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 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.

Molecular Dynamics Study of Interfacial Thermal Resistance of Mercapto-Alkanol Self-Assembled Monolayer and Water

2009 ◽  
Author(s):  
Touru Kawaguchi ◽  
Gota Kikugawa ◽  
Ikuya Kinefuchi ◽  
Taku Ohara ◽  
Shinichi Yatuzuka ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Thermal Resistance ◽  
Chem Phys ◽  
Nonequilibrium Molecular Dynamics ◽  
Interfacial Thermal Resistance ◽  
Water Molecules ◽  
Self Assembled Monolayer ◽  
Self Assembled ◽  
Dynamics Simulations

The interfacial thermal resistance of 11-mercaptoundecanol (-S(CH2)11OH) self-assembled monolayer (SAM) adsorbed on Au(111) substrate and water was investigated using nonequilibrium molecular dynamics simulations. The interfacial thermal resistance was found to be a half of that in the system which consists of 1-dodecanthiol (-S(CH2)11CH3) SAM adsorbed on Au(111) and toluene [Kikugawa G. et al., J. Chem. Phys. (2009)]. The effective thermal energy transfer originates from hydrogen-bond structure between the SAM and water molecules in spite of weak structurization of water molecules near the SAM surface.

Mechanistic details of energy transfer and soft landing in ala2-H+ collisions with a F-SAM surface

2015 ◽  
Vol 17 (38) ◽  
pp. 24576-24586 ◽  
Author(s):  
S. Pratihar ◽  
N. Kim ◽  
S. C. Kohale ◽  
W. L. Hase
Keyword(s):  
Energy Transfer ◽  
Chem Phys ◽  
Chemical Dynamics ◽  
Soft Landing ◽  
Self Assembled Monolayer ◽  
Collisional Energy ◽  
Self Assembled ◽  
Dynamics Simulations ◽  
Collisional Energy Transfer ◽  
Phys Chem Chem Phys

Previous chemical dynamics simulations (Phys. Chem. Chem. Phys., 2014, 16, 23769–23778) were analyzed to delineate mechanistic details of collisional energy transfer and trapping/soft landing for collisions of N-protonated dialanine (ala2-H+) with a C8 perfluorinated self-assembled monolayer.

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