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 |
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Reaction of O(3P) with a n-Hexylthiloate Self-Assembled Monolayer (SAM) Journal of Molecular Structure 556, 43 (2000) |
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Cl- + CH3Br ---> ClCH3 + Br- SN2 Reaction Journal of Chemical Physics 118, 2688 (2003) |
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Ne + n-Hexylthiolate Self-Assembled Monolayer (SAM) Scattering Journal of Chemical Physics 107, 9677 (1997) |
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Diglycine-H+ + Diamond {111} Surface-Induced Dissociation Journal of the the American Soc. Mass Spectrom. 19, 1402 (2003) |
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Glycine-H+ + Diamond {111} Surface-Induced Dissociation Journal of Physical Chemistry A 106, 9983 (2002) |
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[HO--CH3--F]- ---> CH3OH + F - Exit-Channel Dynamics Science 296, 875 (2002) |
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Sliding Friction of Hydroxylated a-Alumina Surfaces Tribology Letters 7, 153 (2000) |
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Cl- + CH3Cl ---> ClCH3 + Cl- Central Barrier Dynamics Journal of Chemical Physics 96, 8275
(1992) |
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O(3P) + C2H6 Reaction Dynamics for 5 ev Collisions Journal of Physical Chemistry A 108, 9863(2004) |
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Cl- + C2H5Cl ---> ClC2H5 + Cl- Central Barrier Dynamics Canadian Journal of Chemistry 82, 1 (2004) |
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Energy Partitioning in HX Elimination. Mass Effects Collaboration with Don Setser |
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Collaboration with Saulo Vázquez
and Emilio
Martínez-Núňez |
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Collaboration with Emilio Martínez-Núňez Journal of Physical Chemistry C 111, 354 (2007) |
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H + HBr ---> H2 + Br Reaction Dynamics Collaboration with
Dick Zare Research Group |
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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) |
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Cl- + CH3I ---> ClCH3 + I- SN2 Reaction Collaboration with Roland Wester Research Group, University of Innsbruck Science 319, 183 (2008) |
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Journal of Chemical Physics 125, 014317 (2006) |
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NH4+ + CH4 reactive and non-reactive collisions with B3LYP/6-31 Gd Journal of Chemical Physics A 113, 7543-7547 (2009) |
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Physical Chemistry Chemical Physics 12,1 (2010) |
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Octaglycine-H+ + Diamond {111} Surface-Induced Dissociation Journal of the American Society for Mass Spectrometry 20, 939 (2009) |
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| More animations will come soon ............ | |
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