Explaining the sequence of protonation affinities of cytosine with QTAIM

Complexation of common metal cations by cyanins: Binding affinity and molecular structure

“…QTAIM atomic charges of the Cy − ligand become reduced in the complexation process, as exemplified in Figure for OC‐6 [FeCy(H 2 O) 4 ] 2+ and [FeCy 2 (H 2 O) 2 ] + formation (the carbons of the methoxyl groups bonded to C5 and C3, C3’, and C4’ are exceptions to this rule. The reasons for these exceptions can be found considering the same scheme proposed for explaining electron density reorganization in molecular protonations) . Moreover (Tables and ), the results indicate that the larger the net charge transfer (CT), from Cy − to the metal cation, the more favored the metal‐complex formation (the higher binding energy, Δ b E/ Δ b G ).…”

“…[27,28] In the three cases where ρ b values can be compared, that is when an oxidation number differs for the same pair of atoms (Co, Fe and Cr complexes), we observe ( Table 2) The reasons for these exceptions can be found considering the same scheme proposed for explaining electron density reorganization in molecular protonations). [49,50] Moreover (Tables 2 and 4), the results indicate that the larger the net charge transfer (CT), from Cy − to the metal cation, the more favored the metal-complex formation (the higher binding energy, Δ b E/Δ b G). Also, we notice (see Supporting Information Table S4) that coordination number partially modified this trend, as water molecules contribute in reducing the positive charge of the metal and thus, the higher the coordination number the lower CT from Cy − .…”

An Electron‐Density‐Based Study on the Ionic Reactivity of 1,3‐Azoles

“…Trends (vi) and (vii) can be explained, because the deformation experienced by the electron-density distribution is continuous and displays higher intensities along the bonds (Figure 2), suggesting that the electron density flows through the set of chemical bonds. [38] Thus, Δ prot N(Y) is positive, because atom Y is at a junction that receives electron density through three bonds and sends it to the proton through only one. Δ prot N(C6) is also positive for all of the protonations at the ring of 1-methylimidazole (see Table S3 of the Supporting Information) as a consequence of the electron density gained by this atom from its two/three attached hydrogen atoms exceeding that lost by its own basin through the C6-N1 bond.…”

“…Nevertheless, Δ prot N(Ω) values (Table 3) do not provide a common explanation for the experimental and theoretical evidence, which indicates a clear preference for protonation on N3 over that on X1 ( Table 2). In fact, total depletions of electron density at the hydrogen atoms, ΣΔ prot N(H), that are usually associated with larger stabilization, [38][39][40] are very similar for protonations on N3 and X1 in every molecule, both in the gas phase and with PCM, and would even slightly favor protonation on X1 in some cases. Therefore, we have looked at the variations of atomic energies between n+H3 and n+H1, Δ 3-1 E(Ω), (Table 4), which reveal that different stabilization mechanisms favor N3-protonation in each case.…”

On the transferability of QTAIMC descriptors derived from X-ray diffraction data and DFT calculations: substituted hydropyrimidine derivatives

“…It provides meaningful physical and chemical information about such structural elements as atoms, chemical bonds and atomic groups, and makes possible the estimation of the properties of new compounds using available results obtained for the same class of molecule (Wiberg et al, 1987;Chang & Bader, 1992;Matta & Bader, 2003;Popelier, 1999;O'Brien & Popelier, 1999. QTAIMC allows the description of the features of the ED distribution derived from both accurate X-ray diffraction measurements and nonempirical quantum chemical calculations in a uniform way, and therefore is commonly applied to characterize both intraand intermolecular interactions in a wide variety of compounds, including bioactive compounds such as genetically encoded amino acids (Matta & Bader, 2000, 2002Flaig et al, 2002;de Carvalho et al, 2007;Pakiari et al, 2008), peptides (Lorenzo et al, 2006;Vener et al, 2007), DNA bases (Hü bschle et al, 2008;Gonzalez Moa et al, 2008), alkaloids (Scheins et al, 2005;Rincon et al, 2009), natural estrogens (Zhurova, Matta et al, 2006), large biomolecules such as NAD + and -nicotinamide adenine dinucleotide (Guillot et al, 2003), and vitamins (Milanesio et al, 1997;Dittrich et al, 2007). Rykounov & Tsirelson (2009) have recently investigated the electron density and electronic energy properties of three functionally substituted hydropyrimidines (1), (2) and (3) ( Fig.…”