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: A0Localization 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-conformersIt 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 machinesSynthetic Nanoscale objects that can perform several tasksIn nature: proteins are the most representative systemsHighly 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 chainsThey are flexible and with reduced dimensionsThey self-organize on monolayer and cristallizeThe switching process is similar to conformational changes in proteinsNo bond-breaking during the switching process, only non-covalent interactions, time from microsecond to millisecond in solution

Technological interestsLangmuir 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 directions1. 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 cyclophaneNo charge transfer between the counterions and the systemElectric field of the solvent as a possible reaction coordinate

PerspectivesSwitching process in solution and with monolayerFree energy profiles respect to a few reaction coordinates

(new method by A. Laio and M. Parrinello, PNAS 2002)