The Effect of Cluster Size on the Intra-Cluster Ionic Polymerization Process

Polyaromatic hydrocarbons (PAHs) are widespread in the interstellar medium (ISM). The abundance and relevance of PAHs call for a clear understanding of their formation mechanisms, which, to date, have not been completely deciphered. Of particular interest is the formation of benzene, the basic building block of PAHs. It has been shown that the ionization of neutral clusters can lead to an intra-cluster ionic polymerization process that results in molecular growth. Ab-initio molecular dynamics (AIMD) studies in clusters consisting of 3–6 units of acetylene modeling ionization events under ISM conditions have shown maximum aggregation of three acetylene molecules forming bonded C6H6+ species; the larger the number of acetylene molecules, the higher the production of C6H6+. These results lead to the question of whether clusters larger than those studied thus far promote aggregation beyond three acetylene units and whether larger clusters can result in higher C6H6+ production. In this study, we report results from AIMD simulations modeling the ionization of 10 and 20 acetylene clusters. The simulations show aggregation of up to four acetylene units producing bonded C8H8+. Interestingly, C8H8+ bicyclic species were identified, setting a precedent for their astrochemical identification. Comparable reactivity rates were shown with 10 and 20 acetylene clusters

Understanding gas-phase reactivity of uracil coupling QM+MMchemical dynamics simulations of Collision Induced Dissociation with experiments

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Water confinement in small polycyclic aromatic hydrocarbons

The confinement of water molecules is vital in fields from biology to nanotechnology. The conditions allowing confinement in small finite polycyclic aromatic hydrocarbons (PAHs) are unclear, yet are crucial for understanding confinement in larger systems. Here, we report a computational study of water cluster confinement within PAHs dimers. Our results serve as a model for larger carbon allotropes and for understanding molecular interactions in confined systems. We identified size and structural motifs allowing confinement and demonstrated the motifs in various PAHs systems. We show that optimal OH⋯π interactions between water clusters and the PAH dimer permit optimal confinement to occur. However, the lack of such interactions leads to the formation of CH⋯O interactions, resulting in less ideal confinement. Confinement of layered clusters is also possible, provided that the optimal OH⋯π interactions are conserved

STUDYING THE REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL vs. NON-STATISTICAL APPROACH

International audienceØ RRKM and KINETIC MONTE CARLO (KMC) SIMULATIONS : statistical reactivity. Ø INTRODUCTION-NH 3-HNCO Ensemble of trajectories V = V ion + V Ar-ion QM MM Potential energy function Ø QM-MM CHEMICAL DYNAMICS SIMULATIONS [1] : non-statistical mechanisms Collision system Ø RESULTS • Studying the reactivity of biomolecules in the gas phase allows to get rid of the effects of the environment: intrinsic properties of the molecule. • System: Uracil in DNA has cytotoxic and mutagenic potential. AM1, PM3 and DFT Collision gas Fragment ion Fragments ions (product ions) Activated fragment ion (continues to fragment) Fragmenting ion Activated ion Precursor ion Neutral loss Ø ESI-MS/MS: mass of the fragments. Collision cell Ø Our AIM • Explain non-statistical and statistical reactivity of protonated Uracil in the gas phase and obtain predictive MS-MS spectra. • For trajectories that did not react before IVR (intramolecular vibrational relaxation) takes place but have enough energy to react later on. • Following automatic protocol [3] to find all fragmentation pathways, TSs and minima. Then this is used as input fot RRKM and KMC simulations. (1) (6)-CO loss (m/z 85) (2) (3) (4) (5) from RRKM analysis: H + transfer ns (out of simulation time) NH 3 loss H 2 O loss React. <1%-no NH 3 loss All isomers: [5] mechanism (m/z 70 and m/z 44) [2] • As suggested by experiments, m/z 70 is obtained by a retro Diels-Alder (rDA) mechanism. • rDA reaction does not follow the minimum energy path along the reaction coordinate, while stepwise mechanisms do. In experiments, both mechanisms can co-exist. • Initial protonation state of the ion plays a crucial role in determining the fragmentation pathway. • NH 3 loss is a selective reaction, while H 2 O loss it is not. Ø CONCLUSIONS Refs. [1] Hase et al. JPCA (1999) [2] Rossich Molina et al. Example of NH 3 loss mechanism for isomer 4. Product yields of the different fragmentation channels of the C 4 H 5 N 2 O 2 + system obtained in the KMC simulation as a function of the excitation energy. a) Average final (internal) energies of [uracil]H + as a function of the collision energy (in the center of mass framework) for Ar + [uracil]H + collisional system. (b) Percent energy transfer values to [uracil]H + internal degrees of freedom. Symbols and solid lines correspond to the chemical dynamics simulation (CDS), and energy transfer model results, respectively

