Chemical Dynamics Simulations of CO2in the Ground and First Excited Bend States Colliding with a Perfluorinated Self-Assembled Monolayer

2010 ◽  
Vol 114 (43) ◽  
pp. 18455-18464 ◽  
Author(s):  
J. J. Nogueira ◽  
S. A. Vázquez ◽  
U. Lourderaj ◽  
W. L. Hase ◽  
E. Martínez-Núñez
Keyword(s):  
Chemical Dynamics ◽  
Self Assembled Monolayer ◽  
Self Assembled ◽  
Dynamics Simulations

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.

Chemical Dynamics Simulations of Energy Transfer in Collisions of Protonated Peptide−Ions with a Perfluorinated Alkylthiol Self-Assembled Monolayer Surface

2008 ◽  
Vol 112 (25) ◽  
pp. 9377-9386 ◽  
Author(s):  
Li Yang ◽  
Oleg A. Mazyar ◽  
U. Lourderaj ◽  
Jiangping Wang ◽  
M. T. Rodgers ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Protonated Peptide ◽  
Chemical Dynamics ◽  
Peptide Ions ◽  
Self Assembled Monolayer ◽  
Self Assembled ◽  
Dynamics Simulations

Chemical Dynamics Simulations of CO2Scattering off a Fluorinated Self-Assembled Monolayer Surface

2007 ◽  
Vol 111 (1) ◽  
pp. 354-364 ◽  
Author(s):  
Emilio Martínez-Núñez ◽  
Asif Rahaman ◽  
William L. Hase
Keyword(s):  
Chemical Dynamics ◽  
Self Assembled Monolayer ◽  
Self Assembled ◽  
Dynamics Simulations

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.

Nanotribology of self-assembled monolayer with a probe tip investigated using molecular dynamics simulations

Micron ◽  
2013 ◽  
Vol 44 ◽  
pp. 410-418 ◽  
Author(s):  
Cheng-Da Wu ◽  
Te-Hua Fang ◽  
Jen-Fin Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembled Monolayer ◽  
Self Assembled ◽  
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>

A Hybrid Continuum-Molecular Analysis of Interfacial Force Microscope Experiments on a Self-Assembled Monolayer

2004 ◽  
Vol 73 (5) ◽  
pp. 769-777 ◽  
Author(s):  
Mingji Wang ◽  
Kenneth M. Liechti ◽  
Vibha Srinivasan ◽  
John M. White ◽  
Peter J. Rossky ◽  
...  
Keyword(s):  
Cohesive Zone Model ◽  
Zone Model ◽  
Self Assembled Monolayer ◽  
Compressive Response ◽  
Assembled Monolayers ◽  
Self Assembled ◽  
Adhesive Interactions ◽  
Dynamics Simulations ◽  
Force Profiles ◽  
Interfacial Force

Nanoindentation experiments were performed on a defect-free, molecular self-assembled monolayer of octadecyltrichlorosilane (OTS) on silicon using an interfacial force microscope (IFM). The IFM provided repeatable and elastic force profiles corresponding to the adhesive and compressive response of these 2.5nm thick monolayers. As a first step in the analysis of the force profiles, the OTS was assumed to be linearly elastic and isotropic, and adhesive interactions were accounted for via a cohesive zone model. However, the assumption of linearity gave rise to force profiles that did not match the measurements. As a result, the mechanical behavior of the OTS was extracted from molecular-dynamics simulations and represented as a hypoelastic material, which, when used in finite element analyses of the IFM experiments, was able to fully reproduce the force profiles. This suggests that the continuum representation of the mechanical and adhesive behavior of self-assembled monolayers may be directly obtained from molecular analyses.

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