Electrophilic Properties of 2'-Deoxyadenosine···Thymine Dimer: Photoelectron Spectroscopy and DFT Studies.

The anion radical of the 2'-deoxyadenosine···thymine (dAT•-) pair has been investigated experimentally and theoretically in the gas phase. By employing negative-ion photoelectron spectroscopy (PES), we have registered a spectrum typical for the valence-bound anion, featuring a broad peak at the electron-binding energy (EBE) between ∼1.5 and 2.2 eV with the maximum at ∼1.9 eV. The measured value of the adiabatic electron affinity (AEA) for dAT was estimated to be ∼1.1 eV. Calculations performed at the M06-2X/6-31++G(d,p) level revealed that the structure, where thymine is coordinated to the sugar of dA by two hydrogen bonds, is responsible for the observed PES signal. The AEAG and the vertical detachment energy of 0.91 and 1.68 eV, respectively, calculated for this structure reproduce the experimental values well. The role of the possible proton transfer in the stabilization of anionic radical complexes is discussed.

Excess Electron Attachment to the Nucleoside Pair 2'-Deoxyadenosine (dA)-2'-Deoxythymidine (dT).

The 2'-deoxyadenosine···2'-deoxythymidine (dAdT(•-)) radical anion nucleoside pair has been investigated both experimentally and theoretically in the gas phase. The vertical detachment energy (VDE) and adiabatic electron affinity (AEA) were determined by anion photoelectron spectroscopy (PES). The measured photoelectron spectrum features a broad band having an onset at ∼1.1 eV and a maximum at the electron binding energy (EBE) ranging from 1.7 to 1.9 eV. Calculations performed at the M06-2X/6-31++G** level reveal that the observed PES signal is probably due to a dAdT(•-) complex in which the thymine of the dT nucleoside forms hydrogen bonds that engage its O7 and O8 atoms as well as the 3'- and 5'-hydroxyl groups of 2'-deoxyadenosine (dA), while dT's 3'-hydroxyl group interacts with the N1 of dA. In this heterodimer, the excess electron is entirely located on thymine. The biologically relevant Watson-Crick arrangement of the dAdT(•-) dimer was found to be substantially less stable (by ∼19 kcal mol(-1) in Gibbs free energy scale) than the above-mentioned configuration; hence, it is not populated in the gas phase.

Photoelectron spectroscopy of boron aluminum hydride cluster anions.

Boron aluminum hydride clusters are studied through a synergetic combination of anion photoelectron spectroscopy and density functional theory based calculations. Boron aluminum hydride cluster anions, BxAlyHz(-), were generated in a pulsed arc cluster ionization source and identified by time-of-flight mass spectrometry. After mass selection, their photoelectron spectra were measured by a magnetic bottle-type electron energy analyzer. The resultant photoelectron spectra as well as calculations on a selected series of stoichiometries reveal significant geometrical changes upon substitution of aluminum atoms by boron atoms.

The viability of aluminum Zintl anion moieties within magnesium-aluminum clusters.

Through a synergetic combination of anion photoelectron spectroscopy and density functional theory based calculations, we have investigated the extent to which the aluminum moieties within selected magnesium-aluminum clusters are Zintl anions. Magnesium-aluminum cluster anions were generated in a pulsed arc discharge source. After mass selection, photoelectron spectra of MgmAln (-) (m, n = 1,6; 2,5; 2,12; and 3,11) were measured by a magnetic bottle, electron energy analyzer. Calculations on these four stoichiometries provided geometric structures and full charge analyses for the cluster anions and their neutral cluster counterparts, as well as photodetachment transition energies (stick spectra). Calculations revealed that, unlike the cases of recently reported sodium-aluminum clusters, the formation of aluminum Zintl anion moieties within magnesium-aluminum clusters was limited in most cases by weak charge transfer between the magnesium atoms and their aluminum cluster moieties. Only in cases of high magnesium content, e.g., in Mg3Al11 and Mg2Al12 (-), did the aluminum moieties exhibit Zintl anion-like characteristics.

Aluminum Zintl anion moieties within sodium aluminum clusters.

Through a synergetic combination of anion photoelectron spectroscopy and density functional theory based calculations, we have established that aluminum moieties within selected sodium-aluminum clusters are Zintl anions. Sodium-aluminum cluster anions, Na(m)Al(n)(-), were generated in a pulsed arc discharge source. After mass selection, their photoelectron spectra were measured by a magnetic bottle, electron energy analyzer. Calculations on a select sub-set of stoichiometries provided geometric structures and full charge analyses for both cluster anions and their neutral cluster counterparts, as well as photodetachment transition energies (stick spectra), and fragment molecular orbital based correlation diagrams.

