Stabilization of an excess electron on uracil by water. Ab initio study

Morgado, Claudio A.; Pichugin, Kostyantyn; Adamowicz, Ludwik

doi:10.1039/b316910c

Cited by 26 publications

(44 citation statements)

References 15 publications

(13 reference statements)

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“…Moreover, it is now well established from experiment and theory that the VB state of U − •H 2 O is lower in energy than the DB state. 14,21,23,24 Here, as in our previous work on I − •U, however, there is unfortunately no direct match of VB anion rise and DB anion decay time scales, as has been observed for I − •Adenine and I − •CH 3 NO 2 . 12,45 Calculations by Takayanagi et al for the DB and VB anions of U − •H 2 O indicate that for various U − •H 2 O DB anion isomers, the barrier height for a DB to VB anion conversion can vary from 0.43 to 3.00 kcal/mol.…”

Section: B Formation and Energetics Of The Vb Anionmentioning

confidence: 52%

“…The U − •H 2 O VB anion was measured to have a vertical detachment energy (VDE), the energy difference between the anion and the neutral species at the equilibrium geometry of the anion, of approximately 850 meV. Theory has suggested for both uracil-water 23,24 and thymine-water anion clusters 25 that the VB anion is preferentially stabilized over the DB anion as a result of the interaction energy of the solvating species being greater for the higher density excess electron distribution in the VB anion than in the DB anion.…”

Section: Introductionmentioning

confidence: 99%

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Dynamics of electron attachment and photodissociation in iodide-uracil-water clusters via time-resolved photoelectron imaging

Kunin

Neumark

2018

The Journal of Chemical Physics

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The dynamics of low energy electron attachment to monohydrated uracil are investigated using time-resolved photoelectron imaging to excite and probe iodide-uracil-water (I·U·HO) clusters. Upon photoexcitation of I·U·HO at 4.38 eV, near the measured cluster vertical detachment energy of 4.40 eV ± 0.05 eV, formation of both the dipole bound (DB) anion and valence bound (VB) anion of I·U·HO is observed and characterized using a probe photon energy of 1.58 eV. The measured binding energies for both anions are larger than those of the non-hydrated iodide-uracil (I·U) counterparts, indicating that the presence of water stabilizes the transient negative ions. The VB anion exhibits a somewhat delayed 400 fs rise when compared to I·U, suggesting that partial conversion of the DB anion to form the VB anion at early times is promoted by the water molecule. At a higher probe photon energy, 3.14 eV, I re-formation is measured to be the major photodissociation channel. This product exhibits a bi-exponential rise; it is likely that the fast component arises from DB anion decay by internal conversion to the anion ground state followed by dissociation to I, and the slow component arises from internal conversion of the VB anion.

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Section: B Formation and Energetics Of The Vb Anionmentioning

confidence: 52%

Section: Introductionmentioning

confidence: 99%

Dynamics of electron attachment and photodissociation in iodide-uracil-water clusters via time-resolved photoelectron imaging

Kunin

Neumark

2018

The Journal of Chemical Physics

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“…Thus, investigating the effects of microsolvation on the electron affinities of NABs is central to understanding the mechanism of radiation-induced DNA damage in aqueous solution and in living organisms. There have been theoretical studies reported of solvation effects on the electron affinities of uracil, [25][26][27][28][29][30][31] as well as studies of its gas-phase electron affinities. [32][33][34][35] However, most of these investigations considered only one solvating water molecule [25][26][27] or focused on the dipole-bound states, which are not relevant to biological systems.…”

Section: Introductionmentioning

confidence: 98%

“…[32][33][34][35] However, most of these investigations considered only one solvating water molecule [25][26][27] or focused on the dipole-bound states, which are not relevant to biological systems. 28,29 Some researchers 30 employed the polarized continuum model ͑PCM͒, which cannot account for explicit microsolvation effects such as hydrogen bonding between solute and solvent molecules. In the present study, we have investigated the effect of microsolvation by explicitly considering various structures of uracil hydrated with up to five water molecules.…”

Section: Introductionmentioning

confidence: 99%

Effects of microsolvation on uracil and its radical anion: Uracil∙(H2O)n (n=1–5)

