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Molecular dynamics study of
molecular switches
Matteo Ceccarelli
Gabriele Petraglio and Michele Parrinello
CSCS (Manno, Switzerland)
ETH (Zurich, Switzerland)
Overview
Introduction and Motivations:
•[2]Catenanes and molecular switches
•Molecular machines
•Technological interests of [2]Catenanes: devices
•Perspectives
Our project:
•Details of algorithms and simulations
•State of the project: static calculations and
kinetic in vacuum and in solution
[2]Catenane
Neutral state: A0
Localization of the HOMO
Molecular Switch
Molecular system
having 2 main co-conformers
State A0
State B+
Choosing suitable units it is possible to have different
electronic structures for the two co-conformers
It is possible to move (switch) from one co-conformer to the
other reversibly upon external stimuli (oxido-reduction or
electric field) and without bond-breaking
Molecular Machines
Molecular switches belong to the wider class of molecular
machines
Synthetic Nanoscale objects that can perform several tasks
In nature: proteins are the most representative systems
Highly specialized systems with high performance (natural
selection), self-assembly and self-organizing
Electron and proton pump proteins (photosynthesis)
Transport proteins (hemoglobine)
Ion channels to transmit signals or select molecules
(antibiotics, sugars, amino acids etc.)
The term molecular machine or molecular motor was coined by
the group of Prof. Balzani (Univ. of Bologna, IT) in the ’90s
Structure and functionalities
[2]Catenanes are cheap, obtained easily by self-assembly of simple
sub-systems, tetracationic cyclophane (the cage, +4),
tetrathiofulvalene (TTF) and dioxynaphtalene (NP) units
connected by polyether chains
They are flexible and with reduced dimensions
They self-organize on monolayer and cristallize
The switching process is similar to conformational
changes in proteins
No bond-breaking during the switching process, only non-covalent
interactions, time from microsecond to millisecond in solution
Technological interests
Langmuir Blodgett monolayer can be transferred onto
polysilicon wires
Our Project
Switching Process of [2]Catenanes in different
conditions
Static calculations: Electronic structure calculations
and force-field parameters for classical MD (done)
Kinetics in vacuum (done)
Kinetics in solution (in progress)
Free Energy profiles in solution (next step)
Perspectives: two different directions
1. Other switches and molecular machines
(collaboration with Prof. Balzani, Univ. of Bologna)
2. Kinetics on LB monolayer: are the processes the
same when the systems are confined?
The switching process
The switching process 2
Energetics and mechanism
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Conclusions
With the action-based method we investigated microscopically
the switching process of the [2]catenane in vacuum
Two electrostatic barriers were found along the reaction path
(12 kcal/mol each)
Counterions are involved in the process: they decrease the
electrostatic barriers between NP-TTF and the charged
cyclophane
No charge transfer between the counterions and the system
Electric field of the solvent as a possible reaction coordinate
Perspectives
Switching process in solution and with monolayer
Free energy profiles respect to a few reaction coordinates
(new method by A. Laio and M. Parrinello, PNAS 2002)