Two-body dissociation of isoxazole following double photoionization - an experimental PEPIPICO and theoretical DFT and MP2 study.

The dissociative double photoionization of isoxazole molecules has been investigated experimentally and theoretically. The experiment has been carried out in the 27.5-36 eV photon energy range using vacuum ultraviolet (VUV) synchrotron radiation excitation combined with ion time-of-flight (TOF) spectrometry and photoelectron-photoion-photoion coincidence (PEPIPICO) technique. Five well-resolved two-body dissociation channels have been identified in the isoxazole's coincidence maps, and their appearance energies have been determined. The coincidence yield curves of these dissociation channels have been obtained in the photon energy ranges from their appearance energies up to 36 eV. The double photoionization of isoxazole produces a C3H3NO2+ transient dication, which decomposes into fragments differing from previously reported photofragmentation products of isoxazole. We have found no evidence of pathways leading to the C3H2NO+, HCN+, C2H2O+, C3HN+, or C2H2+ fragments or their neutral counterparts that have been observed in previous neutral photodissociation and single photoionization studies. Instead, the dissociation of isoxazole after the ejection of two electrons is bond-selective and is governed by two reactions, HCO+ + H2CCN+ and H2CO+ + HCCN+, whose appearance energies are 28.6 (±0.3) and 29.4 (±0.3) eV, respectively. A third dissociation channel turns out to be a variant of the most intense channel (HCO+ + H2CCN+), where one of the fragment ions contains a heavy isotope. Two minor dissociation channels occurring at higher energies, CO+ + CH3CN+ and CN+ + H3CCO+, are also identified. The density functional and ab initio quantum chemical calculations have been performed to elucidate the dissociative charge-separating mechanisms and determine the energies of the observed photoproducts. The present work unravels hitherto unexplored photodissociation mechanisms of isoxazole and thus provides deeper insight into the photophysics of five-membered heterocyclic molecules containing two heteroatoms.

Hydrogen bonding and protonation effects in amino acids' anthraquinone derivatives - Spectroscopic and electrochemical studies.

Six novel amino acid chromophores were synthesized and their spectroscopic, acid-base, and electrochemical properties are discussed in this work. In studied compounds, selected amino acid residues (l-Aspartic acid, l-Glutamic acid, l-Glutamine, l-Histidine, l-Lysine, l-Arginine) are attached to the 1-(piperazine) 9,10-anthraquinone skeleton via the amide bond between the carboxyl group of amino acid and nitrogen atom of the piperazine ring. All derivatives have been characterized using a variety of spectroscopic techniques (mass spectrometry, 1HNMR, UV-Vis, IR spectroscopy), acid-base (electrochemical and UV-Vis) titrations, and cyclic voltammetry methods. Basing on observed experimental effects, supported by quantum chemical simulations, the structure-properties links were established. They are indicative of the specific interactions within and/or in-between amino acid side groups, which are prone to form both, intra- and intermolecular hydrogen bonds as well as electrostatic interactions with the anthraquinone system.

Stability of the Parent Anion of the Potential Radiosensitizer 8-Bromoadenine Formed by Low-Energy (<3 eV) Electron Attachment.

8-Bromoadenine (8BrA) is a potential DNA radiosensitizer for cancer radiation therapy due to its efficient interaction with low-energy electrons (LEEs). LEEs are a short-living species generated during the radiation damage of DNA by high-energy radiation as it is applied in cancer radiation therapy. Electron attachment to 8BrA in the gas phase results in a stable parent anion below 3 eV electron energy in addition to fragmentation products formed by resonant exocyclic bond cleavages. Density functional theory (DFT) calculations of the 8BrA- anion reveal an exotic bond between the bromine and the C8 atom with a bond length of 2.6 Å, where the majority of the charge is located on bromine and the spin is mainly located on the C8 atom. The detailed understanding of such long-lived anionic states of nucleobase analogues supports the rational development of new therapeutic agents, in which the enhancement of dissociative electron transfer to the DNA backbone is critical to induce DNA strand breaks in cancerous tissue.

