X-ray crystal structure, vibrational spectra and DFT calculations of 3-chloro-7-azaindole: a case of dual N-H⋯N hydrogen bonds in dimers

Insights into the spontaneity of hydrogen bond formation between formic acid and phthalimide derivatives

We evaluated a group of phthalimide derivatives, which comprise a convenient test set for the study of the multiple factors involved in the energetics of hydrogen bond formation. Accordingly, we carried out quantum chemical calculations on the hydrogen bonded complexes formed between a sample of phthalimide derivatives with formic acid with the intent of identifying the most important electronic and structural factors related to how their strength and spontaneity vary across the series. The geometries of all species considered were fully optimized at DFT B3LYP/6-31++G(d,p), RM1, RM1-DH2, and RM1-D3H4 level, followed by frequency calculations to determine their Gibbs free energies of hydrogen bond formation using Gaussian 2009 and MOPAC 2012. Our results indicate that the phthalimide derivatives that form hydrogen bond complexes most favorably, have in their structures only one C=O group and at least one NH group. On the other hand, the phthalimide derivatives predicted to form hydrogen bonds least favorably, possess in their structures two carbonyl groups, C=O, and no NH group. The ability to donate electrons and simultaneously receive one acidic hydrogen is the most important property related to the spontaneity of hydrogen bond formation. We further chose two cyclic compounds, phthalimide and isoindolin-1-one, in which to study the main changes in molecular, structural and spectroscopic properties as related to the formation of hydrogen bonds. Thus, the greatest ability of the isoindolin-1-one compound in forming hydrogen bonds is evidenced by the larger effect on the structural, vibrational, and chemical shifts properties associated with the O-H group. In summary, the electron-donating ability of the hydrogen bond acceptor emerged as the most important property differentiating the spontaneity of hydrogen bond formation in this group of complexes.

DFT study and topological analysis of the bonding in DNA Hoogsteen-type base pairs

The purpose of our work is to characterize and present a theoretical comparative study of a variety of compounds based on DNA base pairs linked with some transition metal ions in gas phase: C–M–G (Cytosine–metal–Guanine) where [Formula: see text](I), Zn(II), Cd(II) and A–M–T (Adenine–metal–Thyminate) where [Formula: see text](II), Ru(I), Ni(I), Y(II), Zn(I), Cd(I), Cu(II). Geometry optimization and frequency calculations were carried out at DFT/ZORA/BLYP-D/TZ2P level. M–N and M–O bonds were investigated with the quantum chemical topology (QCT): Quantum theory of atoms in molecules (QTAIM) and electron localization functions (ELF). The hydrogen bonds: N10–H[Formula: see text]O7 for A–M–T complexes and N7–H[Formula: see text]O10 for C–M–T ones were visualized and discussed, QTAIM and ELF prove the existence of O7–H[Formula: see text]N10 hydrogen bond for some A–M–T systems, since the bond critical point (BCP) of N7–H having [Formula: see text], so it has a covalent character confirming the existence of a tautomer process of these complexes. Bonding energy [Formula: see text], Pauli repulsion [Formula: see text], electrostatic [Formula: see text], and orbital [Formula: see text] interactions were represented and compared together. Hirschfeld’s charges showed the existence of charge transfer process in the bridge moieties. It seems that, in contrast to natural base pairs that are stabilized by hydrogen bonding, Hoogsteen-type base pairs are held together by coordinative bond with metal ions.