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 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)(-).

Electron-induced elimination of the bromide anion from brominated nucleobases. A computational study.

The enhancement of radiodamage to DNA labeled with halonucleobases is attributed to the reactive radical produced from a halonucleobase by the attachment of an electron. We examined at the B3LYP/6-31++G** level electron capture by four brominated nucleobases (BrNBs): 8-bromo-9-methyladenine, 8-bromo-9-methylguanine, 5-bromo-1-methylcytosine, and 5-bromo-1-methyluracil followed by the release of the bromide anion and a nucleobase radical. We demonstrate that neutral BrNBs in both gas and aqueous phases are better electron acceptors than unsubstituted NBs and that resulting anion radicals, BrNBs(•-), can easily transform into the product complex of the bromide anion and the nucleobase radical ([Br(-)···NB(•)]). The overall thermodynamic stimulus for the process starting with the neutral BrNB and ending with the isolated bromide anion and the NB(•) radical is similar in the case of all four BrNBs studied, which suggests their comparable radiosensitizing capabilities.

Local excitation of the 5-bromouracil chromophore in DNA. Computational and UV spectroscopic studies.

The UV electronic transition energies and their oscillator strengths for two stacked dimers having B-DNA geometries and consisting of 5-bromouracil ((Br)U) and a purine base were studied at the MS-CASPT2/6-311G(d) level with an active space of 12 orbitals and 12 electrons. The calculated energy of the first vertical (π,π*) transitions for the studied dimers remain in fair agreement with the maxima in the difference spectra measured for duplexes with the 5'-A(Br)U-3' or 5'-G(Br)U-3' sequences. Our MS-CASPT2 results show that the charge transfer (CT) states in which an electron is transferred from A/G to (Br)U are located at much higher energies than the first (π,π*) transitions, which involve local excitation (LE) of (Br)U. Moreover, CT transitions are characterized by small oscillator strengths, which implies that they could not be excited directly. The results of the current studies suggest that the formation of the reactive uracil-5-yl radical in DNA is preceded by the formation of the highly oxidative LE state of (Br)U, which is followed by electron transfer, presumably from guanine.

Single strand break in DNA coupled to the O-P bond cleavage. A computational study.

In the present study, we consider the formation of a single strand break (SSB) in DNA via an alternative mechanism involving O-P bond splitting that was observed as a minor route to DNA damage induced by low-energy electrons (LEEs) or γ radiation. We postulate and characterize, at the B3LYP/6-31++G(**) level, a path that starts with LEE attachment to the nucleotide of thymine resulting in a stable valence radical anion localized on pyrimidine. In the next step, a proton is attached to the C5 position of thymine, producing a neutral monohydroradical of this nucleotide. This event triggers the subsequent intramolecular transfer of a sugar hydrogen atom from C3' or C5' to the C6 site of thymine. In the final elemental reaction, O-P bond dissociation takes place, which yields the phosphoryl radical and a cyclic ketone or aldehyde. Identification of the latter species as well as 5,6-dihydropyrimidines in DNA solutions irradiated with ionizing radiation could provide experimental confirmation of the suggested mechanism.

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.

TG-FTIR, DSC, and quantum-chemical studies on the thermal decomposition of quaternary ethylammonium halides.

The thermal decomposition of quaternary ethylammonium chloride, bromide, and iodide has been studied using the experimental techniques of thermal gravimetry coupled to Fourier transform infrared spectroscopy (TG-FTIR) and differential scanning calorimetry (DSC) as well as the density functional theory (DFT) and MP2 quantum-chemical methods. These compounds decompose in a one-step process, and the almost perfect agreement between the experimental IR spectra and those predicted at the B3LYP/6-311G(d,p) level demonstrates for the first time that decomposition produces an equimolar mixture of triethylamine and a haloethane. The respective experimental enthalpies of dissociation of the chloride, bromide, and iodide are 158, 181, and 195 kJ/mol. These values correlate well with the calculated enthalpies of dissociation based on crystal lattice energies and quantum-chemical thermodynamic barriers. The experimental activation barriers were derived from the least-squares fit of the F1 kinetic model (first-order process) to thermogravimetric traces. These estimates are 184, 286, and 387 kJ/mol for chloride, bromide, and iodide, respectively, and agree well with the theoretical calculations. It has been demonstrated that the theoretical approach assumed in this work is capable of predicting the relevant characteristics of the thermal decomposition of solids with experimental accuracy. DFT methodology is recommended for the quantum-chemical part of the model: B3LYP for evaluating the thermodynamic barriers and MPW1K for assessing the activation characteristics. These quantum-chemical data then have to be combined with crystal lattice energies. The latter should be calculated using both electrostatic and repulsion-dispersion terms.

Lipophilicity and metabolic route prediction of imidazolium ionic liquids.

AIMS AND BACKGROUND: Ionic liquid application in industry will offer several excellent solutions, but it also means that they will enter the environment sooner or later. Responsible product design should always take into consideration not only technological demands, but also the risks arising out of possible toxicity and ecotoxicity. In our strategy we are aiming to understand the fate of these entities through their life cycle in the environment as a complimentary element of their design. This paper presents results on the lipophilicity of selected imidazolium ionic liquids, a parameter that plays a key role in environmental and biological distribution. Additionally, the prediction of the most stable metabolite of a 1-butyl-3-methylimidazolium (BMIM) cation--a congener representative of this group of compounds is presented. MATERIALS AND METHODS: Lipophilicity was evaluated by means of reversed phase and immobilized artificial membrane chromatography and further compared to calculated data. Theoretical prediction of lipophilicity was undertaken using fragmental methodology combined with manual calculations of the geometric bond factor for quaternary ammonium and the electronic bond factor due to the presence of a charge. RESULTS AND DISCUSSION: All the substances studied are characterized by very low partition coefficients, and lipophilicity varies linearly with elongation of the n-alkyl chain. Prediction of metabolic routes was based solely on thermodynamic data of the radical intermediates formed during the reaction with the cytochrome P450 system. The energetically most stable radical structure is generated by hydrogen abstraction from the ac position of the BMIM cation. CONCLUSIONS AND RECOMMENDATIONS: The experimentally measured and theoretically estimated lipophilicity coefficients obtained for all the compounds studied generally indicate a relatively low lipophilicity and thus preferable partition to the aqueous phase. By means of thermodynamic data, it was also confirmed that the energetically most stable radical structure is generated by hydrogen abstraction from the alpha position on the alkyl chain in the 1-alkyl-3-methylimidazolium cation, as a result of which the C1 atom is preferentially oxidized.

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.