Sensitizing DNA Towards Low-Energy Electrons with 2-Fluoroadenine.

2-Fluoroadenine ((2F) A) is a therapeutic agent, which is suggested for application in cancer radiotherapy. The molecular mechanism of DNA radiation damage can be ascribed to a significant extent to the action of low-energy (<20 eV) electrons (LEEs), which damage DNA by dissociative electron attachment. LEE induced reactions in (2F) A are characterized both isolated in the gas phase and in the condensed phase when it is incorporated into DNA. Information about negative ion resonances and anion-mediated fragmentation reactions is combined with an absolute quantification of DNA strand breaks in (2F) A-containing oligonucleotides upon irradiation with LEEs. The incorporation of (2F) A into DNA results in an enhanced strand breakage. The strand-break cross sections are clearly energy dependent, whereas the strand-break enhancements by (2F) A at 5.5, 10, and 15 eV are very similar. Thus, (2F) A can be considered an effective radiosensitizer operative at a wide range of electron energies.

Hydrogen migration in formation of NH(A³Π) radicals via superexcited states in photodissociation of isoxazole molecules.

Formation of the excited NH(A(3)Π) free radicals in the photodissociation of isoxazole (C3H3NO) molecules has been studied over the 14-22 eV energy range using photon-induced fluorescence spectroscopy. The NH(A(3)Π) is produced through excitation of the isoxazole molecules into higher-lying superexcited states. Observation of the NH radical, which is not a structural unit of the isoxazole molecule, corroborates the hydrogen atom (or proton) migration within the molecule prior to dissociation. The vertical excitation energies of the superexcited states were determined and the dissociation mechanisms of isoxazole are discussed. The density functional and ab initio quantum chemical calculations have been performed to study the mechanism of the NH formation.

Reactions in gas phase and condensed phase C6F5X (X = NCO, CH2CN) triggered by low energy electrons.

Electron attachment to gas phase perfluorophenylisocyanate (C(6)F(5)NCO) and perfluorophenyloacetonitrile (C(6)F(5)CH(2)CN) generates metastable parent anions within a very narrow resonance close to zero energy. At higher energies (2-7 eV), dissociative electron attachment (DEA) resonances are present, associated with the rupture of the C(6)F(5)-X bond (X = NCO, CH(2)CN) with the excess electron finally localised on either of the two fragments. The most intense fragment ion from C(6)F(5)CH(2)CN (M) is (M - HF)(-), which arises from the loss of a neutral HF from the transient anion and requires the concerted cleavage of two bonds and formation of a new molecule (HF). Most remarkably, this rather complex DEA reaction is by about two orders of magnitude more intense than the single bond cleavages (C(6)F(5)-X) leading to the complementary DEA reactions C(6)F(5) + X(-) and C(6)F(5)(-) + X. From both condensed molecules we observe desorption of F(-) and CN(-) and, additionally, O(-) from C(6)F(5)NCO. The desorption yields also show a resonant behaviour with the peak maxima in the range 8-12 eV, i.e., near or above the ionization energy, indicating that in electron stimulated desorption (ESD) highly excited resonances are involved. Ab initio calculations are performed in order to get information on the shape and energy of the molecular orbitals involved in low energy (<2 eV) electron attachment.

Excision of CN(-) and OCN(-) from acetamide and some amide derivatives triggered by low energy electrons.

Low energy electron attachment to acetamide and some of its derivatives shows unique features in that the unimolecular reactions of the transient anions are remarkably complex, involving multiple bond cleavages and the formation of new molecules. Each of the three compounds acetamide (CH(3)C(O)NH(2)), glycolamide (CH(2)OHC(O)NH(2)) and cyanoacetamide (CH(2)CNC(O)NH(2)) shows a pronounced resonance located near 2 eV and decomposing into CN(-) along a concerted reaction forming a neutral H(2)O molecule and the corresponding radical (methyl and methoxy). From glycolamide an additional reaction pathway resulting in the loss of water is operative, in this case generating two fragments and observable via the complementary anion (M-H(2)O)(-). The pseudohalogen OCN(-) is formed at comparatively lower intensity having a specific energy profile for each of the target molecules. In dibromocyanoacetamide (CBr(2)CNC(O)NH(2)) the situation changes completely as now comparatively intense CN(-) and OCN(-) signals appear already near zero eV. Electronic structure calculations predict that in dibromocyanoacetamide the extra electron resides in a molecular orbital (MO) which is strongly localized at the Br sites. For the other compounds, the relevant MOs are appreciably delocalized showing pi*(C=O) character.

