Preparation of Nafion Membranes for Reproducible Ammonia Quantification in Nitrogen Reduction Reaction Experiments.

This study highlights the importance of following a strict protocol for Nafion membrane pretreatment for electrochemical nitrogen reduction reaction experiments. Atmospheric ammonia pollution can be introduced to the experimental setup through membranes and interpreted falsely as catalysis product from N2 . The sources of ammonia contamination vary drastically between locations worldwide and even within the same location between days depending on temperature, wind direction, fertilizer use, and manure accumulation in its vicinity. The study shows that significant amounts of ammonium is accumulated in the membranes after commonly practiced pretreatment methods, where the amount depends on the ammonia concentration in the surrounding of the experiment. Therefore, we introduce a new pretreatment method which removes all the ammonium in the membrane. The membranes can be stored for several days but a short final step in the method needs to be carried out right before NRR experiments.

NCO(-), a key fragment upon dissociative electron attachment and electron transfer to pyrimidine bases: site selectivity for a slow decay process.

We report gas phase studies on NCO(-) fragment formation from the nucleobases thymine and uracil and their N-site methylated derivatives upon dissociative electron attachment (DEA) and through electron transfer in potassium collisions. For comparison, the NCO(-) production in metastable decay of the nucleobases after deprotonation in matrix assisted laser desorption/ionization (MALDI) is also reported. We show that the delayed fragmentation of the dehydrogenated closed-shell anion into NCO(-) upon DEA proceeds few microseconds after the electron attachment process, indicating a rather slow unimolecular decomposition. Utilizing partially methylated thymine, we demonstrate that the remarkable site selectivity of the initial hydrogen loss as a function of the electron energy is preserved in the prompt as well as the metastable NCO(-) formation in DEA. Site selectivity in the NCO(-) yield is also pronounced after deprotonation in MALDI, though distinctly different from that observed in DEA. This is discussed in terms of the different electronic states subjected to metastable decay in these experiments. In potassium collisions with 1- and 3-methylthymine and 1- and 3-methyluracil, the dominant fragment is the NCO(-) ion and the branching ratios as a function of the collision energy show evidence of extraordinary site-selectivity in the reactions yielding its formation.

Mass spectrometric study on sodium ion induced central nucleotide deletion in the gas phase.

We report a mass spectrometric study on sodium ion induced central nucleotide deletion from protonated oligonucleotides (ONTs) and the concurrent recombination of the terminal nucleotides. To shed some light on the mechanism behind this intriguing fragmentation channel, we have studied the metastable decay of a number of different protonated hexameric and octameric oligonucleotides with 0-6 and 0-8 of their exchangeable protons replaced with sodium ions, respectively. In selected cases, we have also studied the further fragmentation of the parent ions after initial base loss. Our findings are concurrent with a reaction mechanism where the initial step is the elimination of a protonated, high proton affinity (PA) base from the center of the ONTs. This is followed by an elimination of a (next neighbour) nucleotide that contains a second high PA base and the concurrent recombination of the terminal nucleotides. To our knowledge, such central nucleotide deletion in the gas phase has only been reported in one previous study (Flosadóttir et al., J. Am. Soc. Mass Spectrom 20:689-696, 2009), and this is the first systematic approach to understand the mechanism behind this channel.

Experimental and theoretical study of the metastable decay of negatively charged nucleosides in the gas phase.

Fragmentation of metastable anions of all deoxynucleosides and nucleosides constituting DNA and RNA has been studied experimentally and by computer simulations. The ions were formed through deprotonation in matrix assisted laser desorption/ionisation (MALDI). Clear difference in fragmentation patterns was obtained for nucleosides containing purine vs. pyrimidine bases. To elucidate the role of various potential deprotonation sites, systematic blocking by chemical modification was performed and this gave unambiguous correlation between deprotonation sites and fragments observed. Classical dynamics simulations of the fragmentation process, using density functional theory to describe the electronic degrees of freedom, were performed for the various deprotonation sites. These were found to reproduce the observed fragmentation patterns remarkably well.

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.

Sodium controlled selective reactivity of protonated deoxy-oligonucleotides in the gas phase.

Metastable fragmentation of the positively charged, hexameric oligonucleotides 5'-d(TTXYTT) (X and Y are dC, dG, or dA) and 5'-d(CTCGTT), 5'-d(TTCGTC) and 5'-d(CTCGTC) is studied after matrix assisted laser desorption/ionization (MALDI). The influence of the degree of sodiation, i.e., when the acidic protons are one by one exchanged against sodium ions, is systematically studied for the exchange of up to seven protons against sodium ions. Exchanging the acidic protons against sodium gradually quenches the backbone cleavage through the w and a-B channels, and quantitative quenching of these channels is generally achieved with the exchange of four protons against sodium ions. At the same time, the exchange of protons against sodium ions promotes the loss of a neutral, high proton affinity base. The formation of the w and a-B fragments is found to be highly dependent on the sequence of the central bases. A single mechanism consistent with these observations is proposed. In addition to the quenching of the classical w and a-B reaction channels, a drastic and abrupt on/off-switching of new reaction channels is observed as the degree of sodiation successively increases. These channels involve selective loss of the two central bases and the excision of a phosphodiester group and a sugar unit from the center of the oligonucleotides. Synchronously, the two terminal fragments recombine to form a tetramer containing the two terminal nucleosides from each end of the hexamer. Possible mechanism explaining these remarkable channels are discussed.