Potassium-uracil/thymine ring cleavage enhancement as studied in electron transfer experiments and theoretical calculations

Low-lying Negative Ion States Probed in Potassium - Ethanol Collisions

Dissociative electron transfer in collisions between neutral potassium atoms and neutral ethanol molecules yields mainly OH-, followed by C2H5O-, O-, CH3 - and CH2 -. The dynamics of negative ions have been investigated by recording time-of-flight mass spectra in a wide range of collision energies from 17.5 to 350 eV in the lab frame, where the branching ratios show a relevant energy dependence for low/intermediate collision energies. The dominant fragmentation channel in the whole energy range investigated has been assigned to the hydroxyl anion in contrast to oxygen anion from dissociative electron attachment (DEA) experiments. This result shows the relevant role of the electron donor in the vicinity of the temporary negative ion formed allowing access to reactions which are not thermodynamically attained in DEA experiments. The electronic state spectroscopy of such negative ions, was obtained from potassium cation energy loss spectra in the forward scattering direction at 205 eV impact energy, showing a prevalent Feshbach resonance at 9.36±0.10 eV withσ O H * / σ C H * ${{\sigma }_{OH}^{^{\ast}}/{\sigma }_{CH}^{^{\ast}}}$ character, while a less pronouncedσ O H * ${{\sigma }_{OH}^{^{\ast}}}$ contribution assigned to a shape resonance has been obtained at 3.16±0.10 eV. Quantum chemical calculations for the lowest-lying unoccupied molecular orbitals in the presence of a potassium atom have been performed to support the experimental findings.

Isotope Effect in D2O Negative Ion Formation in Electron Transfer Experiments: DO-D Bond Dissociation Energy

H2O/D2O negative ion time-of-flight mass spectra from electron transfer processes at different collision energies with neutral potassium yield OH-/OD-, O-, and H-/D-. The branching ratios show a relevant energy dependence with an important isotope effect in D2O. Electronic state spectroscopy of water has been further investigated by recording potassium cation energy loss spectra in the forward scattering direction at an impact energy of 205 eV (lab frame), with quantum chemical calculations for the lowest-lying unoccupied molecular orbitals in the presence of a potassium atom supporting most of the experimental findings. The DO-D bond dissociation energy has been determined for the first time to be 5.41 ± 0.10 eV. The collision dynamics revealed the character of the singly excited (1b2-1) molecular orbital and doubly excited states in such K-H2O and K-D2O collisions.

Anionic states of C6Cl6 probed in electron transfer experiments

This is the first comprehensive investigation on the anionic species formed during collisions of fast neutral potassium (K) atoms with neutral hexachlorobenzene (C₆Cl₆) molecules in the laboratory frame range from 10 up to 100 eV. In such ion-pair formation experiments we also report a novel K⁺ energy loss spectrum obtained in the forward scattering giving evidence of the most accessible electronic states. The vertical electron affinity of (-3.76 ± 0.20) eV has been obtained and assigned to a purely repulsive transition from the C₆Cl₆ ground state to a state of the temporary negative ion yielding Cl^- formation. These experimental findings are also supported by state-of-the art theoretical calculations on the electronic structure of C₆Cl₆ in the presence of a potassium atom and are used for analysing the lowest unoccupied molecular orbitals participating in the collision process. From the time-of-flight mass spectra recorded in the wide collision energy range, more than 80% of the total anion yield is due to the undissociated parent anion C₆Cl₆^-, C₆Cl₅^- and Cl^- formation. Other fragment anions such as C₆Cl₄^-, C₃Cl₂^-, C₂Cl^- and Cl₂^- that undergo complex internal reactions with the temporary negative ion formed after electron transfer account for less than 20% of the total yield. The joint experimental and theoretical methodologies employed in these electron transfer studies provide the most comprehensive and unique assignments of the hexachlorobenzene anionic species and the role of C₆Cl₆ electronic states in collision induced dissociation to date.

