Investigation of simple and water assisted tautomerism in a derivative of 1,3,4-oxadiazole: A DFT study

Chahkandi, Behzad; Tayyari, Sayyed Faramarz; Bakhshaei, Maliheh; Chahkandi, Mohammad

doi:10.1016/j.jmgm.2013.04.002

Cited by 24 publications

(11 citation statements)

References 48 publications

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“…12,13,24,25 These studies showed that water molecules decrease the activation energies of the proton transfers. 12,13,24,25 These studies showed that water molecules decrease the activation energies of the proton transfers.…”

Section: Tablementioning

confidence: 99%

“…12,13,24,25 These studies showed that water molecules decrease the activation energies of the proton transfers. 13,25 In these cases, since there is not enough space around the isomers to accommodate extra water molecules, an unstable TS structure is formed. One and two water molecules usually have considerable catalysis effect on proton transfer reactions while increase in the number of water molecules (n≥3) does not guarantee the decrease in the activation energies.…”

Section: Tablementioning

confidence: 99%

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Effect of hydration on the stability and tautomerisms of different isomers of uracil

Valadbeigi

Farrokhpour

2014

RSC Adv.

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Thermodynamic and structural properties of isolated, hydrated and solvated forms of twelve isomers of uracil were studied, theoretically. It was found that the di-keto tautomer is the most stable isomer in gas and aqueous phases and in hydrated forms. Internal proton transfers and O-H rotations in uracil were studied employing B3LYP and MP2 methods in gas phase. Activation energies (E a ) and Gibbs free energies (∆G # ) of the isomerization processes were calculated. The calculated activation energies of the proton transfer reactions were in the range of 110-180 kJ/mol and the energy barriers of internal O-H rotations were generally smaller than 40 kJ/mol. The high energy barriers of the proton transfers indicate that proton transfers are hard to achieve.Therefore, catalysis effect of one, two and three water molecules on the proton transfer processes in the hydrated isomers of uracil was investigated. The calculations showed that water molecules lower the energy barriers of the proton transfer reactions and catalyze the tautomerism processes in uracil.

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Section: Tablementioning

confidence: 99%

Section: Tablementioning

confidence: 99%

Effect of hydration on the stability and tautomerisms of different isomers of uracil

Valadbeigi

Farrokhpour

2014

RSC Adv.

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“…Thus, it is apparent that inclusion of a second helper molecule has a strong impact on reducing the barrier which in this case seems to be in the range of previously mentioned experimental results in solution. Other authors had gone even a step further and included a third water molecule as the helper for the proton transfer in keto/amino derivative of 1,3,4-oxadiazole [32]. In the case of proton transfer from the external amino group to the ring nitrogen atom, the first water molecule decreased the barrier from 59.8 to 22.4 kcal/mol at the B3LYP/6-311?…”

Section: Introductionmentioning

confidence: 99%

The kinetics of water-assisted tautomeric 1,2-proton transfer in azoles: a computational approach

Ozimiński

2016

Struct Chem

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A complete set of azoles undergoing 1,2-proton transfer, consisting of pyrazole, 1,2,3-triazole, 1,2,4-triazole, tetrazole and pentazole, was computationally investigated regarding proton transfer mechanism in gas phase and water solution. Complexes of one azole molecule with 1-4 water molecules were employed to facilitate the proton transfer by lowering the activation energy, which for the isolated azole molecule is prohibitively large. The calculations were performed at the MP2/aug-cc-pVDZ and B3LYP/6-311??G(d,p) levels of theory which showed very good concordance. It follows that in the most probable transition state one azole molecule is accompanied by two water molecules. The activation barrier in water solution modelled by PCM method was lowered to 18.8 kcal/mol in the case of pyrazole and more for azoles containing more nitrogen atoms in the ring, reaching 6.8 kcal/mol in the case of pentazole. The analysis of the IRC reaction paths showed that proton transfer in the gas phase has more synchronous character and in the water solution is rather stepwise. It also follows from the analysis of bond lengths in the transition state that in the case of pyrazole the transition state is more cation-like and for other azoles, especially pentazole, is more anion-like. In the water environment, the initial step of proton transfer is moving the proton from azole to the water cluster in all cases except pyrazole, where the proton moves first from the water cluster to the azole molecule.

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“…H 2 O molecules can act as both proton acceptors and proton donors, in other words, a H 2 O molecule can transfer one proton from one site of the catalyzed molecule to another site (Valadbeigi et al, 2014b). However, it was found that three or more H 2 O molecules does not enhance this catalysis effect (Chahkandi et al, 2013). Fig.…”

Section: Figurementioning

confidence: 98%

The effect of water-mediated catalysis on the intramolecular proton-transfer reactions of the isomers of 5-chlorouracil: a theoretical study

Zhang

2019

Acta Crystallogr C

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The geometrical structures and thermal energies (E), enthalpies (H) and Gibbs free energies (G) of 13 isomers of 5-chlorouracil (5ClU) in the gas and water phases were investigated using the density functional theory (DFT) method at the M06-2X/6-311++g(3df,3pd) level. The isomers of 5ClU can be microhydrated at different molecular target sites. The mono-and dihydrated forms are the most stable in both the gas and water phases, and, because of the intermolecular interactions, the hydrations lead to a degree of change in the stability trend. Two types of isomerizations were considered: the internal H-O bond rotations in which the H atom rotates 180 around the C-O bond and the intramolecular proton-transfer reactions in which an H atom is transferred between an O atom and a neighbouring N atom. The forward and backward energy barriers for isomerizations of nonhydrated 5ClU were calculated. In addition, 16 optimized transition-state structures for water-mediated catalysis on isomerizations of 5ClU were investigated. The forward and backward protontransfer energy barriers of water-mediated catalysis on isomerizations of 5ClU were obtained. The results indicate that the catalytic effect of two H 2 O molecules is much greater than that of one H 2 O molecule in isomerizations of 5ClU.

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Investigation of simple and water assisted tautomerism in a derivative of 1,3,4-oxadiazole: A DFT study

Cited by 24 publications

References 48 publications

Effect of hydration on the stability and tautomerisms of different isomers of uracil

Effect of hydration on the stability and tautomerisms of different isomers of uracil

The kinetics of water-assisted tautomeric 1,2-proton transfer in azoles: a computational approach

The effect of water-mediated catalysis on the intramolecular proton-transfer reactions of the isomers of 5-chlorouracil: a theoretical study

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