Metal Complexation and H-bonding Effects on Electronic Structure of Cytosine Studied in the Gas Phase

The influence of H-bonding and complexation with cations (probed by HF, F–, Li+, Na+ and K+) on structural and π-electron changes in the six most stable cytosine tautomers has been studied in the gas phase using the B3LYP/6-311++G(2d,2p) computational level. The presence of two exo- groups (ami-no/imino and carbonyl/hydroxyl) in cytosine tautomers significantly increases their sensitivity to structur¬al changes due to intra- and intermolecular interactions. These interactions induce large changes in aroma¬ticity of the rings and in the CX (X = N, O) bond lengths of exocyclic groups. Three types of H-bonds, considering their strength, could be distinguished: (i) charge-assisted X–•••HF, X = N or O, as the strong¬est, (ii) neutral X•••HF, where X is the nitrogen atom of the ring or imino group or the keto form oxygen atom and (iii) also neutral X•••HF, where X being either amino N or alternatively hydroxylic O. Hydrogen bond energy decreases approximately twice in the above listed sequence of interactions. Structural conse¬quences of H-bonding and metal complexation have been observed not only in the immediate region of the interaction but also in other parts of the molecule (the shape of the amino group, changes in CO and CN bond lengths). Complexation of the cytosine tautomers with cations leads to monotonic changes in aromaticity in line with an increase of their ionic radii

Why 1,2‑quinone derivatives are more stable than their 2,3‑analogues?

In this work, we have studied the relative stability of 1,2- and 2,3-quinones. While 1,2-quinones have a closed-shell singlet ground state, the ground state for the studied 2,3-isomers is open-shell singlet, except for 2,3-naphthaquinone that has a closed-shell singlet ground state. In all cases, 1,2-quinones are more stable than their 2,3-counterparts. We analyzed the reasons for the higher stability of the 1,2-isomers through energy decomposition analysis in the framework of Kohn–Sham molecular orbital theory. The results showed that we have to trace the origin of 1,2-quinones’ enhanced stability to the more efficient bonding in the π-electron system due to more favorable overlap between the SOMOπ of the ·C4n−2H2n–CH·· and ··CH–CO–CO· fragments in the 1,2-arrangement. Furthermore, whereas 1,2-quinones present a constant trend with their elongation for all analyzed properties (geometric, energetic, and electronic), 2,3-quinone derivatives present a substantial breaking in monotonicity.European Union in the framework of European Social Fund through the Warsaw University of Technology Development Programme. O.A. S., H. S. and T.M. K

Energetic and Geometric Characteristics of Substituents, Part 3: The Case of NO₂ and NH₂ Groups in Their Mono-Substituted Derivatives of Six-Membered Heterocycles

Substituted heterocyclic arenes play important roles in biochemistry, catalysis, and in the design of functional materials. Exemplary six-membered heteroaromatic molecules, that differ from benzene by inclusion of one heteroatom, are pyridine, phosphorine, arsabenzene, and borabenzene. This theoretical study concerns the influence of the heteroatom present in these molecules on the properties of substituents of two types: electron-donating (ED) NH2 group and electron-accepting (EA) NO2 group, attached at the 2-, 3-, or 4-position. The effect is evaluated by the energy of interaction (Erel) between the substituent and the substituted system and electronic properties of the substituents described by the charge of the substituent active region (cSAR) index. In addition, several geometric descriptors of the substituent and heteroaromatic ring, as well as changes in the aromaticity, are considered. The latter are assessed using the Electron Density of Delocalized Bonds (EDDBs) property of delocalized π electrons. The obtained results show that the electronegativity (EN) of the heteroatom has a profound effect on the EA/ED properties of the substituents. This effect is also reflected in the geometry of studied molecules. The Erel parameter indicates that the relative stability of the molecules is highly related to the electronic interactions between the substituent and the heteroarene. This especially applies to the enhancement or weakening of π-resonance due to the EN of the heteroatom. Additionally, in the 2-heteroarene derivatives, specific through-space ortho interactions contribute to the heteroatom effects

Energetic and Geometric Characteristics of the Substituents: Part 2: The Case of NO2, Cl, and NH2 Groups in Their Mono-Substituted Derivatives of Simple Nitrogen Heterocycles

Variously substituted N-heterocyclic compounds are widespread across bio- and medicinal chemistry. The work aims to computationally evaluate the influence of the type of N-heterocyclic compound and the substitution position on the properties of three model substituents: NO2, Cl, and NH2. For this reason, the energetic descriptor of global substituent effect (Erel), geometry of substituents, and electronic descriptors (cSAR, pEDA, sEDA) are considered, and interdependences between these characteristics are discussed. Furthermore, the existence of an endocyclic N atom may induce proximity effects specific for a given substituent. Therefore, various quantum chemistry methods are used to assess them: the quantum theory of atoms in molecules (QTAIM), analysis of non-covalent interactions using reduced density gradient (RDG) function, and electrostatic potential maps (ESP). The study shows that the energetic effect associated with the substitution is highly dependent on the number and position of N atoms in the heterocyclic ring. Moreover, this effect due to interaction with more than one endo N atom (e.g., in pyrimidines) can be assessed with reasonable accuracy by adding the effects calculated for interactions with one endo N atom in substituted pyridines. Finally, all possible cases of proximity interactions for the NO2, Cl, and NH2 groups are thoroughly discussed

Energetic and Geometric Characteristics of Substituents, Part 3: The Case of NO2 and NH2 Groups in Their Mono-Substituted Derivatives of Six-Membered Heterocycles

Substituted heterocyclic arenes play important roles in biochemistry, catalysis, and in the design of functional materials. Exemplary six-membered heteroaromatic molecules, that differ from benzene by inclusion of one heteroatom, are pyridine, phosphorine, arsabenzene, and borabenzene. This theoretical study concerns the influence of the heteroatom present in these molecules on the properties of substituents of two types: electron-donating (ED) NH2 group and electron-accepting (EA) NO2 group, attached at the 2-, 3-, or 4-position. The effect is evaluated by the energy of interaction (Erel) between the substituent and the substituted system and electronic properties of the substituents described by the charge of the substituent active region (cSAR) index. In addition, several geometric descriptors of the substituent and heteroaromatic ring, as well as changes in the aromaticity, are considered. The latter are assessed using the Electron Density of Delocalized Bonds (EDDBs) property of delocalized π electrons. The obtained results show that the electronegativity (EN) of the heteroatom has a profound effect on the EA/ED properties of the substituents. This effect is also reflected in the geometry of studied molecules. The Erel parameter indicates that the relative stability of the molecules is highly related to the electronic interactions between the substituent and the heteroarene. This especially applies to the enhancement or weakening of π-resonance due to the EN of the heteroatom. Additionally, in the 2-heteroarene derivatives, specific through-space ortho interactions contribute to the heteroatom effects