Yanao, Tomohiro and Koon, Wang Sang and Marsden, Jerrold E. (2009) Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters. Journal of Chemical Physics, 130 (14). p. 144111. ISSN 0021-9606. http://resolver.caltech.edu/CaltechAUTHORS:20090818-113933909
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This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a general message. First, we introduce a general method of hyperspherical mode analysis to analyze the energy transfer among internal modes of polyatomic molecules. In this method, the (3n−6) internal modes of an n-atom molecule are classified generally into three coarse level gyration-radius modes, three fine level twisting modes, and (3n−12) fine level shearing modes. We show that a large amount of kinetic energy flows into the gyration-radius modes when the cluster undergoes structural transitions by changing its mass distribution. Based on this fact, we construct a reactive mode as a linear combination of the three gyration-radius modes. It is shown that before the reactive mode acquires a large amount of kinetic energy, activation or inactivation of the twisting modes, depending on the geometry of the isomer, plays crucial roles for the onset of a structural transition. Specifically, in a symmetric isomer with a spherical mass distribution, activation of specific twisting modes drives the structural transition into an elongated isomer by inducing a strong internal centrifugal force, which has the effect of elongating the mass distribution of the system. On the other hand, in an elongated isomer, inactivation of specific twisting modes initiates the structural transition into a symmetric isomer with lower potential energy by suppressing the elongation effect of the internal centrifugal force and making the effects of the potential force dominant. This driving mechanism for reactions as well as the present method of hyperspherical mode analysis should be widely applicable to molecular reactions in which a system changes its overall mass distribution in a significant way.
|Additional Information:||© 2009 American Institute of Physics. Received 19 January 2009; accepted 20 February 2009; published online 13 April 2009. We wish to acknowledge stimulating discussions at the Telluride Workshop on “the complexity of dynamics and kinetics in many dimensions,” in which one of the authors T.Y. participated in 2007. In particular, we are grateful to R. Stephen Berry, Tamiki Komatsuzaki, Mikito Toda, George Haller, Sergy Grebenschikov, Laurent Wiesenfeld, Holger Waalkens, and Thomas Bartsch for their encouraging discussions. This work was partially supported by NSF Grant No. DMS-0505711. One of the authors T.Y. gratefully acknowledges the support from JSPS Fellowships for Research Abroad, and the research opportunity at Fukui Institute for Fundamental Chemistry, Kyoto University.|
|Subject Keywords:||intramolecular forces; isomerism; molecular clusters; molecular configurations; potential energy surfaces; reaction rate constants|
|Usage Policy:||No commercial reproduction, distribution, display or performance rights in this work are provided.|
|Deposited By:||Tony Diaz|
|Deposited On:||18 Aug 2009 22:38|
|Last Modified:||26 Dec 2012 11:12|
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