Collective coordinates and the mechanism for conformational transitions of complex molecules

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.; Kevrekidis, Ioannis G.

doi:10.1002/pamm.200700486

Cited by 2 publications

(2 citation statements)

References 4 publications

(4 reference statements)

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“…The equations of motion for the hyperangular modes would also be useful to highlight the qualitative difference of their dynamics from that of the gyration radii. Indeed, the structure of the equations of motion for the hyperangular modes 61 is largely different from those for the gyration radii. The most striking difference is that the kinematic terms in the equations of motion for the hyperangular modes appear to vanish after averaging.…”

Section: Discussionmentioning

confidence: 99%

Gyration-radius dynamics in structural transitions of atomic clusters

Yanao

Koon

Marsden

et al. 2007

The Journal of Chemical Physics

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This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.

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Section: Discussionmentioning

confidence: 99%

Gyration-radius dynamics in structural transitions of atomic clusters

Yanao

Koon

Marsden

et al. 2007

The Journal of Chemical Physics

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“…Various extensions [30][31][32][33] and applications of the partition method have been made. They mainly regarded systems as neutral and ionic atom clusters and doped rare gas matrices.…”

Section: Survey Of Applicationsmentioning

confidence: 99%

Hyperspherical and related views of the dynamics of nanoclusters

et al. 2009

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In this paper, we give an account of recent progress in understanding properties of nanoaggregates, following their dynamical behavior by classical mechanics simulations and utilizing tools based on extensions of hyperspherical and related techniques, originally developed for the quantum mechanical treatment of few-body atomic and molecular systems. After an outline of the underlying theory, recent applications exemplifying statistical and thermodynamic aspects of nanoclusters are discussed.

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Collective coordinates and the mechanism for conformational transitions of complex molecules

Cited by 2 publications

References 4 publications

Gyration-radius dynamics in structural transitions of atomic clusters

Gyration-radius dynamics in structural transitions of atomic clusters

Hyperspherical and related views of the dynamics of nanoclusters

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