Direct dynamics simulations of the unimolecular dissociation of dioxetane: Probing the non-RRKM dynamics

2018 ◽  
Vol 148 (16) ◽  
pp. 164309 ◽  
Author(s):  
Shreyas Malpathak ◽  
Xinyou Ma ◽  
William L. Hase
Keyword(s):  
Unimolecular Dissociation ◽  
Direct Dynamics ◽  
Dynamics Simulations

Modeling the Effects of O-sulfonation on the CID of Serine

2020 ◽  
Author(s):  
Kenneth Lucas ◽  
George Barnes
Keyword(s):  
Sulfo Group ◽  
High Energy ◽  
Empirical Method ◽  
Side Chain ◽  
Energy Structure ◽  
Direct Dynamics ◽  
Theoretical Mass ◽  
Intermolecular Proton Transfer ◽  
Dynamics Simulations ◽  
Semi Empirical

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of \textit{O}-sulfonation on the collision induced dissociation for serine. Towards this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m\z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m\z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The \mz 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also seen that the RM1 semi empirical method was not able to obtain all of the major peaks seen in experiment for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.

Mechanism of Thiolate-Disulfide Exchange: Addition–Elimination or Effectively SN2? Effect of a Shallow Intermediate in Gas-Phase Direct Dynamics Simulations

2012 ◽  
Vol 116 (47) ◽  
pp. 11492-11499 ◽  
Author(s):  
Manikandan Paranjothy ◽  
Matthew R. Siebert ◽  
William L. Hase ◽  
Steven M. Bachrach
Keyword(s):  
Gas Phase ◽  
Disulfide Exchange ◽  
Direct Dynamics ◽  
Dynamics Simulations

Evaluating the Accuracy of Hessian Approximations for Direct Dynamics Simulations

2012 ◽  
Vol 9 (1) ◽  
pp. 54-64 ◽  
Author(s):  
Yu Zhuang ◽  
Matthew R. Siebert ◽  
William L. Hase ◽  
Kenneth G. Kay ◽  
Michele Ceotto
Keyword(s):  
Direct Dynamics ◽  
Dynamics Simulations

Potential energy surface stationary points and dynamics of the F−+ CH3I double inversion mechanism

2017 ◽  
Vol 19 (30) ◽  
pp. 20127-20136 ◽  
Author(s):  
Yong-Tao Ma ◽  
Xinyou Ma ◽  
Anyang Li ◽  
Hua Guo ◽  
Li Yang ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Stationary Points ◽  
Direct Dynamics ◽  
Dynamics Simulations ◽  
Inversion Mechanism

Direct dynamics simulations were performed to study the SN2 double inversion mechanism SN2-DI, with retention of configuration, for the F−+ CH3I reaction.

scholarly journals Determination of Kinetic Properties in Unimolecular Dissociation of Complex Systems from Graph-Theory Based Analysis of an Ensemble of Reactive Trajectories.

2021 ◽  
Author(s):  
Ariel F. Perez-Mellor ◽  
Riccardo Spezia
Keyword(s):  
Graph Theory ◽  
Complex Systems ◽  
Kinetic Properties ◽  
Unimolecular Dissociation ◽  
Theoretical Mass ◽  
Reactive Trajectories ◽  
Direct Counting ◽  
Dynamics Simulations ◽  
State Kinetic

<div>We describe and apply a general approach based on graph-theory to obtain kinetic and structural properties from direct dynamics simulations. In particular, we focus on the unimolecular fragmentation of complex systems in which, prior to dissociation, different events can take place, and notably isomerizations and formation of ion-molecule complex.</div><div>3-state and 4-state kinetic models are thus obtained and rate constants for global or specific pathways are obtained from direct counting and flux calculation, both being in agreement.<br />Finally, we show how a theoretical mass spectrum can also be obtained automatically.<br /></div>

scholarly journals Curve crossing in a manifold of coupled electronic states: direct quantum dynamics simulations of formamide

2018 ◽  
Vol 212 ◽  
pp. 191-215 ◽  
Author(s):  
K. Eryn Spinlove ◽  
Gareth W. Richings ◽  
Michael A. Robb ◽  
Graham A. Worth
Keyword(s):  
Quantum Dynamics ◽  
Organic Molecules ◽  
Potential Surface ◽  
Electronic States ◽  
Small Organic Molecules ◽  
Direct Dynamics ◽  
Dynamics Simulations ◽  
Curve Crossing

Fully quantum direct dynamics simulations generate the potential surface manifold for the photo-excited dynamics of small organic molecules.

scholarly journals Direct Dynamics Simulations of the Thermal Fragmentation of a Protonated Peptide Containing Arginine

ACS Omega ◽  
2020 ◽  
Vol 5 (3) ◽  
pp. 1463-1471
Author(s):  
Meng Gu ◽  
Jiaxu Zhang ◽  
William L. Hase ◽  
Li Yang
Keyword(s):  
Protonated Peptide ◽  
Direct Dynamics ◽  
Thermal Fragmentation ◽  
Dynamics Simulations

scholarly journals Experiments and Direct Dynamics Simulations That Probe η2-Arene/Aryl Hydride Equilibria of Tungsten Benzene Complexes

2020 ◽  
Vol 142 (38) ◽  
pp. 16437-16454
Author(s):  
Jacob A. Smith ◽  
Anna Schouten ◽  
Justin H. Wilde ◽  
Karl S. Westendorff ◽  
Diane A. Dickie ◽  
...  
Keyword(s):  
Direct Dynamics ◽  
Dynamics Simulations
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