Molecular dynamics study of molecular switches

1. Molecular dynamics study of molecular switches Matteo Ceccarelli Gabriele Petraglio and Michele Parrinello CSCS (Manno, Switzerland) ETH (Zurich, Switzerland)

2. 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

3. [2]Catenane Neutral state: A0 Localization of the HOMO

4. 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

5. 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

6. 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

7. Technological interests • Langmuir Blodgett monolayer can be transferred onto polysilicon wires

8. 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 • Other switches and molecular machines (collaboration with Prof. Balzani, Univ. of Bologna) • Kinetics on LB monolayer: are the processes the same when the systems are confined?

9. The switching process

10. The switching process 2

11. 1 3 2 4 5 6 5 4 1 6 3 2 Energetics and mechanism

12. 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)