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

Abstract

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

N‐Methylimidazolidin‐4‐one organocatalysts: gas‐phase fragmentations of radical cations by experiment and theory

“…We employ a model internal excess energy (IEE) distribution, which is parametrised so that on average, temperatures of 2000 to 3000 K will be reached during the production trajectories. This temperature range is usual in BO‐MD simulations of unimolecular decomposition reactions . The production runs starts with the removal of an electron from the HOMO of the respective molecule at one of the snapshot geometries, and the excess energy is applied by scaling the nuclear velocities until the predefined temperature is reached.…”

Shattering During Surface-Induced Dissociation: An Examination of Peptide Size and Structure

“…The A 5 K structure was obtained via Avogadro [18] and then optimized using the RM1 semi-empirical method [19]. RM1 was selected since it was used in the soft-landing work of Frederickson et al as well as numerous other direct dynamics simulations of protonated peptides [20][21][22][23][24][25][26].…”

RM1 Semiempirical Model: Chemistry, Pharmaceutical Research, Molecular Biology and Materials Science

“…Homayoon et al 270 studied the thermal dissociation of the doubly protonated tripeptide threonine-isoleucinelysine ion, labeled as TIK(H + ) 2 , in four different temperatures, ranging between 1250 and 2500 K. The authors determined how many fragmentation pathways exist in each temperature they considered and observed that the number of different fragmentation pathways increases with increasing temperature. 270 Several kinetic parameters were calculated using RM1 and AM1 semiempirical methods as quantum chemical models. In special, the authors pointed out that the activation energy values determined from the simulated Arrhenius plots displayed good agreement with the predicted reaction barriers when RM1 was used in the simulations.…”