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.     

Switch From Pauli-Lowering to LUMO-Lowering Catalysis in Brønsted Acid-Catalyzed Aza-Diels-Alder Reactions

Brønsted acid-catalyzed inverse-electron demand (IED) aza-Diels-Alder reactions between 2-aza-dienes and ethylene were studied using quantum chemical calculations. The computed activation energy systematically decreases as the basic sites of the diene progressively become protonated. Our activation strain and Kohn-Sham molecular orbital analyses traced the origin of this enhanced reactivity to i) “Pauli-lowering catalysis” for mono-protonated 2-aza-dienes due to the induction of an asynchronous, but still concerted, reaction pathway that reduces the Pauli repulsion between the reactants; and ii) “LUMO-lowering catalysis” for multi-protonated 2-aza-dienes due to their highly stabilized LUMO(s) and more concerted synchronous reaction path that facilitates more efficient orbital overlaps in IED interactions. In all, we illustrate how the novel concept of “Pauli-lowering catalysis” can be overruled by the traditional concept of “LUMO-lowering catalysis” when the degree of LUMO stabilization is extreme as in the case of multi-protonated 2-aza-dienes.     

Transient spectroscopic characterization of the ring‐opening reaction of tetrahydrochromeno[2,3‐dimethyl]indole

Tetrahydrochromeno is a structural variant of spiropyran that undergoes a reversible ring‐opening to generate a colored nitrophenolate intermediate. Earlier work confirmed this intermediate through trimethylsilyl cyanide trapping under continuous irradiation. We have performed transient absorption spectroscopy to further characterize the mechanism of the ring‐opening reaction. Excitation at 355 nm produced a transient species with an absorption maximum at 445 nm, which we assign to the nitrophenolate unit of the ring‐opened product. The transient absorption decays after ~970 ns with small optical density changes corresponding to a 0.15 quantum yield. Exposure to oxygen did not exhibit a significant deleterious effect on the photoisomerization of the chromeno dye. Time‐dependent density functional theory corroborated spectroscopic assignments of the starting chromeno and the putative ring‐opened intermediate. The excited state behavior of this system parallels the structurally similar oxazine system reported by Raymo and coworkers. The one significant difference is the longer lifetime of the photochemically generated intermediate from chromeno. Copyright © 2015 John Wiley & Sons, Ltd.     

Photophysics of Azobenzene Constrained in a UiO Metal–Organic Framework: Effects of Pressure,Solvation and Dynamic Disorder

Photophysical studies of chromophoric linkers in metal–organic frameworks (MOFs) are undertaken commonly in the context of sensing applications, in search of readily observable changes of optical properties in response to external stimuli. The advantages of the MOF construct as a platform for investigating fundamental photophysical behaviour have been somewhat overlooked. The linker framework offers a unique environment in which the chromophore is geometrically constrained and its structure can be determined crystallographically, but it exists in spatial isolation, unperturbed by inter-chromophore interactions. Furthermore, high-pressure studies enable the photophysical consequences of controlled, incremental changes in local environment or conformation to be observed and correlated with structural data. This approach is demonstrated in the present study of the trans-azobenzene chromophore, constrained in the form of the 4,4’-azobenzenedicarboxylate (abdc) linker, in a UiO topology framework. Previously unobserved effects of pressure-induced solvation and conformational distortion on the lowest energy, nπ* transition are reported, and interpreted the light of crystallographic data. It was found that trans-azobenzene remains non-fluorescent (with a quantum yield less than 10⁻⁴) despite the prevention of trans-cis isomerization by the constraining MOF structure. We propose that efficient non-radiative decay is mediated by the local, pedal-like twisting of the azo group that is evident as dynamic disorder in the crystal structure.     

The Chemical Bond: When Atom Size Instead of Electronegativity Difference Determines Trend in Bond Strength

We have quantum chemically analyzed element−element bonds of archetypal H_nX−YH_n molecules (X, Y=C, N, O, F, Si, P, S, Cl, Br, I), using density functional theory. One purpose is to obtain a set of consistent homolytic bond dissociation energies (BDE) for establishing accurate trends across the periodic table. The main objective is to elucidate the underlying physical factors behind these chemical bonding trends. On one hand, we confirm that, along a period (e. g., from C−C to C−F), bonds strengthen because the electronegativity difference across the bond increases. But, down a period, our findings constitute a paradigm shift. From C−F to C−I, for example, bonds do become weaker, however, not because of the decreasing electronegativity difference. Instead, we show that the effective atom size (via steric Pauli repulsion) is the causal factor behind bond weakening in this series, and behind the weakening in orbital interactions at the equilibrium distance. We discuss the actual bonding mechanism and the importance of analyzing this mechanism as a function of the bond distance.     

Protected Amine Labels: A Versatile Molecular Scaffold for Multiplexed Nominal Mass and Sub-Da Isotopologue Quantitative Proteomic Reagents

We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (1) robust targeting of peptide N-termini and lysyl side chains, (2) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (3) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (4) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da, are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition, we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally, we provide exemplar data that extend the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers.

A Pressure-Induced Inverse Order–Disorder Transition in Double Perovskites

Given the consensus that pressure improves cation ordering in most of known materials, a discovery of pressure-induced disordering could require recognition of an order–disorder transition in solid-state physics/chemistry and geophysics. Double perovskites Y₂CoIrO₆ and Y₂CoRuO₆ polymorphs synthesized at 0, 6, and 15 GPa show B-site ordering, partial ordering, and disordering, respectively, accompanied by lattice compression and crystal structure alteration from monoclinic to orthorhombic symmetry. Correspondingly, the long-range ferrimagnetic ordering in the B-site ordered samples are gradually overwhelmed by B-site disorder. Theoretical calculations suggest that unusual unit-cell compressions under external pressures unexpectedly stabilize the disordered phases of Y₂CoIrO₆ and Y₂CoRuO₆.     

PIII/PV=O Catalyzed Cascade Synthesis of N‐Functionalized Azaheterocycles

An organocatalytic method for the modular synthesis of diverse N‐aryl and N‐alkyl azaheterocycles (indoles, oxindoles, benzimidazoles, and quinoxalinediones) is reported. The method employs a small‐ring organophosphorus‐based catalyst (1,2,2,3,4,4‐hexamethylphosphetane P‐oxide) and a hydrosilane reductant to drive the conversion of ortho‐functionalized nitroarenes into azaheterocycles through sequential intermolecular reductive C?N cross coupling with boronic acids, followed by intramolecular cyclization. This method enables the rapid construction of azaheterocycles from readily available building blocks, including a regiospecific approach to N‐substituted benzimidazoles and quinoxalinediones.     

A Pressure‐Induced Inverse Order–Disorder Transition in Double Perovskites

Given the consensus that pressure improves cation ordering in most of known materials, a discovery of pressure‐induced disordering could require recognition of an order–disorder transition in solid‐state physics/chemistry and geophysics. Double perovskites Y₂CoIrO₆ and Y₂CoRuO₆ polymorphs synthesized at 0, 6, and 15 GPa show B‐site ordering, partial ordering, and disordering, respectively, accompanied by lattice compression and crystal structure alteration from monoclinic to orthorhombic symmetry. Correspondingly, the long‐range ferrimagnetic ordering in the B‐site ordered samples are gradually overwhelmed by B‐site disorder. Theoretical calculations suggest that unusual unit‐cell compressions under external pressures unexpectedly stabilize the disordered phases of Y₂CoIrO₆ and Y₂CoRuO₆.