Dipole bound, nucleic acid base anions studied via negative ion photoelectron spectroscopy

Intrinsic electrophilic properties of nucleosides: Photoelectron spectroscopy of their parent anions

The nucleoside parent anions 2(')-deoxythymidine(-), 2(')-deoxycytidine(-), 2(')-deoxyadenosine(-), uridine(-), cytidine(-), adenosine(-), and guanosine(-) were generated in a novel source, employing a combination of infrared desorption, electron photoemission, and a gas jet expansion. Once mass selected, the anion photoelectron spectrum of each of these was recorded. In the three cases in which comparisons were possible, the vertical detachment energies and likely adiabatic electron affinities extracted from these spectra agreed well with the values calculated both by Richardson et al. [J. Am. Chem. Soc. 126, 4404 (2004)] and by Li et al. [Radiat. Res. 165, 721 (2006)]. Through the combination of our experimental results and their theoretical calculations, several implications emerge. (1) With the possible exception of dG(-), the parent anions of nucleosides exist, and they are stable. (2) These nucleoside anions are valence anions, and in most cases the negative charge is closely associated with the nucleobase moiety. (3) The nucleoside parent anions we have generated and studied are the negative ions of canonical, neutral nucleosides, similar to those found in DNA.

Effects of Microsolvation on the Adenine−Uracil Base Pair and Its Radical Anion: Adenine−Uracil Mono- and Dihydrates

Microhydration effects upon the adenine-uracil (AU) base pair and its radical anion have been investigated by explicitly considering various structures of their mono- and dihydrates at the B3LYP/DZP++ level of theory. For the neutral AU base pair, 5 structures were found for the monohydrate and 14 structures for the dihydrate. In the lowest-energy structures of the neutral mono- and dihydrates, one and two water molecules bind to the AU base pair through a cyclic hydrogen bond via the N(9)-H and N(3) atoms of the adenine moiety, while the lowest-lying anionic mono- and dihydrates have a water molecule which is involved in noncyclic hydrogen bonding via the O4 atom of the uracil unit. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of the AU base pair are predicted to increase upon hydration. While the VDE and AEA of the unhydrated AU pair are 0.96 and 0.40 eV, respectively, the corresponding predictions for the lowest-lying anionic dihydrates are 1.36 and 0.75 eV, respectively. Because uracil has a greater electron affinity than adenine, an excess electron attached to the AU base pair occupies the pi* orbital of the uracil moiety. When the uracil moiety participates in hydrogen bonding as a hydrogen bond acceptor (e.g., the N(6)-H(6a)...O(4) hydrogen bond between the adenine and uracil bases and the O(w)-H(w)...N and O(w)-H(w)...O hydrogen bonds between the AU pair and the water molecules), the transfer of the negative charge density from the uracil moiety to either the adenine or water molecules efficiently stabilizes the system. In addition, anionic structures which have C-H...O(w) contacts are energetically more favorable than those with N-H...O(w) hydrogen bonds, because the C-H...O(w) contacts do not allow the unfavorable electron density donation from the water to the uracil moiety. This delocalization effect makes the energetic ordering for the anionic hydrates very different from that for the corresponding neutrals.

Understanding electron attachment to the DNA double helix: the thymidine monophosphate-adenine pair in the gas phase and aqueous solution

Electron attachment to the 2'-deoxythymidine-5'-monophosphate-adenine pairs (5'-dTMPH-A and 5'-dTMP(-)-A) has been investigated at a carefully calibrated level of theory (B3LYP/DZP++) to investigate the electron-accepting properties of thymine (T) in the DNA double helix under physiological conditions. All molecular structures have been fully optimized in vacuo and in solution. The adiabatic electron affinity of 5'-dTMPH-A in the gas phase has been predicted to be 0.67 eV. Solvent effects greatly increase the electron capture ability of 5'-dTMPH-A. In fact, the adiabatic electron affinity increases to 2.04 eV with solvation. The influence of the solvent environment on the electron-attracting properties of 5'-dTMPH-A arises not only from the stabilization of the corresponding radical anion through charge-dipole interactions, but also by changing the distribution of the unpaired electron in the molecular system. The unpaired electron is covalently bound even during vertical attachment, due to the solvent effects. Solvent effects also weaken the pairing interaction in the thymidine monophosphate-adenine complexes. The phosphate deprotonation is found to have a relatively minor influence on the capture of electrons by the 5'-dTMPH-A species in aqueous solution. The electron distributions, natural population analysis, and geometrical features of the models examined illustrate that the influence of the phosphate deprotonation is limited to the phosphate moiety in aqueous solution. Therefore, it is reasonable to expect that electron attachment to nucleotides will be independent of monovalent counterions in the vicinity of the phosphate group in aqueous solution.

