The Specific Solvation Effects on the Structures and Properties of Adenine−Uracil Complexes:  A Theoretical <i>ab Initio</i> Study

Zhanpeisov, Nurbosyn U.; Leszczyński, Jerzy

doi:10.1021/jp9806260

Cited by 58 publications

(80 citation statements)

References 38 publications

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“…This structure is 7.5 kcal/ mol less stable than the canonic AT pair. These predictions are in complete correspondence with the results published in ref 37 and those obtained in the current investigation. Similar results have been obtained for the hydration of the GC base pair.…”

Section: Stabilizing and Destabilizing Factors For The Doubleproton Tsupporting

confidence: 93%

“…A similar investigation has been performed in our previous study at the MP2/6-31G(d)//HF/6-31G(d) level for the hydration of the AU, A*U*, CiC, and C*iC* base pairs (iC denotes isocytosine, which has the same structural pattern as the sixmembered heterocyclic part of guanine). 37 The results of the relative energies obtained previously 35 can be very easily explained using the maps presented in Figures 5 and 6 and, therefore, applied directly to the currently studied base pairs. However, to clarify the discussion, it should be mentioned that only the data concerning the positions of water molecules obtained previously have been used to construct the initial aqueous hydration shells surrounding the AT, A*T*, GC, and G*C* DNA base pairs.…”

Section: Stabilizing and Destabilizing Factors For The Doubleproton Tmentioning

confidence: 76%

See 1 more Smart Citation

Double-Proton Transfer in Adenine−Thymine and Guanine−Cytosine Base Pairs. A Post-Hartree−Fock ab Initio Study

et al. 2004

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The results of a comprehensive study on the double-proton transfer in Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs at room temperature in gas phase and with the inclusion of environmental effects are obtained. The double-proton-transfer process has been investigated in the AT and GC base pairs at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. It has been predicted that the hydrogen-bonded bases possess nonplanar geometries due to sp3 hybridization of nitrogen atoms and because of the soft intermolecular vibrations in the molecular complexes. An analysis of the energetic parameters of the local minima suggests that rare AT base pair conformation is not populated due to the shallowness of this minimum, which completely disappears from the Gibbs free energy surface. The stabilization of canonic or rare forms of the DNA bases by water molecules and metal cations has been predicted by calculating the optimal configuration of charges (using differential product/transition state stabilization approach) followed by calculations of the interactions between the base pair and a water/sodium cation.

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Section: Stabilizing and Destabilizing Factors For The Doubleproton Tsupporting

confidence: 93%

Section: Stabilizing and Destabilizing Factors For The Doubleproton Tmentioning

confidence: 76%

Double-Proton Transfer in Adenine−Thymine and Guanine−Cytosine Base Pairs. A Post-Hartree−Fock ab Initio Study

et al. 2004

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“…It was found that the elongation of the C=O bonds could reach up to 0.02 Å , and changes in the geometry of the amino group due to the formation of the hydrogen bonds is notable. The same results have been obtained for adenine-uracil, isocytosine-cytosine, and guanine-cytosine base pairs interacting with several water molecules [20,21].…”

Section: Introductionsupporting

confidence: 81%

Structure and hydrogen bonding in polyhydrated complexes of guanine

et al. 2007

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Molecular structure of complexes of guanine with 12, 13, 16, and 17 water molecules were calculated using B3LYP/6-311G(d,p) level of theory. Interaction with water results in some deformation of geometrical parameters of guanine, which can be described as contribution of zwitter-ionic resonant form into the structure of DNA base. Saturation of water binding sites within guanine creates possibilities for the formation of the NÁÁÁH-O hydrogen bond where the nitrogen atom of amino group acts as proton acceptor. The NBO analysis of guanine-water interactions reveals that hydrogen bonds involving the N(3) and N(7) atoms of guanine represent a case of mixed NÁÁÁH-O/pÁÁÁH-O hydrogen bonds where contribution of p-system into total energy of interaction varies from 3% to 41%. This contribution significantly depends on orientation of the hydrogen atom of water molecule with respect to plane of purine bicycle and influence of neighboring water molecules.

