On a quantum-chemical nature of a stereochemical nonrigidity of canonical nucleotide bases

Hovorun, Dmytro М.; Mishchuk, Ya. R.; Kondratyuk, I. V.

doi:10.7124/bc.000441

Cited by 20 publications

(8 citation statements)

References 12 publications

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“…Notably, in these two TSs amino group of A is significantly pyramidilized. In this case, pyramidalization of the amino group of A is around the same, as in the case of the TS of its anisotropic rotation around the C6N6 bond in free state . Gibbs free energies of activation for these processes consist 19.07 and 19.71 kcal·mol −1 , accordingly.…”

Section: Resultsmentioning

confidence: 83%

Unexpected A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions between the classical A·T DNA base pairs: A QM/QTAIM comprehensive study

Brovarets’

Tsiupa

Hovorun

2018

Int J of Quantum Chemistry

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In this study, using QM/QTAIM calculations in the continuum with ε = 1 under normal conditions, we have revealed for the first time the nondissociative A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions. It was established that they proceed via the essentially nonplanar transition states (С1 symmetry) through the intermediates, which are wobbled conformers (С1 symmetry) theoretically predicted in our previous work (Brovarets’ et al., Frontiers in Chemistry, 2018, 6:8, 10.3389/fchem.2018.00008) of the classical А·Т DNA base pairs—Watson–Crick А·Т(WC), reverse Watson–Crick А·Т(rWC), Hoogsteen А·Т(Н) and reverse Hoogsteen А·Т(rН). At this, the A·T(H)↔A·T(rWC) and A·T(WC)↔A·T(rH) conformational transformations are controlled by the transition states (TSs) stabilized by the participation of the intermolecular (T)N3H···N6(A) H‐bond (∼3.70 kcal·mol−1) between the imino group N3H of T and pyramidilized amino group N6H2 of A. Gibbs free energies of activation for these processes consist 12.22 and 11.11 kcal·mol−1, accordingly, under normal conditions. TSs, which control the A·T(WC)↔A·T(rWC) and A·T(H)↔A·T(rH) conformational transitions are stabilized by the participation of the intermolecular (T)N3H···N6(A) H‐bond (5.82 kcal·mol−1) and bifurcating intermolecular (T)N3H···N6(A) (5.00) and (T)N3H···N7(A) (0.61 kcal·mol−1) H‐bonds, accordingly. Notably, in these two TSs amino group N6H2 of A is significantly pyramidilized; Gibbs free energies of activation for these reactions are 19.07 and 19.71 kcal·mol−1, accordingly.

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Section: Resultsmentioning

confidence: 83%

Unexpected A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions between the classical A·T DNA base pairs: A QM/QTAIM comprehensive study

Brovarets’

Tsiupa

Hovorun

2018

Int J of Quantum Chemistry

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“…In uracil, the excited‐state structural dynamics are dominated by the C5 and C6 in‐plane bends, as well as the C4O10 stretch. Whereas the role of the C4O10 stretch in the photochemistry of uracil is not currently understood, because this bond is unaffected in all photochemical products of uracil, the C5 and C6 in‐plane bends may reflect the formation of the zwitterionic state that has been implicated in the pyrimidine photohydrate formation . Ideally, we would be able to observe the out‐of‐plane bends, as these internal coordinates may be more diagnostic for pyramidalization motions of the C5 and C6 carbon atoms.…”

Section: Discussionmentioning

confidence: 99%

Resonance Raman Intensities Demonstrate that C5 Substituents Affect the Initial Excited‐State Structural Dynamics of Uracil More than C6 Substituents

Teimoory

Loppnow

2016

ChemPhysChem

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Resonance Raman derived initial excited-state structural dynamics provide insight into the photochemical mechanisms of pyrimidine nucleobases, in which the photochemistry appears to be dictated by the C5 and C6 substituents. The absorption and resonance Raman spectra and excitation profiles of 5,6-dideuterouracil were measured to further test this photochemical dependence on the C5 and C6 substituents. The resulting set of excited-state reorganization energies of the observed internal coordinates were calculated and compared to those of other 5- and 6-substituted uracils. The results show that the initial excited-state dynamics along the C5C6 stretch responds to changes in mass at C5 and C6 in the same manner but that the in-plane bends at C5 and C6 are more sensitive to substituents at the C5 position than at the C6 position. In addition, the presence of two deuterium substituents at C5 and C6 decreases the initial excited-state structural dynamics along these in-plane bends, in contrast to what is observed in the presence of two CH3 groups on C5 and C6. The results are discussed in the context of DNA nucleobase photochemistry.

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“…The monomethylation of Gua and Ade amino groups doesn't change the character of interaction with carboxylateion, increasing it considerably. To the point, the significant role of inversion and anisotropic rotation of the nucleotide bases' amino groups in DNA structure and fuctioning is discussed in the papers [34][35][36][37][38].…”

Section: Stepanyugin 1998mentioning

confidence: 99%

Model considerations on physico-chemical nature of protein-nucleic acid contacts through amino acid carboxylic groups: spectroscopic data

et al. 1998

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This paper generalizes the results of a series of the works on spectroscopic (IR, UV, NMR, Raman) investigations of complexes of nucleotide bases, their numerous methyl and glycosyl derivatives with amino acid carboxylic groups modelling point protein-nucleic acid contacts. The specificity of interactions between bases and two forms of carboxylic group-neutral and deprotonated-was determined. The structures of the complexes investigated were established, and the role of various atomic groups in their formation was elucidated as well. Special consideration has been given to the frequent occurrence of proton transfer in the studied complexes. The significance of the data obtained in understanding of elementary mechanisms of protein-nucleic acid interactions is discussed.

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On a quantum-chemical nature of a stereochemical nonrigidity of canonical nucleotide bases

Cited by 20 publications

References 12 publications

Unexpected A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions between the classical A·T DNA base pairs: A QM/QTAIM comprehensive study

Unexpected A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions between the classical A·T DNA base pairs: A QM/QTAIM comprehensive study

Resonance Raman Intensities Demonstrate that C5 Substituents Affect the Initial Excited‐State Structural Dynamics of Uracil More than C6 Substituents

Model considerations on physico-chemical nature of protein-nucleic acid contacts through amino acid carboxylic groups: spectroscopic data

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