Vibrational Feshbach resonances in uracil and thymine

Sharp peaks in the dissociative electron attachment (DEA) cross sections of uracil and thymine at energies below 3 eV are assigned to vibrational Feshbach resonances (VFRs) arising from coupling between the dipole bound state and the temporary anion state associated with occupation of the lowest sigma* orbital. Three distinct vibrational modes are identified, and their presence as VFRs is consistent with the amplitudes and bonding characteristics of the sigma* orbital wave function. A deconvolution method is also employed to yield higher effective energy resolution in the DEA spectra. The site dependence of DEA cross sections is evaluated using methyl substituted uracil and thymine to block H atom loss selectively. Implications for the broader issue of DNA damage are briefly discussed.

The 2'-deoxyadenosine-5'-phosphate anion, the analogous radical, and the different hydrogen-abstracted radical anions: molecular structures and effects on DNA damage

The 2'-deoxyadenosine-5'-phosphate (5'-dAMP) anion and its related radicals have been studied by reliably calibrated theoretical approaches. This study reveals important physical characteristics of 5'-dAMP radical related processes. One-electron oxidation of the 5'-dAMP anion is found on both the phosphoryl group and the adenine base with electron detachment energies close to that of phosphate. Partial removal of electron density from the adenine fragment leads to an extended pi system which includes the amine group of the adenine. Although the radical-centered carbon increases the extent of bonding with its adjacent atoms, it usually weakens the chemical bonds between the atoms at the alpha- and beta-positions. This tendency should be important in predicting the reactivity of the sugar-based radicals. The overall stability sequence of the H-abstracted 5'-dAMP anionic radicals is consistent with the analogous results for the H-abstracted neutral radicals of the adenosine nucleoside: aliphatic radicals > aromatic radicals. The negatively charged phosphoryl group attached to atom C(5)' of the ribose does not change this energetic sequence. All the H-abstraction produced 5'-dAMP radical anions are distonic radical anions. Studies have shown that the charge-radical-separating feature of the distonic radical anions is biologically relevant. This result should be important in understanding the reactive properties of these H-abstraction-produced anion radicals.

Computational studies of DNA photolyase

The electron transfer catalyzed (ETC) repair of the DNA photolesion cyclobutane pyrimidine dimer (CPD) is mediated by the enzyme DNA photolyase. Due to its importance as part of the cancer prevention mechanism in many organisms, but also due to its unique mechanism, this DNA photoreactivation is a topic of intense study. The progress in the application of computational methods to three aspects of the ETC repair of CPD is reviewed: (i) electronic structure calculations of the cycloreversion of the CPD radical cation and radical anion, (ii) MD simulations of the DNA photolyase and its complex to photodamaged DNA, and (iii) the structure and dynamics of photodamaged DNA. The contributions of this work to the overall understanding of the reaction and its relationship to the available experimental work are highlighted.

Quantum mechanical energy-based screening of combinatorially generated library of tautomers. TauTGen: a tautomer generator program

We describe a procedure of finding low-energy tautomers of a molecule. The procedure consists of (i) combinatorial generation of a library of tautomers, (ii) screening based on the results of geometry optimization of initial structures performed at the density functional level of theory, and (iii) final refinement of geometry for the top hits at the second-order Möller-Plesset level of theory followed by single-point energy calculations at the coupled cluster level of theory with single, double, and perturbative triple excitations. The library of initial structures of various tautomers is generated with TauTGen, a tautomer generator program. The procedure proved to be successful for these molecular systems for which common chemical knowledge had not been sufficient to predict the most stable structures.

MS-CASPT2 calculation of excess electron transfer in stacked DNA nucleobases

Calculations using the complete active space self-consistent field (CASSCF) and complete active space second-order perturbation (CASPT2) methods, and the multistate formulation of CASPT2 (MS-CASPT2), are performed for the ground and excited states of radical anions consisting of two pi-stacked nucleobases. The electronic couplings for excess electron transfer (EET) in the pi-stacks are estimated by using the generalized Mulliken-Hush approach. We compare results obtained within the different methods with data derived using Koopmans' theorem approximation at the Hartree-Fock level. The results suggest that although the one-electron scheme cannot be applied to calculate electron affinities of nucleobases, it provides reasonable estimates for EET energies. The electronic couplings calculated with KTA lie between the CASPT2 and the MS-CASPT2 based values in almost all cases.

