Non-statistical Fragmentation Research Articles

Addressing electronic and dynamical evolution of molecules and molecular clusters: DFTB simulations of energy relaxation in polycyclic aromatic hydrocarbons.

We present a review of the capabilities of the density functional based Tight Binding (DFTB) scheme to address the electronic relaxation and dynamical evolution of molecules and molecular clusters following energy deposition via either collision or photoabsorption. The basics and extensions of DFTB for addressing these systems and in particular their electronic states and their dynamical evolution are reviewed. Applications to PAH molecules and clusters, carbonaceous systems of major interest in astrochemical/astrophysical context, are reported. A variety of processes are examined and discussed such as collisional hydrogenation, fast collisional processes and induced electronic and charge dynamics, collision-induced fragmentation, photo-induced fragmentation, relaxation in high electronic states, electronic-to-vibrational energy conversion and statistical versus non-statistical fragmentation. This review illustrates how simulations may help to unravel different relaxation mechanisms depending on various factors such as the system size, specific electronic structure or excitation conditions, in close connection with experiments.

Vacuum UV studies of protonated serine clusters

In a recent work, we have shown that photon absorption can cause a chemical bond to be created between the two monomers within a protonated serine dimer, a process known as intra-cluster bond formation, despite this process not occurring following thermal excitation via low energy collision-induced dissociation (LE-CID). Here we show further evidence for non-statistical photon-induced dissociation (PID) of the protonated serine dimer. In addition we discuss LE-CID and PID studies of the protonated serine octamer, showing that in this case as well, PID leads to non-statistical fragmentation and to the formation of two bonds between three neighboring monomers.

Non-ergodic fragmentation of protonated reserpine using femtosecond laser activation

Specific fragmentation patterns are fingerprints that allow for unambiguous identification of molecules, for instance in analytical methods. To reveal and possibly control such specific fragmentation, it is essential to understand the physical processes involved during the activation step. We have performed “on-the-fly” (without trapping device) femtosecond (fs) laser activation/mass spectrometry experiments on gas phase protonated reserpine, a model molecular ion for analytical purpose, at different wavelengths and laser pulse intensities. In contrast to collision induced dissociation (CID) or 267 nm fs-laser activation, evidence of non-statistical fragmentation is observed when using 800 nm fs-laser activation. The associated mechanisms are discussed in terms of fragmentation induced by Coulomb repulsion after ultrafast ionization of the protonated molecule. Our results illustrate that the present “on-the-fly” experimental scheme can help in the understanding of the physics behind fs-laser activation.

Non-statistical fragmentation in photo-activated flavin mononucleotide anions.

The spectroscopy and photo-induced dissociation of flavin mononucleotide anions in vacuo are investigated over the 300-500nm wavelength range. Comparison of the dependence of fragment ion yields as a function of deposited photon energy with calculated dissociation energies and collision-induced dissociation measurements performed under single-collision conditions suggests that a substantial fraction of photo-activated ions decompose through non-statistical fragmentation pathways. Among these pathways is the dominant photo-induced fragmentation channel, the loss of a fragment identified as formylmethylflavin. The fragment ion specific action spectra reveal electronic transition energies close to those for flavins in solution and previously published gas-phase measurements, although the photo-fragment yield upon excitation of the S2 ← S0 transition appears to be suppressed.

Site-selective soft X-ray absorption as a tool to study protonation and electronic structure of gas-phase DNA.

The conformation and the electronic structure of gas-phase oligonucleotides depends strongly on the protonation site. 5'-d(FUAG) can either be protonated at the A-N1 or at the G-N7 position. We have stored protonated 5'-d(FUAG) cations in a cryogenic ion trap held at about 20 K. To identify the protonation site and the corresponding electronic structure, we have employed soft X-ray absorption spectroscopy at the nitrogen K-edge. The obtained spectra were interpreted by comparison to time-dependent density functional theory calculations using a short-range exchange correlation functional. Despite the fact that guanine has a significantly higher proton affinity than adenine, the agreement between experiment and theory is better for the A-N1 protonated system. Furthermore, an inverse site sensitivity is observed in which the yield of the nucleobase fragments that contain the absorption site appears substantially reduced, which could be explained by non-statistical fragmentation processes, localized on the photoabsorbing nucleobase.

Non-statistical fragmentation of C60 and the formation of endohedral defect fullerenes

SynopsisWe report the first observation of the endohedral defect fullerene complex and the first measurement of the threshold displacement energy of a fullerene.

Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide.

Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analogue methanobactin peptide-5, amb5) and in particular to explore the role of zinc binding in reactivity. Fragmentation pathways, their mechanisms, and collision energy transfer are discussed. The probability distributions of the pathways are compared with the results of the experimental IM-MS, MS/MS spectrum and previous thermal simulations. Collisional activation gives both statistical and non-statistical fragmentation pathways with non-statistical shattering mechanisms accounting for a relevant percentage of reactive trajectories, becoming dominant at higher energies. The tetra-coordination of zinc changes qualitative and quantitative fragmentation, in particular the shattering. The collision energy threshold for the shattering mechanism was found to be 118.9 kcal mol-1 which is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal mol-1 identified previously during thermal simulations. This difference can be attributed to the tetra-coordinated zinc complex that hinders the availability of the sidechains to undergo direct collision with the Ar projectile.

Chemical dynamics simulations of CID of peptide ions: comparisons between TIK(H+)2 and TLK(H+)2 fragmentation dynamics, and with thermal simulations.

Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N2, and previous thermal activation simulation results; Z. Homayoon, S. Pratihar, E. Dratz, R. Snider, R. Spezia, G. L. Barnes, V. Macaluso, A. Martin-Somer and W. L. Hase, J. Phys. Chem. A, 2016, 120, 8211-8227. Upon thermal activation unimolecular fragmentation is statistical and in accord with RRKM unimolecular rate theory. Simulations show that in collisional activation some non-statistical fragmentation occurs, including shattering, which is not present when the ions dissociate statistically. Products formed by non-statistical shattering mechanisms may be related to characteristic mass spectrometry peaks which distinguish the two isomers I and L.

Model Simulations of the Thermal Dissociation of the TIK(H+)2 Tripeptide: Mechanisms and Kinetic Parameters.

Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly protonated tripeptide threonine-isoleucine-lysine ion, TIK(H+)2, for temperatures of 1250-2500 K, corresponding to classical energies of 1778-3556 kJ/mol. The number of different fragmentation pathways increases with increase in temperature. At 1250 K there are only three fragmentation pathways, with one contributing 85% of the fragmentation. In contrast, at 2500 K, there are 61 pathways, and not one dominates. The same ion is often formed via different pathways, and at 2500 K there are only 14 m/z values for the product ions. The backbone and side-chain fragmentations occur by concerted reactions, with simultaneous proton transfer and bond rupture, and also by homolytic bond ruptures without proton transfer. For each temperature the TIK(H+)2 fragmentation probability versus time is exponential, in accord with the Rice-Ramsperger-Kassel-Marcus and transition state theories. Rate constants versus temperature were determined for two proton transfer and two bond rupture pathways. From Arrhenius plots activation energies Ea and A-factors were determined for these pathways. They are 62-78 kJ/mol and (2-3) × 1012 s-1 for the proton transfer pathways and 153-168 kJ/mol and (2-4) × 1014 s-1 for the bond rupture pathways. For the bond rupture pathways, the product cation radicals undergo significant structural changes during the bond rupture as a result of hydrogen bonding, which lowers their entropies and also their Ea and A parameters relative to those for C-C bond rupture pathways in hydrocarbon molecules. The Ea values determined from the simulation Arrhenius plots are in very good agreement with the reaction barriers for the RM1 method used in the simulations. A preliminary simulation of TIK(H+)2 collision-induced dissociation (CID), at a collision energy of 13 eV (1255 kJ/mol), was also performed to compare with the thermal dissociation simulations. Though the energy transferred to TIK(H+)2 in the collisions is substantially less than the energy for the thermal excitations, there is substantial fragmentation as a result of the localized, nonrandom excitation by the collisions. CID results in different fragmentation pathways with a significant amount of short time nonstatistical fragmentation. Backbone fragmentation is less important, and side-chain fragmentation is more important for the CID simulations as compared to the thermal simulations. The thermal simulations provide information regarding the long-time statistical fragmentation.

Hydrogenated pyrene: Statistical single-carbon loss below the knockout threshold

An ongoing discussion revolves around the question of what effect hydrogenation has on carbon backbone fragmentation in polycyclic aromatic hydrocarbons (PAHs). In order to shed more light on this issue, we have measured absolute single carbon loss cross sections in collisions between native or hydrogenated pyrene cations (C16H+ 10+m , m = 0, 6, 16) and He as functions of center-of-mass energies down to 20 eV. Classical molecular dynamics (MD) simulations give further insight into energy transfer processes and also yield m-dependent threshold energies for prompt (femtoseconds) carbon knockout. Such fast, non-statistical fragmentation processes dominate CH x -loss for native pyrene (m = 0), while much slower statistical fragmentation processes contribute significantly to single-carbon loss for the hydrogenated molecules (m = 6 and m = 16). The latter is shown by measurements of large CH x -loss cross sections far below the MD knockout thresholds for C16H+ 16 and C16H+ 26.

