Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study

Gas phase chemistry in the cold interstellar clouds is dominated by ion-molecule and radical-radical interactions, though some neutralneutral reactions are also barrier-free and efficient at cold temperatures. It has been suggested that it is impossible to synthesize detectable abundances of the pre-biotic HCN oligomer adenine (H 5 C 5 N 5 ) in the interstellar medium via successive neutral-neutral reactions. We attempted therefore to use quantum chemical techniques to explore if adenine can possibly form in the interstellar space by radical-radical and radical-molecule interaction schemes, both in the gas phase and in the grains. We report results of ab initio calculations for the formation of adenine starting from some of the simple neutral molecules and radicals detected in the interstellar space. The reaction path is found to be totally exothermic and barrier free, which increases the probability of occurrence in the cold interstellar clouds (10−50 K). We also estimated the reaction rates.

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“…2. These are found to agree well with the experimental (Vogt et al 2009) and calculated (Sponer & Hobza 1994) …”

Section: Formation Of Adeninesupporting

confidence: 83%

Quantum chemical study of a new reaction pathway for the adenine formation in the interstellar space

Gupta

Tandon

Rawat

et al. 2011

A&A

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“…The thorough analysis of our results and also interpretation of the data reported in literature (Bludský et al, 1996;Hobza & Šponer, 1999;Hovorun et al, 1995aHovorun et al, , 1995bHovorun et al, , 1999Hovorun & Kondratyuk, 1996;Larsen et al, 1976;Lister et al, 1974;Šponer & Hobza, 1994;S. Wang & Schaefer III, 2006;Zierkiewicz et al, 2008) allow us to offer the following conclusions.…”

Section: Planarity or Nonplanarity Of Dna Basessupporting

confidence: 67%

“…Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. The DNA bases were believed to be planar for many years, until the nonplanarity of their amino groups has been predicted in the 1990s (Aamouche et al, 1997;Hobza & Šponer, 1999;Hovorun et al, 1995aHovorun et al, , 1995bHovorun et al, , 1999Hovorun & Kondratyuk, 1996;Komarov & Polozov, 1990;Komarov et al, 1992;Šponer & Hobza, 1994;Šponer et al, 2001). Direct experimental results for the nucleic acid bases amino moieties are not available, but indirect experimental evidence does exist.…”

Section: Dna Bases With Amino Group: Planar or Nonplanar?mentioning

confidence: 99%

“…The internal nonplanarity of the amino group originates from the partial sp 3 hybridization of the amino group nitrogen atom (Govorun et al, 1992;Hovorun et al, 1995aHovorun et al, , 1995bHovorun et al, , 1999Hovorun & Kondratyuk, 1996;Gorb & Leszczynski, 1998a, 1998bHobza & Šponer, 1999;Šponer & Hobza, 1994).…”

Section: Dna Bases With Amino Group: Planar or Nonplanar?mentioning

confidence: 99%

See 1 more Smart Citation

Elementary Molecular Mechanisms of the Spontaneous Point Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding

Brovarets’¹,

Kolomiets²,

Hovorun³

2012

Quantum Chemistry - Molecules for Innovations

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“…An inspection of the dihedral angles in Table 1 proves that all the tautomers/rotamers structures are nonplanar. It is reported that [79] results of electron correlation calculations (MP2/6-31G * ) give nonplanar geometries for several nucleotide bases specifically, for cytosine, which showed a significant pyramidalization of the amino group from MP2/6-31G * calculations. Using enormous computer resources, a complete MP2/6-31G * * frequency calculation was carried out [80] for cytosine, confirming that the planar structure is a saddle point.…”

Section: Geometrical Aspects Of Diphosphocytosine Tautomericmentioning

confidence: 99%

Structure and Stability of Chemically Modified DNA Bases: Quantum Chemical Calculations on 16 Isomers of Diphosphocytosine

Al‐Sehemi

El-Gogary

Wolschann

et al. 2013

ISRN Physical Chemistry

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We studied for the first time 16 tautomers/rotamers of diphosphocytosine by four computational methods. Some of these tautomers/rotamers are isoenergetic although they have different structures. High-level electron correlation MP2 and MP4(SDQ) ab initio methods and density functional methods employing a B3LYP and the new M06-2X functional were used to study the structure and relative stability of 16 tautomers/rotamers of diphosphocytosine. The dienol tautomers of diphosphocytosine are shown to be much more stable than the keto-enol and diketo forms. The tautomers/rotamers stability could be ranked as PC3 = PC12 < PC2 = PC11 < PC1 < PC10 < PC8 < PC9 < PC15 < PC16 < PC6 ∼ PC7 < PC13 < PC4 ∼ PC14 < PC5. This stability order was discussed in the light of stereo and electronic factors. Solvation effect has been modeled in a high dielectric solvent, water using the polarized continuum model (PCM). Consideration of the solvent causes some reordering of the relative stability of diphosphocytosine tautomers: PC3 ∼ PC12 ∼ PC2 ∼ PC11 < PC1 < PC10 < PC8 < PC9 < PC15 ∼ PC16 < PC13 < PC6 ∼ PC7 ∼ PC14 < PC4 ∼ PC5.

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Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study

Cited by 249 publications

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Quantum chemical study of a new reaction pathway for the adenine formation in the interstellar space

Quantum chemical study of a new reaction pathway for the adenine formation in the interstellar space

Elementary Molecular Mechanisms of the Spontaneous Point Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding

Structure and Stability of Chemically Modified DNA Bases: Quantum Chemical Calculations on 16 Isomers of Diphosphocytosine

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