Anion photoelectron imaging of deprotonated thymine and cytosine

We report the anion photoelectron spectra of deprotonated thymine and cytosine at 3.496 eV photodetachment energy using velocity-mapped imaging. The photoelectron spectra of both species exhibit bands resulting from detachment transitions between the anion ground state and the ground state of the neutral radical. Franck-Condon simulations identify the anion isomers that contribute to the observed photoelectron spectrum. For both thymine and cytosine, the photoelectron spectra are consistent with anions formed by removal of a proton from the N atom that normally attaches to the sugar in the nucleotide (N1). For deprotonated thymine, the photoelectron spectrum shows a band due to a ring breathing vibration excited during the photodetachment transition. The electron affinity for the dehydrogenated thymine radical is determined as 3.250 +/- 0.015 eV. For deprotonated cytosine, the photoelectron spectrum lacks any resolved structure and the electron affinity of the dehydrogenated cytosine radical is determined to be 3.037 +/- 0.015 eV. By combining the electron affinity with previously measured gas phase acidities of thymine and cytosine, we determine the bond dissociation energy for the N-H bond that is broken.

Determination of Redox Potentials for the Watson−Crick Base Pairs, DNA Nucleosides, and Relevant Nucleoside Analogues

Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.

Estimates of electronic coupling for excess electron transfer in DNA

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 (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a pi stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). 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 (LUMOs) 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.

Bound anionic states of adenine

Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the newfound anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike the dipole-bound state, could exist in condensed phases and might be relevant to radiobiological damage. The discovery of these valence anionic states of adenine was facilitated by the development of (i) an experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a combinatorial/quantum chemical approach for identification of the most stable tautomers of organic molecules.

Coupled-cluster and explicitly correlated perturbation-theory calculations of the uracil anion

A valence-type anion of the canonical tautomer of uracil has been characterized using explicitly correlated second-order Moller-Plesset perturbation theory (RI-MP2-R12) in conjunction with conventional coupled-cluster theory with single, double, and perturbative triple excitations. At this level of electron-correlation treatment and after inclusion of a zero-point vibrational energy correction, determined in the harmonic approximation at the RI-MP2 level of theory, the valence anion is adiabatically stable with respect to the neutral molecule by 40 meV. The anion is characterized by a vertical detachment energy of 0.60 eV. To obtain accurate estimates of the vertical and adiabatic electron binding energies, a scheme was applied in which electronic energy contributions from various levels of theory were added, each of them extrapolated to the corresponding basis-set limit. The MP2 basis-set limits were also evaluated using an explicitly correlated approach, and the results of these calculations are in agreement with the extrapolated values. A remarkable feature of the valence anionic state is that the adiabatic electron binding energy is positive but smaller than the adiabatic electron binding energy of the dipole-bound state.

Microhydration of cytosine and its radical anion: Cytosine∙(H2O)n (n=1–5)

Microhydration effects on cytosine and its radical anion have been investigated theoretically, by explicitly considering various structures of cytosine complexes with up to five water molecules. Each successive water molecule (through n=5) is bound by 7-10 kcal mol(-1) to the relevant cytosine complex. The hydration energies are uniformly higher for the analogous anion systems. While the predicted vertical detachment energy (VDE) of the isolated cytosine is only 0.48 eV, it is predicted to increase to 1.27 eV for the lowest-lying pentahydrate of cytosine. The adiabatic electron affinity (AEA) of cytosine was also found to increase from 0.03 to 0.61 eV for the pentahydrate, implying that the cytosine anion, while questionable in the gas phase, is bound in aqueous solution. Both the VDE and AEA values for cytosine are smaller than those of uracil and thymine for a given hydration number. These results are in qualitative agreement with available experimental results from photodetachment-photoelectron spectroscopy studies of Schiedt et al. [Chem. Phys. 239, 511 (1998)].

Valence Anions in Complexes of Adenine and 9-Methyladenine with Formic Acid: Stabilization by Intermolecular Proton Transfer

Photoelectron spectra of adenine-formic acid (AFA(-)) and 9-methyladenine-formic acid (MAFA(-)) anionic complexes have been recorded with 2.540 eV photons. These spectra reveal broad features with maxima at 1.5-1.4 eV that indicate formation of stable valence anions in the gas phase. The neutral and anionic complexes of adenine/9-methyladenine and formic acid were also studied computationally at the B3LYP, second-order Møller-Plesset, and coupled-cluster levels of theory with the 6-31++G** and aug-cc-pVDZ basis sets. The neutral complexes form cyclic hydrogen bonds, and the most stable dimers are bound by 17.7 and 16.0 kcal/mol for AFA and MAFA, respectively. The theoretical results indicate that the excess electron in both AFA(-) and MAFA(-) occupies a pi* orbital localized on adenine/9-methyladenine, and the adiabatic stability of the most stable anions amounts to 0.67 and 0.54 eV for AFA(-) and MAFA(-), respectively. The attachment of the excess electron to the complexes induces a barrier-free proton transfer (BFPT) from the carboxylic group of formic acid to a N atom of adenine or 9-methyladenine. As a result, the most stable structures of the anionic complexes can be characterized as neutral radicals of hydrogenated adenine (9-methyladenine) solvated by a deprotonated formic acid. The BFPT to the N atoms of adenine may be biologically relevant because some of these sites are not involved in the Watson-Crick pairing scheme and are easily accessible in the cellular environment. We suggest that valence anions of purines might be as important as those of pyrimidines in the process of DNA damage by low-energy electrons.