Combined Experimental and Theoretical Studies on Electron Transfer in Potassium Collisions with CCl4

Negative ion formation in electron transfer experiments from fast neutral potassium (K) atom collisions with neutral tetrachloromethane (CCl₄) molecules has been investigated in the laboratory frame range of 8-1000 eV. Comprehensive calculations on the electronic structure were performed for CCl₄ in the presence of a potassium atom and used to help analyze the lowest unoccupied molecular orbitals participating in the collision process. Additionally, K⁺ energy loss produced in the forward direction has served to further our knowledge on the electronic state spectroscopy of CCl₄. A vertical electron affinity of -0.79 ± 0.20 eV has been obtained and assigned to a purely repulsive transition from CCl₄ ground state to the ²T₂ state of the temporary negative ion yielding Cl^- formation. Other features in the energy loss spectrum were observed for the first time and related to Cl₂^-, CCl₂^-, and CCl₃^- formation. Special attention is also given to the unresolved feature corresponding to a positive electron affinity of 0.24 ± 0.2 eV, assigned to a vibrationally hot transition from CCl₄ ground state into the triply degenerate ²T₂ excited state of the negative ion. The combined time-of-flight mass spectrometry together with K⁺ energy loss data represents the most comprehensive assignment of the tetrachloromethane anion yields and the role of CCl₄ electronic states in collision induced dissociation to date.

A Spontaneous Ring-Opening Reaction Leads to a Repair-Resistant Thymine Oxidation Product in Genomic DNA

The alphabet of modified DNA bases goes beyond the conventional four letters, with biological roles being found for many such modifications. Herein, we describe the observation of a modified thymine base that arises from spontaneous N1 -C2 ring opening of the oxidation product 5-formyl uracil, after N3 deprotonation. We first observed this phenomenon in silico through ab initio calculations, followed by in vitro experiments to verify its formation at a mononucleoside level and in a synthetic DNA oligonucleotide context. We show that the new base modification (Trex , thymine ring expunged) can form under physiological conditions, and is resistant to the action of common repair machineries. Furthermore, we found cases of the natural existence of Trex while screening a number of human cell types and mESC (E14), thus suggesting potential biological relevance of this modification.

Electron Transfer Induced Decomposition in Potassium-Nitroimidazoles Collisions: An Experimental and Theoretical Work

Electron transfer induced decomposition mechanism of nitroimidazole and a selection of analogue molecules in collisions with neutral potassium (K) atoms from 10 to 1000 eV have been thoroughly investigated. In this laboratory collision regime, the formation of negative ions was time-of-flight mass analyzed and the fragmentation patterns and branching ratios have been obtained. The most abundant anions have been assigned to the parent molecule and the nitrogen oxide anion (NO₂^–) and the electron transfer mechanisms are comprehensively discussed. This work focuses on the analysis of all fragment anions produced and it is complementary of our recent work on selective hydrogen loss from the transient negative ions produced in these collisions. Ab initio theoretical calculations were performed for 4-nitroimidazole (4NI), 2-nitroimidazole (2NI), 1-methyl-4- (Me4NI) and 1-methyl-5-nitroimidazole (Me5NI), and imidazole (IMI) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.

The Role of Electron Transfer in the Fragmentation of Phenyl and Cyclohexyl Boronic Acids

In this study, novel measurements of negative ion formation in neutral potassium-neutral boronic acid collisions are reported in electron transfer experiments. The fragmentation pattern of phenylboronic acid is comprehensively investigated for a wide range of collision energies, i.e., from 10 to 1000 eV in the laboratory frame, allowing some of the most relevant dissociation channels to be probed. These studies were performed in a crossed molecular beam set up using a potassium atom as an electron donor. The negative ions formed in the collision region were mass analysed with a reflectron time-of-flight mass spectrometer. In the unimolecular decomposition of the temporary negative ion, the two most relevant yields were assigned to BO^- and BO₂^-. Moreover, the collision-induced reaction was shown to be selective, i.e., at energies below 100 eV, it mostly formed BO^-, while at energies above 100 eV, it mostly formed BO₂^-. In order to further our knowledge on the complex internal reaction mechanisms underlying the influence of the hybridization state of the boron atom, cyclohexylboronic acid was also investigated in the same collision energy range, where the main dissociation channel yielded BO₂^-. The experimental results for phenyl boronic acid are supported by ab initio theoretical calculations of the lowest unoccupied molecular orbitals (LUMOs) accessed in the collision process.

