Evidence for C?Cl/C?Br⋅⋅⋅π Interactions as an Important Contribution to Protein–Ligand Binding Affinity

Attractive chlorine : Noncovalent interactions between chlorine or bromine atoms and aromatic rings in proteins open up a new method for the manipulation of molecular recognition. Substitution at distinct positions of two factor Xa inhibitors improves the free energy of binding by interaction with a tyrosine unit. The generality of this motif was underscored by multiple crystal structures as well as high‐level quantum chemical calculations (see picture).

     

Ion‐Pairing of Phosphonium Salts in Solution: C?H⋅⋅⋅Halogen and C?H⋅⋅⋅π Hydrogen Bonds

The ¹H NMR chemical shifts of the C(α)? H protons of arylmethyl triphenylphosphonium ions in CD₂Cl₂ solution strongly depend on the counteranions X^?. The values for the benzhydryl derivatives Ph₂CH? PPh₃⁺ X^?, for example, range from δ_H=8.25 (X^?=Cl^?) over 6.23 (X^?=BF₄^?) to 5.72 ppm (X^?=BPh₄^?). Similar, albeit weaker, counterion‐induced shifts are observed for the ortho‐protons of all aryl groups. Concentration‐dependent NMR studies show that the large shifts result from the deshielding of the protons by the anions, which decreases in the order Cl^? > Br^? ? BF₄^? > SbF₆^?. For the less bulky derivatives PhCH₂? PPh₃⁺ X^?, we also find C? H???Ph interactions between C(α)? H and a phenyl group of the BPh₄^? anion, which result in upfield NMR chemical shifts of the C(α)? H protons. These interactions could also be observed in crystals of (p‐CF₃‐C₆H₄)CH₂? PPh₃⁺ BPh₄^?. However, the dominant effects causing the counterion‐induced shifts in the NMR spectra are the C? H???X^? hydrogen bonds between the phosphonium ion and anions, in particular Cl^? or Br^?. This observation contradicts earlier interpretations which assigned these shifts predominantly to the ring current of the BPh₄^? anions. The concentration dependence of the ¹H NMR chemical shifts allowed us to determine the dissociation constants of the phosphonium salts in CD₂Cl₂ solution. The cation–anion interactions increase with the acidity of the C(α)? H protons and the basicity of the anion. The existence of C? H???X^? hydrogen bonds between the cations and anions is confirmed by quantum chemical calculations of the ion pair structures, as well as by X‐ray analyses of the crystals. The IR spectra of the Cl^? and Br^? salts in CD₂Cl₂ solution show strong red‐shifts of the C? H stretch bands. The C? H stretch bands of the tetrafluoroborate salt PhCH₂? PPh₃⁺ BF₄^? in CD₂Cl₂, however, show a blue‐shift compared to the corresponding BPh₄^? salt.     

Probing the C?H⋅⋅⋅π Weak Hydrogen Bond in Anesthetic Binding: The Sevoflurane–Benzene Cluster

Cooperativity between weak hydrogen bonds can be revealed in molecular clusters isolated in the gas phase. Here we examine the structure, internal dynamics, and origin of the weak intermolecular forces between sevoflurane and a benzene molecule, using multi‐isotopic broadband rotational spectra. This heterodimer is held together by a primary C H⋅⋅⋅π hydrogen bond, assisted by multiple weak C H⋅⋅⋅F interactions. The multiple nonbonding forces hinder the internal rotation of benzene around the isopropyl C H bond in sevoflurane, producing detectable quantum tunneling effects in the rotational spectrum.     

An Interplay of Cooperativity between Cation⋅⋅⋅π, Anion⋅⋅⋅π and C?H⋅⋅⋅Anion Interactions

Mixed cation (Li⁺, Na⁺ and K⁺) and anion (F^?, Cl^?, Br^?) complexes of the aromatic π‐surfaces (top and bottom) are studied by using dispersion‐corrected density functional theory. The selectivity of the aromatic surface to interact with a cation or an anion can be tuned and even reversed by the electron‐donating/electron‐accepting nature of the side groups. The presence of a methyl group in the ? OCH₃, ? SCH₃, ? OC₂H₅ in the side groups of the aromatic ring leads to further cooperative stabilization of the otherwise unstable/weakly stable anion???π complexes by bending of the side groups towards the anion to facilitate C? H???anion interactions. The cooperativity among the interactions is found to be as large as 100 kcal mol^?1 quantified by dissection of the three individual forces from the total interaction energy. The crystal structures of the fluoride binding tripodal and hexapodal ligands provide experimental evidence for such cooperative interactions.     

Hydrogen‐Bond Dynamics of C?H⋅⋅⋅O Interactions: The Chloroform⋅⋅⋅Acetone Case

Spectroscopic evidence for C? H ??? O hydrogen bonding in chloroform ??? acetone [Cl₃CH ??? O?C(CH₃)₂] mixtures was obtained from vibrational inelastic neutron scattering (INS) spectra. Comparison between the INS spectra of pure samples and their binary mixtures reveals the presence of new bands at about 82, 130 and 170 cm^?1. Assignment of the 82 cm^?1 band to the νO ??? H anti‐translational mode is considered and discussed. In addition, the βC? H mode of CHCl₃ at 1242 cm^?1 is split in the spectra of the mixtures, and the high‐wavenumber component is assigned to the hydrogen‐bonded complex. The plot of the integrated intensity of this component shows a maximum for x=0.5, in agreement with the 1:1 stoichiometry of the chloroform ??? acetone complex, with a calculated complexation constant of 0.15 dm³ mol^?1. Results also show that the complex behaves as an independent entity, that is, despite being weak, such interactions play a key role in supramolecular chemistry.     

