Intramolecular vibrational energy redistribution from a high frequency mode in the presence of an internal rotor: Classical thick-layer diffusion and quantum localization

We study the effect of an internal rotor on the classical and quantum intramolecular vibrational energy redistribution (IVR) dynamics of a model system with three degrees of freedom. The system is based on a Hamiltonian proposed by Martens and Reinhardt (J. Chem. Phys. {\bf 93}, 5621 (1990).) to study IVR in the excited electronic state of para-fluorotoluene. We explicitly construct the state space and show, confirming the mechanism proposed by Martens and Reinhardt, that an excited high frequency mode relaxes via diffusion along a thick layer of chaos created by the low frequency-rotor interactions. However, the corresponding quantum dynamics exhibits no appreciable relaxation of the high frequency mode. We attribute the quantum suppression of the classical thick-layer diffusion to the rotor selection rules and, possibly, dynamical localization effects.Comment: To appear in J. Chem. Phys. (August 28, 2007); 4 pages and 3 figure

Theoretical Investigation of Dissociation <i>versus</i> Intramolecular Rearrangements in Aminohydroxymethylene

Aminohydroxymethylene (H2N–C̈–OH) is the simplest aminooxycarbene which is a heteroatom stabilized carbene. This highly reactive molecule was prepared in an Ar matrix in a recent experimental work. Unimolecular reactivity of this astrochemically important molecule was investigated and only fragmentations were identified contrary to the observations of both fragmentations and intramolecular rearrangements in other hydroxycarbenes. These rearrangement reactions form the corresponding imine and carbonyl compounds. In the present work, direct chemical dynamics simulations of unimolecular chemistry of aminohydroxymethylene were performed in the gas phase to study atomic level dissociation mechanisms. Classical trajectories were generated on-the-fly using potentials and gradients computed at the density functional B3LYP/6-31+G* level of electronic structure theory. Simulation results showed that intramolecular rearrangements accompany fragmentations during the unimolecular decay process of aminohydroxymethylene. However, the average lifetime of the intermediate isomers were found to be only few picoseconds which might not have been long enough for detection in the experiments

Dissociation Chemistry of 3‑Oxetanone in the Gas Phase

3-Oxetanone is a strained cyclic molecule which plays an important role in synthetic chemistry. A few studies exist in the literature about the equilibrium properties of this molecule and the dissociation patterns of substituted 3-oxetanones. For the unsubstituted 3-oxetanone, formation of ketene (CH₂CO) and formaldehyde (HCHO) was considered to be the major dissociation pathway. In a recent work, pyrolysis products of 3-oxetanone molecule in the gas phase were investigated by Fourier transform infrared spectroscopy and photoionization mass spectrometry. In this study, an additional dissociation channel forming ethylene oxide (c-C₂H₄O) and carbon monoxide CO was reported. In the present work, gas phase dissociation chemistry of 3-oxetanone was investigated by electronic structure theory, <i>ab initio</i> classical chemical dynamics simulations, and Rice–Ramsperger–Kassel–Marcus (RRKM) rate constant calculations. The barrier height for the ethylene oxide channel was found to be much higher than the ketene pathway. The dynamics simulations were performed at three different total energies, viz., 150, 200, and 300 kcal/mol, and multiple reaction pathways and varying branching ratios observed. A new dissociation channel involving a ring-opened isomer of ethylene oxide was identified in the simulations. This pathway has a lower energy barrier and was dominant in our dynamics simulations

E-Z Isomerization in Guanidine: Second-order Saddle Dynamics, Non-statisticality, and Time-frequency Analysis

Our recent work on the E-Z isomerization reaction of guanidine using ab initio chemical dynamics simulations [Rashmi et al, Regul. Chaotic Dyn. 2021, 26, 119] emphasized the role of second-order saddle (SOS) in the isomerization reaction; however could not unequivocally establish the non-statistical nature of the dynamics followed in the reaction. In the present study, we performed thousands on-the-fly trajectories using forces computed at the MNDO level to investigate the influence of second-order saddle in the E-Z isomerization reaction of guanidine and the role of intramolecular vibrational energy redistribution (IVR) on the reaction dynamics. The simulations reveal that while majority of the trajectories follow the traditional transition state pathways, 15% of the trajectories follow the SOS path. The dynamics was found to be highly non-statistical with the survival probabilities of the reactants showing large deviations from those obtained within the RRKM assumptions. In addition, a detailed analysis of the dynamics using time-dependent frequencies and the frequency ratio spaces reveal the existence of multiple resonance junctions that indicate the existence of regular dynamics and long-lived quasi-periodic trajectories in the phase space associated with non-RRKM behavior

