Water molecule elimination from the protonated methanol dimer ion-An example of a size-selective intracluster reaction.

The abundance of extraterrestrial methanol makes the reaction between methanol molecules in a molecular cluster a possible key step in the search for mechanisms for the formation of more complex molecules under the conditions of the interstellar medium as well as circumstellar and planetary atmospheres. The reaction leading to the formation of the dimethyl ether ion from a methanol molecule interacting with a protonated methanol ion via the elimination of a water molecule is a basic mechanism for the formation of complex organic molecules. Here, we experimentally examine such reactions in the gas phase, analyzing the production and reactivity of protonated cluster ions formed by the ionization of a supersonic jet of methanol. Focusing especially on the post-collisional relaxation of the protonated methanol dimer and trimer ions after high-energy single collisions, the results indicate a strong size selectivity favoring the occurrence of this reaction only in the dimer ion. To elucidate this behavior, the velocity distribution of the eliminated water molecule was measured using an event-by-event coincidence analysis. These results are interpreted using quantum chemical calculations of the dissociation pathways. It turns out that in the dimer case, two transition states are able to contribute to this intracluster reaction. In the trimer case, methanol evaporation appears as the most energetically favorable relaxation pathway.

Glycine Peptide Chain Formation in the Gas Phase via Unimolecular Reactions.

Peptide chain formation from amino acids such as glycine is a key step in the emergence of life. Unlike their synthesis by living systems, how peptide chains grow under abiotic conditions is an open question given the variety of organic compounds discovered in various astrophysical environments, comets and meteorites. We propose a new abiotic route in the presence of protonated molecular dimers of glycine in a cold gaseous atmosphere without further need for a solid catalytic substrate. The results provide evidence for the preferential formation of mixed protonated dimers of glycine consisting of a dipeptide and a glycine molecule instead of pure protonated glycine dimers. Additional measurements mimicking a cosmic-ray impact in terms of internal excitation show that a single gas-phase collision induces polymerization via dehydration in both the mixed and pure dimer ions. Peptide chain growth is thus demonstrated to occur via a unimolecular gas-phase reaction in an excited cluster ion.

Energy Dispersion in Pyridinium-Water Nanodroplets upon Irradiation.

Postirradiation dissociation of molecular clusters has been mainly studied assuming energy redistribution in the entire cluster prior to the dissociation. Here, the evaporation of water molecules from out-of-equilibrium pyridinium-water cluster ions was investigated using the recently developed correlated ion and neutral time-of-flight (COINTOF) mass spectrometry technique in combination with a velocity-map imaging (VMI) device. This special setup enables the measurement of velocity distributions of the evaporated molecules upon high-velocity collisions with an argon atom. The distributions measured for pyridinium-water cluster ions are found to have two distinct components. Besides a low-velocity contribution, which corresponds to the statistical evaporation of water molecules after nearly complete redistribution of the excitation energy within the clusters, a high-velocity contribution is also found in which the molecules are evaporated before the energy redistribution is complete. These two different evaporation modes were previously observed and described for protonated water cluster ions. However, unlike in the case of pure water clusters, the low-velocity part of the distributions for pyridinium-doped water clusters is itself composed of two distinct Maxwell-Boltzmann distributions, indicating that evaporated molecules originate in this case from out-of-equilibrium processes. Statistical molecular dynamics simulations were performed to (i) understand the effects caused in the ensuing evaporation process by the various excitation modes at different initial cluster constituents and to (ii) simulate the distributions resulting from sequential evaporations. The presence of a hydrophobic impurity in water clusters is shown to impact water molecule evaporation due to the energy storage in the internal degrees of freedom of the impurity.

Decomposition of protonated ronidazole studied by low-energy and high-energy collision-induced dissociation and density functional theory.