Unimolecular dissociation of peptides: statistical vs. non-statistical fragmentation mechanisms and time scales.

In the present work we have investigated mechanisms of gas phase unimolecular dissociation of a relatively simple dipeptide, the di-proline anion, by means of chemical dynamics simulations, using the PM3 semi-empirical Hamiltonian. In particular, we have considered two activation processes that are representative limits of what occurs in collision induced dissociation experiments: (i) thermal activation, corresponding to several low energy collisions, in which the system is prepared with a microcanonical distribution of energy; (ii) collisional activation where a single shock of hundreds of kcal mol-1 (300 kcal mol-1 in the present case) can transfer sufficient energy to allow dissociation. From these two activation processes we obtained different product abundances, and for one particular fragmentation pathway a clear mechanistic difference for the two activation processes. This mechanism corresponds to the leaving of an OH- group and subsequent formation of water by taking a proton from the remaining molecule. This last reaction is always observed in thermal activation while in collisional activation it is less favoured and the formation of OH- as a final product is observed. More importantly, we show that while in thermal activation unimolecular dissociation follows exponential decay, in collision activation the initial population decays with non-exponential behaviour. Finally, from the thermal activation simulations it was possible to obtain rate constants as a function of temperature that show Arrhenius behaviour. Thus activation energies have also been extracted from these simulations.

Non-statistical fragmentation of large molecules in collisions with atoms

Non-statistical fragmentation processes are important when Polycyclic Aromatic Hydrocarbon (PAH) molecules, fullerenes, or other large molecules collide with atoms at center- of-mass energies from a few tens to a few hundreds of eV. The typical result is the prompt, billiard-ball-like knockout of single atoms (CHx-loss). This is distinct from the well-known statistical fragmentation patterns of these molecules, which are dominated by H- and C2H2-loss for PAHs and C2-loss for fullerenes. We have explored the role of non-statistical fragmentation of PAHs and fullerenes in a series of experimental and theoretical studies. In general, the yield of non-statistical fragments depends sensitively on their stability against secondary statistical fragmentation following knockout.

Non-Statistical Oligopeptide Fragmentation by IR Photons with λ=16–18 μm

Abstract In this article we analyse the vibration excitation and following dissociation of protonated oligopeptide molecules induced by IR photons with λ=16–18 μm. The analysis is based on our previous works in which we considered a specific non-statistical dissociation process in organic molecules containing substructures consisting of chained identical diatomic dipoles such as (CH2)n. Such dipole chains can serve as IR antennas for external radiation in the IR frequency range. The acquired vibration energy accumulated in IR antennas can be large enough to dissociate molecules within a femtosecond time interval by a non-statistical process, which is driven by a radiationless low-energy transport mechanism inside the peptide molecules. We point out in this article that the suggested IR-induced dissociation mechanism can be applied to obtain sequence information of protonated oligopeptides.

Isomer effects in fragmentation of Polycyclic Aromatic Hydrocarbons

We have observed significant differences in the fragmentation patterns of isomeric Polycyclic Aromatic Hydrocarbon (PAH) cations following collisions with helium atoms at center-of-mass energies around 100eV. This is in contrast to the situation at other collision energies or in photo-absorption experiments where isomeric effects are very weak and where the lowest-energy dissociation channels (H- and C2H2-loss) dominate in statistical fragmentation processes. In the 100eV range, non-statistical fragmentation also competes and is uniquely linked to losses of single carbon atoms (CHx-losses). We find that such CHx-losses are correlated with the ionic ground state energy within a given group of isomers. We present results for three C16H10+, four C18H12+ and five C20H12+ isomers colliding with He.

Collision Induced Dissociation of PAHs and Biomolecules

SynopsisWe have performed an extensive set of experiments with focus on collisions between PAH or biomolecular cations and He atoms at center-of-mass energies around 100 eV. In this energy range, non-statistical fragmentation processes are important.

Fragmentation of anthracene C₁₄H₁₀, acridine C₁₃H₉N and phenazine C₁₂H₈N₂ ions in collisions with atoms.

