Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment

Ab initio molecular dynamics simulations are used to investigate the fragmentation dynamics following the double ionization of 2-deoxy-D-ribose (DR), a major component in the DNA chain. Different ionization scenarios are considered to provide a complete picture. First focusing on isolated DR2+, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei. These patterns differ for the two isomers studied. To compare thermal and electronic excitation effects, Ehrenfest dynamics are also performed, allowing to remove the two electrons from selected molecular orbitals. Two intermediate-energy orbitals, localized on the carbon chain, were selected. The dissociation pattern corresponds to the most frequent pattern obtained when adding thermal excitation. On the contrary, targeting the four deepest orbitals, localized on the oxygen atoms, leads to selective ultrafast C-O and/or O-H bond dissociation. To probe the role of environment, a system consisting of a DR molecule embedded in liquid water is then studied. The two electrons are removed from either the DR or the water molecules directly linked to the sugar through hydrogen bonds. Although the dynamics onset is similar to that of isolated DR when removing the same deep orbitals localized on the sugar oxygen atoms, the subsequent fragmentation patterns differ. Sugar damage also occurs following the Coulomb explosion of neighboring H2O2+ molecules due to interaction with the emitted O or H atoms.

Controlling the diversity of ion-induced fragmentation pathways by N-methylation of amino acids

We present a combined experimental and theoretical study of the fragmentation of singly and doubly N-methylated glycine (sarcosine and N,N-dimethyl glycine, respectively) induced by low-energy (keV) O⁶⁺ ions. Multicoincidence mass spectrometry techniques and quantum chemistry simulations (ab initio molecular dynamics and density functional theory) allow us to characterise different fragmentation pathways as well as the associated mechanisms. We focus on the fragmentation of doubly ionised species, for which coincidence measurements provide unambiguous information on the origin of the various charged fragments. We have found that single N-methylation leads to a larger variety of fragmentation channels than in no methylation of glycine, while double N-methylation effectively closes many of these fragmentation channels, including some of those appearing in pristine glycine. Importantly, the closure of fragmentation channels in the latter case does not imply a protective effect by the methyl group.

Ultrafast molecular dynamics in ionized 1- and 2-propanol: from simple fragmentation to complex isomerization and roaming mechanisms

Upon photoexcitation, molecules can undergo numerous complex processes, such as isomerization and roaming, leading to changes in the molecular and electronic structure. Here, we report on the time-resolved ultrafast nuclear dynamics, initiated by laser ionization, in the two structural isomers, 1- and 2-propanol, using a combination of pump-probe spectroscopy and coincident Coulomb explosion imaging. Our measurements, paired with quantum chemistry calculations, identify the mechanisms for the observed two- and three-body dissociation channels for both isomers. In particular, the fragmentation channel of 2-propanol associated with the loss of CH₃ shows possible evidence of methyl roaming. Moreover, the electronic structure of this roaming methyl fragment could be responsible for the enhanced ionization also observed for this channel. Finally, comparison with similar studies done on ethanol and acetonitrile helps establish a correlation between the length of the alkyl chain and the likelihood of hydrogen migration.

A general approach to study molecular fragmentation and energy redistribution after an ionizing event

We propose to combine quantum chemical calculations, statistical mechanical methods, and photoionization and particle collision experiments to unravel the redistribution of internal energy of the furan cation and its dissociation pathways. This approach successfully reproduces the relative intensity of the different fragments as a function of the internal energy of the system in photoelectron-photoion coincidence experiments and the different mass spectra obtained when ions ranging from Ar+ to Xe25+ or electrons are used in collision experiments. It provides deep insights into the redistribution of the internal energy in the ionized molecule and its influence on the dissociation pathways and resulting charged fragments. The present pilot study demonstrates the efficiency of a statistical exchange of excitation energy among various degrees of freedom of the molecule and proves that the proposed approach is mature to be extended to more complex systems.

