HOMA Index Establishes Similarity to a Reference Molecule

Abstract

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.

Unveiling the Intermolecular Interactions between Drug 5-Fluorouracil and Watson–Crick/Hoogsteen Base Pairs: A Computational Analysis

“…To realize the charge transfer between the base pair and the 5FU drug and to identify the other intermolecular interactions that are accountable for stabilization, we carried out the electron density difference (EDD), quantitative molecular electrostatic potential (MESP), atoms in molecules (AIM) analysis, noncovalent interaction–reduced density gradient (NCI–RDG) analysis, and energy density decomposition (EDA) analysis . It has been well documented that H-bonding interactions increase the cyclic 4 n + 2π electron delocalization and boost aromaticity.…”

“…To realize the charge transfer between the base pair and the 5FU drug and to identify the other intermolecular interactions that are accountable for stabilization, we carried out the electron density difference (EDD), 67 quantitative molecular electrostatic potential (MESP), 68 atoms in molecules (AIM) analysis, 69 noncovalent interaction–reduced density gradient (NCI–RDG) analysis, 70 and energy density decomposition (EDA) analysis. 71 It has been well documented that H-bonding interactions increase the cyclic 4 n + 2π electron delocalization and boost aromaticity. Hence, we have computed the harmonic oscillator model of aromaticity (HOMA) and nucleus-independent chemical shifts (NICS) analysis for the nucleobase pairs and compared it with the 5FU–nucleobase pair complexes to understand how the H-bonding between 5FU and nucleobases affect the bonding between nucleobase pairs.…”

COMPAS-3: a dataset of peri-condensed polybenzenoid hydrocarbons

“…33,34 Nonetheless, certain aspects of their structure–property relationships remain poorly understood, which impedes rational design of improved PBH-based candidates. Recent reports on the synthesis 35–38 and characterization of challenging PBHs and on computational developments 39–42 aimed at further elucidation of their properties underline the ongoing interest in PBH systems and the importance of obtaining reliable and useful data for them.…”