On the Importance of Halogen Bonding Interactions in Two X-ray Structures Containing All Four (F, Cl, Br, I) Halogen Atoms

Abstract

This manuscript reports the synthesis and X-ray characterization of two octahydro-1H-4,6-epoxycyclopenta[c]pyridin-1-one derivatives that contain the four most abundant halogen atoms (Ha) in the structure with the aim of studying the formation of Ha···Ha halogen bonding interactions. The anisotropy of electron density at the heavier halogen atoms provokes the formation of multiple Ha···Ha contacts in the solid state. That is, the heavier Ha-atoms exhibit a region of positive electrostatic potential (σ-hole) along the C–Ha bond and a belt of negative electrostatic potential (σ-lumps) around the atoms. The halogen bonding assemblies in both compounds were analyzed using density functional theory (DFT) calculations, molecular electrostatic potential (MEP) surfaces, the quantum theory of “atom-in-molecules” (QTAIM), the noncovalent interaction plot (NCIplot), and the electron localization function (ELF).

Combined crystallographic and computational investigation of the solvent disorder present in a new tipiracil hydrochloride methanol solvate–hydrate

“…37 The dissociation energy of the Cl⋯O contact is 2.5 kcal mol −1 , in line with previous computations of halogen bonding interactions. 38 This interaction is weaker than the conventional HBs but stronger than the CH⋯O contacts. Total formation energy of the assembly shown in Fig.…”

Oxalic Acid, a Versatile Coformer for Multicomponent Forms with 9-Ethyladenine

“…The experimental crystallographic coordinates have been used to evaluate the interactions in the solid state. This level of theory and methodology was used before to investigate similar interactions [32][33][34][35]. The Bader's quantum theory of "Atoms in molecules" (QTAIM) [36] and the noncovalent interaction index (NCIPlot) index [37] methods were used to characterize the hydrogen bonding interactions by means of the AIMall program [38].…”

On the reliability of atoms in molecules, noncovalent index, and natural bond orbital to identify and quantify noncovalent bonds

“…For example, it is common in the literature to consider the bond critical point density as a measure of bond strength [23][24][25][26][27] and possibly even with spectroscopic perturbations. 28 In an alternate scheme, the energies of some of these bonds are sometimes assessed via a simple relationship with the potential energy density 24,[29][30][31] or other quantities extracted from AIM analysis. 24,27,[32][33][34] It would indeed be comforting for analysis of noncovalent bonds if the methods indicated above provided definitive indicators of the presence of such a bond, and if the data could be treated in a quantitative manner to compare strengths of such bonds.…”

“…For example, it is common in the literature to consider the bond critical point density as a measure of bond strength 23–27 and possibly even with spectroscopic perturbations 28 . In an alternate scheme, the energies of some of these bonds are sometimes assessed via a simple relationship with the potential energy density 24,29–31 or other quantities extracted from AIM analysis 24,27,32–34 …”