We report experimental total, absolute, fragmentation cross sections for anthracene C14H10, acridine C13H9N, and phenazine C12H8N2 ions colliding with He at center-of-mass energies close to 100 eV. In addition, we report results for the same ions colliding with Ne, Ar, and Xe at higher energies. The total fragmentation cross sections for these three ions are the same within error bars for a given target. The measured fragment mass distributions reveal significant contributions from both delayed (≫10(-12) s) statistical fragmentation processes as well as non-statistical, prompt (∼10(-15) s), single atom knockout processes. The latter dominate and are often followed by secondary statistical fragmentation. Classical Molecular Dynamics (MD) simulations yield separate cross sections for prompt and delayed fragmentation which are consistent with the experimental results. The intensity of the single C/N-loss peak, the signature of non-statistical fragmentation, decreases with the number of N atoms in the parent ion. The fragment intensity distributions for losses of more than one C or N atom are rather similar for C14H10 and C13H9N but differ strongly for C12H8N2 where weak C-N bonds often remain in the fragments after the first fragmentation step. This greatly increases their probability to fragment further. Distributions of internal energy remaining in the fragments after knockout are obtained from the MD simulations.

Absolute fragmentation cross sections in atom-molecule collisions: scaling laws for non-statistical fragmentation of polycyclic aromatic hydrocarbon molecules.

We present scaling laws for absolute cross sections for non-statistical fragmentation in collisions between Polycyclic Aromatic Hydrocarbons (PAH/PAH(+)) and hydrogen or helium atoms with kinetic energies ranging from 50 eV to 10 keV. Further, we calculate the total fragmentation cross sections (including statistical fragmentation) for 110 eV PAH/PAH(+) + He collisions, and show that they compare well with experimental results. We demonstrate that non-statistical fragmentation becomes dominant for large PAHs and that it yields highly reactive fragments forming strong covalent bonds with atoms (H and N) and molecules (C6H5). Thus nonstatistical fragmentation may be an effective initial step in the formation of, e.g., Polycyclic Aromatic Nitrogen Heterocycles (PANHs). This relates to recent discussions on the evolution of PAHNs in space and the reactivities of defect graphene structures.

Nonstatistical fragmentation of large molecules

We present experimental evidence for the dominance of prompt single-atom knockout in fragmenting collisions between large polycyclic aromatic hydrocarbon cations and He atoms at center-of-mass energies close to 100 eV. Such nonstatistical processes are shown to give highly reactive fragments. We argue that nonstatistical fragmentation is dominant for any sufficiently large molecular system under similar conditions.

Non-statistical fragmentation of PAHs and fullerenes in collisions with atoms

Non-statistical fragmentation processes may be important when Polycyclic Aromatic Hydrocarbon molecules (PAHs), fullerenes, or other large complex molecules collide with atoms and atomic ions. For collisions with hydrogen or helium this occurs for center-of-mass energies between a few tens to a few hundreds of electron volts and typically results in losses of single atoms. In such processes one forms much more reactive fragments than in statistical fragmentation, which instead are dominated by losses of C2- or C2H2-molecules (H-atoms) from fullerenes and PAHs, respectively. An enhanced reactivity has recently been demonstrated for van der Waals clusters of C60 molecules where prompt knockouts of single C-atoms from one of the fullerenes yield highly reactive C59+ fragments, which easily form covalent bonds with a C60 molecule inside the clusters.

Electron-impact-ionization dynamics of five C2to C4perfluorocarbons

Perfluorocarbons (PFCs) are man-made compounds whose ion physics exhibit complex interplays between statistical and nonstatistical fragmentation and intramolecular rearrangement processes. One probe of such processes is the energy-dependent electron-impact-ionization cross section. Partial electron-impact-ionization cross sections are reported for the fragments arising from five C${}_{2}$ to C${}_{4}$ PFCs, namely, C${}_{2}$F${}_{6}$, C${}_{3}$F${}_{8}$, C${}_{3}$F${}_{6}$, CF${}_{2}$=CF-CF=CF${}_{2}$, and CF${}_{3}$-C\ensuremath{\equiv}C-CF${}_{3}$, over the energy range from threshold to \ensuremath{\sim}210 eV. Care was taken to maximize ion collection efficiency and to minimize discrimination against ions produced with high kinetic-energy release, and the measured cross sections have been calibrated using independent absolute total (gross) ionization efficiency curves measured previously in the same laboratory with an instrument that was designed to essentially have unit detection efficiency. Total ionization cross sections have also been modeled using the binary-encounter Bethe model, and the shortcomings of the model when applied to perfluorinated compounds are discussed. Analysis of the mass spectral fragmentation patterns in combination with ab initio energetics suggests that nonstatistical dissociative ionization processes play a significant role in the fragmentation dynamics of saturated PFCs. In contrast, unsaturated PFCs exhibit long-lived parent ions, which tend to undergo a higher degree of statistical dissociation following ionization, involving considerable intramolecular rearrangement.