Kim

Schaefer

2006

The Journal of Chemical Physics

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Microsolvation effects on the stabilities of uracil and its anion have been investigated by explicitly considering the structures of complexes of uracil with up to five water molecules at the B3LYPDZP++ level of theory. For all five systems, the global minimum of the neutral cluster has a different equilibrium geometry from that of the radical anion. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of uracil are predicted to increase gradually with the number of hydrating molecules, qualitatively consistent with experimental results from a photodetachment-photoelectron spectroscopy study [J. Schiedt et al., Chem. Phys. 239, 511 (1998)]. The trend in the AEAs implies that while the conventional valence radical anion of uracil is only marginally bound in the gas phase, it will form a stable anion in aqueous solution. The gas-phase AEA of uracil (0.24 eV) was higher than that of thymine by 0.04 eV and this gap was not significantly affected by microsolvation. The largest AEA is that predicted for uracil(H2O)5, namely, 0.96 eV. The VDEs range from 0.76 to 1.78 eV.

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“…[26] The influence of water microsolvation on electron attachment to nucleobases has also been investigated extensively at different levels of theory. [44][45][46][47][48][49][50][51][52][53][54][55][56][57] Recently, the electron affinities of thymine-adenine and guanine-cytosine base pairs stacking between different bases were studied by the resolution of identity MP2 (RI-MP2) approach. [58,59] As a crucial step in achieving a realistic description of electron attachment to nucleotide oligomers, dinucleoside phosphate deoxycytidylyl-3',5'-deoxyguanosine (dCpdG), dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine (dGpdC), dinucleoside phosphate deoxythytidylyl-3',5'-de-…”

mentioning

confidence: 99%

Electron Attachment to a Hydrated DNA Duplex: The Dinucleoside Phosphate Deoxyguanylyl‐3′,5′‐Deoxycytidine

Wong

Xie

et al. 2010

Chemistry A European J

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The minimal essential section of DNA helices, the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine dimer octahydrate, [dGpdC](2), has been constructed, fully optimized, and analyzed by using quantum chemical methods at the B3LYP/6-31+G(d,p) level of theory. Study of the electrons attached to [dGpdC](2) reveals that DNA double strands are capable of capturing low-energy electrons and forming electronically stable radical anions. The relatively large vertical electron affinity (VEA) predicted for [dGpdC](2) (0.38 eV) indicates that the cytosine bases are good electron captors in DNA double strands. The structure, charge distribution, and molecular orbital analysis for the fully optimized radical anion [dGpdC](2)(·-) suggest that the extra electron tends to be redistributed to one of the cytosine base moieties, in an electronically stable structure (with adiabatic electron affinity (AEA) 1.14 eV and vertical detachment energy (VDE) 2.20 eV). The structural features of the optimized radical anion [dGpdC](2)(·-) also suggest the probability of interstrand proton transfer. The interstrand proton transfer leads to a distonic radical anion [d(G-H)pdC:d(C+H)pdG](·-), which contains one deprotonated guanine anion and one protonated cytosine radical. This distonic radical anion is predicted to be more stable than [dGpdC](2)(·-). Therefore, experimental evidence for electron attachment to the DNA double helices should be related to [d(G-H)pdC:d(C+H)pdG](·-) complexes, for which the VDE might be as high as 2.7 eV (in dry conditions) to 3.3 eV (in fully hydrated conditions). Effects of the polarizable medium have been found to be important for increasing the electron capture ability of the dGpdC dimer. The ultimate AEA value for cytosine in DNA duplexes is predicted to be 2.03 eV in aqueous solution.

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Stabilization of an excess electron on uracil by water. Ab initio study

Cited by 26 publications

References 15 publications

Dynamics of electron attachment and photodissociation in iodide-uracil-water clusters via time-resolved photoelectron imaging

Dynamics of electron attachment and photodissociation in iodide-uracil-water clusters via time-resolved photoelectron imaging

Effects of microsolvation on uracil and its radical anion: Uracil∙(H2O)n (n=1–5)

Electron Attachment to a Hydrated DNA Duplex: The Dinucleoside Phosphate Deoxyguanylyl‐3′,5′‐Deoxycytidine

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