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     The animations for each reaction were prepared from trajectories calculated as part of a chemical dynamics simulation. A trajectory determines the positions of all the atoms as a function of time and one can study atomic-level mechanisms for chemical reactions and molecular collisions. To compare with an experiment, a large number of trajectories must be calculated to properly average all the different possibilities for the initial positions, velocities, orientations, etc. of the reactant molecules. The following animations are for representative trajectories among the large number which were calculated. 

      The animations were prepared using the VMD software developed by the Klaus Schulten research group, University of Illinois. http://www.ks.uiuc.edu/Research/vmd

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Representative Animations

Reaction of O(3P) with a n-Hexylthiloate Self-Assembled Monolayer (SAM)

Journal of Molecular Structure 556, 43 (2000)

Cl- + CH3Br ---> ClCH3 + Br-  SN2 Reaction

Journal of Chemical Physics 118, 2688 (2003)

 

Ne + n-Hexylthiolate Self-Assembled Monolayer (SAM) Scattering

Journal of Chemical Physics 107, 9677 (1997)
Phys. Chem. Chem. Phys. 2, 901 (2000)
Chemical Physics Letters 329, 84 (2000)
Journal of Physical Chemistry B 106, 8029 (2002)
Journal of Physical Chemistry A 107, 10600(2003)
Journal of Chemical Physics 120, 2417 (2004)

Diglycine-H+ + Diamond {111} Surface-Induced Dissociation

Journal of the the American Soc. Mass Spectrom. 19, 1402 (2003)

Glycine-H+ + Diamond {111} Surface-Induced Dissociation

Journal of Physical Chemistry A 106, 9983 (2002)

[HO--CH3--F]- ---> CH3OH + F - Exit-Channel Dynamics

Science 296, 875 (2002)

Sliding Friction of Hydroxylated a-Alumina Surfaces

Tribology Letters 7, 153 (2000)
Journal of Physical Chemistry B 105, 12032 (2001)
Phys. Chem. Chem. Phys. 4, 5377 (2002)
Journal of Chemical Physics 122, 094713 (2005)

Cl- + CH3Cl ---> ClCH3 + Cl- Central Barrier Dynamics

Journal of Chemical Physics 96, 8275 (1992)
Journal of the American Chemical Society 123, 5735 (2001)

O(3P) + C2H6 Reaction Dynamics for 5 ev Collisions

Journal of Physical Chemistry A 108, 9863(2004)

Cl- + C2H5Cl ---> ClC2H5 + Cl- Central Barrier Dynamics

Canadian Journal of Chemistry 82, 1 (2004)

Energy Partitioning in HX Elimination. Mass Effects

Collaboration with Don Setser
Journal of Chemical Physics 124, 064313 (2006)

Xe + Cr+(CO)6 CID

Collaboration with Saulo Vázquez and Emilio Martínez-Núňez
Journal of Chemical Physics 123, 154311 (2005)

CO2 + F-SAM (C8) Scattering

Collaboration with Emilio Martínez-Núňez
Journal of Physical Chemistry C 111, 354 (2007)

H + HBr ---> H2 + Br Reaction Dynamics

Collaboration with Dick Zare Research Group
Journal of the American Chemical Society 127, 16368 (2005)

F- + CH3OOH Collisions. Non-IRC Dynamics

Collaboration with Shuji Kato, Wibe A. DeJong, and Theresa L. Windus
Journal of the American Chemical Society 129, 9976 (2007)

Cl- + CH3I ---> ClCH3 + I- SN2 Reaction

Collaboration with Roland Wester Research Group, University of Innsbruck
Science 319, 183 (2008)

Ozonolysis of Propene

Journal of Chemical Physics 125, 014317 (2006)

NH4+ + CH4 reactive and non-reactive collisions with B3LYP/6-31 Gd

Journal of Physical Chemistry A 113, 7543-7547 (2009)

gly2-H+ + F-SAM Collisions with RAM1

Journal of Chemical Physics 134, 094106 (2011)

Non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer

Physical Chemistry Chemical Physics 12, 1 (2010)

Octaglycine-H+ + Diamond {111} Surface-Induced Dissociation

Journal of the American Society for Mass Spectrometry 20, 939 (2009)

OH- + CH3I ---> CH3OH + I- SN2 Reaction

Collaboration with the Roland Wester and Al Viggiano Research Groups

OH-(H2O) + CH3I ---> CH3OH + I- + H2O SN2 Reaction

Collaboration with the Roland Wester and Al Viggiano Research Groups

Collision of High Energy Xenon on Ice [Solid H2O] Surface at 140 K

Collaboration with the Steve Sibena Research Group

Mechanistic Details of ala2-H+ Collisions with a F-SAM Surface

Collaboration with Julia Lashia

Thermal Fragmentation of the Doubly Protonated Tripeptide Threonine-Isoleucine-Lysine, TIK(H+)2

Collaboration with the Riccardo Spezia research group
Journal of Physical Chemistry A 120, 8211 (2016)


More animations will come soon ............