Photoelectron spectroscopic and density functional theoretical studies of the 2'-deoxycytidine homodimer radical anion.

The intact (parent) 2'-deoxycytidine homodimer anion, (dC)2 (●-), was generated in the gas phase (in vacuo) using an infrared desorption∕photoemission source and its photoelectron spectrum was recorded using a pulsed, magnetic bottle photoelectron spectrometer. The photoelectron spectrum (PES) revealed a broad peak with the maximum at an electron binding energy between 1.6 and 1.9 eV and with a threshold at ∼1.2 eV. The relative energies and vertical detachment energies of possible anion radicals were calculated at the B3LYP/6-31++G(∗∗) level of theory. The most stable anion radicals are the complexes involving combinations of the sugar[middle dot][middle dot][middle dot]base and base[middle dot][middle dot][middle dot]base interactions. The calculated adiabatic electron affinities and vertical detachment energies of the most stable (dC)2 (●-) anions agree with the experimental values. In contrast with previous experimental-computational studies on the anionic complexes involving nucleobases with various proton-donors, the electron-induced proton transferred structures of (dC)2 (●-) are not responsible for the shape of PES.

Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions.

We report the photoelectron spectrum (PES) of the homogeneous dimer anion radical of uridine, (rU)(2)(●-). It features a broad band consisting of an onset of ∼1.2 eV and a maximum at the electron binding energy (EBE) ranging from 2.0 to 2.5 eV. Calculations performed at the B3LYP∕6-31++G∗∗ level of theory suggest that the PES is dominated by dimeric radical anions in which one uridine nucleoside, hosting the excess charge on the base moiety, forms hydrogen bonds via its O8 atom with hydroxyl of the other neutral nucleoside's ribose. The calculated adiabatic electron affinities (AEAGs) and vertical detachment energies (VDEs) of the most stable homodimers show an excellent agreement with the experimental values. The anionic complexes consisting of two intermolecular uracil-uracil hydrogen bonds appeared to be substantially less stable than the uracil-ribose dimers. Despite the fact that uracil-uracil anionic homodimers are additionally stabilized by barrier-free electron-induced proton transfer, their relative thermodynamic stabilities and the calculated VDEs suggest that they do not contribute to the experimental PES spectrum of (rU)(2)(●-).

Photoelectron spectroscopy and computational modeling of thymidine homodimer anions.

The intact thymidine homodimer anion (dT(2)(-)) was generated in the gas phase using an infrared desorption/photoemission source and recorded by a pulsed photoelectron spectrometer. The photoelectron spectrum (PES) revealed a broad signal with the maximum at electron binding energy ∼2.0 eV and the threshold value at 1.1 eV. The relative energies and vertical detachment energies of the possible anion structures were calculated at the B3LYP/6-31++G(d,p) level. Here we report that the most stable anion radical homodimer geometries observed in the PES are the anionic nucleoside coordinated by the O8 atom of thymine to the deoxyribose of the second neutral nucleoside. Unlike previous experimental-computational studies on anionic complexes involving nucleobases with proton donors, the electron-induced proton-transferred structures are not responsible for the shape of the PES of dT(2)(-).

Magnetic structure variation in manganese-oxide clusters.

Negative-ion photoelectron spectroscopy and ab initio simulations are used to study the variation in magnetic structure in Mn(x)O(y) (x = 3, 4[semicolon] y = 1, 2) clusters. The ferrimagnetic and antiferromagnetic ground-state structures of Mn(x)O(y) are 0.16-1.20 eV lower in energy than their ferromagnetic isomers. The presence of oxygen thus stabilizes low-spin isomers relative to the preferred high-spin ordering of bare Mn(3) and Mn(4). Each cluster has a preferred overall magnetic moment, and no evidence is seen of competing states with different spin multiplicities. However, non-degenerate isomags, which possess the same spin multiplicity but different arrangements of local moments, do contribute additional features and peak broadening in the photoelectron spectra. Proper accounting for all possible isomags is shown to be critical for accurate computational prediction of the spectra.

Valence anions of N-acetylproline in the gas phase: computational and anion photoelectron spectroscopic studies.

We report the photoelectron spectrum of anionic N-acetylproline, (N-AcPro)(-), measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that N-acetylproline forms a valence anion in the gas phase. The neutrals and anions of N-AcPro were also studied computationally at the B3LYP∕6-31++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π* orbital localized at the acetyl group of N-AcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic N-AcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.