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“…Therefore the result supports C 3 H 4 N 2 O + production from multi-photon ionized uracil-adenine complexes. Zhanpeisov and Leszczynski [42] and…”

Section: Fig 5 Compares Mpi and Eii Measurements Carried Out On Uracmentioning

confidence: 99%

Dissociative multi-photon ionization of isolated uracil and uracil-adenine complexes

Ryszka

Pandey

Rizk

et al. 2016

International Journal of Mass Spectrometry

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Recent multi-photon ionization (MPI) experiments on uracil revealed a fragment ion at m/z 84 that was proposed as a potential marker for ring opening in the electronically excited neutral molecule. The present MPI measurements on deuterated uracil identify the fragment as C 3 H 4 N 2 O + (uracil + less CO), a plausible dissociative ionization product from the theoretically predicted open-ring isomer. Equivalent measurements on thymine do not reveal an analogous CO loss channel, suggesting greater stability of the excited DNA base. MPI and electron impact ionization experiments have been carried out on uracil-adenine clusters in order to better understand the radiation response of uracil within RNA.Evidence for C 3 H 4 N 2 O + production from multi-photon-ionized uracil-adenine clusters is tentatively attributed to a significant population of π-stacked configurations in the neutral beam. Graphical AbstractHighlights UV multi-photon ionization measurements on deuterated uracil have identified a CO loss pathway that may indicate ring opening in the electronically excited neutral molecule. The first dissociative ionization experiments on uracil-adenine complexes have revealed that the CO loss channel is also accessible in these clusters.Keywords: Uracil; adenine-uracil clusters; fragmentation; multi-photon ionization; electron impact ionization; mass spectrometry Ryszka et al. Int. J. Mass. Spectrom. 396 (2016) 48 2 IntroductionThe dynamics and stabilities of nucleobases following excitation to their bright S 2 (ππ* of the ring-opening crossing seam [9] and the geometry of the predicted isomer indicates likely CO abstraction. Therefore MPI production of this fragment ion was proposed as a potential experimental marker for ring opening in neutral excited uracil, suggesting possibilities for diverse measurements exploring the process in depth (e.g. using coincidence and / or time-resolved methods). The first aim of the present work was to test if the new fragment ion is indeed due to CO loss by studying MPI of deuterated uracil (dominantly C 4 D 4 N 2 O 2 ). These results have the added value of identifying several previously debated fragments from the radical cation, while further evidence to assign specific peaks is provided by high-resolution MPI mass spectra. The paper also presents equivalent MPI measurements on thymine, for which no analogous ring-opening process has been predicted [9]. A distinctly higher pump energy (5.64 eV, 220 nm) was applied than in the previous MPI studies of thymine (4.34-4.77 eV, 285.7-260 nm) [6, 12, 13, 14, 15, 16, 17], increasing the likelihood of isomeric transitions during radiationless deactivation. Finally, MPI and electron impact ionization (EII) experiments were carried out on uracil-adenine clusters as a step towards better understanding the dissociative ionization pathways of uracil within RNA. Whereas several spectroscopic studies have been carried out on adenine-thymine complexes in supersonic beams [18,19,20], to our knowledge no previous experiments on isolated u...

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The Specific Solvation Effects on the Structures and Properties of Adenine−Uracil Complexes: A Theoretical ab Initio Study

Cited by 58 publications

References 38 publications

Double-Proton Transfer in Adenine−Thymine and Guanine−Cytosine Base Pairs. A Post-Hartree−Fock ab Initio Study

Double-Proton Transfer in Adenine−Thymine and Guanine−Cytosine Base Pairs. A Post-Hartree−Fock ab Initio Study

Structure and hydrogen bonding in polyhydrated complexes of guanine

Dissociative multi-photon ionization of isolated uracil and uracil-adenine complexes

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