Theoretical treatment of IO-X (X = N2, CO, CO2, H2O) complexes

Iodine monoxide (IO) is an important component of the biogeochemical cycle of iodine. For instance, it is present in the troposphere, where it plays a crucial role in the physical chemical processes involving iodine containing compounds. Here, we present a theoretical study on a series of atmospherically relevant complexes of IO with N₂, CO, CO₂ and H₂O, where their structural and spectroscopic properties and their interaction energies are computed. Calculations are carried out by means of ab initio post Hartree-Fock (RCCSD(T) and RMP2) methods and density functional theory DFT (PBE0 and M05-2X) based approaches with and without the inclusion of dispersion correction. After comparison to RCCSD(T), we highlight the good performance of M05-2X(+D3) DFT in describing the bonding between IO and X (X = N₂, CO, CO₂, H₂O). Moreover, we found that the IO-X (X = N₂, CO, CO₂, H₂O) complexes are formed by non-covalent interactions between the two monomers. In sum, we characterized two types of complexes: I-bonded and O-bonded, where the former is more stable. The atmospheric implications of the present findings are also discussed such as in the formation of the iodine oxide particles (IOPs).

Hybrid Molecular Dynamics for Elucidating Cooperativity Between Halogen Bond and Water Molecules During the Interaction of p53-Y220C and the PhiKan5196 Complex

The cooperativity between hydrogen and halogen bonds plays an important role in rational drug design. However, mimicking the dynamic cooperation between these bonds is a challenging issue, which has impeded the development of the halogen bond force field. In this study, the Y220C–PhiKan5196 complex of p53 protein was adopted as a model, and the functions of three water molecules that formed hydrogen bonds with halogen atoms were analyzed by the simulation method governed by the hybrid quantum mechanical/molecular mechanical molecular dynamics. A comparison with the water-free model revealed that the strength of the halogen bond in the complex was consistently stronger. This confirmed that the water molecules formed weak hydrogen bonds with the halogen atom and cooperated with the halogen atom to enhance the halogen bond. Further, it was discovered that the roles of the three water molecules were not the same. Therefore, the results obtained herein can facilitate a rational drug design. Further, this work emphasizes on the fact that, in addition to protein pockets and ligands, the role of voids should also be considered with regard to the water molecules surrounding them.

On the ability of pnicogen atoms to engage in both σ and π-hole complexes. Heterodimers of ZF2C6H5 (Z = P, As, Sb, Bi) and NH3

When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH₃ base lies opposite one F atom. In addition to this σ-hole complex, the ZF₂C₆H₅ molecule can distort in such a way that the NH₃ approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4-13 kcal/mol. On the other hand, this large interaction energy is countered by the considerable deformation energy required for the Lewis acid to adopt the geometry necessary to form the π-hole complex. The overall energetics of the complexation reaction are thus more exothermic for the σ-hole dimers than for the π-hole dimers.

Competition between tetrel bond and pnicogen bond in complexes of TX3-ZX2 and NH3

The complexes formed between TX₃-ZX₂ (T = C, Si, Ge; Z = P, As, Sb; X = F, Cl) and NH₃ were studied at the MP2/aug-cc-pVTZ(PP) level. For each TX₃-ZX₂, two types of complex were obtained. For CX₃-ZX₂, NH₃ is inclined to approach the σ-hole on the Z atom, forming a pnicogen bond. For TX₃-ZX₂ (T = Si and Ge), however, the base favors engaging in a tetrel bond with the σ-hole on the T atom although the corresponding pnicogen-bonded complex is also stable. When NH₃ approaches the CX₃ terminal of CX₃-ZX₂, weak interactions are observed that may be classified as van der Waals interactions. The relative stability of both types of complexes is not affected by the substituent X. The tetrel bond is very strong and the largest interaction energy is up to -144 kJ mol^-1. Dispersion is dominant in the weak van der Waals complexes, while tetrel- and pnicogen-bonded complexes are dominated by electrostatic interactions, with comparable contributions from polarization.

Substituent effect of the stacking interaction between carbon monoxide and benzene

Noncovalent interactions (NCIs) between carbon monoxide and substituted benzene were investigated at the M06-2X/6-311++G(d,p) level. rThe results of interaction energy analysis indicated different effects for the electron-donating (-NH₂, -OH, -CH₃) and electron-withdrawing (-F, -CN, -NO₂) groups on the CO⋯PhX complex. Atoms in molecules analysis confirmed the NCIs between CO and PhX. NCI analysis revealed that these interactions belong to van der Waals interactions. The electron density shift of the complexes was investigated with electron density difference analysis. Ternary CO⋯PhX⋯Bz complexes were designed to study the interplay between CO⋯π and π⋯π stacking interactions.

Intermolecular interactions between σ- and π-holes of bromopentafluorobenzene and pyridine: computational and experimental investigations

The characters of σ- and π-holes of bromopentafluorobenzene (C6F5Br) enable it to interact with an electron-rich atom or group like pyridine which possesses an electron lone-pair N atom and a π ring. Theoretical studies of intermolecular interactions between C6F5Br and C5H5N have been carried out at the M06-2X/aug-cc-pVDZ level without and with the counterpoise method, together with single point calculations at M06-2X/TZVP, wB97-XD/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels. The σ- and π-holes of C6F5Br exhibiting positive electrostatic potentials make these sites favorably interact with the N atom and the π ring of C5H5N with negative electrostatic potentials, leading to five different dimers connected by a σ-holen bond, a σ-holeπ bond or a π-holeπ bond. Their geometrical structures, characteristics, nature and spectroscopy behaviors were systematically investigated. EDA analyses reveal that the driving forces in these dimers are different. NCI, QTAIM and NBO analyses confirm the existence of intermolecular interactions formed via σ- and π-holes of C6F5Br and the N atom and the π ring of C5H5N. The experimental IR and Raman spectra gave us important information about the formation of molecular complexes between C6F5Br and C5H5N. We expect that the results could provide valuable insights into the investigation of intermolecular interactions involving σ- and π-holes.

Computational investigations of intermolecular interactions between electron-accepting bromo- and iodo-pentafluorobenzene and electron-donating furan and thiophene

C₆F₅X (X = Br, I) exhibits intriguing σ- and π-hole characters, which enable it to accept electrons from the electron-rich atoms or groups in C₄H₄O and C₄H₄S via various intermolecular interactions.

Interactions between haloperfluorobenzenes and fluoranthene in luminescent cocrystals from π-hole⋯π to σ-hole⋯π bonds

From π-hole⋯π to σ-hole⋯π bonds between haloperfluorobenzenes and fluoranthene in luminescent cocrystals.