On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study

We characterized anionic states of thymine using various electronic structure methods, with the most accurate results obtained at the CCSD(T)/aug-cc-pVDZ level of theory followed by extrapolations to complete basis set limits. We found that the most stable anion in the gas phase is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion, aT(c5)(nl), is characterized by an electron vertical detachment energy (VDE) of 1251 meV and it is adiabatically stable with respect to the canonical neutral nT(can) by 2.4 kcal/mol. It is also more stable than the dipole-bound (aT(dbs)(can)), and valence anion aT(val)(can) of the canonical tautomer. The VDE values for aT(dbs)(can)and T(val)(can) are 55 and 457 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2458 meV has a proton transferred from N3H to C5 aT(c5)(n3). It is less stable than aT(val)(can) by 3.3 kcal/mol. The mechanism of formation of anionic tautomers with the carbons C5 or C6 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of the anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral; becomes the most stable, being followed by aT(c5)(nl), aT(c5)(n3), aT(can), and aT(c5)(nl).

Low-energy electron collisions with gas-phase uracil

We have studied gas-phase collisions between slow electrons and uracil molecules with a view to understanding the resonance structure of the scattering cross section. Our symmetry-resolved results for elastic scattering, computed in the fixed-nuclei, static-exchange and static-exchange-plus-polarization approximations, provide locations for the expected pi* shape resonances and indicate the possible presence of a low-energy sigma* resonance as well. Electron-impact excitation calculations were carried out for low-lying triplet and singlet excitation channels and yield a very large singlet cross section. We discuss the connection between the resonances found in our elastic cross section and features observed in dissociative attachment.

Hydrogen loss from nucleobase nitrogens upon electron attachment to isolated DNA and RNA nucleotide anions

Electron transfer to isolated nucleotide monoanions in collisions with Na vapor induces hydrogen loss from nitrogen of the transient nucleobase anion. The cross section for this process is linearly correlated with the number of N-H hydrogens and is highest for guanine. The process is much faster than microseconds since only dehydrogenated dianions survived for mass spectrometric detection. The lifetime of the adenosine 5(')-monophospate dianions was measured to be 0.2 ms in an electrostatic ion storage ring but also a longer-lived component with a lifetime of at least 10 ms was identified. Implications of dissociation along the N-H coordinate for a nucleotide in DNA are briefly discussed in terms of Watson-Crick base pairs.

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

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.

Probing chemical dynamics with negative ions

Experiments are reviewed in which key problems in chemical dynamics are probed by experiments based on photodetachment and/or photoexcitation of negative ions. Examples include transition state spectroscopy of biomolecular reactions, spectroscopy of open shell van der Waals complexes, photodissociation of free radicals, and time-resolved dynamics in clusters. The experimental methods used in these investigations are described along with representative systems that have been studied.

Electron attachment to gas-phase uracil

We present results about dissociative electron attachment (DEA) to gas-phase uracil (U) for incident electron energies between 0 and 14 eV using a crossed electron/molecule beam apparatus. The most abundant negative ion formed via DEA is (U-H)-, where the resonance with the highest intensity appears at 1.01 eV. The anion yield of (U-H)- shows a number of peaks, which can be explained in part as being due to the formation of different (U-H)- isomers. Our results are compared with high level ab initio calculations using the G2MP2 method. There was no measurable amount of a parent ion U-. We also report the occurrence of 12 other fragments produced by dissociative electron attachment to uracil but with lower cross sections than (U-H)-. In addition we observed a parasitic contaminating process for conditions where uracil was introduced simultaneously with calibrant gases SF6 and CCl4 that leads to a sharp peak in the (U-H)- cross section close to 0 eV. For (U-H)- and all other fragments we determined rough measures for the absolute partial cross section yielding in the case of (U-H)- a peak value of sigma (at 1.01 eV)=3 x 10(-20) m2.

Photoelectron spectra of hydrated electron clusters: Fitting line shapes and grouping isomers

The photoelectron spectra of (H2O)(n = 2-69) - and (D2O)(n = 2-23) - are presented, and their spectral line shapes are analyzed in detail. This analysis revealed the presence of three different groupings of species, each of which are seen over the range, n = 11-16. These three groups are designated as dipole boundlike states, seen from n = 2-16, intermediate states, found from n = 6-16, and bulk embryonts, starting at n = 11 and continuing up through the largest sizes studied. Almost two decades ago [J. V. Coe et al., J. Chem. Phys. 92, 3980 (1990)], before the present comprehensive analysis, we concluded that the latter category of species were embryonic hydrated electrons with internalizing excess electrons (thus the term embryonts). Recent experiments with colder expansion (high stagnation chamber pressures) conditions by Neumark and coworkers [J. R. R. Verlet et al., Science 307, 93 (2005)] have also found three groups of isomers including the long-sought-after surface states of large water cluster anions. This work confirms that the species here designated as embryonts are in the process of internalizing the excess electron states as the cluster size increases (for n > or = 11).

