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1. Large transition state stabilization from a weak hydrogen bond

   Vik, E. C.; Li, P.; Maier, J. M.; Madukwe, D.O.; Rassolov, V. A.; Pellechia, P. J.; Masson, E.; Shimizu, K. D. (July 2020, Chemical science)

   A series of molecular rotors was designed to study and measure the rate accelerating effects of an intramolecular hydrogen bond. The rotors form a weak neutral O–H/O]C hydrogen bond in the planar transition state (TS) of the bond rotation process. The rotational barrier of the hydrogen bonding rotors was dramatically lower (9.9 kcal mol
   1) than control rotors which could not form hydrogen bonds. The magnitude of the stabilization was significantly larger than predicted based on the independently measured strength of a similar OH/OC hydrogen bond (1.5 kcal mol-1). The origins of the large transition state stabilization were studied via experimental substituent effect and computational perturbation analyses. Energy decomposition analysis of the hydrogen bonding interaction revealed a significant reduction in the repulsive component of the hydrogen bonding interaction. The rigid framework of the molecular rotors positions and preorganizes the interacting groups in the transition state. This study demonstrates that with proper design a single hydrogen bond can lead to a TS stabilization that is greater than the intrinsic interaction energy, which has applications in catalyst design and in the study of enzyme mechanisms. 

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2. Counterintuitive torsional barriers controlled by hydrogen bonding

   https://doi.org/10.1039/d0cp03285a  

   Barbero, Héctor; Meunier, Antoine; Kotturi, Kondalarao; Smith, Ashton; Kyritsakas, Nathalie; Killmeyer, Adam; Rabbani, Ramin; Nazimuddin, Md; Masson, Eric (September 2020, Physical Chemistry Chemical Physics)

   null (Ed.)

   The torsional barriers along the C aryl –C aryl axis of a pair of isosteric disubstituted biphenyls were determined by variable temperature 1 H NMR spectroscopy in three solvents with contrasted hydrogen bond accepting abilities (1,1,2,2-tetrachloroethane-d 2 , nitrobenzene-d 5 and dimethyl sulfoxide-d 6 ). One of the biphenyl scaffolds was substituted at its ortho and ortho ′ positions with N ′-acylcarbohydrazide groups that could engage in a pair of intramolecular N–H⋯O=C hydrogen bonding interactions at the ground state, but not at the transition state of the torsional isomerization pathway. The torsional barrier of this biphenyl was exceedingly low despite the presence of the hydrogen bonds (16.1, 15.6 and 13.4 kcal mol −1 in the three aforementioned solvents), compared to the barrier of the reference biphenyl (15.3 ± 0.1 kcal mol −1 on average). Density functional theory and the solvation model developed by Hunter were used to decipher the various forces at play. They highlighted the strong stabilization of hydrogen bond donating solutes not only by hydrogen bond accepting solvents, but also by weakly polar, yet polarizable solvents. As fast exchanges on the NMR time scale were observed above the melting point of dimethyl sulfoxide-d 6 , a simple but accurate model was also proposed to extrapolate low free activation energies in a pure solvent (dimethyl sulfoxide-d 6 ) from higher ones determined in mixtures of solvents (dimethyl sulfoxide-d 6 in nitrobenzene-d 5 ). 

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3. Transition State Stabilizing Effects of Oxygen and Sulfur Chalcogen Bond Interactions

   https://doi.org/10.1002/chem.202402011  

   Lin, Binzhou; Liu, Hao; Scott, Harrison_M; Karki, Ishwor; Vik, Erik_C; Madukwe, Daniel_O; Pellechia, Perry_J; Shimizu, Ken_D (September 2024, Chemistry – A European Journal)

   Abstract Non‐covalent chalcogen bond (ChB) interactions have found utility in many fields, including catalysis, organic semiconductors, and crystal engineering. In this study, the transition stabilizing effects of ChB interactions of oxygen and sulfur were experimentally measured using a series of molecular rotors. The rotors were designed to form ChB interactions in their bond rotation transition states. This enabled the kinetic influences to be assessed by monitoring changes in the rotational barriers. Despite forming weaker ChB interactions, the smaller chalcogens were able to stabilize transition states and had measurable kinetic effects on the rotational barriers. Sulfur stabilized the bond rotation transition state by as much as −7.2 kcal/mol without electron‐withdrawing groups. The key was to design a system where the sulfur ‐hole was aligned with the lone pairs of the chalcogen bond acceptor. Oxygen rotors also could form transition state stabilizing ChB interactions but required electron‐withdrawing groups. For both oxygen and sulfur ChB interactions, a strong correlation was observed between transition state stabilizing abilities and electrostatic potential (ESP) of the chalcogen, providing a useful predictive parameter for the rational design of future ChB systems. 

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4. What Is the Catalytic Mechanism of Enzymatic Histone N‐Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field?

   https://doi.org/10.1002/chem.202101174  

   Ramanan, Rajeev; Waheed, Sodiq_O; Schofield, Christopher_J; Christov, Christo_Z (June 2021, Chemistry – A European Journal)

   Abstract Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2‐oxoglutarate dependent Jumonji‐C (JmjC) Nϵ‐methyl lysine histone demethylases also have N‐methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N‐methyl arginine demethylation by human KDM4E and compare the results with those reported for N‐methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen‐bond between the substrate Ser1 and Tyr178. The calculations imply that in either C−H or N−H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N‐methyl arginine demethylation, electron transfer occurs via a σ‐channel; the transition state for the N−H pathway is ∼10 kcal/mol higher than for the C−H pathway due to the higher bond dissociation energy of the N−H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier‐lowering effect on the C−H pathway, by contrast, such EEFs inhibit the N−H activation rate. The overall results imply that KDM4 catalyzed N‐methyl arginine demethylation and N‐methyl lysine demethylation occur via similar C−H abstraction and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates. 

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5. The non-covalently bound SO⋯H ₂ O system, including an interpretation of the differences between SO⋯H ₂ O and O ₂ ⋯H ₂ O

   https://doi.org/10.1039/C8CP05749D  

   Misiewicz, Jonathon P.; Noonan, Julia A.; Turney, Justin M.; Schaefer, Henry F. (November 2018, Physical Chemistry Chemical Physics)

   Despite the interest in sulfur monoxide (SO) among astrochemists, spectroscopists, inorganic chemists, and organic chemists, its interaction with water remains largely unexplored. We report the first high level theoretical geometries for the two minimum energy complexes formed by sulfur monoxide and water, and we report energies using basis sets as large as aug-cc-pV(Q+d)Z and correlation effects through perturbative quadruple excitations. One structure of SO⋯H 2 O is hydrogen bonded and the other chalcogen bonded. The hydrogen bonded complex has an electronic energy of −2.71 kcal mol −1 and a zero kelvin enthalpy of −1.67 kcal mol −1 , while the chalcogen bonded complex has an electronic energy of −2.64 kcal mol −1 and a zero kelvin enthalpy of −2.00 kcal mol −1 . We also report the transition state between the two structures, which lies below the SO⋯H 2 O dissociation limit, with an electronic energy of −1.26 kcal mol −1 and an enthalpy of −0.81 kcal mol −1 . These features are much sharper than for the isovalent complex of O 2 and H 2 O, which only possesses one weakly bound minimum, so we further analyze the structures with open-shell SAPT0. We find that the interactions between O 2 and H 2 O are uniformly weak, but the SO⋯H 2 O complex surface is governed by the superior polarity and polarizability of SO, as well as the diffuse electron density provided by sulfur's extra valence shell. 

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