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1. Unraveling the structural and chemical features of biological short hydrogen bonds

   https://doi.org/10.1039/C9SC01496A  

   Zhou, Shengmin; Wang, Lu (August 2019, Chemical Science)

   The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein–ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds. 

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2. Preferential N–H⋯:C hydrogen bonding involving ditopic NH -containing systems and N -heterocyclic carbenes

   https://doi.org/10.1039/d0ra08490e  

   Kinney, Zacharias J.; Rheingold, Arnold L.; Protasiewicz, John D. (November 2020, RSC Advances)

   null (Ed.)

   Hydrogen bonding plays a critical role in maintaining order and structure in complex biological and synthetic systems. N -heterocyclic carbenes (NHCs) represent one of the most versatile tools in the synthetic chemistry toolbox, yet their potential as neutral carbon hydrogen bond acceptors remains underexplored. This report investigates this capability in a strategic manner, wherein carbene-based hydrogen bonding can be assessed by use of ditopic NH -containing molecules. N–H bonds are unique as there are three established reaction modes with carbenes: non-traditional hydrogen bonding adducts (X–H⋯:C), salts arising from proton transfer ([H–C] + [X] − ), or amines from insertion of the carbene into the N–H bond. Yet, there are no established rules to predict product distributions or the strength of these associations. Here we seek to correlate the hydrogen bond strength of symmetric and asymmetric ditopic secondary amines with 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene ( IPr , a representative NHC). In symmetric and asymmetric ditopic amine adducts both the solid-state (hydrogen bond lengths, NHC interior angles) and solution-state ( 1 H Δ δ of NH signals, 13 C signals of carbenic carbon) can be related to the p K a of the parent amine. 

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3. Large transition state stabilization from a weak hydrogen bond

   https://doi.org/10.1039/D0SC02806A  

   Vik, Erik C.; Li, Ping; Maier, Josef M.; Madukwe, Daniel O.; Rassolov, Vitaly A.; Pellechia, Perry J.; Masson, Eric; Shimizu, Ken 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 O–H⋯OC 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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4. 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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5. Anomalous chemically induced electron spin polarization in proton-coupled electron transfer reactions: insight into radical pair dynamics

   https://doi.org/10.1039/d0sc02691c  

   Brugh, Alexander M.; Forbes, Malcolm D. (June 2020, Chemical Science)

   Time-resolved electron paramagnetic resonance (TREPR) spectroscopy has been used to study the proton coupled electron transfer (PCET) reaction between a ruthenium complex (Ru(bpz)(bpy) 2 ) and several substituted hydroquinones (HQ). After excitation at 355 nm, the HQ moiety forms a strong hydrogen bond to the exposed N atoms in the bpz heterocycle. At some point afterwards, a PCET reaction takes place in which an electron from the O atom of the hydrogen bond transfers to the metal center, and the proton forming the hydrogen bond remains on the bpz ligand N atom. The result is a semiquinone radical (HQ˙), whose TREPR spectrum is strongly polarized by the triplet mechanism (TM) of chemically induced dynamic electron spin polarization (CIDEP). Closer examination of the CIDEP pattern reveals, in some cases, a small amount of radical pair mechanism (RPM) polarization. We hypothesize that when the HQ moiety has electron donating groups (EDGs) substituted on the ring, S–T − RPM polarization is observed in HQ˙. These anomalous intensities are accounted for by spectral simulation using polarization from S–T − mixing. The generation of S–T − RPM is attributed to slow radical separation after PCET due to stabilization of the positive charge on the ring by EDGs. Results from a temperature dependence support the hypothesis. 

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