Microsolvation effects on the electron capturing ability of thymine: Thymine-water clusters

The effects of solvation on the stability of thymine and its negative ion have been investigated by explicitly considering the structures of complexes of thymine with up to five water molecules and the respective anions at the B3LYP/DZP++ level of theory. The vertical detachment energy of thymine was predicted to increase gradually with the hydration number, consistent with experimental observations from a photodetachment-photoelectron spectroscopy study J. Schiedt et al., [Chem. Phys. 239, 511 (1998)]. The adiabatic electron affinity of thymine was also found to increase with the hydration number, which implies that while the conventional valence anion of thymine is only marginally bound in the gas phase, it may form a stable anion in aqueous solution.

Binding of Gold Clusters with DNA Base Pairs: A Density Functional Study of Neutral and Anionic GC−Aun and AT−Aun (n = 4, 8) Complexes

Binding of clusters of gold atoms (Au) with the guanine-cytosine (GC) and adenine-thymine (AT) Watson-Crick DNA base pairs was studied using the density functional theory (DFT). Geometries of the neutral GC-Au(n) and AT-Au(n) and the corresponding anionic (GC-Au(n))(-1) and (AT-Au(n))(-1) (n = 4, 8) complexes were fully optimized in different electronic states, that is, singlet and triplet states for the neutral complexes and doublet and quartet states for the anionic complexes, using the B3LYP density functional method. The 6-31+G basis set was used for all atoms except gold. For gold atoms, the Los Alamos effective core potential (ECP) basis set LanL2DZ was employed. Vibrational frequency calculations were performed to ensure that the optimized structures corresponded to potential energy surface minima. The gold clusters around the neutral GC and AT base pairs have a T-shaped structure, which satisfactorily resemble those observed experimentally and in other theoretical studies. However, in anionic GC and AT base pairs, the gold clusters have extended zigzag and T-shaped structures. We found that guanine and adenine have high affinity for Au clusters, with their N3 and N7 sites being preferentially involved in binding with the same. The calculated adiabatic electron affinities (AEAs) of the GC-Au(n)complexes (n = 4, 8) were found to be much larger than those of the isolated base pairs.

Dipole-Bound Anions of β-Alanine: Canonical and Zwitterionic Conformers

The remarkable stabilities of the dipole-bound anions of the canonical and zwitterionic conformers of beta-alanine are predicted at the high level of theories, in which the former is the global minimum and the latter, the anti zwitterionic anion, is the local minimum. In contrast to the dipole-bound anions of glycine, the gauche zwitterionic anion of beta-alanine is an unstable conformer. The vertical electron detachment energies for the canonical and anti zwitterionic anions are 58 and 1145 meV, respectively. The photodetachment electron spectrum of the canonical anion is theoretically simulated on the basis of the Franck-Condon factor calculations.

Microsolvation Effect, Hydrogen-Bonding Pattern, and Electron Affinity of the Uracil−Water Complexes U−(H2O)n (n = 1, 2, 3)

To achieve a systematic understanding of the influence of microsolvation on the electron accepting behaviors of nucleobases, the reliable theoretical method (B3LYP/DZP++) has been applied to a comprehensive conformational investigation on the uracil-water complexes U-(H(2)O)(n) (n = 1, 2, 3) in both neutral and anionic forms. For the neutral complexes, the conformers of hydration on the O2 of uracil are energetically favored. However, hydration on the O4 atom of uracil is more stable for the radical anions. The electron structure analysis for the H-bonding patterns reveal that the CH...OH(2) type H-bond exists only for di- and trihydrated uracil complexes in which a water dimer or trimer is involved. The electron density structure analysis and the atoms-in-molecules (AIM) analysis for U-(H(2)O)(n) suggest a threshold value of the bond critical point (BCP) density to justify the CH...OH(2) type H-bond; that is, CH...OH(2) could be considered to be a H-bond only when its BCP density value is equal to or larger than 0.010 au. The positive adiabatic electron affinity (AEA) and vertical detachment energy (VDE) values for the uracil-water complexes suggest that these hydrated uracil anions are stable. Moreover, the average AEA and VDE of U-(H(2)O)(n) increase as the number of the hydration waters increases.