Photoelectron spectroscopic and computational studies of the Pt@Pb10⁻¹ and Pt@Pb12¹â»/²â» anions.

A combination of anion photoelectron spectroscopy and density functional theory calculations has elucidated the geometric and electronic structure of gas-phase endohedral Pt/Pb cage cluster anions. The anions, Pt@Pb10⁻¹ and Pt@Pb12¹â» were prepared from "preassembled" clusters generated from crystalline samples of [K(2,2,2-crypt)]2[Pt@Pb12] that were brought into the gas phase using a unique infrared desorption/photoemission anion source. The use of crystalline [K(2,2,2-crypt)]2[Pt@Pb12] also provided access to K[Pt@Pb(n)](-) anions in the gas phase (i.e., the K⁺ salts of the Pt@Pb(n)²â» anions). Anion photoelectron spectra of Pt@Pb10⁻¹, Pt@Pb12¹â», and K[Pt@Pb12]¹â» are presented. Extensive density functional theory calculations on Pt@Pb10³â»/²â»/¹â»/° and Pt@Pb12²â»/¹â» provided candidate structures and anion photoelectron spectra for Pt@Pb10⁻¹ and Pt@Pb12¹â». Together, the calculated and measured photoelectron spectra show that Pt@Pb10⁻¹ and Pt@Pb12²â»/¹â» endohedral complexes maintain their respective D(4d) and slightly distorted I(h) symmetries in the gas phase even for the charge states with open shell character. Aside from the fullerenes, the Pt@Pb12²â» endohedral complex is the only bare cluster that has been structurally characterized in the solid state, solution, and the gas phase.

Joint photoelectron and theoretical study of (Rh(m)Co(n))⁻ (m=1-5, n=1-2) cluster anions and their neutral counterparts.

Anion photoelectron spectroscopic experiments and calculations based on density functional theory have been used to investigate and uniquely identify the structural, electronic, and magnetic properties of both neutral and anionic (Rh(m)Co(n)) and (Rh(m)Co(n))(-) (m=1-5, n=1-2) clusters, respectively. Negative ion photoelectron spectra are presented for electron binding energies up to 3.493 eV. The calculated electron affinities and vertical detachment energies are in good agreement with the measured values. Computational results for geometric structures and magnetic moments of both cluster anions and their neutrals are presented.

Photoelectron and computational studies of the copper-nucleoside anionic complexes, Cu(-)(cytidine) and Cu(-)(uridine).

The copper-nucleoside anions, Cu(-)(cytidine) and Cu(-)(uridine), have been generated in the gas phase and studied by both experimental (anion photoelectron spectroscopy) and theoretical (density functional calculations) methods. The photoelectron spectra of both systems are dominated by single, intense, and relatively narrow peaks. These peaks are centered at 2.63 and 2.71 eV for Cu(-)(cytidine) and Cu(-)(uridine), respectively. According to our calculations, Cu(-)(cytidine) and Cu(-)(uridine) species with these peak center [vertical detachment energy (VDE)] values correspond to structures in which copper atomic anions are bound to the sugar portions of their corresponding nucleosides largely through electrostatic interactions; the observed species are anion-molecule complexes. The combination of experiment and theory also reveal the presence of a slightly higher energy, anion-molecule complex isomer in the case of the Cu(-)(cytidine). Furthermore, our calculations found that chemically bond isomers of these species are much more stable than their anion-molecule complex counterparts, but since their calculated VDE values are larger than the photon energy used in these experiments, they were not observed.

Photoelectron spectroscopic studies of 5-halouracil anions.

The parent negative ions of 5-chlorouracil, UCl(-) and 5-fluorouracil, UF(-) have been studied using anion photoelectron spectroscopy in order to investigate the electrophilic properties of their corresponding neutral halouracils. The vertical detachment energies (VDE) of these anions and the adiabatic electron affinities (EA) of their neutral molecular counterparts are reported. These results are in good agreement with the results of previously published theoretical calculations. The VDE values for both UCl(-) and UF(-) and the EA values for their neutral molecular counterparts are much greater than the corresponding values for both anionic and neutral forms of canonical uracil and thymine. These results are consistent with the observation that DNA is more sensitive to radiation damage when thymine is replaced by halouracil. While we also attempted to prepare the parent anion of 5-bromouracil, UBr(-), we did not observe it, the mass spectrum exhibiting only Br(-) fragments, i.e., 5-bromouracil apparently underwent dissociative electron attachment. This observation is consistent with a previous assessment, suggesting that 5-bromouracil is the best radio-sensitizer among these three halo-nucleobases.