Ultrafast Laser-Induced Isomerization Dynamics in Acetonitrile

Isomerization induced by laser ionization in acetonitrile (CH₃CN) was investigated using pump-probe spectroscopy in combination with ion-ion coincident Coulomb explosion imaging. We deduced five primary channels indicating direct C-C breakup, single and double hydrogen migration, and H and H₂ dissociation in the acetonitrile cation. Surprisingly, the hydrogen-migration channels dominate over direct fragmentation. This observation is supported by quantum chemistry calculations showing that isomerization through single and double hydrogen migration leads to very stable linear and ring isomers, with most of them more stable than the original linear structure following ionization of the parent molecule. This is unlike most molecules investigated previously using similar schemes. By varying the delay between the pump and probe pulses, we have also determined the time scales of the corresponding dynamical processes. Isomerization typically occurs in a few hundred femtoseconds, a time scale that is comparable to that found for H and H₂ dissociation and direct molecular fragmentation.

Polypeptide formation in clusters of β-alanine amino acids by single ion impact

The formation of peptide bonds by energetic processing of amino acids is an important step towards the formation of biologically relevant molecules. As amino acids are present in space, scenarios have been developed to identify the roots of life on Earth, either by processes occurring in outer space or on Earth itself. We study the formation of peptide bonds in single collisions of low-energy He2+ ions (α-particles) with loosely bound clusters of β-alanine molecules at impact energies typical for solar wind. Experimental fragmentation mass spectra produced by collisions are compared with results of molecular dynamics simulations and an exhaustive exploration of potential energy surfaces. We show that peptide bonds are efficiently formed by water molecule emission, leading to the formation of up to tetrapeptide. The present results show that a plausible route to polypeptides formation in space is the collision of energetic ions with small clusters of amino acids.

Time-resolved molecular dynamics of single and double hydrogen migration in ethanol

Being the lightest, most mobile atom that exists, hydrogen plays an important role in the chemistry of hydrocarbons, proteins and peptides and most biomolecules. Hydrogen can undergo transfer, exchange and migration processes, having considerable impact on the chemical behavior of these molecules. Although much has been learned about reaction dynamics involving one hydrogen atom, less is known about those processes where two or more hydrogen atoms participate. Here we show that single and double hydrogen migrations occurring in ethanol cations and dications take place within a few hundred fs to ps, using a 3D imaging and laser pump-probe technique. For double hydrogen migration, the hydrogens are not correlated, with the second hydrogen migration promoting the breakup of the C-O bond. The probability of double hydrogen migration is quite significant, suggesting that double hydrogen migration plays a more important role than generally assumed. The conclusions are supported by state-of-the-art molecular dynamics calculations.

Fully versus constrained statistical fragmentation of carbon clusters and their heteronuclear derivatives

The Microcanonical Metropolis Monte Carlo (MMMC) method has been shown to describe reasonably well fragmentation of clusters composed of identical atomic species. However, this is not so clear in the case of heteronuclear clusters as some regions of phase space might be inaccessible due to the different mobility of the different atomic species, the existence of large isomerization barriers, or the quite different chemical nature of the possible intermediate species. In this paper, we introduce a constrained statistical model that extends the range of applicability of the MMMC method to such mixed clusters. The method is applied to describe fragmentation of isolated clusters with high, moderate, and no heteronuclear character, namely, C_nH_m, C_nN, and C_n clusters for which experimental fragmentation branching ratios are available in the literature. We show that the constrained statistical model describes fairly well fragmentation of C_nH_m clusters in contrast with the poor description provided by the fully statistical model. The latter model, however, works pretty well for both C_n and C_nN clusters, thus showing that the ultimate reason for this discrepancy is the inability of the MMMC method to selectively explore the whole phase space. This conclusion has driven us to predict the fragmentation patterns of the C₄N cluster for which experiments are not yet available.

Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments

The fragmentation of the isolated 5-bromouracil (5BrU) molecule and pure and nano-hydrated 5BrU clusters induced by low energy ¹²C⁴⁺ ions has been studied.