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The true nature of rotary movements in rotaxanes.

ABSTRACT: Disentangling the different movements observed in rotaxanes is critical to characterize their function as molecular and biological motors. How to achieve unidirectional rotation is an important question for successful construction of a highly efficient molecular motor. The motions within a rotaxane composed of a benzylic amide ring threaded on a fumaramide moiety were investigated employing atomistic molecular dynamics simulations. The free-energy profiles describing the rotational process of the ring about the thread were determined from multi-microsecond simulations. Comparing the theoretical free-energy barriers with their experimental counterpart, the syn-anti isomerization of the amide bond within the ring was ruled out. The free-energy barriers arise in fact from the disruption of hydrogen bonds between the ring and the thread. Transition path analysis reveals that complete description of the reaction coordinate requires another collective variable. The free-energy landscape spanned by the two variables characterizing the coupled rotational and shuttling processes of the ring in the rotaxane was mapped. The calculated free-energy barrier, amounting to 9.3 kcal mol^-1, agrees well with experiment. Further analysis shows that shuttling is coupled with the isomerization of the ring, which is not limited to a simplistic chair-to-chair transition. This work provides a cogent example that contrary to chemical intuition, molecular motion can result from complex, entangled movements requiring for their accurate description careful modeling of the underlying reaction coordinate. The methodology described here can be used to evaluate the different components of the multifaceted motion in rotaxanes, and constitutes a robust tool for the rational design of molecular machines.

SUBMITTER: Liu P

PROVIDER: S-EPMC6090524 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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The true nature of rotary movements in rotaxanes.

Liu Peng P Shao Xueguang X Chipot Christophe C Cai Wensheng W

Chemical science 20151013 1

Disentangling the different movements observed in rotaxanes is critical to characterize their function as molecular and biological motors. How to achieve unidirectional rotation is an important question for successful construction of a highly efficient molecular motor. The motions within a rotaxane composed of a benzylic amide ring threaded on a fumaramide moiety were investigated employing atomistic molecular dynamics simulations. The free-energy profiles describing the rotational process of th ...[more]

PMID: 30155010

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Project description:Experiments on choice-predictive brain signals have played an important role in the debate on free will. In a seminal study, Benjamin Libet and colleagues found that a negative-going EEG signal, the readiness potential (RP), can be observed over motor-related brain regions even hundreds of ms before the time of the conscious decision to move. If the early onset of the readiness potential is taken as an indicator of the "brain's decision to move" this could mean that this decision is made early, by unconscious brain activity, rather than later, at the time when the subject believes to have decided. However, an alternative kind of interpretation, involving ongoing stochastic fluctuations, has recently been brought to light. This stochastic decision model (SDM) takes its inspiration from leaky accumulator models of perceptual decision making. It suggests that the RP originates from an accumulation of ongoing stochastic fluctuations. In this view, the decision happens only at a much later stage when an accumulated noisy signal (plus imperative) reaches a threshold. Here, we clarify a number of confusions regarding both the evidence for the stochastic decision model as well as the interpretation that it offers. We will explore several points that we feel are in need of clarification: (a) the empirical evidence for the role of stochastic fluctuations is so far only indirect; (b) the interpretation of animal studies is unclear; (c) a model that is deterministic during the accumulation stage can explain the data in a similar way; (d) the primary focus in the literature has been on the role of random fluctuations whereas the deterministic aspects of the model have been largely ignored; (e) contrary to the original interpretation, the deterministic component of the model is quantitatively the dominant input into the accumulator; and finally (f) there is confusion regarding the role of "imperative" in the SDM and its link to "evidence" in perceptual decision making. Our aim is not to rehabilitate the role of the RP in the free will debate. Rather we aim to address some confusions regarding the evidence for accumulators playing a role in these preparatory brain processes.

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The true nature of rotary movements in rotaxanes.

Publications

The true nature of rotary movements in rotaxanes.

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