Electronic structure and properties of isoelectronic magic clusters: Al13X (X=H,Au,Li,Na,K,Rb,Cs).

The equilibrium structure, stability, and electronic properties of the Al(13)X (X=H,Au,Li,Na,K,Rb,Cs) clusters have been studied using a combination of photoelectron spectroscopy experiment and density functional theory. All these clusters constitute 40 electron systems with 39 electrons contributed by the 13 Al atoms and 1 electron contributed by each of the X (X=H,Au,Li,Na,K,Rb,Cs) atom. A systematic study allows us to investigate whether all electrons contributed by the X atoms are alike and whether the structure, stability, and properties of all the magic clusters are similar. Furthermore, quantitative agreement between the calculated and the measured electron affinities and vertical detachment energies enable us to identify the ground state geometries of these clusters both in neutral and anionic configurations.

The anionic (9-methyladenine)-(1-methylthymine) base pair solvated by formic acid. A computational and photoelectron spectroscopy study.

The photoelectron spectrum for (1-methylthymine)-(9-methyladenine)...(formic acid) (1MT-9MA...FA) anions with the maximum at ca. 1.87 eV was recorded with 2.54 eV photons and interpreted through the quantum-chemical modeling carried out at the B3LYP/6-31+G(d,p) level. The relative free energies of the anions and their calculated vertical detachment energies suggest that only seven anionic structures contribute to the observed PES signal. We demonstrate that electron binding to the (1MT-9MA...FA) complex can trigger intermolecular proton transfer from formic acid, leading to the strong stabilization of the resulting radical anion. The SOMO distribution indicates that an excess electron may localize not only on the pyrimidine but also on the purine moiety. The biological context of DNA-environment interactions concerning the formation of single-strand breaks induced by excess electrons has been briefly discussed.

Combined experimental and theoretical investigation of three-dimensional, nitrogen-doped, gallium cluster anions.

Anion photoelectron spectra of Ga(x)N(y)(-) cluster anions, in which x = 4-12, y = 1 and x = 7-12, y = 2, were measured. Ab initio studies were conducted on Ga(x)N(y)(-) cluster anions in which x = 4-7, y = 1 and Ga(7)N(2)(-), providing their structures and electronic properties. The photoelectron spectra were interpreted in terms of the computational results. This allowed for identification of the isomers present in the beam experiments for specific Ga(x)N(-) cluster anions (x = 4-7). The unexpected presence of Ga(x)N(2)(-) species is also reported.

Photoelectron spectroscopy of homogeneous nucleic acid base dimer anions.

We report the photoelectron spectra of homogeneous dimer anions of the nucleobases: uracil, thymine, cytosine, adenine, and guanine, i.e., U(2)(-), T(2)(-), C(2)(-), A(2)(-), and G(2)(-) along with DFT calculations on U(2)(-) and T(2)(-). Based on these calculations the photoelectron spectrum of T(2)(-) was assigned as being due to both a proton transferred and a non-proton transferred isomer, while the photoelectron spectrum of U(2)(-) was assigned in terms of a single dominant barrier-free proton transferred isomer. Photoelectron spectra were also measured with a different source and on a different type of photoelectron spectrometer for U(2)(-), T(2)(-), A(2)(-), (1-MeT)(2)(-) and (1,3-Me(2)U)(2)(-).

Low-energy-barrier proton transfer induced by electron attachment to the guanine...cytosine base pair.

The photoelectron spectrum of the anion of the guanine...cytosine base pair (GC)(*-) is recorded for the first time. The observed variation in the spectral peak-height ratios with the source conditions suggests the presence of two or more anionic isomers. Two maxima of the broad bands in the photoelectron spectrum were measured at about 1.9 and about 2.6 eV. These values are very well reproduced by the vertical detachment energies of the B3LYP/6-31++G(d,p) calculated low-energy anionic structures, which are 1) the Watson-Crick base-pair anion with proton transferred from N1 of guanine to N3 of cytosine, 2) its analogue in which the proton is transferred from N9 of guanine to N7 of guanine, and 3) the global minimum geometry, which is formed from the latter anion by rotation of guanine about the axis approximately defined by C2 of guanine and C4 of cytosine. Furthermore, a minor difference in the stabilities of the two lowest energy anions explains the experimentally observed source (temperature) dependence of the PES spectrum. A rational procedure, based on the chemistry involved in the formation of anionic dimers, which enables the low-energy anions populated in the photoelectron spectrum to be identified is proposed. In contrast to the alternative combinatorial approach, which in the studied case would lead to carrying out quantum chemical calculations for 2000-2500 structures, the procedure described here reduces the computational problem to only 15 geometries.