Intrinsic Dynamic Nature of Neutral Hydrogen Bonds Elucidated with QTAIM Dual Functional Analysis: Role of the Compliance Force Constants and QTAIM-DFA Parameters in Stability

Intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs and its behavior, elucidated with QTAIM dual functional analysis and QC calculations

The intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs (Nu-Nu') is elucidated with QTAIM dual functional analysis (QTAIM-DFA). Perturbed structures generated using coordinates derived from the compliance constants (C ii ) are employed for QTAIM-DFA. The method is called CIV. Two, three, or four HBs are detected for Nu-Nu'. Each HB in Nu-Nu' is predicted to have the nature of CT-TBP (trigonal bipyramidal adduct formation through charge transfer (CT)), CT-MC (molecular complex formation through CT), or t-HBwc (typical HB with covalency), while the vdW nature is predicted for the C-H⋯X interactions, for example. Energies for the formation of the pairs (ΔE) are linearly correlated with the total values of C ii -1 in Nu-Nu'. The total C ii -1 values are obtained by summing each C ii -1 value, similarly to the case of Ohm's law for the parallel connection in the electric resistance. The total ΔE value for a nucleobase pair could be fractionalized to each HB, based on each C ii -1 value. The perturbed structures generated with CIV are very close to those generated with the partial optimization method, when the changes in the interaction distances are very small. The results provide useful insights for better understanding DNA processes, although they are highly enzymatic.

Nature of intramolecular O-H⋯π interactions as elucidated by QTAIM dual functional analysis with QC calculations

The intrinsic dynamic and static nature of intramolecular OH-*-π interactions is elucidated using a QTAIM dual functional analysis (QTAIM-DFA) after clarifying the structural features. Asterisks (*) are employed to emphasize the presence of bond critical points (BCPs) on the bond paths (BPs), which correspond to the interactions in question. Data from the fully optimized structures correspond to the static nature of the interactions. In our treatment, data from the perturbed structures, which are based around the fully optimized structure, are employed for the analysis in addition to those from the fully optimized structure, which represent the dynamic nature of the interaction. Seven intramolecular OH-*-C(π) interactions were detected in six-membered rings, with six BPs and BCPs for each, among the 72 conformers of the species examined here (1-15). The interactions are predicted to have a vdW or t-HBnc (typical hydrogen bonds with no covalency) nature, which appeared in the pure closed shell region. They appear to be stronger than the corresponding intermolecular interactions. Nine BPs with BCPs were also detected for the intramolecular O-*-X interactions (X = C(π) and H(π), joined to C(π)) in the 5-7-membered rings. The E(2) values of the interactions, as obtained by NBO, are discussed in relation to the stabilities of the conformers and the BPs with BCPs.

The nature of G⋯E–Y σ(3c–4e) in o-MenGCH2C6H4EY (MenG = Me2N and MeE; E = O, S, Se and Te; Y = F, Cl, Br, EMe and Me) with contributions from CT and compliance constants in noncovalent G⋯E interactions

The intrinsic dynamic and static nature of G–*–E–*–Y σ(3c–4e) interactions was elucidated with the quantum theory of atoms in molecules dual functional analysis (QTAIM-DFA), employing o-Me_nGCH₂C₆H₄EY (Me_nG = Me₂N and MeE; E = O, S, Se and Te; Y = F, Cl, Br, I, EMe and Me). Asterisks (*) are employed to emphasize the existence of bond critical points (BCPs) on the bond paths (BPs), corresponding to the interactions in question. Data from the fully optimized structure correspond to the static nature of interactions. The dynamic nature is called the intrinsic dynamic nature if the perturbed structures are generated using the coordinates derived from the compliance constants. Basis sets of the Sapporo-TZP type with diffusion functions are employed for the heteroatoms at the MP2 level. The noncovalent G–*–E interactions in GEY σ(3c–4e) are predicted to demonstrate van der Waals bonding to CT-TBP (trigonal bipyramidal adduct formation through charge transfer) nature, while the E–*–Y bonds have the covalent nature. Some E–F bonds show strong ionic character when G–*–E is predicted to be stronger than E–*–Y. The contributions of the CT terms to the G–*–E interactions, evaluated with NBO, are discussed in relation to the predicted nature. The E(2) values based on NBO are strongly correlated to the compliance constants for the G–*–E interactions if suitably treated separately.

The nature of E⋯E′ in 1-RECH₂-2-R′E′C₆H₄ (E/E′ = O, S, Se and Te) is clarified with QTAIM approach and NBO analysis, after structural determinations.