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

scholarly journals Fast Fragmentation During Surface-Induced Dissociation: An Examination of Peptide Size and Structure

2020 ◽  
Author(s):  
George Barnes ◽  
Amanda Shlaferman ◽  
Monica Strain
Keyword(s):  
Self Assembled Monolayer ◽  
Collision Event ◽  
Direct Dynamics ◽  
Surface Induced Dissociation ◽  
Self Assembled ◽  
Dynamics Simulations ◽  
Size And Structure

We present the results of direct dynamics simulations of surface-induced dissociation for protonated versions of A$_\mathrm{n}$K, KA$_\mathrm{n}$ (n = 1, 3, and 5), AcA$_\mathrm{7}$K, and AcKA$_\mathrm{7}$ for collisions with a fluorinated self-assembled monolayer surface. We focus on elucidating fast fragmentation events, which takes place in coincidence with the collision event. Such events generate a large number of products, and hence, are not easily understood through chemical intuition. Our simulations show distinct differences between the A$_{\mathrm{n}}$K/AcA$_\mathrm{7}$K and KA$_{\mathrm{n}}$/AcKA$_7$ series of peptides, with the former being more reactive, and the latter more selective. Backbone rearrangements and sidechain fragmentation are also seen.<br>

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

2020 ◽  
Author(s):  
George Barnes ◽  
Amanda Shlaferman ◽  
Monica Strain
Keyword(s):  
Self Assembled Monolayer ◽  
Collision Event ◽  
Direct Dynamics ◽  
Surface Induced Dissociation ◽  
Self Assembled ◽  
Dynamics Simulations ◽  
Size And Structure

We present the results of direct dynamics simulations of surface-induced dissociation for protonated versions of A$_\mathrm{n}$K, KA$_\mathrm{n}$ (n = 1, 3, and 5), AcA$_\mathrm{7}$K, and AcKA$_\mathrm{7}$ for collisions with a fluorinated self-assembled monolayer surface. We focus on elucidating fast fragmentation events, which takes place in coincidence with the collision event. Such events generate a large number of products, and hence, are not easily understood through chemical intuition. Our simulations show distinct differences between the A$_{\mathrm{n}}$K/AcA$_\mathrm{7}$K and KA$_{\mathrm{n}}$/AcKA$_7$ series of peptides, with the former being more reactive, and the latter more selective. Backbone rearrangements and sidechain fragmentation are also seen.<br>

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

2020 ◽  
Author(s):  
George Barnes ◽  
Amanda Shlaferman ◽  
Monica Strain
Keyword(s):  
Self Assembled Monolayer ◽  
Collision Event ◽  
Direct Dynamics ◽  
Surface Induced Dissociation ◽  
Self Assembled ◽  
Dynamics Simulations ◽  
Size And Structure

We present the results of direct dynamics simulations of surface-induced dissociation for protonated versions of A$_\mathrm{n}$K, KA$_\mathrm{n}$ (n = 1, 3, and 5), AcA$_\mathrm{7}$K, and AcKA$_\mathrm{7}$ for collisions with a fluorinated self-assembled monolayer surface. We focus on elucidating fast fragmentation events, which takes place in coincidence with the collision event. Such events generate a large number of products, and hence, are not easily understood through chemical intuition. Our simulations show distinct differences between the A$_{\mathrm{n}}$K/AcA$_\mathrm{7}$K and KA$_{\mathrm{n}}$/AcKA$_7$ series of peptides, with the former being more reactive, and the latter more selective. Backbone rearrangements and sidechain fragmentation are also seen.<br>

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

2020 ◽  
Author(s):  
George Barnes ◽  
Amanda Shlaferman ◽  
Monica Strain
Keyword(s):  
Self Assembled Monolayer ◽  
Collision Event ◽  
Direct Dynamics ◽  
Surface Induced Dissociation ◽  
Self Assembled ◽  
Dynamics Simulations ◽  
A Charge ◽  
Size And Structure

We present the results of direct dynamics simulations of surface-induced dissociation for A<sub>n</sub>K, KA<sub>n</sub> (n = 1, 3, and 5), AcA<sub>7</sub>K, and AcKA<sub>7</sub> for collisions with a fluorinated self-assembled monolayer surface. Our focus is on elucidating shattering fragmentation events, which takes place in coincidence with the collision event and frequently occurs in a charge remote fashion. Shattering events typically generate a large number of fragmentation products, and hence, are not easily understood through chemical intuition. Our simulations show distinct differences between the A<sub>n</sub>K/AcA<sub>7</sub>K and KA<sub>n</sub>/AcKA<sub>7</sub> series of peptides, with the former being more reactive, while the latter is more selective regarding the type of bond that will break. In addition, we examine the possible backbone rearrangements seen as well as sidechain fragmentation.

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.

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