Structure and energetics of gas phase halogen-bonding in mono-, bi-, and tri-dentate anion receptors as studied by BIRD

Principles and Applications of CF2X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery

As an orthogonal principle to the established (hetero)aryl halides, we herein highlight the usefulness of CF2X (X = Cl, Br, or I) moieties. Using tool compounds bearing CF2X moieties, we study their chemical/metabolic stability and their logP/solubility, as well as the role of XB in their small molecular crystal structures. Employing QM techniques, we analyze the observed interactions, provide insights into the conformational flexibilities and preferences in the potential interaction space. For their application in molecular design, we characterize their XB donor capacities and its interaction strength dependent on geometric parameters. Implementation of CF2X acetamides into our HEFLibs and biophysical evaluation (STD-NMR/ITC), followed by X-ray analysis, reveals a highly interesting binding mode for fragment 23 in JNK3, featuring an XB of CF2Br toward the P-loop, as well as chalcogen bonds. We suggest that underexplored chemical space combined with unconventional binding modes provides excellent opportunities for patentable chemotypes for therapeutic intervention.

Preparation and Characterization of the Halogen-Bonding Motif in the Isolated Cl-·IOH Complex with Cryogenic Ion Vibrational Spectroscopy

In the presence of a halide ion, hypohalous acids can adopt two binding motifs upon formation of the ion-molecule complexes [XHOY]^- (X, Y = Cl, Br, I): a hydrogen (HB) bond to the acid OH group and a halogen (XB) bond between the anion and the acid halogen. Here we isolate the X-bonded Cl^-·IOH ion-molecule complex by collisions of I^-·(H₂O)_n clusters with HOCl vapor and measure its vibrational spectrum by IR photodissociation of the H₂-tagged complex. Anharmonic analysis of its vibrational band pattern reveals that formation of the XB complex results in dramatic lowering of the HOI bending fundamental frequency and elongation of the O-I bond (by 168 cm^-1 and 0.13 Å, respectively, relative to isolated HOI). The frequency of the O-I stretch (estimated 436 cm^-1) is also encoded in the spectrum by the weak v = 0 → 2 overtone transition at 872 cm^-1.

Phosphine Oxides as Spectroscopic Halogen Bond Descriptors: IR and NMR Correlations with Interatomic Distances and Complexation Energy

An extensive series of 128 halogen-bonded complexes formed by trimethylphosphine oxide and various F-, Cl-, Br-, I- and At-containing molecules, ranging in energy from 0 to 124 kJ/mol, is studied by DFT calculations in vacuum. The results reveal correlations between R–X⋅⋅⋅O=PMe₃ halogen bond energy ΔE, X⋅⋅⋅O distance r, halogen’s σ-hole size, QTAIM parameters at halogen bond critical point and changes of spectroscopic parameters of phosphine oxide upon complexation, such as ³¹P NMR chemical shift, ΔδP, and P=O stretching frequency, Δν. Some of the correlations are halogen-specific, i.e., different for F, Cl, Br, I and At, such as ΔE(r), while others are general, i.e., fulfilled for the whole set of complexes at once, such as ΔE(ΔδP). The proposed correlations could be used to estimate the halogen bond properties in disordered media (liquids, solutions, polymers, glasses) from the corresponding NMR and IR spectra.

Crystal Engineering with Multipoint Halogen Bonding: Double Two-Point Donors and Acceptors at Work

The combination of singly or doubly bidentate halogen-bond donors with double bidentate acceptors was investigated as a supramolecular synthon in crystal engineering. The crystal topologies obtained feature novel halogen-bonding motifs like double two-point recognition and infinite chains or networks based on two-point interactions. Induced conformational changes in the double bidentate halogen-bond donors could be exploited to obtain different 1D and 2D networks. All solid-state studies were accompanied by DFT calculations to predict and rationalize the outcome.

Halide anion discrimination by a tripodal hydroxylamine ligand in gas and condensed phases

Electrospray ionization of solutions containing a tripodal hydroxylamine ligand, H3TriNOx ([((2-tBuNOH)C6H4CH2)3N]) denoted as L, and a hydrogen halide HX: HCl, HBr and/or HI, yielded gas-phase anion complexes [L(X)]- and [L(HX2)]-. Collision induced dissociation (CID) of mixed-halide complexes, [L(HXaXb)]-, indicated highest affinity for I- and lowest for Cl-. Structures and energetics computed by density functional theory are in accord with the CID results, and indicate that the gas-phase binding preference is a manifestation of differing stabilities of the HX molecules. A high halide affinity of [L(H)]+ in solution was also demonstrated, though with a highest preference for Cl- and lowest for I-, the opposite observation of, but not in conflict with, what is observed in gas phase. The results suggest a connection between gas- and condensed-phase chemistry and computational approaches, and shed light on the aggregation and anion recognition properties of hydroxylamine receptors.

