack of convenient methods for their generation. Thanks to advances in photoredox catalysis, enabling facile access to alkoxy radicals from bench-stable precursors and free alcohols under mild conditions, research interest in this field has been renewed. This review comprehensively summarizes the recent progress in alkoxy radical-mediated transformations under visible light irradiation. Elementary steps for alkoxy radical generation from either radical precursors or free alcohols are central to reaction development; thus, each section is categorized and discussed accordingly. Throughout this review, we have focused on the different mechanisms of alkoxy radical generation as well as their impact on synthetic utilizations. Notably, the catalytic generation of alkoxy radicals from abundant alcohols is still in the early stage, providing intriguing opportunities to exploit alkoxy radicals for diverse synthetic paradigms.

Electrophotochemical Ring-Opening Bromination of tert-Cycloalkanols

An electrophotochemical ring-opening bromination of unstrained tert-cycloalkanols has been developed. This electrophotochemical method enables the oxidative transformation of cycloalkanols with 5- to 7-membered rings into synthetically useful ω-bromoketones without the use of chemical oxidants or transition-metal catalysts. Alkoxy radical species would be key intermediates in the present transformation, which generate through homolysis of the O-Br bond in hypobromite intermediates under visible light irradiation.