On the Applicability of Resonance Forms in Pyrimidinic Bases. II. QTAIM Interpretation of the Sequence of Protonation Affinities

2006

J. Phys. Chem. A

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QTAIM properties for uracil and 18 derivatives containing the substituents -NH(2), -OH, -OCH(3), -SH, -F, -Cl, -CH(3) -NO(2), and -Li in position 5 or 6 were computed on MP2/6-31++G//MP2/6-31G charge densities. The results indicate that -OH, -OCH(3), and -NH(2) groups are really retrieving charge from the ring. Also, the activating ability of the substituent groups, usually considered as the variation of electron population at the carbon where the electrophilic attack takes place, C, was studied. The study shows that the activating ability is reflected by the variation of pi charge or quadrupole moment at C, and also by the variation of the Laplacian of the charge density in the secondary charge concentration points around C (SCC-C). They indicate a similar, but not exactly equal, graduation of activating ability. The relative behavior of the substituents is basically the same as in benzene, though benzene has more tendency to concentrate charge in the SCC-C regions than uracil, where this tendency is larger for 6- than for 5-derivatives. sigma(+/-)(R) Taft parameters are found to display good correlations with the above indicated activating indexes. Finally, the resonance model predicts most of the main variations displayed by QTAIM atomic pi electron populations of derivatives with regard to uracil, but there are still some significant variations of the pi electron charge that it cannot predict.

Section: Computational and Geometrical Detailsmentioning

confidence: 99%

On the Electron Donor and the Electrophilic Substitution Activating Abilities of Substituents in Uracil

Moa

2006

J. Phys. Chem. A

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“…As previously observed in a long series of compounds, QTAIM charges do not support the resonance forms usually employed to describe azides and isocyanates. Thus, QTAIM charges for N5 and N6 in the azide are, respectively, −0.1 and +0.2 au in the azide, and that of N3 is −1.2 au in the isocyanate.…”

Section: Resultsmentioning

confidence: 73%

Do one‐step mechanisms always involve simultaneous evolution of electron density? QTAIM/IQA analysis of the Curtius rearrangement

López‐Fernández

Int J of Quantum Chemistry

Graña

2020

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The Curtius rearrangement reaction is studied by using quantum theory of atoms in molecules (QTAIM) analysis of the electron density and the interacting quantum atoms (IQA) formalism. Although the rearrangements take place in one stage, two phases are distinguished when the rearranged atom is H: the first one corresponds to the separation of N2, and the second one to the N‐H/C‐H bond rearrangement. The transition state (TS) for the reaction does not represent an intermediate between reagent and product for the migration but for the isolation of the N2 molecule. When the migration is undergone by a fluorine atom, no electronic phases can be distinguished and the process is really concerted. As the migration happens closer to the TS, the TS is more similar to the product. The IQA analysis reveals different electron density evolutions for H and F migrations, and the scarce relevance (in terms of energy) of the point where BCPs appear or disappear.

“…In all of them, the final ρ gained by the proton is between 0.310 and 0.325 au. Therefore, as pointed out in previous papers on the protonations of oxygen and nitrogen containing compounds, and contrasting with traditional Lewis structures, the molecular electron density distribution of the protonated form is more compatible with a positive charge on the proton than on any heteroatom. − …”

Section: Resultsmentioning

confidence: 91%

Influence of the O-Protonation in the O═C–O-MeZPreference. A QTAIM Study

Ferro-Costas

2012

J. Phys. Chem. A

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One of the three O-protonations of methyl formate (MF) gives rise to a system where the Z preference is switched off and the E conformer becomes the most stable arrangement. The quantum theory of atoms in molecules scheme for splitting the physical space of a molecule into atomic subspaces has been employed to analyze this trend, as well as the effect of the protonation in MF. The most important changes in energy and electron density upon protonation do not take place when MF reorganizes its nuclei, but when the proton is introduced explicitly. The same trend is observed when the H attached to the carbonyl C is replaced by electron donating and withdrawing groups (CN, F, OH, CH(3), and CF(3)). The origin of the inversion in the conformational preference relies in the changes experienced by two interactions: (i) the methyl group with the proton and (ii) that between the atoms of the ether C-O bond.