Molecular Machines: Energy Dissipation and Directional Motion

2. Machines take in energy and dissipate it while doing mechanical work, e.g. apply a force over a distance – are not in thermodynamic equilibrium Molecular machines are supposed to work in a thermally noisy environment, e.g. in a beaker or human body at room temperature or elevated temperatures, in this kind of environment, Brownian motion due to thermal energy (kT) is significant (and the molecular machines themselves are very very small) ! Synthetic chemistry is typically in thermodynamic equilibrium, the trick is to find conditions where a high yield of the desired product is assured, First there is some kind of massive “quasi-parallel processing” resulting in substantial quantities of the desired product, the reaction product is then taken out of the beaker (separated from the raw materials) the operation of the molecular motors in not in thermodynamic equilibrium, but they need to operate in a crowded and noisy environment (Brownian motion) asymmetries and/or chirality is designed into the molecular motors to allow for the ratchet principle, movement is possible only in one direction because it is blocked in the opposite direction

3. Kudernac, T.; Ruangsupapichat, N.; Parschau, M.; Maci. Electrically Driven Directional Motion of a Four-Wheeled Molecule on a Metal Surface. Nature 2011, 479 (7372), 208–211. A four-wheeled molecule moving on a metal surface.https://www.youtube.com/watch?v=I5JgJsjq3Q4 This machine has four rotary motors that move preferentially in one direction (due to a ratchet mechanism), input of a stream of photons (absorbed energy) moves it forward. Drexler’s fantasies are, on the other hand, produced by non-existing “miniature mechanical engineering” and are very highly symmetric so that they would be pretty useless in a noisy and crowded environment (due to Brownian motion) No wonder that the Nobel committee went for an approach that actually works !!!

4. Koumura, N.; Zijlstra, R. W. J.; Delden, R. A. van; Harada, N.; Feringa, B. L. Light-Driven Monodirectional Molecular Rotor. Nature 1999, 401 (6749), 152–155 Ratchet principle that works at room temperature, no extra heating required, photons serve as energy source to “stress the molecule”

5. Let’s start with molecules that contain mechanical bonds catenane, a new class of molecule

6. Dietrich-Buchecker, C. O.; Sauvage, J. P.; Kintzinger, J. P. Une nouvelle famille de molécules: Les métallo-caténanes. Tetrahedron Lett. 1983, 24 (46), 5095–5098.

7. Photo of a Roman “Il nodo di Salomone” mosaic, featuring a King Solomon Knot

8. rotaxanes, another new class of molecules Jiménez, M. C.; Dietrich-Buchecker, C.; Sauvage, J.-P. Towards Synthetic Molecular Muscles: Contraction and Stretching of a Linear Rotaxane Dimer. Angew. Chem. Int. Ed. 2000, 39 (18), 3284–3287

11. Actions are controlled by changing ph value in watery solution (concentration of protons), which results in change of concentration of electrons as well

12. The force exerted is approximately 200 pN. Badjić, J. D.; Balzani, V.; Credi, A.; Silvi, S.; Stoddart, J. F. A Molecular Elevator. Science 2004, 303 (5665), 1845–1849

13. Delden, R. A. van; Wiel, M. K. J.; Pollard, M. M.; Vicario, J.; Koumura, N.; Feringa, B. L.Unidirectional Molecular Motor on a Gold Surface. Nature 2005, 437 (7063), 1337–1340