Nitroimidazoles are important compounds in medicine, biology, and the food industry. The growing need for their structural assignment, as well as the need for the development of the detection and screening methods, provides the motivation to understand their fundamental properties and reactivity. Here, we investigated the decomposition of protonated ronidazole [Roni+H]+ in low-energy and high-energy collision-induced dissociation (CID) experiments. Quantum chemical calculations showed that the main fragmentation channels involve intramolecular proton transfer from nitroimidazole to its side chain followed by a release of NH2CO2H, which can proceed via two pathways involving transfer of H+ from (1) the N3 position via a barrier of TS2 of 0.97 eV, followed by the rupture of the C-O bond with a thermodynamic threshold of 2.40 eV; and (2) the -CH3 group via a higher barrier of 2.77 eV, but with a slightly lower thermodynamic threshold of 2.24 eV. Electrospray ionization of ronidazole using deuterated solvents showed that in low-energy CID, only pathway (1) proceeds, and in high-energy CID, both channels proceed with contributions of 81% and 19%. While both of the pathways are associated with small kinetic energy release of 10-23 meV, further release of the NO• radical has a KER value of 339 meV.

Impact of a hydrophobic ion on the early stage of atmospheric aerosol formation.

Atmospheric aerosols are one of the major factors affecting planetary climate, and the addition of anthropogenic molecules into the atmosphere is known to strongly affect cloud formation. The broad variety of compounds present in such dilute media and their specific underlying thermalization processes at the nanoscale make a complete quantitative description of atmospheric aerosol formation certainly challenging. In particular, it requires fundamental knowledge about the role of impurities in water cluster growth, a crucial step in the early stage of aerosol and cloud formation. Here, we show how a hydrophobic pyridinium ion within a water cluster drastically changes the thermalization properties, which will in turn change the corresponding propensity for water cluster growth. The combination of velocity map imaging with a recently developed mass spectrometry technique allows the direct measurement of the velocity distribution of the water molecules evaporated from excited clusters. In contrast to previous results on pure water clusters, the low-velocity part of the distributions for pyridinium-doped water clusters is composed of 2 distinct Maxwell-Boltzmann distributions, indicating out-of-equilibrium evaporation. More generally, the evaporation of water molecules from excited clusters is found to be much slower when the cluster is doped with a pyridinium ion. Therefore, the presence of a contaminant molecule in the nascent cluster changes the energy storage and disposal in the early stages of gas-to-particle conversion, thereby leading to an increased rate of formation of water clusters and consequently facilitating homogeneous nucleation at the early stages of atmospheric aerosol formation.

Velocity of a Molecule Evaporated from a Water Nanodroplet: Maxwell-Boltzmann Statistics versus Non-Ergodic Events.

The velocity of a molecule evaporated from a mass-selected protonated water nanodroplet is measured by velocity map imaging in combination with a recently developed mass spectrometry technique. The measured velocity distributions allow probing statistical energy redistribution in ultimately small water nanodroplets after ultrafast electronic excitation. As the droplet size increases, the velocity distribution rapidly approaches the behavior expected for macroscopic droplets. However, a distinct high-velocity contribution provides evidence of molecular evaporation before complete energy redistribution, corresponding to non-ergodic events.

Proton Migration in Clusters Consisting of Protonated Pyridine Solvated by Water Molecules.

Proton transfer (PT) from protonated pyridine to water molecules is observed after excitation of microhydrated protonated pyridine (Py) clusters PyH(+) (H2 O)n (n=0-5) is induced by a single collision with an Ar atom at high incident velocity (95×10(3)  m s(-1) ). Besides the fragmentation channel associated with the evaporation of water molecules, the charged-fragment mass spectrum shows competition between the production of the PyH(+) ion (or its corresponding charged fragments) and the production of H(+) (H2 O) or H(+) (H2 O)2 ions. The increase in the production of protonated water fragments as a function of the number of H2 O molecules in the parent cluster ion as well sd the observation of a stable H(+) (H2 O)2 fragment, even in the case of the dissociation of PyH(+) (H2 O)2 , are evidence of the crucial role of PT in the relaxation process, even for a small number of solvating water molecules.

Fragmentation mechanisms of cytosine, adenine and guanine ionized bases.

The different fragmentation channels of cytosine, adenine and guanine have been studied through DFT calculations. The electronic structure of bases, their cations, and the fragments obtained by breaking bonds provides a good understanding of the fragmentation process that can complete the experimental approach. The calculations allow assigning various fragments to the given peaks. The comparison between the energy required for the formation of fragments and the peak intensity in the mass spectrum is used. For cytosine and guanine the elimination of the HNCO molecule is a major route of dissociation, while for adenine multiple loss of HCN or HNC can be followed up to small fragments. For cytosine, this corresponds to the initial bond cleavage of N3-C4/N1-C2, which represents the main dissociation route. For guanine the release of HNCO is obtained through the N1-C2/C5-C6 bond cleavage (reverse order also possible) leading to the largest peak of the spectrum. The corresponding energies of 3.5 and 3.9 eV are typically in the range available in the experiments. The loss of NH3 or HCN is also possible but requires more energy. For adenine, fragmentation consists of multiple loss of the HCN molecule and the main route corresponding to HC8N9 loss is followed by the release of HC2N1.