C?X⋅⋅⋅O Halogen Bonding: Interactions of Trifluoromethyl Halides with Dimethyl Ether

The formation of weakly bound molecular complexes between dimethyl ether (DME) and the trifluoromethyl halides CF₃Cl, CF₃Br and CF₃I dissolved in liquid argon and in liquid krypton is investigated, using Raman and FTIR spectroscopy. For all halides evidence is found for the formation of C? X???O halogen‐bonded 1:1 complexes. At higher concentrations of CF₃Br, a weak absorption due to a 1:2 complex is also observed. Using spectra recorded at temperatures between 87 and 125 K, the complexation enthalpies for the complexes are determined to be ?6.8(3) kJ mol^?1 (DME?CF₃Cl), ?10.2(1) kJ mol^?1 (DME?CF₃Br), ?15.5(1) kJ mol^?1 (DME?CF₃I), and ?17.8(5) kJ mol^?1 [DME(?CF₃Br)₂]. Structural and spectral information on the complexes is obtained from ab initio calculations at the MP2/ 6‐311++G(d,p) and MP2/6‐311++G(d,p)+LanL2DZ* levels. By applying Monte Carlo free energy perturbation calculations to account for the solvent influences, and statistical thermodynamics to estimate the zero‐point vibrational and thermal influences, the ab initio complexation energies are converted into complexation enthalpies for the solutions in liquid argon. The resulting values are compared with the experimental data deduced from the cryosolutions.     

Dimensional Matching of Polycyclic Aromatics with Rectangular Metallacycles: Insertion Modes Determined by [C?H⋅⋅⋅π] Interactions

A family of Pd^II/Pt^II dinuclear receptors, designed to give a smooth increase in their cavity lengths (from 7.46–13.78 Å), is presented. Their inclusion complexes with a representative set of polycyclic aromatic substrates (naphthalene, carbazol, pyrene, and benzo[a]pyrene), were characterized and studied in aqueous solution and the solid state. By taking into account the dimensions of both receptors and substrates, an excellent complementarity was found between the size of the receptors and their ability to complex a given substrate. Furthermore, this dimensional matching results in specific binding modes depending on the ability of the guest to establish stabilizing [C? H???π] interactions with the host.     

Spin–Spin Coupling Constants Transmitted through Ir?H⋅⋅⋅H?N Dihydrogen Bonds

Relativity matters: Calculations of NMR shielding tensors and spin–spin coupling constants transmitted through Ir? H???H? N dihydrogen bonds are presented. The picture shows one of the simplified models employed. It is shown that the spin–orbit relativistic effects influence the NMR shielding constants far more than the spin–spin coupling constants.

     

Molecular Pair Analysis: C?H⋅⋅⋅F Interactions in the Crystal Structure of Fluorobenzene? And Related Matters

The crystal structure of fluorobenzene is compared with isomorphous crystal structures of molecules of roughly similar shape. The lowest-energy fluorobenzene dimers are identified by theoretical calculations. Molecular pair analysis of the crystal structure of fluorobenzene and of an isomorphous virtual low-energy polymorph of benzene suggests that the important intermolecular interactions in the two structures are closely similar. In particular, the intermolecular C-H...F interactions in the fluorobenzene crystal have approximately the same structure-directing ability and influence on the intermolecular energy as the corresponding C-H...H interactions in benzene. Molecular pair analysis of the isomorphous crystal structures of benzonitrile, alloxan, and cyclopentene-1,2,3-trione indicates that essentially the same crystal structure can be adopted with quite different patterns of pair energies and atom-atom interactions. The question as to whether the packing radius of organic fluorine is larger or smaller than that of hydrogen, is addressed, but not answered.     

Self‐Assembly of Halogenated Cobaltacarborane Compounds: Boron‐Assisted C?H⋅⋅⋅X?B Hydrogen Bonds?

Full structural characterisation and complete synthetic procedures for three monohalogenated cobaltacarborane compounds closo-[3-Co(eta5-C5H5)-8-X-1,2-C2B9H10] (X=Cl (1), Br (2), I (3)) and the dibromo derivative closo-[3-Co(eta5-C5H5)-8,9-Br2-1,2-C2B9H9] (4) are reported. The supramolecular structures of 1, 3, and 4 reveal the existence of intermolecular C--HX--B interactions. The role of these interactions has been investigated through a CSD search and subsequent analysis of the reported crystalline compounds. The results show that halogens become reasonably good hydrogen-bond acceptors when bonded to boron and, in this respect, are comparable in strength to metal-bound halogens.     

Predicting C?H/π Interactions with Nonlocal Density Functional Theory

We examine the performance of a recently developed nonlocal density functional in predicting a model noncovalent interaction, namely the weak bond between an aromatic π system and an aliphatic C? H group. The new functional is a significant improvement over traditional density functionals, providing results which compare favorably to high‐level quantum‐chemistry techniques, but at considerably lower computational cost. Interaction energies in several model C? H/π systems are in good general agreement with coupled‐cluster calculations, though equilibrium distances are consistently overpredicted when using the revPBE functional for exchange. The new functional predicts changes in energy upon addition of halogen substituents correctly.