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1. Design of a halogen bond catalyzed DNA endonuclease

   Walker, Margaret G; Mendez, Cesar Gustavo; Ho, Alexander N; Czarny, Ryan S; Rappé, Anthony K; Ho, Pui Shing (April 2025, Proceedings of the National Academy of Sciences of the United States of America)

   In this study, we expand the repertoire of biological catalysts by showing that a halo- gen bond (X-bond) can functionally replace the magnesium (Mg2+) cofactor in mouse endonuclease G (mEndoG). We mutated the metal coordinating glutamate E136 in mEndoG to a meta-halotyrosine (mXY, X = chlorine or iodine) to form a mXY-mEndoG construct that is both acid and base catalyzed. Under basic conditions, the enzyme is inactivated by the metal chelator ethylene diamine tetraacetic acid (EDTA), indicating that the halogen substituent facilitates deprotonation of the tyrosyl hydroxyl group, allowing recruitment of Mg2+ to restore the metal-dependent catalytic center. At low pHs, we observe that the mXY-mEndoG is resistant to EDTA inactivation and that the iodinated constructed is significantly more active than the chlorinated analogue. These results implicate a hydrogen bond (H-bond) enhanced X-bond as the catalyst in the mXY-mEndoG, with asparagine N103 serving as the H-bond donor that communicates the protonation state of histidine H104 to the halogen. This model is supported by mutation studies and electrostatic potential (ESP) calculations on models for the protonated and unprotonated mXY···N103···H104 system compared to the Mg2+ coor- dination complex of the wild type. Thus, we have designed and engineered an enzyme that utilizes an unnatural catalyst in its active site—a catalytic X-bonding enzyme, or cX-Zyme—by controverting what constitutes a metal catalyst in biochemistry. 

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2. Critical comparison of RX⋯Y and RH⋯Y directionality in halogen and hydrogen bonds using modern computational chemistry methods

   https://doi.org/doi.org/10.1016/j.cplett.2020.137221  

   Riley, Kevin E. (April 2020, Chemical physics letters)

   Symmetry adapted perturbation theory anlysis and intermolecular overlap volume calculations are used to investigate the origins of halogen- and hydrogen bond directionality. The central finding is that exchange-repulsion is primarily responsible for destabilizing both types of interaction as the R-x⋯Y (x = H, Cl, Br) angle deviates from linearity. The particular shape of the electron density envelope on the halogen/hydrogen bond donor plays a large role in dictating the degree to which a complex is destabilized upon R-x⋯Y rotation, with halogen bonds exhibiting a roughly linear destabilization and hydrogen bonds exhibiting destabilization that is approximately quadratic. 

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3. Pushing the limits of the hydrogen bond enhanced halogen bond—the case of the C–H hydrogen bond

   https://doi.org/10.1039/d2sc03792k  

   Decato, Daniel A.; Sun, Jiyu; Boller, Madeleine R.; Berryman, Orion B. (September 2022, Chemical Science)

   C–H hydrogen bonds to iodine halogen bond donors are shown to improve halogen bonding and molecular preorganization. 

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4. Co-operative halogen bonds and nonconventional sp -C—H...O hydrogen bonds in 1:1 cocrystals formed between diethynylpyridines and N -halosuccinimides

   https://doi.org/10.1107/S2053229622006635  

   Bosch, Eric; Bowling, Nathan P. (July 2022, Acta Crystallographica Section C Structural Chemistry)

   The rapid evaporation of 1:1 solutions of diethynylpyridines and N -halosuccinimides, that react together to form haloalkynes, led to the isolation of unreacted 1:1 cocrystals of the two components. The 1:1 cocrystal formed between 2,6-diethynylpyridine and N -iodosuccinimide (C 4 H 4 INO 2 ·C 9 H 5 N) contains an N -iodosuccinimide–pyridine I...N halogen bond and two terminal alkyne–succinimide carbonyl C—H...O hydrogen bonds. The three-dimensional extended structure features interwoven double-stranded supramolecular polymers that are interconnected through halogen bonds. The cocrystal formed between 3,5-diethynylpyridine and N -iodosuccinimide (C 4 H 4 INO 2 ·C 9 H 5 N) also features an I...N halogen bond and two C—H...O hydrogen bonds. However, the components form essentially planar double-stranded one-dimensional zigzag supramolecular polymers. The cocrystal formed between 3,5-diethynylpyridine and N -bromosuccinimide (C 4 H 4 BrNO 2 ·C 9 H 5 N) is isomorphous to the cocrystal formed between 3,5-diethynylpyridine and N -iodosuccinimide, with a Br...N halogen bond instead of an I...N halogen bond. 

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5. A comparison between hydrogen and halogen bonding: the hypohalous acid–water dimers, HOX⋯H ₂ O (X = F, Cl, Br)

   https://doi.org/10.1039/C9CP00422J  

   Wolf, Mark E.; Zhang, Boyi; Turney, Justin M.; Schaefer, Henry F. (March 2019, Physical Chemistry Chemical Physics)

   Hypohalous acids (HOX) are a class of molecules that play a key role in the atmospheric seasonal depletion of ozone and have the ability to form both hydrogen and halogen bonds. The interactions between the HOX monomers (X = F, Cl, Br) and water have been studied at the CCSD(T)/aug-cc-pVTZ level of theory with the spin free X2C-1e method to account for scalar relativistic effects. Focal point analysis was used to determine CCSDT(Q)/CBS dissociation energies. The anti hydrogen bonded dimers were found with interaction energies of −5.62 kcal mol −1 , −5.56 kcal mol −1 , and −4.97 kcal mol −1 for X = F, Cl, and Br, respectively. The weaker halogen bonded dimers were found to have interaction energies of −1.71 kcal mol −1 and −3.03 kcal mol −1 for X = Cl and Br, respectively. Natural bond orbital analysis and symmetry adapted perturbation theory were used to discern the nature of the halogen and hydrogen bonds and trends due to halogen substitution. The halogen bonds were determined to be weaker than the analogous hydrogen bonds in all cases but close enough in energy to be relevant, significantly more so with increasing halogen size. 

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