Mechanism of Isomerization in Dithietane-1,3-Dioxide

Contreras, J. G.; Gerli, Lorena A.; Hurtado, S. Marcela; Madariaga, Sandra T.

doi:10.4067/s0717-97072004000400011

Cited by 3 publications

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“…The hydrogen bonds between the nucleobases are polar (N-H … N and/or N-H … O), presenting bond distances close to 2.0 Å and bond angles in the range of 164-175 degrees (Table 1), the non-bonded distances N … N y N … O are ca. 3.0 Å, similar to those found in GC, AU and AT base pairs [35][36] . X-ray diffraction study 38 reveals that in the solid state as well in the monohydrate of the pair formed by two molecules of 9-ethyl-guanine, the bond distance N 2 -H … O 6 , is larger than N 7 … N 1 -H, in good agreement to our results (Table 1), a difference of 0.34 Å in the GG II pair has been determined.…”

Section: Resultssupporting

confidence: 69%

“…N9-H 34 . In the same way, it has been found previously, in purine and azapurine pairing [35][36][37] , the geometric parameters of those atoms not involved in the hydrogen bonds are not affected significatively after the hydrogen bonding formation. The hydrogen bonds between the nucleobases are polar (N-H … N and/or N-H … O), presenting bond distances close to 2.0 Å and bond angles in the range of 164-175 degrees (Table 1), the non-bonded distances N … N y N … O are ca.…”

Section: Resultssupporting

confidence: 65%

“…The different energetic stability between GC and AU pairs is ca. 11.0 kcal/mol at HF/6-31G(d,p) level [35][36] . These results could explain the thermodynamic stability differences of some RNA internal loops 15 that vary between -1.3 and +3.4 kcal/mol and whose three-dimensional structure is determined by interactions WC/H GG and WC/H AA pairs, in addition to WC/ WC GC and AU pairs.…”

Section: Resultsmentioning

confidence: 99%

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Theoretical Study of the Structural and Energetics Properties of the Interaction Sides of Guanine and Adenine in Gg and Aa Trans Base Pairs

Madariaga¹,

Contreras²

2012

J. Chil. Chem. Soc.

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In the present work we have carried out an ab initio study on the structural and energetic properties of the hydrogen bonding formed between the different interaction sides of Guanine (G) and Adenine (A) in the GG and AA trans non Watson-Crick base pairs. The energies derived at the HF/6-31G(d,p) level, show that while Watson-Crick sides contribute significantly to the stabilization of the hydrogen bonding, however, Sugar and Hoogsteen sides interacciones are weaker. The inclusion of electronic correlation at the second order Møller-Plesset perturbation method, confirm the importance of including this correlation at MP2/6-31G(d,p) and MP2/6-311G(d,p) levels. It is concluded that two Guanine molecules form hydrogen bonds energetically more favorable than AA pairs within the same kind of interaction, while those having the sugar-sugar GG interaction become better solvated in aqueous solution. The results also allow understanding the functional role of this type of interaction in the oligonucleotide.

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Section: Resultssupporting

confidence: 69%

Section: Resultssupporting

confidence: 65%

Section: Resultsmentioning

confidence: 99%

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Theoretical Study of the Structural and Energetics Properties of the Interaction Sides of Guanine and Adenine in Gg and Aa Trans Base Pairs

Madariaga¹,

Contreras²

2012

J. Chil. Chem. Soc.

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“…Enthalpies and free energy changes of interconversion were obtained from the corresponding sums of electronic and thermal enthalpies and free energies, respectively. The solute-solvent interactions were calculated with the polarized continuum method (PCM )-SCRF method for which its capacity to reproduce solvation energies 15 has been proved. In general PCM behaves well, failing just in few cases.…”

Section: Methodsmentioning

confidence: 99%

CONFORMATIONAL PREFERENCE IN 4,6-DIMETHYL-l,3-THIOXANE

Contreras¹,

Gerli²

2008

J. Chil. Chem. Soc.

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Trans-4,6-dimethyl-1,3-thioxane shows two conformations as a result of the heterocyclic ring inversion. The I and II conformers interconversion process has been studied by means of ab initio methods. The thermodynamics of this reaction calculated at the MP2/6-311+G ** // HF/6-31G ** and B3LYP/6-311+G ** // B3LYP/6-31G ** levels yield ∆G o values of ca.-1.5 kcal/mol in the gas phase, implying that II is the most important species in the gas phase and that its relative concentration is ca. 93%. In solution of low and medium polarity solvents, PCM method predicts an 85% concentration for this species, consistent with an 83% estimated from 1 H-NMR spectra. The experimental NMR properties (δ and 1 J C-H) have not been reported since I and II separation could not be achieved. The results obtained for two long range 4 J 2ax,6eq and 6 J 2eq,5eq coupling constants of ca. 0.5 Hz are in good agreement with 0.41 Hz, calculated in the present work. The calculated chemical shifts for the C2 and C5 protons show that δHeq < δHax implying that some anomalous effects are operating, though the δ seems to be moderately insensitive C-H bond distances changes. The spin-spin coupling constants are much more sensitive to changes occurring in the ring. Thus, normal and reverse Perlin effects for 1 J C-H are predicted for C2-H and C5-H are operating, respectively. The σC5-Heq → σ * C-S interaction would be the responsible for the very small elongation of the C5-Heq over the C5-Hax bond distances.

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