Mechanisms for the Deamination Reaction of Cytosine with H2O/OH−and 2H2O/OH−: A Computational Study

Almatarneh, Mansour H.; Flinn, Christopher G.; Poirier, Raymond A.

doi:10.1021/ci7003219

Cited by 44 publications

(51 citation statements)

References 29 publications

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“…G3MP2//B3LYP method was also used due to the fact that it could give reliable energetic properties for such systems [2,5]. We have demonstrated that the energy difference between B3LYP and G3MP2 method for nonassisted hydrolytic deamination of adenine could not be neglected in our previous paper.…”

Section: Effects Of Dispersion Energiesmentioning

confidence: 99%

“…The base deamination has been studied extensively [1][2][3][4][5], in which few are about the water-assisted hydrolytic deamination. Zhang et al [4] have studied the hydrolytic deamination of adenine with 1-4 water molecules at B3LYP/6-31G(d,p) level.…”

Section: Introductionmentioning

confidence: 99%

“…They found that as for adenine with two water molecules, the reactants should pass through two transition states for both pathways. Almatarneh et al [5] have studied the mechanism for the deamination reaction of cytosine with 2H 2 O and OHusing theoretical method. They found that all pathways undergo the formation of a tetrahedral intermediate followed by several conformational changes, and the obtained energy barrier agrees well with the experimental value.…”

Section: Introductionmentioning

confidence: 99%

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Theoretical study of water-assisted hydrolytic deamination mechanism of adenine

Zheng

Meng

2009

Struct Chem

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The water-assisted hydrolytic deamination mechanism of adenine was studied using density functional method at B3LYP/6-311G(d,p) level. Intrinsic reaction coordinate (IRC) calculations were performed on the transition states to verify whether it is the real transition states that connect the corresponding intermediates. Single-point calculations were carried out on the previous optimized geometries obtained during IRC calculations. The activation energies have also been calculated using G3MP2//B3LYP/6-311G(d,p) method. The water molecules attack the adenine and a tetrahedral intermediate forms. Then, two different intermediates have been obtained through different bond rotations. In pathway a, the second water molecule takes part in the formation of transition state and acts as a bridge to transfer hydrogen atom, while in pathway b, the second water molecule does not involve in the creation of transition state and only acts as a medium. The energy barriers are 23.40 and 37.17 kcal/mol for pathways a and b, respectively.

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Section: Effects Of Dispersion Energiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Theoretical study of water-assisted hydrolytic deamination mechanism of adenine

Zheng

Meng

2009

Struct Chem

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“…1,2-Elimination and 1,3-proton shift reactions are of fundamental interest in organic chemistry and are ubiquitous processes in gas-phase chemistry of cationic or anionic species [1][2][3][4][5]. Among these reactions that can undergo the 1,2-elimination and 1,3-proton shift is the decomposition (pyrolysis) of ethylamine (C 2 H 7 N).…”

Section: Introductionmentioning

confidence: 99%

High level ab initio, DFT, and RRKM calculations for the unimolecular decomposition reaction of ethylamine

Almatarneh

Altarawneh

Poirier

et al. 2014

Journal of Computational Science

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A c c e p t e d M a n u s c r i p t 3 AbstractMechanisms for the decomposition reaction of ethylamine, CH 3 CH 2 NH 2 , were investigated using ab initio, DFT, and RRKM calculations.Optimized geometries of reactants, transition states, intermediates, and products were determined at HF, MP2, and B3LYP levels of theory using the 6-31G(d) and 6-31+G(d) basis sets. Single point energies were also determined at G3MP2B3 and G3B3 levels of theory.Thermodynamic properties, activation energies, enthalpies and Gibbs energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface.The conformational change and planarity of the ethylamine moiety along with the twist angle of the amino group about the CN axis are examined. Four pathways for the decomposition reaction of ethylamine were studied. All pathways involve a 1,2-elimination reaction and 1,3-proton shift to produce ethene, ethanimine, ethenamine, and methanimine. All pathways are single-step mechanisms. Elimination of the NH 3 dominates the decomposition behaviour up to 1200 K whereas after this temperature, secession of the C-N gradually holds more importance. While pathways signifying departures of NH 3 and NH 2 exhibit pressure-dependent behaviour, branching ratios for these two channels are generally not influenced by variation in pressure higher than the atmospheric pressure.

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“…The previous works of the 1,3-proton shift has shown that the barrier could drop significantly when the water molecule is involved, acting as a mediator [53][54][55][56][57][58][59][60][61][62][63][64][65]. Figure 5 shows the one-step nucleophilic addition mechanism for the monohydrated reaction between the methanol and CI.…”

Section: Potential Energy Surface For the Reaction Of Methanol With Cmentioning

confidence: 99%

A Computational Study of the Ozonolysis of Phenanthrene

et al. 2017

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A computational study of the ozonolysis of phenanthrene has been carried out using DFT methods (B3LYP and M06-2X). The reaction mechanism for the ozonolysis was studied in both gas phase and in solution, using the polarizable continuum solvation model. The structures for all proposed reaction mechanisms were optimized using M06-2X and B3LYP methods with 6-31G(d), 6-31+G(d), and 6-31G(2df,p) basis sets. In solution, all structures were optimized using B3LYP/6-31+G(d,p) and polarizable continuum solvation model. Six different mechanistic pathways were explored for the ozonolysis of phenanthrene that forms aldehyde compounds. The activation energy of the formation of the primary ozonide intermediate in pathway A is 13 kJ mol −1 in the polarizable continuum model with the B3LYP/6-31+G(d,p) method. This reaction is followed by a dissociation into a zwitterionic Criegee intermediate with an activation energy of 76 kJ mol −1 in polarizable continuum model with B3LYP/6-31+G(d,p). Furthermore, the nucleophilic addition reactions of methanol to the Criegee intermediate have been studied along two pathways, B1 and B2. The water-mediated mechanism for pathways B2 and C2, where the water molecule acts as a mediator through a 1,5-proton shift, dropped the activation barriers by 18 and 26 kJ mol −1 , respectively, based on B3LYP/6-31G(2df,p) method. The solvation model (polarizable continuum) reduces the energy barriers for all pathways except for the reaction of methanol with the Criegee intermediate. This study provides an insight into understanding the mechanism of transformation of this pollutant into non-toxic compounds.

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Mechanisms for the Deamination Reaction of Cytosine with H₂O/OH⁻and 2H₂O/OH⁻: A Computational Study

Cited by 44 publications

References 29 publications

Theoretical study of water-assisted hydrolytic deamination mechanism of adenine

Theoretical study of water-assisted hydrolytic deamination mechanism of adenine

High level ab initio, DFT, and RRKM calculations for the unimolecular decomposition reaction of ethylamine

A Computational Study of the Ozonolysis of Phenanthrene

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