Stabilization of very rare tautomers of 1-methylcytosine by an excess electron

We characterized valence anionic states of 1-methylcytosine using various electronic structure methods. We found that the most stable valence anion is related to neither the canonical amino-oxo nor a rare imino-oxo tautomer, in which a proton is transferred from the N4 to N3 atom. Instead, it is related to an imino-oxo tautomer, in which the C5 atom is protonated. This anion is characterized by an electron vertical detachment energy (VDE) of 2.12 eV and it is more stable than the anion based on the canonical tautomer by 1.0 kcal/mol. The latter is characterized by a VDE of 0.31 eV. Another unusual low-lying imino-oxo tautomer with a VDE of 3.60 eV has the C6 atom protonated and is 3.6 kcal/mol less stable than the anion of the canonical tautomer. All these anionic states are adiabatically unbound with respect to the canonical amino-oxo neutral, with the instability of 5.8 kcal/mol for the most stable valence anion. The mechanism of formation of anionic tautomers with carbon atoms protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to the C5 or C6 atom. The six-member ring structure of anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Indeed the neutral systems collapse without a barrier to a linear or a bicyclo structure, which might be viewed as lesions to DNA or RNA. Within the PCM hydration model, the anions become adiabatically bound with respect to the corresponding neutrals, and the two most stable tautomers have a carbon atom protonated.

Valence- and Dipole-Bound Anions of the Thymine−Water Complex: Ab Initio Characterization of the Potential Energy Surfaces

The potential energy surfaces of the neutral and anionic thymine-water complexes are investigated using high-level ab initio calculations. Both dipole-bound (DB) and valence-bound (VB) anionic forms are considered. Four minima and three first-order stationary points are located, and binding energies are computed. All minima, for both anions, are found to be vertically and adiabatically stable. The binding energies are much higher for valence-bound than for dipole-bound anions. Adiabatic electron affinities are in the 66-287 meV range for VB anions and the 4-60 meV range for DB anions, and vertical detachment energies are in the 698-977 meV and 10-70 meV range for VB and DB anions, respectively. For cases where literature data are available, the computed values are in good agreement with previous experimental and theoretical studies. It is observed that electron attachment modifies the shape of the potential energy surfaces of the systems, especially for the valence-bound anions. Moreover, for both anions the size of the energy barrier between the two lowest energy minima is strongly reduced, rendering the coexistence of different structures more probable.

Negatively Charged Xanthine. I. Anions Formed by Canonical Isomers

The possibility of an excess electron binding to canonical isomers of xanthine in the gas phase was studied at the coupled-cluster level with single and double excitations using the 6-31++G** basis sets supplemented with the 4(sp)3d set of diffuse functions. It was found that xanthine should exist in the gas phase as one canonical tautomer while all the other tautomers are not likely to be detected experimentally because of their significant thermodynamic instability. On the other hand, all canonical tautomers (except one) were found to be capable of forming electronically stable anionic states of dipole-bound nature. However, the only thermodynamically stable anion (with vertical electron binding energy estimated to be 0.041 eV) based on xanthine tautomers is the one supported by the most stable neutral species.

Theoretical study of guanine–Cu and uracil–Cu (neutral, anionic, and cationic). Is it possible to carry out a photoelectron spectroscopy experiment?

The structure and bonding of guanine-Cu and uracil-Cu (neutral, anionic, and cationic) are discussed on the basis of the calculated structures and energies. The interaction of the metal atom with guanine and uracil has been analyzed using the B3LYP density-functional approach. The removal of one electron from the neutral complexes produces the stabilization of one of the isomers, while the addition of one electron leads to a system where the metal atom is weakly bounded to guanine or uracil, according to the metal-bases bond distance that is long (2.29-2.90). For guanine-Cu and uracil-Cu, the vertical ionization energy of the anion is close to the dissociation energy of one hydrogen atom from guanine-Cu or uracil-Cu. In these cases, it could be possible to produce the detachment of one electron from the anion and also the removal of one hydrogen atom. This is important since the photoelectron spectroscopy of atomic or mixed-atomic cluster anions has proven to be a very effective tool in the study of small systems. For the analysis of copper atoms with DNA bases such as guanine and uracil, it is expected that the photoelectron spectra of the anion-bases complexes strongly resemble the spectrum of Cu(-1), just shifted to higher electron binding energies due to the product stabilization. Hopefully, this information will be useful for the experimental groups.

