NMR-assisted crystallography—the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry—holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5′-phosphate–dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid–base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate C β and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.
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Quantum mechanical effects in acid–base chemistry
Acid–base chemistry has immense importance for explaining and predicting the chemical products formed by an acid and a base when mixed together. However, the traditional chemistry theories used to describe acid–base reactions do not take into account the effect arising from the quantum mechanical nature of the acidic hydrogen shuttling potential and its dependence on the acid base distance. Here, infrared and NMR spectroscopies, in combination with first principles simulations, are performed to demonstrate that quantum mechanical effects, including electronic and nuclear quantum effects, play an essential role in defining the acid–base chemistry when 1-methylimidazole and acetic acid are mixed together. In particular, it is observed that the acid and the base interact to form a complex containing a strong hydrogen bond, in which the acidic hydrogen atom is neither close to the acid nor to the base, but delocalized between them. In addition, the delocalization of the acidic hydrogen atom in the complex leads to characteristic IR and NMR signatures. The presence of a hydrogen delocalized state in this simple system challenges the conventional knowledge of acid–base chemistry and opens up new avenues for designing materials in which specific properties produced by the hydrogen delocalized state can be harvested.
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- Award ID(s):
- 1904800
- NSF-PAR ID:
- 10338529
- Date Published:
- Journal Name:
- Chemical Science
- Volume:
- 13
- Issue:
- 23
- ISSN:
- 2041-6520
- Page Range / eLocation ID:
- 6998 to 7006
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract An anionic Rh−Ga complex catalyzed the hydrodefluorination of challenging C−F bonds in electron‐rich aryl fluorides and trifluoromethylarenes when irradiated with violet light in the presence of H2, a stoichiometric alkoxide base, and a crown‐ether additive. Based on theoretical calculations, the lowest unoccupied molecular orbital (LUMO), which is delocalized across both the Rh and Ga atoms, becomes singly occupied upon excitation, thereby poising the Rh−Ga complex for photoinduced single‐electron transfer (SET). Stoichiometric and control reactions support that the C−F activation is mediated by the excited anionic Rh−Ga complex. After SET, the proposed neutral Rh0intermediate was detected by EPR spectroscopy, which matched the spectrum of an independently synthesized sample. Deuterium‐labeling studies corroborate the generation of aryl radicals during catalysis and their subsequent hydrogen‐atom abstraction from the THF solvent to generate the hydrodefluorinated arene products. Altogether, the combined experimental and theoretical data support an unconventional bimetallic excitation that achieves the activation of strong C−F bonds and uses H2and base as the terminal reductant.
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Abstract An anionic Rh−Ga complex catalyzed the hydrodefluorination of challenging C−F bonds in electron‐rich aryl fluorides and trifluoromethylarenes when irradiated with violet light in the presence of H2, a stoichiometric alkoxide base, and a crown‐ether additive. Based on theoretical calculations, the lowest unoccupied molecular orbital (LUMO), which is delocalized across both the Rh and Ga atoms, becomes singly occupied upon excitation, thereby poising the Rh−Ga complex for photoinduced single‐electron transfer (SET). Stoichiometric and control reactions support that the C−F activation is mediated by the excited anionic Rh−Ga complex. After SET, the proposed neutral Rh0intermediate was detected by EPR spectroscopy, which matched the spectrum of an independently synthesized sample. Deuterium‐labeling studies corroborate the generation of aryl radicals during catalysis and their subsequent hydrogen‐atom abstraction from the THF solvent to generate the hydrodefluorinated arene products. Altogether, the combined experimental and theoretical data support an unconventional bimetallic excitation that achieves the activation of strong C−F bonds and uses H2and base as the terminal reductant.
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In exploring the conformational behavior of cyclic tungsten bis-alkyne complexes, two dialkynylamides (14a and 14c) and two dialkynylesters (14b and 14d) derived from 1,1’-ferrocenedicarboxylic acid were prepared. They were subsequently reacted with W(CO)3(dmtc)2 to yield the desired cyclic tungsten bis-alkyne complexes 8-11. In the cyclization of 14a to yield 8 a dimeric macrocyclic complex, 15, featuring two tungsten bis-alkyne complexes in the ring, also was isolated. The conformational behavior of these complexes was assessed by analysis of the 1H NMR resonances for the alkyne hydrogens, which appear around 11 ppm. The spectra for complexes 10, 11 and 15 show multiple singlets of varying integrations for these protons, while the spectra for complexes 8 and 9 show only two resonances of equal integration for the alkyne hydrogens. The spectra for 8 and 9 changed very little when examined at higher temperatures, indicating that the solution conformation is robust. A ROESY spectrum was obtained for 8. It did not show any crosspeaks between the two alkyne hydrogens. The NMR data shows that the alkyne ligands in 10, 11 and 15 are able to rotate about the tungsten-alkyne bond; these complexes adopted several different solution conformations relating to syn and anti arrangements of the alkyne ligands. In contrast, complexes 8 and 9 adopt only one solution conformation, and the alkyne ligands in these species do not rotate about the tungsten-alkyne bond. The NMR spectra for 8 and 9 also show that these complexes are asymmetric. The 1H NMR spectra for 8 and 9 show that each hydrogen atom has its own unique resonance in the 1H NMR spectrum. There are 8 resonances for the 8 Cp protons, 4 resonances for the methylene protons, 2 resonances for the alkyne protons, and in the case of 8, 2 resonances for the NH protons. The two NH protons on complex 8 were found to have widely different chemical shifts. A DMSO titration was performed and it showed that one of the two NH protons in 8 is involved in an intramolecular hydrogen bond. Given that the diester 9 adopts a similar conformation as the diamide 8, this intramolecular hydrogen bond appears to result from the conformation imposed by cyclization of the ring system. Overall, the data show that the ring system for 8 and 9 provides a unique, rigid, robust, and air stable cyclic molecule where the alkyne ligands are limited to one orientation, presumably the syn orientation. The lack of mobility for the alkyne ligands limits the cyclic molecule to only one solution conformation. Complexes 8 and 9 are the first reported examples of cyclic tungsten bis-alkyne complexes that only adopt a single, robust conformation in solution.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D2SC01784A