Selective Bond Excision in Nitroimidazoles by Electron Transfer Experiments

We have performed comprehensive charge-transfer experiments yielding negative ion formation in collisions of fast neutral potassium atoms with nitroimidazole and methylated derivative molecules. The anionic pattern reveals that in the unimolecular decomposition of the precursor parent anion, single and multiple bond cleavages are attained. Selective excision of hydrogen atoms from the N1 position in 4-nitroimidazole (4NI) is completely blocked upon methylation in 1-methyl-4-nitroimidazole (1m4NI) and 1-methyl-5-nitroimidazole (1m5NI). Additionally, only 4NI and 2-nitroimidazole (2NI) are efficient in selectively producing neutral ^•OH and NO^• radicals in contrast to 1m4NI and 1m5NI. These findings present a novel experimental evidence of selective chemical bond breaking by just tuning the proper collision energy in atom-molecule collision experiments. The present work contributes to the current need of pinpointing a class of charge-transfer collisions that exhibit selective reactivity of the kind demonstrated here, extending to tailored chemical control for different applications such as tumor radiation therapy through nitroimidazole-based radiosensitization.

Ion-Pair Formation in Neutral Potassium-Neutral Pyrimidine Collisions: Electron Transfer Experiments

We report novel data on ion-pair formation in hyperthermal (30–800 eV) neutral potassium collisions with neutral pyrimidine (Pyr, C₄H₄N₂) molecules. In this collision regime, negative ions formed by electron transfer from the alkali atom to the target molecule were time-of-flight mass analyzed and the fragmentation patterns and branching ratios have been obtained. The most abundant product anions have been assigned to CN⁻ and C₂H⁻ and the electron transfer mechanisms are comprehensively discussed. Particular importance is also given to the efficient loss of integrity of the pyrimidine ring in the presence of an extra electron, which is in contrast to dissociative electron attachment experiments yielding the dehydrogenated parent anion. Theoretical calculations were performed for pyrimidine in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process. In order to further our knowledge about the collision dynamics, potassium cation (K⁺) energy loss spectrum has been obtained and within this context, we also discuss the role of the accessible electronic states. A vertical electron affinity of (−5.69 ± 0.20) eV was obtained and may be assigned to a π3*(b₁) state that leads to CN⁻ formation.

Communication: Site-selective bond excision of adenine upon electron transfer

This work demonstrates that selective excision of hydrogen atoms at a particular site of the DNA base adenine can be achieved in collisions with electronegative atoms by controlling the impact energy. The result is based on analysing the time-of-flight mass spectra yields of potassium collisions with a series of labeled adenine derivatives. The production of dehydrogenated parent anions is consistent with neutral H loss either from selective breaking of C-H or N-H bonds. These unprecedented results open up a new methodology in charge transfer collisions that can initiate selective reactivity as a key process in chemical reactions that are dominant in different areas of science and technology.

Electron transfer driven decomposition of adenine and selected analogs as probed by experimental and theoretical methods

We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH₂ loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K⁺ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.

Proton-Induced Collisions on Potential Prebiotic Species

With regard to the fascinating question of the origin of life, special interest has been devoted to potential prebiotic molecules which could drive the emergence of life. In the widely discussed hypothesis of a possible exogen apparition of life, the transport of those prebiotic species and their survival under spatial conditions is of strong interest. In particular their stability under solar radiation or in collisions with bare nucleus has to be considered. In that sense, taking account of the abundance of protons in ionized clouds of the interstellar medium, we have developed a detailed theoretical study of the charge transfer collision dynamics induced by impact of protons on a series of possible prebiotic compounds. Three main types of molecules have been considered: first of all the DNA and RNA building blocks with on a one hand the nucleobases uracil and thymine, and on the other hand the 2-deoxy-D-ribose sugar skeleton in its furanose and pyranose forms. The study has been extended to the 2-aminooxazole suggested to be a possible precursor of RNA nucleotides. The theoretical treatment involves ab-initio quantum chemistry molecular calculations followed by a semiclassical collision dynamics. Some qualitative trends may be suggested for the proton-induced damage of such prebiotic species.