Structural and Energetic Characterization of a DNA Nucleoside Pair and Its Anion: Deoxyriboadenosine (dA) − Deoxyribothymidine (dT)

The geometries of the DNA nucleoside pairs between 2'-deoxyriboadenosine (dA) and 2'-deoxyribothymidine (dT) and its anion (dAdT-) were fully optimized using carefully calibrated density functional methods. The addition of an electron to dAdT results in remarkable changes to the two hydrogen bonding distances, the H...O distance decreasing by 0.303 angstroms and the N...H distance increasing by 0.229 angstroms. The electron affinity of the dAdT pair was studied to reveal the correct trends of adiabatic electron affinity (EA(ad)) under the influence of the additional components to the individual bases. The consequence of negative charge in terms of structural variations, energetic changes, and charge distribution were explored. The EA(ad) of dAdT is predicted to be positive (0.60 eV), and it exhibits a substantial increase compared with those of the corresponding bases A and T and the nucleic acid base pair AT. The effects of pairing and the addition of the sugar moiety on the EA(ad) are well described as the summation of the individual influences. The influence of the pairing on the EA is comparable to that of the addition of 2-deoxyribose. The excess charge is mainly located on the thyminyl moiety in the anionic dAdT pair. The positive vertical electron affinity (VEA = 0.20 eV) for dAdT suggests that it is able to form a stable anion through electron attachment. A large vertical detachment energy (VDE = 1.14 eV) has been determined for the anionic dAdT nucleoside pair. Therefore, one may expect that the stable anionic dAdT nucleoside pair should be able to undergo the subsequent glycosidic bond cleavage process.

Intermolecular Proton Transfer in Anionic Complexes of Uracil with Alcohols

A series of 18 alcohols (ROH) has been designed with an enthalpy of deprotonation in the gas phase (H(DP)) in the range 13.8-16.3 eV. The effects of excess electron attachment to the binary alcohol-uracil (ROH...U) complexes have been studied at the density functional level with a B3LYP exchange-correlation functional and at the second-order Møller-Plesset perturbation theory level. The photoelectron spectra of anionic complexes of uracil with 3 alcohols (ethanol, 2,2,3,3,3-pentafluoropropanol, and 1,1,1,3,3,3-hexafluoro-2-propanol) have been measured with 2.54 eV photons. For ROHs with deprotonation enthalpies larger than 14.8 eV, only the ROH...U- minimum exists on the potential energy surface of the anionic complex. For alcohols with deprotonation enthalpies in the range 14.3-14.8 eV, two minima might exist on the anionic potential energy surface, which correspond to the RO-...HU* and ROH...U- structures. For ROHs with deprotonation enthalpies smaller than 14.3 eV, the excess electron attachment to the ROH...U complex always induces a barrier-free proton transfer from the hydroxyl group of ROH to the O8 atom of U, with the product being RO-...HU*.

Marked Influences on the Adenine−Cytosine Base Pairs by Electron Attachment and Ionization

The reverse wobble and the reverse Hoogsteen adenine-cytosine mispairs regarding their radical cations and anions are studied with the hybrid three-parameter B3LYP density functional method and 6-31+G(d), 6-311+G(2df,2p) basis sets. Hydrogen bonding mispairs are remarkably influenced by electron attachment and ionization. Only one stronger hydrogen bond N6-H (in adenine)...N3 (in cytosine) exists in the radical pair, while the strengths of two N-H...N hydrogen bonds in the neutral pair are comparable. Geometrical coplanarity is found for the neutral and cationic pairs, in contrast to the anionic pairs in which the cytosine moiety exhibits significant deformation due to electron attachment. Dissociation energies for the neutral and radical pairs are slightly higher than those of the adenine-thymine pairs but much smaller than those of the guanine-cytosine pairs. Valence-bound anions of these two adenine-cytosine pairs are thermodynamically stable by 0.1-0.2 eV with respect to the neutral pairs. On the basis of the comparison between the experimental data of the solvated clusters and the calculated values, these two pairs can be quantitatively equivalent to the clusters in which each base is solvated by five water molecules.

Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair: A Density Functional Study

Adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pair surrounded by 5 and 13 water molecules have been studied by density functional theory (DFT). Geometries of neutral AT x nH2O and anionic (AT x nH2O)- complexes (n = 5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory. The optimized structures of the neutral (AT x nH2O) and (AT x nH2O)- complexes were found to be somewhat nonplanar. Some of the water molecules are displaced away from the AT ring plane and linked with one another by hydrogen bonds. The optimized structures of the complexes are found to be in a satisfactory agreement with the observed experimental and molecular dynamics simulation results. In the optimized anionic complexes, the thymine (T) moiety was found to be puckered, whereas the adenine (A) moiety remained almost planar. Natural population analysis (NPA) performed using the B3LYP/6-31+G** method shows that the thymine moiety in the anionic (AT x nH2O)- complexes (n = 5 and 13) has most of the excess electronic charge, i.e., approximately -0.87 and approximately -0.81 (in the unit of magnitude of the electronic charge), respectively. The zero-point energy corrected adiabatic electron affinities of the hydrated AT base pair were found to be positive both for n = 5 and 13 and have the values of 0.97 and 0.92 eV, respectively, which are almost three times the AEA of the AT base pair. The results show that the presence of water molecules appreciably enhances the EA of the base pair.