Electron capture by pentafluoronitrobenzene and pentafluorobenzonitrile.

Electron attachment to pentafluorobenzonitrile (C(6)F(5)CN) and pentafluoronitrobenzene (C(6)F(5)NO(2)) is studied in the energy range 0-16 eV by means of a crossed electron-molecular beam experiment with mass spectrometric detection of the anions. We find that pentafluoronitrobenzene exclusively generates fragment anions via dissociative electron attachment (DEA), while pentafluorobenzonitrile forms a long lived parent anion within a narrow energy range close to 0 eV and additionally undergoes DEA at higher energies. This is in contrast to the behaviour of the non-fluorinated analogues as in nitrobenzene the non-decomposed anion is formed while in benzonitrile only DEA is observed. The associated reactions involve simple bond cleavages but also complex unimolecular decompositions associated with structural and electronic rearrangement also resulting in the deterioration of the cyclic structure.

Cylindrical projection of electrostatic potential and image analysis tools for damaged DNA: the substitution of thymine with thymine glycol.

Changes of electrostatic potential around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through electronic structure computations. Quantum mechanical structural optimizations of fragments of five pairs of nucleotides with thymine or thymine glycol were performed at the density functional level of theory with a B3LYP exchange-correlation functional and 6-31G(d,p) basis sets. The electrostatic potential (EP) around DNA fragments was projected on a cylindrical surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were compared using image analysis methods to identify and measure modifications of the EP that result from the occurrence of thymine glycol. It was found that distortions of phosphate groups and displacements of the accompanying countercations by up to approximately 0.5 angstroms along the axis of DNA are clearly reflected in the EP maps. Modifications of the EP in the major groove of DNA near the damaged site are also reported.

Bond and site selectivity in dissociative electron attachment to gas phase and condensed phase ethanol and trifluoroethanol.

The formation of negative ions following electron impact to ethanol (CH(3)CH(2)OH) and trifluoroethanol (CF(3)CH(2)OH) is studied in the gas phase by means of a crossed electron-molecular beam experiment and in the condensed phase via Electron Stimulated Desorption (ESD) of fragment ions from the corresponding molecular films under UHV conditions. Gas phase ethanol exhibits two pronounced resonances, located at 5.5 eV and 8.2 eV, associated with a remarkable selectivity in the decomposition of the precursor ion. While the low energy resonance exclusively decomposes into O(-), that at higher energy generates OH(-) and a comparatively small signal of [CH(3)CH(2)O](-) due to the loss of a neutral hydrogen. CF(3)CH(2)OH shows a completely different behaviour, as now an intense feature at 1.7 eV appears associated with the loss of a neutral hydrogen atom exclusively occurring at the O site. The H(-) formation from the gas phase compounds is below the detection limit of the present experiment, while in ESD from 3 MonoLayer (ML) films of CH(3)CH(2)OH and CF(3)CH(2)OH the most intense fragment is H(-), appearing from a broad resonant feature between 7 and 12 eV. With CF(3)CH(2)OH, by using the isotopically-labelled analogues CF(3)CD(2)OH and CF(3)CH(2)OD it can be shown that this feature consists of two resonances, one located at 8 eV leading to H(-)/D(-) loss from the O site and a second resonance located at 10 eV leading to the loss of H(-)/D(-) from the CH(2) site.

Energy selective excision of CN- following electron attachment to hexafluoroacetone azine ((CF3)2C=N-N=C(CF3)2).

