The dipole bound-to-covalent anion transformation in uracil

Hendricks, James; Lyapustina, Svetlana; Clercq, Helen L. de; Bowen, Kit H.

doi:10.1063/1.475360

Cited by 248 publications

(276 citation statements)

References 21 publications

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“…And furthermore, the solvation of the uracil anionic state by one water molecule provides an extra stabilization of this state by ca. 0.4 eV [58,59]. Thus, the solvation of U − by the amino acid would have to provide an extra stabilization of 1.3 eV to be consistent with the maxima of the PES peaks at 1.8 eV, which is again improbable.…”

Section: Bfpt In Binary Complexes Of Nucleobases With Proton Donorsmentioning

confidence: 92%

“…On the other hand, it is well known that the valence anions of nucleobases, unstable in the gas phase [33], become adiabatically stable due to even marginal solvation. For instance, employing photoelectron spectroscopy (PES) Bowen et al [34] demonstrated that isolated uracil forms a stable dipole bound anion (DB). When it interacts with the argon atom both DB and valence anions are registered, and for uracil complex with single water molecule only the valence anion signal appears in the PES spectrum.…”

Section: Dna Damage Induced By Low Energy Electronsmentioning

confidence: 99%

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Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Rak

Mazurkiewicz

Kobyłecka

et al. 2008

Challenges and Advances in Computational Chemistry and Physics

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Abstract:The last decade has witnessed immense advances in our understanding of the effects of ionizing radiation on biological systems. As the genetic information carrier in biological systems, DNA is the most important species which is prone to damage by high energy photons. Ionizing radiations destroy DNA indirectly by forming low energy electrons (LEEs) as secondary products of the interaction between ionizing radiation and water. An understanding of the mechanism that leads to the formation of single and double strand breaks may be important in guiding the further development of anticancer radiation therapy. In this article we demonstrate the likely involvement of stable nucleobases anions in the formation of DNA strand breaks -a concept which the radiation research community has not focused on so far. In Section 21.1 we discuss the current status of studies related to the interaction between DNA and LEEs. The next section is devoted to the description of proton transfer induced by electron attachment to the complexes between nucleobases and various proton donorsa process leading to the strong stabilization of nucleobases anions. Then, we review our results concerning the anionic binary complexes of nucleobases with particular emphasize on the GC and AT systems. Next, the possible consequences of interactions between DNA and proteins in the context of electron attachment are briefly discussed. Further, we focus on existing proposal of single strand break formation in DNA. Ultimately, open questions as well perspectives of studies on electron induced DNA damage are discussed

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Section: Bfpt In Binary Complexes Of Nucleobases With Proton Donorsmentioning

confidence: 92%

Section: Dna Damage Induced By Low Energy Electronsmentioning

confidence: 99%

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Rak

Mazurkiewicz

Kobyłecka

et al. 2008

Challenges and Advances in Computational Chemistry and Physics

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“…There exist two types of radical-anion states of nucleobases: ͑i͒ dipole-bound anions where the excess electron is located far outside the molecule and ͑ii͒ valence ͑co-valently bound͒ anionic state the electron is delocalized over the molecule. The existence of dipole-bound anions was first predicted theoretically by Adamowicz and co-workers 14,15 and subsequently detected in the gas-phase experiments by Desfrançois et al 16 and Hendricks et al 17,18 In the gas phase, the nucleobase anions may be described as electron-dipolebound states. [19][20][21] However, it has been shown that hydrogen bonds between an anion and its surroundings stabilize the valence-bound state.…”

Section: Introductionmentioning

confidence: 99%

Estimates of electronic coupling for excess electron transfer in DNA

Voityuk

2005

The Journal of Chemical Physics

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Electronic coupling V da is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of V da for hole transfer, estimates of electronic couplings for excess electron transfer ͑ET͒ in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a stack. Two approaches are considered. First, we employ the diabatic-state ͑DS͒ method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine ͑AT͒ and guanine-cytosine ͑GC͒. In this approach, similar values of V da are obtained with the standard 6-31G * and extended 6-31+ + G ** basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals ͑LUMOs͒ of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of V da are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements V da for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack.

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“…This behavior evidently indicates that the anion state of band I is a e s À state, since dipole-bound anions usually exhibit a relatively flat trend in electron binding energy with increase in the cluster size and can survive only at low values of n. Besides, the VDEs of band I (0.5-1.1 eV for n ¼ 10-100) are higher than those of dipole-bound anions, which are typically much lower than 0.2 eV. 78,108,109 Consistently, the formation of e s À was experimentally confirmed in liquid CH 3 CN. 104,105 Recent theoretical study of excess electron attachment to CH 3 CN clusters by Takayanagi 114 also supports our assignment.…”

Section: Research Backgroundmentioning

confidence: 99%

“…Another remarkable feature is the large difference in electron binding energy between bands I and II. The coexistence of two different anionic isomers has been reported for several cluster anions, such as (uracil) À Xe, 108 (pyridine) 4 À , 78,79 and (HF) 3 À , 109 in which the differences between VDEs of the isomers have been reported to be %0.2 eV. For the (CH 3 CN) n À clusters, however, the differences between VDEs of bands I and II (%1.8 eV at n ¼ 11-100) are much larger than in these species.…”

Section: Research Backgroundmentioning

confidence: 99%

Formation of Large Molecular Cluster Anions and Elucidation of Their Electronic Structures

Mitsui¹,

Nakajima²

2007

Bulletin of the Chemical Society of Japan

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The present account describes our efforts to understand the microscopic aspects of condense phase phenomena, such as ion solvation in molecular liquids and charge carrier localization in molecular solids, by viewing finite-size molecular clusters as their embryonic forms. In this effort, we efficiently prepared supersonically cooled, isolated molecular cluster anions with up to more than 100 constituent molecules and size-selectively investigated their electronic structures using anion photoelectron spectroscopy. Large anionic clusters of two different types of organic molecule; acetonitrile and naphthalene reported as examples of the noteworthy results obtained in our studies. In these two systems, we found that energetically close anionic isomers coexist over a broad range in size, and their contribution in the photoelectron spectra could be separated using anion beam hole-burning technique. A detailed inspection into the electronic states and size-dependent energetics of each isomer has enabled us to establish a link from the large finite cluster to the infinite bulk system. Molecular clusters are finite aggregates consisting of 2-10 4 molecules and have been regarded as an excellent model system to use for gaining profound insights into weak noncovalent interactions, which play a predominant role in determining the structures and properties of molecular assemblies in chemistry, biology, and soft-material science. In molecular clusters, most of the properties originate from weakly perturbed, easily recognized, and well-defined units. Additionally, the finite number of molecules in the gas phase under collisionfree conditions makes a theoretical treatment much easier than that of bulk liquids and solids. Over the last two decades, therefore, intensive experimental and theoretical studies on molecular clusters have been performed, and a large number of review articles on the spectroscopic study of molecular clusters have been published in last twenty years.

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The dipole bound-to-covalent anion transformation in uracil

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Cited by 248 publications

References 21 publications

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Estimates of electronic coupling for excess electron transfer in DNA

Formation of Large Molecular Cluster Anions and Elucidation of Their Electronic Structures

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