A combined theoretical and experimental study of small anthracene–water clusters

Water-cluster interactions with polycyclic aromatic hydrocarbons (PAHs) are of paramount interest in many chemical and biological processes. We report a study of anthracene monomers and dimers with water (up to four)-cluster systems utilizing molecular beam vacuum-UV photoionization mass spectrometry and density functional calculations. Structural loss in photoionization efficiency curves when adding water indicates that various isomers are generated, while theory indicates only a slight shift in energy in photoionization states of different isomers. Calculations reveal that the energetic tendency of water is to remain clustered and not to disperse around the PAH. Theoretically, we observe water confinement exclusively in the case of four water clusters and only when the anthracenes are in a cross configuration due to optimal OH⋯π interactions, indicating dependence on the size and structure of the PAH. Furthermore theory sheds light on the structural changes that occur in water upon ionization of anthracene, due to the optimal interactions of the resulting hole and water hydrogen atoms

On the gas phase fragmentation of protonated uracil : a statistical perspective

International audienceThe potential energy surface of protonated uracil has been explored with an automated transition state search procedure, resulting in the finding of 1398 stationary points and 751 reactive channels, which can be categorized into isomerizations between pairs of isomers, unimolecular fragmentations and bimolecular reactions. The use of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory and Kinetic Monte Carlo (KMC) simulations allowed us determining the relative abundances of each fragmentation channel as a function of the ion's internal energy. The KMC/RRKM product abundances are compared with novel mass spectrometry (MS) experiments in the collision energy range 1-6 eV. To facilitate the comparison between theory and experiments, further dynamics simulations are carried out to determine the fraction of collision energy converted into the ion's internal energy. The KMC simulations show that the major fragmentation channels are isocyanic acid and ammonia losses, in good agreement with experiments. The third predominant channel is water loss according to both theory and experiments, although the abundance obtained in the KMC simulations is very low, suggesting that non-statistical dynamics might play an important role for this channel. Isocyanic acid (HNCOH+) is also an important product in the KMC simulations, although its abundance is only significant at internal energies not accessible in the MS experiments

REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL & NON-STATISTICAL STUDY

International audienceDNA’s role in heritage and coding protein was described long time ago. The presence of Uracil in DNA gives rise to nucleic bases misparings which can be cytotoxic and mutagenic for the cell. It is therefore important to understand the chemical reactivity of nucleobases, including Uracil. Studying the reactivity in the gas phase allows to get rid of environmental effects, giving direct access to important intrinsic properties of the molecule of interest. In this context, we coupled Tandem Mass Spectrometry Experiments (MS/MS) to mixed Quantum-Classical (QM+MM) Molecular Dynamic Simulations of collisions between protonated Uracil and Argon.Experiments: MS/MS spectra of protonated Uracil, 2-13C-uracil; 3-15N-uracil and 1,3-15N2-213C-uracil generated by electrospray ionization from aqueous solutions, were recorded at different collision energies, ranging from 5 to 30 eV, using an Applied Biosystems/MDS Sciex API2000 triple-quadrupole instrument.Simulations : Chemical dynamic simulations were performed using VENUS coupled with MOPAC or with Gaussian09 for six Uracil’s protonated forms, at AM1, PM3 and B3LYP/6-31g levels of theory. Thousands of trajectories were performed to have statistically valid results.We chose 300K as initial temperature for the ions. Energies for the normal modes of vibration were selected from a 300 K Boltzmann distribution. Random orientations in Euler angles between Argon and protonated Uracil were sampled to account for random orientations of collisions.We achieved a deeper understanding of the fragmentation mechanisms occurring during Collision Induced Dissociation (CID) of protonated Uracil generated by electrospray (ESI). We successfully characterized the main fragmentation paths: ammonia loss (m/z 96), water loss (m/z 95) and cyanic acid loss (m/z 70) as well as other minor paths. The latter corresponds to a retro-Diels-Alder reaction, which has been proposed in the literature, but has recently been questioned. We obtained perfect agreement for fragmentation mechanisms obtained during simulations and those deduced from isotopic labeling.RRKM approach was used to stimate rate constants for different paths and understand the long time scale reactivity.We have already successfully applied this approach to the study of disaccharides, and our new good dynamic results open the door to the possibility of studying the reactivity of other systems, such as Uracil with metals and other DNA building blocks. Our research is moving forward this direction

Characterization of Protonated Model Disaccharides from Tandem Mass Spectrometry and Chemical Dynamics Simulations

International audienceThe fragmentation mechanisms of prototypical disaccharides have been studied herein by coupling tandem mass spectrometry (MS) with collisional chemical dynamics simulations. These calculations were performed by explicitly considering the collisions between the protonated sugar and the neutral target gas, which led to an ensemble of trajectories for each system, from which it was possible to obtain reaction products and mechanisms without pre‐imposing them. The β‐aminoethyl and aminopropyl derivatives of cellobiose, maltose, and gentiobiose were studied to observe differences in both the stereochemistry and the location of the glycosidic linkage. Chemical dynamics simulations of MS/MS and MS/MS/MS were used to suggest some primary and secondary fragmentation mechanisms for some experimentally observed product ions. These simulations provided some new insights into the fundamentals of the unimolecular dissociation of protonated sugars under collisional induced dissociation conditions