Search

We present a detailed spectroscopic analysis of the first absorption band of the six possible conformers of 1,6-diphenyl-1,3,5-hexatriene, obtained by changing the configuration of trans double bonds to cis. To this end, we computed the absorption spectra using FCclasses 3.0 code. First, we assessed the performance of PBE0 and CAM-B3LYP density functional theory functionals with different basis sets to reproduce the experimental spectra. Additionally, we considered different models to compute the spectra. PBE0/def2tZVP with an adiabatic hessian model with internal coordinates yields results in very good agreement with experimental data. Subsequently, we analyzed the different contributions of vibronic transition to the spectral structure, correlating ground state conformation with spectral shape, and studied the effect of temperature on the absorption first band. [ABSTRACT FROM AUTHOR]

An ambimodal transition state (TS) that leads to formation of four different pericyclic reaction products ([4 + 6]-, [2 + 8]-, [8 + 2]-, and [6 + 4]-cycloadducts) without any intervening minima has been designed and explored with DFT computations and quasiclassical molecular dynamics. Direct dynamics simulations propagated from the ambimodal TS show the evolution of trajectories to give the four cycloadducts. The topography of the PES is a key factor in product selectivity. A good correlation is observed between geometrical resemblance of the products to the ambimodal TS (measured by the RMSD) and the ratio of products formed in the dynamics 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. [ABSTRACT FROM AUTHOR]

In the present contribution, we have summarized our recent work on the comprehension of [Ca(formamide)]2+ complex gas-phase unimolecular dissociation. By using different theoretical approaches, we were able to revise the original (and typical for such kind of problems) understanding given in terms of stationary points on the potential energy surface, which did not provide a satisfactory explanation of the experimentally observed reactivity. In particular, we point out how non-statistical and non-intrinsic reaction coordinate mechanisms are of fundamental importance. [ABSTRACT FROM AUTHOR]

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Dissociation chemistry of the diproline anion [Pro 2 -H] - is studied using chemical dynamics simulations coupled with quantum-chemical calculations and RRKM analysis. Pro 2 is chosen due to its reduced size and the small number of sites where deprotonation can take place. The mechanisms leading to the two dominant collision-induced dissociation (CID) product ions are elucidated. Trajectories from a variety of isomers of [Pro - is chosen due to its reduced size and the small number of sites where deprotonation can take place. The mechanisms leading to the two dominant collision-induced dissociation (CID) product ions are elucidated. Trajectories from a variety of isomers of [Pro 2 were followed in order to sample a larger range of possible reactivity. While different mechanisms yielding y - were followed in order to sample a larger range of possible reactivity. While different mechanisms yielding y 1 ion. This mechanism leads to formation of a b - fragment with a diketopiperazine structure. The sole formation of a diketopiperazine b 2 - ion. This mechanism leads to formation of a b 2 - fragment with a diketopiperazine structure. The sole formation of a diketopiperazine b 2 sequence ion is experimentally confirmed by infrared ion spectroscopy of the fragment anion. Furthermore, collisional and internal energy activation simulations are used in parallel to identify the different dynamical aspects of the observed reactivity.

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 N 2 , 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.

In the present contribution, we have summarized our recent work on the comprehension of [Ca(formamide)] 2+ complex gas-phase unimolecular dissociation. By using different theoretical approaches, we were able to revise the original (and typical for such kind of problems) understanding given in terms of stationary points on the potential energy surface, which did not provide a satisfactory explanation of the experimentally observed reactivity. In particular, we point out how non-statistical and non-intrinsic reaction coordinate mechanisms are of fundamental importance.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'., (© 2017 The Author(s).)

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 E a and A-factors were determined for these pathways. They are 62-78 kJ/mol and (2-3) × 10 12 s -1 for the proton transfer pathways and 153-168 kJ/mol and (2-4) × 10 14 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 E a and A parameters relative to those for C-C bond rupture pathways in hydrocarbon molecules. The E a 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.