On Aromaticity of the Aromatic α-Amino Acids and Tuning of the NICS Indices to Find the Aromaticity Order

The σ+π dual aromaticity of typical bi-tetrazole ring molecule TKX-50

Two complexes of dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) were employed to evaluate the aromaticity of their tetrazole rings via deep analysis such as the electronic structure, the ZZ component of the natural chemical shielding tensor (NICSZZ) and component orbitals, localized orbital locator purely contributed by σ-orbitals (LOL-σ) and localized orbital locator purely contributed by π-orbitals (LOL-π), the anisotropy of the induced current density (AICD) and the ZZ component of iso-chemical shielding surface (ICSSZZ) of these tetrazole rings thereof. The conclusion shows: that all tetrazole rings and bi-tetrazole rings in complexes have strong σ and a comparable strength π double aromaticity; all these magnetic shields almost symmetrically increase from the central axis to the tetrazole ring atoms; tetrazole rings in complex II show a little stronger dual aromaticity than that in complex I mainly due to the different orientation of the fragment 2 encompassing two hydroxylamine groups resulting in different effects on the contributions of σ orbitals and π orbitals to total aromaticity of tetrazole rings thereof; the difference in aromaticity is fundamentally caused by the atoms O with stronger electron-withdrawing than atom N in fragment 2 interact with bi-tetrazole ring through O in complex I but through N in complex II.

HOMA Index Establishes Similarity to a Reference Molecule

The article shows that the definition of the HOMA index of geometrical aromaticity satisfies the axioms of a similarity function between the examined and benzene ring. Consequently, for purely mathematical reasons, the index works exceptionally well as an index of aromaticity: it expresses a geometric similarity to the archetypal aromatic benzene. Thus, if the molecule is geometrically similar to benzene, then it is also chemically similar, and therefore, it is aromatic. However, the similarity property legitimizes using the HOMA-like indices to express similarity to molecules other than benzene, whether cyclic or linear and existing or hypothetical. The paper demonstrates an example of HOMA-similarity to cyclohexane, which expresses a (relaxed)-saturicity property not accompanied by strong structural strains or steric hindrances. Further, it is also shown that the HOMA index can evaluate the properties of whole molecules, such as 25 unbranched catacondensed isomers of hexacene. The index exhibits a significant quadratic correlation with the total energy differences of planar isomers from which the nonplanar ones deviate. Moreover, the HOMA index of hexacene isomers significantly correlates with the Kekulé count connected to the resonance energy in the Hückel approximation. As a result, the study shows that the HOMA index can be used not only for aromaticity analyses but also as a general chemical descriptor applicable to rings, chains, composed molecular moieties, or even whole molecules.

On Integral INICS Aromaticity of Pyridodiazepine Constitutional Isomers and Tautomers

The structure, energetics, and aromaticity of c.a. 100 constitutional isomers and tautomers of pyrido[m,n]diazepines (m = 1, 2; n = 2, 3, 4, 5; m ≠ n) were studied at the B3LYP/cc-pVTZ level. The pyrido[1,3]diazepines appear the most, while pyrido[2,4]diazepines are the least stable (ca. 26 kcal/mol). In the pyrido[1,n]diazepine group (n = 2-5), the [1,5] isomers are higher in energy by ca. 4.5 kcal/mol and the [1,4] ones by ca. 7 kcal/mol, and the pyrido[1,2]diazepines are the least stable (ca. 20 kcal/mol). All the most stable pyrido[1,n]diazepines have N-atoms near the ring's junction bond but on opposite sites. The most stable [2,n]-forms are also those with the pyridine ring N6-atom near the junction bond. Surprisingly, for the [1,2]-, [1,3]-, and [1,4]-isomer condensation types of pyridine and diazepine rings, the same N9 > N7 > N6 > N8 stability pattern obeys. The stability remains similar in a water medium simulated with the Polarizable Continuum Model of the solvent and is conserved when calculated using the CAM-B3LYP or BHandHlyp functionals. The ring's aromaticity in the pyridine[m,n]diazepines was established based on the integral INICS index resulting from the NICSzz-scan curves' integration. The integral INICS index is physically justified through its relation to the ringcurrent as demonstrated by Berger, R.J.F., et al. Phys. Chem. Chem. Phys. 2022, 24, 624. The six-membered pyrido rings have negative INICSZZ indices and can be aromatic only if they are not protonated at the N-atom. All protonated pyrido and seven-membered rings exhibit meaningful positive INICSZZ values and can be assigned as antiaromatic. However, some non-protonated pyrido rings also have substantial positive INICSZZ indices and are antiaromatic. A weak linear correlation (R2 = 0.72) between the INICSZZ values of the pyridine I(6) and diazepine I(7) rings exists and is a consequence of the communication between the π-electron systems of the two rings. The juxtaposition of the INICS descriptor of the six- and seven-membered rings and diverse electron density parameters at the Ring Critical Points (RCP) revealed good correlations only with the Electrostatic Potentials from the electrons and nuclei (ESPe and ESPn). The relationships with other RCP parameters like electron density and its Laplacian, total energy, and the Hamiltonian form of kinetic energy density were split into two parts: one nearly constant for the six-membered rings and one linearly correlating for the seven-membered rings. Thus, most of the electron density parameters at the RCP of the six-membered rings of pyridodiazepines practically do not change with the diazepine type and the labile proton position. In contrast, those of the seven-membered rings display aromaticity changes in the antiaromatic diazepine with its ring structural modifications.

Elucidating the Racemization Mechanism of Aliphatic and Aromatic Amino Acids by In Silico Tools

The racemization of biomolecules in the active site can reduce the biological activity of drugs, and the mechanism involved in this process is still not fully comprehended. The present study investigates the impact of aromaticity on racemization using advanced theoretical techniques based on density functional theory. Calculations were performed at the ωb97xd/6-311++g(d,p) level of theory. A compelling explanation for the observed aromatic stabilization via resonance is put forward, involving a carbanion intermediate. The analysis, employing Hammett's parameters, convincingly supports the presence of a negative charge within the transition state of aromatic compounds. Moreover, the combined utilization of natural bond orbital (NBO) analysis and intrinsic reaction coordinate (IRC) calculations confirms the pronounced stabilization of electron distribution within the carbanion intermediate. To enhance our understanding of the racemization process, a thorough examination of the evolution of NBO charges and Wiberg bond indices (WBIs) at all points along the IRC profile is performed. This approach offers valuable insights into the synchronicity parameters governing the racemization reactions.