Analysis of weak interactions involving organic fluorine: Insights from packing features in substituted 4-keto-tetrahydroindoles

Close Amide NH···F Hydrogen Bonding Interactions in 1,8-Disubstituted Naphthalenes

In this note, we present a series of N-(8-fluoronaphthalen-1-yl)benzamide derivatives designed to maximize amide-NH···F hydrogen bond interactions therein. A combination of IR and NMR spectroscopy indicates a linear correlation between the high energy shift in NH stretching frequency and the electron withdrawing nature of the substituent, consistent with the trend predicted by DFT calculations. Additionally, a limiting case of hydrogen bonding is observed when the benzamide derivatives are replaced with trifluoroacetamide, causing an additional red shift of 44 cm^-1 in the NH stretching frequency. Most importantly, ¹H-¹⁹F coupling constants in this series are among the largest measured for amide-NH···F interactions. X-ray crystallography reveals face-to-face alignment of naphthalene rings in these derivatives resulting in part from the NH···F hydrogen bonds. This motif also dictates the formation of sheets composed of stacked naphthalene rings in the crystal structure as opposed to unfluorinated analogues wherein NH···OC hydrogen-bonding interactions force benzamide and naphthalene rings to engage in T-shaped π-π interactions instead. Additionally, the NH proton in the trifluoroacetamide derivative engages in extended H-bond interactions in its crystal structure.

Fluorine bonding enhances the energetics of protein-lipid binding in the gas phase

This paper reports on the first experimental study of the energies of noncovalent fluorine bonding in a protein-ligand complex in the absence of solvent. Arrhenius parameters were measured for the dissociation of gaseous deprotonated ions of complexes of bovine β-lactoglobulin (Lg), a model lipid-binding protein, and four fluorinated analogs of stearic acid (SA), which contained (X =) 13, 15, 17, or 21 fluorine atoms. In all cases, the activation energies (E(a)) measured for the loss of neutral XF-SA from the (Lg + XF-SA)⁷⁻ ions are larger than for SA. From the kinetic data, the average contribution of each > CF₂ group to E(a) was found to be ~1.1 kcal mol⁻¹, which is larger than the ~0.8 kcal mol⁻¹ value reported for > CH₂ groups. Based on these results, it is proposed that fluorocarbon–protein interactions are inherently stronger (enthalpically) than the corresponding hydrocarbon interactions.

The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates

The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.

New copper(II)-radical one dimensional chain: Synthesis, crystal structure, EPR, magnetic properties and DFT calculations

The novel chain compound [Cu(Phtfac)(2)(NITpPy)](n) (where NITpPy = 4-pyridyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide and Phtfac = 4,4,4-trifluoro-1-phenylbutane-1,3-dione) was synthesized and characterized structurally, magnetically and by EPR. The compound contains two non equivalent Cu(II) ions, Cu1 and Cu2, located at inversion centers and bridged by a NITpPy ligand coordinating Cu1 through the pyridine donor atom, and Cu2 through a N-O group, resulting in a head-to-head chain structure. The chain exhibits an unusual spin topology with two alternating pairs of magnetic coupling constants. The magnetic behavior was modeled considering a 16-membered ring with alternating exchange couplings. The best fit parameters indicate a ferromagnetic (J(1) = 29.4 cm(-1)), and antiferromagnetic (J(2) = -4.6 cm(-1)) couplings and an average g = 2.05, corresponding to a ground state with three parallel and one anti-parallel spin for each Cu(2)NITpPy(2) unit. DFT calculations allowed assigning the ferromagnetic coupling to Cu-O-NITpPy and the antiferromagnetic coupling to Cu-N(Py)-NITpPy. Single crystal EPR spectra display only one resonance for most field orientations, as a consequence of the collapse of the signals of the different spins produced by the exchange interactions. The observed g-tensor of this resonance is related to those expected for the Cu(II) and radical ions. Comparison of this compound with other Cu-NIT radicals chains bearing different substituents in the organic radicals, highlights that the beta-diketonate ligand plays an important role in determining the final architecture. Moreover, we show how a knowledge of the spin density distribution in the initial building blocks is essential to rationalize the magnetic behavior of the resulting product.