Low energy electron attachment (DEA) to hexafluoroacetone azine (HFAA) leads to a remarkable energy selective excision of CN(-) within a pronounced resonance located at 1.35 eV. The underlying dissociative electron attachment (DEA) reaction involves multiple bond cleavages and rearrangement within the neutral products. A series of further fragment ions (F(-), CF(3)(-), (CF(3))(2)C(-) and (CF(3))(2)CN(-)) are observed from resonant features above 2 eV and only (CF(3))(2)CN(-) is additionally formed within a narrow resonance below 1 eV. In contrast to CN(-) all the remaining fragment ions can be formed by simple bond cleavages with (CF(3))(2)CN(-) being the result of a symmetric decomposition of the target molecule by cleavage of the (N-N) bond with the excess charge localised on either of the identical fragments. Our ab initio calculations predict an adiabatic electron affinity of HFAA close to 2 eV with the geometry of the relaxed anion considerably distorted with respect to that of the neutral molecule.

Low energy electron-induced reactions in gas phase 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose: a model system for the behavior of sugar in DNA.

Dissociative electron attachment to 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose (TAR) is studied in a crossed electron-molecular beam experiment with mass spectrometric detection of the observed fragment ions. Since in TAR acetyl groups are coupled at the relevant positions to the five membered ribose ring, it may serve as an appropriate model compound to study the response of the sugar unit in DNA towards low energy electrons. Intense resonances close to 0 eV are observed similar to the pure gas phase sugars (2-deoxyribose, ribose, and fructose). Further strong resonances appear in the range of 1.6-1.8 eV (not present in the pure sugars). Based on calculations on transient anions adopting the stabilization method, this feature is assigned to a series of closely spaced shape resonances of pi* character with the extra electron localized on the acetyl groups outside the ribose ring system. Further but weaker resonant contributions are observed in the range of 7-11 eV, representing core excited resonances and/or sigma* shape resonances. The decomposition processes involve single bond ruptures but also more complex reactions associated with substantial rearrangement. The authors hence propose that the sugar unit in DNA plays an active role in the molecular mechanism towards single strand breaks induced by low energy electrons.

Electronic structure differences in ZrO2 vs HfO2.

Although ZrO2 and HfO2 are, for the most part, quite similar chemically, subtle differences in their electronic structures appear to be responsible for differing MO2/Si (M = Zr, Hf) interface stabilities. To shed light on the electronic structure differences between ZrO2 and HfO2, we have conducted joint experimental and theoretical studies. Because molecular electron affinities are a sensitive probe of electronic structure, we have measured them by conducting photoelectron spectroscopic experiments on ZrO2(-) and HfO2(-). The adiabatic electron affinity of HfO2 was determined to be 2.14 +/- 0.03 eV, and that of ZrO2 was determined to be 1.64 +/- 0.03 eV. Concurrently, advanced electronic structure calculations were conducted to determine electron affinities, vibrational frequencies, and geometries of these systems. The calculated CCSD(T) electron affinities of HfO2 and ZrO2 were found to be 2.05 and 1.62 eV, respectively. The molecular results confirm earlier predictions from solid state calculations that HfO2 is more ionic than ZrO2. The excess electron in MO2(-) occupies an sd-type hybrid orbital localized on the M atom (M = Zr, Hf). The structural parameters of ZrO2 and HfO2 and their vibrational frequencies were found to be very similar. Upon the excess electron attachment, the M-O bond length increases by ca. 0.04 A, the OMO angle increases by 2-4 degrees, and frequencies of all vibrational modes become smaller, with the stretching modes being shifted by 30-50 cm(-1) and the bending mode by 15-25 cm(-1). Together, these studies unveil significant differences in the electronic structures of ZrO2 and HfO2 but not in their structural or vibrational characteristics.

Anion of the formic acid dimer as a model for intermolecular proton transfer induced by a pi* excess electron.