Solution vs. gas phase relative stability of the choline/acetylcholine cavitand complexes.

How the information obtained from the gas phase experiments can reflect the processes in solution is a crucial question for analytical chemistry, and particularly the selective host-guest recognition mechanisms which are fundamental in biology. Here we combine ElectroSpray Ionization mass spectrometry (ESI-MS) and the Collision Induced Dissociation (CID) experiments to the density functional theory to investigate the interaction of acetylcholine and the choline cation with a triphosphonate cavitand. While the relative abundance of the cation complexes in the ESI mass spectrum reflects the preferential capture of the acetylcholine ion over the choline ion by the cavitand in the solution, the gas phase CID measurements indicate that after desolvation the choline cation is the most strongly bound to the host. The experimental results are interpreted by theory that underlines the role of the counterion in the stabilization of the complexes in solution and therefore in the selective recognition of substrates of biological interest.

DFT study of the fragmentation mechanism of uracil RNA base.

The fragmentation process of the uracil RNA base has been investigated via DFT calculations in order to assign fragments to the ionisation mass spectrum obtained after dissociation induced by collision experiments. The analysis of the electronic distribution and geometry parameters of the cation allows selection of several bonds that may be cleaved and lead to the formation of various fragments. Differences are observed in the electronic behaviour of the bond breaking as well as the energy required for the cleavage. It is reported that N(3)-C(4) and N(1)-C(2) bonds are more easily cleaved than the C(5)-C(6) bond, since the corresponding energy barriers amount to ΔG = +1.627, +1.710, +5.459 eV, respectively, which makes the C(5)-C(6) bond cleavage almost prohibited. Among all possible formed fragments, the formation of the OCN(+) fragment for the peak at m/z = 42 Da is excluded because of an intermediate that was not observed experimentally and too a large free energy barrier. Based on the required free energy, it is observed that two fragment derivatives: C(2)H(4)N(+) and C(2)H(2)O˙(+) may be formed, with a small preference for C(2)H(4)N(+). This latter product is not formed through a retro Diels Alder reaction in contrast to C(2)H(2)O˙(+). The following sequence is proposed for the peak at 42 Da: C(2)H(4)N(+) (from N(1)-C(2), C(4)-C(5) cleavages) > C(2)H(2)O˙(+) (from N(3)-C(4), N(1)-C(2) and C(5)-C(6) cleavages) > C(2)H(4)N(+) (from N(1)-C(2), N(3)-C(4) and C(4)-C(5)) > C(2)H(2)O˙(+) (from C(5)-C(6), N(1)-C(2) and N(3)-C(4) cleavages) > NCO(+) (from N(1)-C(2), C(4)-C(5) and N(3)-C(4) cleavages). Finally the peak at 28 Da is assigned to CNH(2)(+) derivatives that can be formed through two different paths, the easiest one requiring 5.4 eV.

Decomposition of methionine by low energy electrons.

In this work, we present the results from low energy (<12 eV) electron impact on isolated methionine, Met. We show that dissociative electron attachment is the operative mechanism for the sulfur content amino-acid fragmentation. The two most dominant fragments are attributed to the (Met-H)(-) and (C(4)NOH(5))(-) ions that are formed at energy below 2 eV. The formation of the latter anion is accompanied by the loss of neutral counterparts, which are most likely a water molecule and highly toxic methanethiol, CH(3)SH. Further fragments are associated with the damage at the sulfur end of the amino acid, producing the methyl sulfide anion CH(3)S(-) or sulfur containing neutrals. In the context of radiation induced damage to biological material at the nano-scale level, the present interest of methionine arises from the implication of the molecule in biological processes (e.g., S-adenosyl methionine for the stimulation of DNA methyltransferase reactions or protein synthesis).