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

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.

Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces

2016 ◽  
Vol 45 (13) ◽  
pp. 3595-3608 ◽  
Author(s):  
Subha Pratihar ◽  
George L. Barnes ◽  
William L. Hase
Keyword(s):  
Energy Transfer ◽  
Protonated Peptide ◽  
Chemical Dynamics ◽  
Peptide Ions ◽  
Soft Landing ◽  
Surface Induced Dissociation ◽  
Organic Surfaces ◽  
Dynamics Simulations ◽  
Reactive Landing

Different simulation approaches like MM, QM + MM, and QM/MM, were used to study surface-induced dissociation, soft-landing, and reactive-landing for the peptide-H+ + surface collisions.

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 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

Exploratory Direct Dynamics Simulations of 3O2 Reaction with Graphene at High Temperatures

2018 ◽  
Vol 122 (51) ◽  
pp. 29368-29379 ◽  
Author(s):  
Seenivasan Hariharan ◽  
Moumita Majumder ◽  
Ross Edel ◽  
Tim Grabnic ◽  
S. J. Sibener ◽  
...  
Keyword(s):  
High Temperatures ◽  
Direct Dynamics ◽  
Dynamics Simulations

Direct Dynamics Simulations of Collision- and Surface-Induced Dissociation of N-Protonated Glycine. Shattering Fragmentation†

2002 ◽  
Vol 106 (42) ◽  
pp. 9983-9992 ◽  
Author(s):  
Samy O. Meroueh ◽  
Yanfei Wang ◽  
William L. Hase
Keyword(s):  
Direct Dynamics ◽  
Surface Induced Dissociation ◽  
Dynamics Simulations
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