Investigation of activation energies for dissociation of host-guest complexes in the gas phase using low-energy collision induced dissociation

A low-energy collision induced dissociation (CID) (low-energy CID) approach that can determine both activation energy and activation entropy has been used to evaluate gas-phase binding energies of host-guest (H-G) complexes of a heteroditopic hemicryptophane cage host (Zn (II)@1) with a series of biologically relevant guests. In order to use this approach, preliminary calibration of the effective temperature of ions undergoing resonance excitation is required. This was accomplished by employing blackbody infrared radiative dissociation (BIRD) which allows direct measurement of activation parameters. Activation energies and pre-exponential factors were evaluated for more than 10 H-G complexes via the use of low-energy CID. The relatively long residence time of the ions inside the linear ion trap (maximum of 60 s) allowed the study of dissociations with rates below 1 s^-1 . This possibility, along with the large size of the investigated ions, ensures the fulfilment of rapid energy exchange (REX) conditions and, as a consequence, accurate application of the Arrhenius equation. Compared with the BIRD technique, low-energy CID allows access to higher effective temperatures, thereby permitting one to probe more endothermic decomposition pathways. Based on the measured activation parameters, guests bearing a phosphate (-OPO₃ ^2- ) functional group were found to bind more strongly with the encapsulating cage than those having a sulfonate (-SO₃ ^- ) group; however, the latter ones make stronger bonds than those with a carboxylate (-CO₂ ^- ) group. In addition, it was observed that the presence of trimethylammonium (-N(CH₃ )₃ ⁺ ) or phenyl groups in the guest's structure improves the strength of H-G interactions. The use of this technique is very straightforward, and it does not require any instrumental modifications. Thus, it can be applied to other H-G chemistry studies where comparison of bond dissociation energies is of paramount importance.

Endo or Exo? Structures of Gas-Phase Alkali Metal Cation/Aromatic Half-Belt Complexes

1,1,9,9-Tetramethyl[9](2,11)teropyrenophane (TM9TP), a belt-shaped molecule, has a sizable cavity that molecules or ions could occupy. In this study, the question of whether TM9TP forms gas-phase ion-molecule complexes with metal cations (K⁺ , Rb⁺ , Cs⁺ ) situated inside or outside the TM9TP cavity was addressed using both experimental and computational methods. Complexes were trapped in a Fourier transform ion cyclotron resonance mass spectrometer and their structures were explored by some novel physical chemistry/mass spectrometry methods. Blackbody infrared radiative dissociation kinetics reveal two populations of ions, a fast dissociating fraction and a persistent fraction. Infrared multiphoton dissociation spectra (vibrational spectra) provide very strong evidence that the most abundant population is a complex where the metal cation is inside the TM9TP cavity, endo-TM9TP. Red-shifted C-H stretching bands present in the gas-phase vibrational spectra of these ionic complexes show that there is an interaction between the metal cation and bridge C-H bonds due to the cation sitting inside the cavity of TM9TP. B3LYP/6-31+G(d,p) calculations showed the endo complexes to be the lowest in energy; about 60 kJ mol^-1 more thermodynamically stable and more than 120 kJ mol^-1 kinetically more stable than the exo complex.

Halogen bonding two-point recognition with terphenyl derivatives

Neutral terphenyl-based halogen bond donors form two-point halogen bonding motifs with oxadiazoles in the solid state.

The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N-H and O-H stretching region and computational methods

IRMPD spectroscopy and computational chemistry techniques have been used to determine that the proton- and sodium-bound dimers of proline exist as a mixture of a number of different structures. Simulated annealing computations were found to be helpful in determining the unique structures of the protonated and sodiated dimers, augmenting chemical intuition. The experimental and computational results are consistent with the proton-bound dimer of N-protonated proline bound to zwitterionic proline. There was no spectroscopic evidence in the 3200-3800 cm(-1) region for a canonical structure which is predicted to have a weak N-H stretch at about 3440 cm(-1). A well resolved band at 1733 cm(-1) from a previous spectroscopic study (DOI: 10.1021/ja068715a ) was reassigned from a high energy canonical isomer to the C=O stretch of a lower energy zwitterionic structure. This band is a free carboxylate C=O stretch where protonated proline is hydrogen bonded to the other carboxylate oxygen which is also involved in an intramolecular hydrogen bond. Fifteen structures of the sodium bound proline dimer were computed to be within 10 kJ mol(-1) of Gibbs energy and eight structures were within 5 kJ mol(-1). None of these structures can be ruled out based on the experimental IRMPD spectrum. They all have an N-H stretching band predicted in a position that agrees with the experimental spectrum. However, only structures where one of the proline monomers is in the canonical form and having a free O-H bond can produce the band at ∼3600 cm(-1).

Halogen bonds with coordinative nature: halogen bonding in a S–I+–S iodonium complex

A thorough characterization of unusually strong I⁺–S halogen bonds indicates that halogen bonding is not merely an electrostatic contact but also has a strong coordinative nature, thus expanding the scope of halogen bonding.

Potent affinity material for tracing acetone and related analytes based on molecular recognition by halogen bonds

A helping third hand converts halogen bonds into a superior recognition tool.

Superior perrhenate anion recognition in water by a halogen bonding acyclic receptor

The first example of perrhenate anion binding and fluorescence sensing in water by a halogen bond donor is reported.

Halogen bonding of electrophilic bromocarbons with pseudohalide anions

Spectral, thermodynamic and structural features of the complexes of bromocarbons with polydentate azide, cyanate or thiocyanate anions are presented. They suggest a significant role of the molecular-orbital interactions in formation of these halogen-bonded associates.