The neutral and anionic formic acid dimers have been studied at the second-order Moller-Plesset and coupled-cluster level of theory with single, double, and perturbative triple excitations with augmented, correlation-consistent basis sets of double- and triple-zeta quality. Scans of the potential-energy surface for the anion were performed at the density-functional level of theory with a hybrid B3LYP functional and a high-quality basis set. Our main finding is that the formic acid dimer is susceptible to intermolecular proton transfer upon an excess electron attachment. The unpaired electron occupies a pi(*) orbital, the molecular moiety that accommodates an excess electron "buckles," and a proton is transferred to the unit where the excess electron is localized. As a consequence of these geometrical transformations, the electron vertical detachment energy becomes substantial, 2.35 eV. The anion is barely adiabatically unstable with respect to the neutral at 0 K. However, at standard conditions and in terms of Gibbs free energy, the anion is more stable than the neutral by +37 meV. The neutral and anionic dimers display different IR characteristics. In summary, the formic acid dimer can exist in two quasidegenerate states (neutral and anionic), which can be viewed as "zero" and "one" in the binary system. These two states are switchable and distinguishable.

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level.

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.

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.

Interaction with glycine increases stability of a mutagenic tautomer of uracil. A density functional theory study.

The most stable structures for the gas-phase complexes of minor tautomers of uracil (U) with glycine (G) were characterized at the density functional B3LYP/6-31++G level of theory. These are cyclic structures stabilized by two hydrogen bonds. The relative stability of isolated tautomers of uracil was rationalized by using thermodynamic and structural arguments. The stabilization energies for complexes between the tautomers of U and G result from interplay between the stabilizing two-body interaction energies and destabilizing one-body terms. The latter are related to the energies of (i) tautomerization of the unperturbed moieties and (ii) distortions of the resulting rare tautomers in the complex. The two-body term describes the interaction energy between distorted tautomers. The two-body interaction energy term correlates with perturbations of length of the proton-donor bonds as well as with deprotonation enthalpies and proton affinities of the appropriate monomer sites. It was demonstrated that the relative instability of rare tautomers of uracil is diminished due to their interactions with glycine. In particular, the instability of the third most stable tautomer (U(III)) is decreased from 11.9 kcal/mol for non-interacting uracil to 6.7 kcal/mol for uracil in a complex with the zwitterionic tautomer of glycine. A decrease of instability by 5.2 kcal/mol could result in an increase of concentration of U(III) by almost 5 orders of magnitude. This is the tautomer with proton donor and acceptor sites matching guanine rather than adenine. Moreover, kinetic characteristics obtained for the glycine-assisted conversion of the most stable tautomer of uracil (U(I)) to U(III) indicate that the U(I)<-->U(III) thermodynamic equilibrium could be easily attained at room temperature. The resulting concentration of this tautomer falls in a mutationally significant range.

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels.

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.

Barrier-free intermolecular proton transfer induced by excess electron attachment to the complex of alanine with uracil.

The photoelectron spectrum of the uracil-alanine anionic complex (UA)(-) has been recorded with 2.540 eV photons. This spectrum reveals a broad feature with a maximum between 1.6 and 2.1 eV. The vertical electron detachment energy is too large to be attributed to an (UA)(-) anionic complex in which an intact uracil anion is solvated by alanine, or vice versa. The neutral and anionic complexes of uracil and alanine were studied at the B3LYP and second-order Møller-Plesset level of theory with 6-31++G(*) (*) basis sets. The neutral complexes form cyclic hydrogen bonds and the three most stable neutral complexes are bound by 0.72, 0.61, and 0.57 eV. The electron hole in complexes of uracil with alanine is localized on uracil, but the formation of a complex with alanine strongly modulates the vertical ionization energy of uracil. The theoretical results indicate that the excess electron in (UA)(-) occupies a pi(*) orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of alanine to the O8 atom of uracil. As a result, the four most stable structures of the uracil-alanine anionic complex can be characterized as a neutral radical of hydrogenated uracil solvated by a deprotonated alanine. Our current results for the anionic complex of uracil with alanine are similar to our previous results for the anion of uracil with glycine, and together they indicate that the BFPT process is not very sensitive to the nature of the amino acid's hydrophobic residual group. The BFPT to the O8 atom of uracil may be relevant to the damage suffered by nucleic acid bases due to exposure to low energy electrons.