Direct Dynamics Simulations of the Unimolecular Decomposition of the Randomly Excited 1CH2O2 Criegee Intermediate. Comparison with 3CH2 + 3O2 Reaction Dynamics

2020 ◽  
Vol 124 (9) ◽  
pp. 1821-1828
Author(s):  
Yuxuan Yao ◽  
Sandhiya Lakshmanan ◽  
Subha Pratihar ◽  
William L. Hase
Keyword(s):  
Reaction Dynamics ◽  
Unimolecular Decomposition ◽  
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.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

2015 ◽  
Vol 143 (21) ◽  
pp. 214102 ◽  
Author(s):  
Adithya Vijaykumar ◽  
Peter G. Bolhuis ◽  
Pieter Rein ten Wolde
Keyword(s):  
Molecular Dynamics ◽  
Green’S Function ◽  
Green's Function ◽  
Reaction Dynamics ◽  
Dynamics Simulations

Reaction Dynamics of ATP Hydrolysis in Actin Determined by ab Initio Molecular Dynamics Simulations

2012 ◽  
Vol 8 (9) ◽  
pp. 3373-3383 ◽  
Author(s):  
Holly Freedman ◽  
Teodoro Laino ◽  
Alessandro Curioni
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Atp Hydrolysis ◽  
Reaction Dynamics ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Transition state dynamics and a QM/MM model for the Cl– + C2H5Cl SN2 reaction

2004 ◽  
Vol 82 (6) ◽  
pp. 891-899 ◽  
Author(s):  
Lipeng Sun ◽  
Eunkyung Chang ◽  
Kihyung Song ◽  
William L Hase
Keyword(s):  
Hydrogen Atom ◽  
Transition State ◽  
Reaction Dynamics ◽  
Vibrational Frequencies ◽  
Dynamics Simulation ◽  
Rrkm Theory ◽  
Direct Dynamics ◽  
Sn2 Reaction ◽  
Classical Trajectories ◽  
Link Atom

A MP2/6-31G* direct dynamics simulation is used to study the dynamics of the central barrier [Cl-C2H5-Cl]– for the Cl– + C2H5 SN2 reaction. The majority of the trajectories move off the central barrier to form the Cl––C2H5Cl complex and appear to undergo efficient IVR as assumed by RRKM theory. However, some of the trajectories move directly to products without forming the complex, a non-RRKM result. A hydrogen atom link-atom QM/MM model is described for studying the dynamics of [X-CH2R-Y]– central barriers with the -R substituent. The model is used to calculate vibrational frequencies for the [Cl-C2H5-Cl]– central barrier.Key words: SN2 reaction dynamics, RRKM theory, QM/MM model, central barrier dynamics, direct dynamics classical trajectories.

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

Tight-binding quantum chemical molecular dynamics simulations for the elucidation of chemical reaction dynamics in SiC etching with SF6/O2 plasma

2016 ◽  
Vol 18 (11) ◽  
pp. 7808-7819 ◽  
Author(s):  
Hiroshi Ito ◽  
Takuya Kuwahara ◽  
Kentaro Kawaguchi ◽  
Yuji Higuchi ◽  
Nobuki Ozawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Reaction ◽  
Quantum Chemical ◽  
Tight Binding ◽  
Reaction Dynamics ◽  
Chemical Reaction Dynamics ◽  
Dynamics Simulations ◽  
Quantum Chemical Molecular Dynamics ◽  
O2 Plasma

Simulations based on tight-binding quantum chemical molecular dynamics are performed to elucidate SiC etching mechanisms and to study SiC surface reactions with SF5 radicals and O atoms.

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 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.

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