Classical Dynamics Simulations of Dissociation of Protonated Tryptophan in the Gas Phase

Gas phase decomposition of protonated amino acids are of great interest due to their role in understanding protein and peptide chemistry. Several experimental and theoretical studies have been reported in the literature on this subject. In the present work, decomposition of the aromatic amino acid protonated tryptophan was studied by on-the-fly classical chemical dynamics simulations using density functional theory. Mass spectrometry and electronic structure theory studies have shown multiple dissociation pathways for this biologically relevant molecule. Unlike aliphatic amino acids, protonated tryptophan dissociates via NH₃ elimination rather than the usual iminium ion formation by combined removal of H₂O and CO molecules. Also, a major fragmentation pathway in the present work involves C_α–C_β bond fission. Results of the chemical dynamics simulations reported here are in overall agreement with experiments, and detailed atomic level mechanisms are presented

Analysis of Molecular Interaction of Drugs within β‑Cyclodextrin Cavity by Solution-State NMR Relaxation

The prime focus of the present study is to employ NMR relaxation measurement to address the intermolecular interactions, as well as motional dynamics, of drugs, viz., paracetamol and aspirin, encapsulated within the β-cyclodextrin (β-CD) cavity. In this report, we have attempted to demonstrate the applicability of nonselective (<i>R</i>₁^ns), selective (<i>R</i>₁^se), and bi-selective (<i>R</i>₁^bs) spin–lattice relaxation rates to infer dynamical parameters, for example, the molecular rotational correlation times (τ_c) and cross-relaxation rates (σ<i>_ij</i>) of the encapsulated drugs. Molecular rotational correlation times of the free drugs were calculated using the selective relaxation rate in the fast molecular motion time regime (ω_H²τ_c² ≪ 1 and <i>R</i>₁^ns/<i>R</i>₁^se ≈ 1.500), whereas that of the 1:1 complexed drugs were found from the ratio of <i>R</i>₁^ns/<i>R</i>₁^se in the intermediate motion time regime (ω_H²τ_c² ∼ 1 and <i>R</i>₁^ns/<i>R</i>₁^se ≈ 1.054), and these values were compared with each other to confirm the formation of inclusion complexes. Furthermore, the cross-relaxation rates were used to evaluate the intermolecular proton distances. Also, density functional theory calculations were performed to determine the minimum energy geometry of the inclusion complexes and the results compared with those from experiments. The report, thus, presents the possibility of utilizing NMR relaxation data, a more cost-effective experiment, to calculate internuclear distances in the case of drug–supramolecule complexes that are generally obtained by extremely time consuming two-dimensional nuclear Overhauser enhancement-based methods. A plausible mode of insertion of the drug molecules into the β-CD cavity has also been described based on experimental NMR relaxation data analysis

Gas-Phase Chemical Dynamics Simulations on the Bifurcating Pathway of the Pimaradienyl Cation Rearrangement: Role of Enzymatic Steering in Abietic Acid Biosynthesis

The biosynthesis of abietadiene is the first biosynthetically relevant process shown to involve a potential energy surface with a bifurcating reaction pathway. Herein, we use gas-phase, enzyme-free direct dynamics simulations to study the behavior of the key reaction (bifurcating) step, which is conversion of the C20 pimaradienyl cation to the abietadienyl cation. In a previous study (J. Am. Chem. Soc.2011, 133, 8335), a truncated C10 model was used to investigate this reaction. The current work finds that the complete C20 pimaradienyl cation gives reaction dynamics similar to that reported for the truncated C10 model. We find that in the absence of the enzyme, the C20 abietadienyl cation is generated in almost equal quantity (1.3:1) as an unobserved (in nature) seven-membered ring product. These simulations allude to a need for abietadiene synthase to steer the reaction to avoid generation of the seven-membered ring product. The methodology of post-transition state chemical dynamics simulations is also considered. The trajectories are initiated at the rate-controlling transition state (TS) separating the pimaradienyl and abietadienyl cations. Accurate results are expected for the short-time direct motion from this TS toward the abietadienyl cation. However, the dynamics may be less accurate for describing the unimolecular reactions that occur in moving toward the pimaradienyl cation, due to the unphysical flow of zero-point energy