The intramolecular hydrogen bonded-halogen bond: a new strategy for preorganization and enhanced binding

Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding

Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation in solution and complex formation have been characterized by crystallography, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations. First, we show why these preorganizing modifications do not affect the overall binding mode and how key interactions are preserved. Next, we demonstrate how preorganization thermodynamics can be largely dominated by enthalpy rather than entropy because of the significant population of low-energy conformations. Furthermore, a salt bridge is shielded by actively reducing its surface exposure, thus leading to an enhanced enthalpic binding profile. Our results suggest that the consideration of the ligand solution ensemble by MD simulation is necessary to predict preorganizing modifications that enhance the binding behavior of already promising binders.

Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry

The halogen bond (XB) has become an important tool for molecular design in all areas of chemistry, including crystal and materials engineering and medicinal chemistry. Its similarity to the hydrogen bond (HB) makes the relationship between these interactions complex, at times competing against and other times orthogonal to each other. Recently, our two laboratories have independently reported and characterized a synergistic relationship, in which the XB is enhanced through direct intramolecular HBing to the electron-rich belt of the halogen. In one study, intramolecular HBing from an amine polarizes the iodopyridinium XB donors of a bidentate anion receptor. The resulting HB enhanced XB (or HBeXB) preorganizes and further augments the XB donors. Consequently, the affinity of the receptor for halogen anions was significantly increased. In a parallel study, a meta-chlorotyrosine was engineered into T4 lysozyme, resulting in a HBeXB that increased the thermal stability and activity of the enzyme at elevated temperatures. The crystal structure showed that the chlorine of the noncanonical amino acid formed a XB to the protein backbone, which augmented the HB of the wild-type enzyme. Calorimetric analysis resulted in an enthalpic contribution of this Cl-XB to the stability of the protein that was an order of magnitude greater than previously determined in biomolecules. Quantum mechanical (QM) calculations showed that rotating the hydroxyl group of the tyrosine to point toward rather than away from the halogen greatly increased its potential to serve as a XB donor, equivalent to what was observed experimentally. In sum, the two systems described here show that the HBeXB concept extends the range of interaction energies and geometries to be significantly greater than that of the XB alone. Additionally, surveys of structural databases indicate that the components for this interaction are already present in many existing molecular systems. The confluence of the independent studies from our two laboratories demonstrates the reach of the HBeXB across both chemistry and biochemistry and that intentional engineering of this enhanced interaction will extend the applications of XBs beyond these two initial examples.

Anion Influence on the Packing of 1,3-Bis(4-Ethynyl-3-Iodopyridinium)-Benzene Halogen Bond Receptors

Rigid and directional arylethynyl scaffolds have been widely successful across diverse areas of chemistry. Utilizing this platform, we present three new structures of a dicationic 1,3-bis(4-ethynyl-3-iodopyridinium)-benzene halogen bonding receptor with tetrafluoroborate, nitrate, and hydrogen sulfate. Structural analysis focuses on receptor conformation, anion shape, solvation, and long range packing of these systems. Coupled with our previously reported structures, we conclude that anions can be classified as building units within this family of halogen bonding receptors. Two kinds of antiparallel dimers are observed for these dicationic receptors. An off-centered species is most frequent, present among geometrically diverse anions, and assorted receptor conformations. In contrast, the centered antiparallel dimers are observed with receptors adopting a bidentate conformation in the solid-state. While anions support the solid-state formation of dimers, the molecular geometry and characteristics (planarity, rigidity, and directionality) of arylethynyl systems increases the likelihood of dimer formation by limiting efficient packing arrangements. The significantly larger cation may have considerable influence on the solid-state packing, as similar cationic arylethynyl systems also display these dimers, suggesting.

A Potent Halogen-Bonding Donor Motif for Anion Recognition and Anion Template Mechanical Bond Synthesis

The covalent attachment of electron deficient perfluoroaryl substituents to a bis-iodotriazole pyridinium group produces a remarkably potent halogen bonding donor motif for anion recognition in aqueous media. Such a motif also establishes halogen bonding anion templation as a highly efficient method for constructing a mechanically interlocked molecule in unprecedented near quantitative yield. The resulting bis-perfluoroaryl substituted iodotriazole pyridinium axle containing halogen bonding [2]rotaxane host exhibits exceptionally strong halide binding affinities in competitive 50 % water containing aqueous media, by a factor of at least three orders of magnitude greater in comparison to a hydrogen bonding rotaxane host analogue. These observations further champion and advance halogen bonding as a powerful tool for recognizing anions in aqueous media.

Rapid Identification of Halogen Bonds in Co-Crystalline Powders via 127 I Nuclear Quadrupole Resonance Spectroscopy

¹²⁷ I nuclear quadrupole resonance (NQR) spectroscopy is established as a rapid and robust method to indicate the formation of iodine-nitrogen halogen bonds in co-crystalline powders. Once the relevant spectral frequency range has been established, diagnostic ¹²⁷ I NQR spectra can be acquired in seconds. The method is demonstrated for a series of co-crystals of 1,4-diiodobenzene. Changes in the ¹²⁷ I quadrupolar coupling constant (C_Q ) by up to 74.4 MHz correlate with the length of the C-I donor covalent bond and inversely with the I⋅⋅⋅N halogen-bond length. The predictive power of this technique is validated on two previously unknown co-crystalline powders prepared mechanochemically. Single-crystal growth via co-sublimation and structure determination by single-crystal X-ray diffraction cross-validates the findings. Natural localized molecular-orbital analyses provide insight into the origins of the quadrupolar coupling constants.

Methanesulfonyl-polarized halogen bonding enables strong halide recognition in an arylethynyl anion receptor

A 3,5-bis((2-iodophenyl)ethynyl)pyridinium scaffold was synthesized which introduces the use of methanesulfonyl withdrawing groups to polarize iodine halogen bonding units for anion binding. We investigate the capability of this receptor to bind halides in polar media, while further probing the structure-property relationship of this well-polarized yet under-explored halogen bonding system.

On the capability of metal–halogen groups to participate in halogen bonds

Halogens in a M–X bond are inhibited from forming a halogen bond but can do so in certain circumstances, with or without a σ-hole.

A comparison between hydrogen and halogen bonding: the hypohalous acid–water dimers, HOX⋯H2O (X = F, Cl, Br)

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.

A Long-Lived Halogen-Bonding Anion Triple Helicate Accommodates Rapid Guest Exchange

Anion-templated helical structures are emerging as a dynamic and tractable class of supramolecules that exhibit anion-switchable self-assembly. We present the first kinetic studies of an anion helicate by utilizing halogen-bonding m-arylene-ethynylene oligomers. These ligands formed high-fidelity triple helicates in solution with surprisingly long lifetimes on the order of seconds even at elevated temperatures. We propose an associative ligand-exchange mechanism that proceeded slowly on the same timescale. In contrast, intrachannel anion exchange occurred rapidly within milliseconds or faster as determined by stopped-flow visible spectroscopy. Additionally, the helicate accommodated bromide in solution and the solid state, while the thermodynamic stability of the triplex favored larger halide ions (bromide≈iodide≫chloride). Taken together, we elucidate a new class of kinetically stable helicates. These anion-switchable triplexes maintain their architectures while accommodating fast intrachannel guest exchange.

Halogen bonding at the wet interfaces of an amyloid peptide structure

Halogenation is a promising tool to stabilize – through halogen bonds – the wet interface of amyloid structures.