Abstract
The problem of aromaticity in heterocyclic rings of uracil and its 5-halogenoderivatives (5XU) was analyzed theoretically by calculating modified harmonic oscillator model of aromaticity (HOMA) for Heterocycle Electron Delocalization (HOMHED), nucleus-independent chemical shift parameters (NICS) and the so-called scan experiments, using helium-3 atom as a magnetic probe. The impact of halogen electronegativity on C5 atom’s NBO charges was also investigated. Water, as a polar environment, has a negligible impact on 5XU aromaticity. The most stable diketo tautomer shows a very low aromaticity while the “rare” dihydroxy form (tautomer No 6) is aromatic and resembles benzene. This is in agreement with traditional drawing of chemical formula of uracil’s six-membered ring, directly showing three alternating single and double bonds in its tautomer No 6. No good correlation between magnetic and geometric indexes of aromaticity for the studied 5XU tautomers was found. Linear correlation between the magnitude of NICS minimum, as well as the distance of the minimum above uracil ring plane center from 3He NMR chemical shift scan plot with respect to halogen electronegativity were observed. A strong linear dependence of magnetic index of aromaticity and the electronegativity of 5X substituent was observed.
Highlights
Uracil is an important component of living systems and belongs to small molecules which are responsible for information transfer [1]
On the basis of theoretical modeling using density functional theory (DFT at B3LYP-D3/aug-ccpVQZ level of theory), it was postulated [5] that mutual arrangement of local C=O and N-H functional groups in uracil, as well as in 1,3-diazines, influences the electron density and local dipole moments distribution in such a way that it is energetically more favorable than in both 1,2- and 1,4diazines
Stability of many organic molecules is often related to aromaticity [6,7,8,9,10]
Summary
Uracil is an important component of living systems and belongs to small molecules which are responsible for information transfer [1]. Detection of the occurrence of uracil and pyrimidine in space [2] indirectly supports the fact that such molecules, containing two nitrogen atoms in a six-membered ring are stable and present in both extraterrestrial space matter and in living systems. Stability of many organic molecules is often related to aromaticity [6,7,8,9,10]. Among them are cyclic organic compounds, with double bonds and heteroatoms with lone electron pairs included in their structure, which could be aromatic. There are two commonly used theoretical indexes of aromaticity, the geometric one (HOMA, and closely related parameters, derived from structural dimensions [11,12,13,14]) and magnetic [7, 9, 15, 16] (NICS).
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