AT Base Pair Anions versus (9-Methyl-A)(1-Methyl-T) Base Pair Anions

The anionic base pairs of adenine and thymine, (AT)(-), and 9-methyladenine and 1-methylthymine, (MAMT)(-), have been investigated both theoretically and experimentally in a complementary, synergistic study. Calculations on (AT)(-) found that it had undergone a barrier-free proton transfer (BFPT) similar to that seen in other dimer anion systems and that its structural configuration was neither Watson-Crick (WC) nor Hoogsteen (HS). The vertical detachment energy (VDE) of (AT)(-) was determined by anion photoelectron spectroscopy and found to be in agreement with the VDE value predicted by theory for the BFPT mechanism. An AT pair in DNA is structurally immobilized into the WC configuration, in part, by being bonded to the sugars of the double helix. This circumstance was mimicked by methylating the sites on both A and T where these sugars would have been tied, viz., 9-methyladenine and 1-methylthymine. Calculations found no BFPT in (MAMT)(-) and a resulting (MAMT)(-) configuration that was either HS or WC, with the configurations differing in stability by ca. 2 kcal/mol. The photoelectron spectrum of (MAMT)(-) occurred at a completely different electron binding energy than had (AT)(-). Moreover, the VDE value of (MAMT)(-) was in agreement with that predicted by theory. The configuration of (MAMT)(-) and its lack of electron-induced proton transfer are inter-related. While there may be other pathways for electron-induced DNA alterations, BFPT in the WC/HS configurations of (AT)(-) is not feasible.

On the interaction of electrons with betaine zwitterions

Betaine is a permanent zwitterion. The molecular betaine anion has been generated in a hybrid, infrared desorption-electron photoemission source and its photoelectron spectrum recorded. The photoelectron spectrum of the betaine anion is characteristic of a dipole bound anion, and its vertical detachment energy was measured to be 0.29+/-0.03 eV. Calculations by Rak, Skurski, and Gutowski [J. Chem. Phys. 114, 10673 (2001)] had found the betaine anion to be a dipole bound anion with a vertical detachment energy of 0.28 eV. We also measured the vertical detachment energy of deprotonated betaine to be approximately 1.9 eV.

Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy

Photodetachment photoelectron spectroscopy is used to probe the electronic structure of mono-, di-, and trinucleotide anions in the gas phase. A weak and well defined threshold band was observed in the photoelectron spectrum of 2'-deoxyguanosine 5'-monophosphate at a much lower ionization energy than the other three mononucleotides. Density function theory calculations revealed that this unique spectral feature is caused by electron-detachment from a pi orbital of the guanine base on 2'-deoxyguanosine 5'-monophosphate, whereas the lowest ionization channel for the other three mononucleotides takes place from the phosphate group. This low-energy feature was shown to be a "fingerprint" in all the spectra of dinucleotides and trinucleotides that contain the guanine base. The current experiment provides direct spectroscopic evidence that the guanine base is the site with the lowest ionization potential in oligonucleotides and DNA and is consistent with the fact that guanine is most susceptible to oxidation to give the guanine cation in DNA damage.

Valence and Dipole-Bound Anions of the Most Stable Tautomers of Guanine

Anionic states of guanine, which is the only nucleic acid base of which the anions have not yet been studied in either photoelectron spectroscopic (PES) or Rydberg electron transfer (RET) experiments, have been characterized for the four most stable tautomers of neutral guanine using a broad spectrum of electronic structure methods from the density functional theory, with the B3LYP exchange-correlation functional, to the coupled-cluster method, with single, double, and perturbative triple excitations. Both valence and dipole-bound anionic states were addressed. We identified some of the difficulties facing future PES or RET experiments on the anion of guanine. Even if guanine is successfully transferred to the gas phase without thermal decomposition, it is critical to have the canonical amino-oxo (G) and both amino-hydroxy (GH and GHN7H) tautomers in the beam, not only the most stable, a noncanonical, amino-oxo tautomer (GN7H), as the latter does not support an adiabatically bound anionic state. We also suggested a scheme for enrichment of gas-phase guanine with the canonical tautomer, which is not the most stable in the gas phase, but which is of main interest due to its biological relevance. The tautomers G, GN7H, and GHN7H support vertically bound valence anionic states with the CCSD(T) value of vertical detachment energy of +0.58, +0.21, and +0.39 eV, respectively. These anionic states are, however, adiabatically unbound and thus metastable. The vertical electronic stability of these valence anionic states is accompanied by serious "buckling" of the molecular skeleton. The G and GHN7H tautomers support dipole-bound states with the CCSD(T) values of adiabatic electron affinity of 65 and 36 meV, respectively. A contribution from higher-than-second-order correlation terms represents, respectively, 48 and 68% of the total vertical electron detachment energy determined at the CCSD(T) level.