Beyond switches: Ratcheting a particle energetically uphill with a compartmentalized molecular machine

Journal of the American Chemical Society

Volumn 128, Issue 12, 2006, Pages 4058-4073

  Chatterjee, Manashi N ^a   Kay, Euan R ^a   Leigh, David A ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BROWNIAN MOVEMENT; POPULATION STATISTICS; STATISTICAL METHODS; SUBSTRATES;

BINDING SITES; BIOLOGICAL PUMPS; MACROCYCLES; MOLECULAR MACHINES;

MOLECULAR STRUCTURE;

AMINO ACID; MACROCYCLIC COMPOUND; PEPTIDE; ROTAXANE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CHEMICAL STRUCTURE; ENERGY; ISOMERIZATION; PHENOMENOLOGY; PHOTON; PROTON NUCLEAR MAGNETIC RESONANCE; REACTION ANALYSIS; STRUCTURE ANALYSIS;

EID: 33645453945     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja057664z     Document Type: Article

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155. 1H NMR spectroscopy.
156. e) in fum-E-5 change among Figures 3b, 3c, and 3d, illustrating the sensitivity of the H-bonding between the macrocycle and thread to factors such as moisture, concentration, and possibly, impurities.
157. This calculation assumes that both translational isomers of de-silylated Z-5 are re-silylated at the same rate. If this is not true, if the position of the macrocycle on a station affects the rate of the unlinking reaction, then it is possible to produce a nonbalanced distribution of the macrocycle through just controlling kinetic energy barriers with the position of the ring-an "information ratchet" (ref 25b).
158. The pure single translational isomer fum-E-5 cannot be regenerated by the operation of the machine but it can be separated from the reaction mixture at any stage using standard purification protocols.
159. Starting from state 5A, the linking and initial balance-breaking stimuli can be applied in either order (or simultaneously) in Scheme 8 for the task to be performed by the machine on the substrate, i.e., net transport of the macrocycle along the thread. In fact, any orthogonal transformations that transpire between two unlinking operations are commutative. Indeed, in a classic energy ratchet mechanism (ref 25b)-say using an oscillating electric field to directionally transport a charged particle-the linking/unlinking and balance-breaking steps happen simultaneously which, of course, would have exactly the same effect as doing them sequentially as envisaged in Scheme 8. Balance-breaking and linking/unlinking steps also occur simultaneously during the operation of molecular shuttles containing cyclodextrins incorporated onto azobenzene or stilbene threads (refs 13d, 13i, 13l, 13n, 20b, 20c, 20d, 20f, and 20g).
160. Although escapement occurs during the operation of 5, it is not escapement of a quantity that had been previously ratcheted by the operation of the motor. Prior to escapement, the macrocycles located on the olefin station in 5 have only been statistically unbalanced by the action of the motor, not ratcheted.
161. Combinational logic circuits (NAND, NOR, OR, XOR, EOR, two- and three-input INH, etc.) are assembled by connecting combinations of AND, NOT, and OR gates in various ways. These, in turn, are assembled by connecting simple "on"-"off" switches in various ways. See: (a) Ben-Ari, M. Mathematical Logic for Computer Science; Prentice-Hall: Hemel Hempstead, 1993.
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168. A series of stimuli-responsive molecular shuttles have been shown to exhibit relatively long-lived nonequilibrium ("metastable") states when operating in self-assembled monolayers or a polymer electrolyte or at low temperatures (see refs 15i, 15j, and 15k). This may account for the junction hysteresis observed in solid-state electronic devices that utilize such rotaxanes (refs 20k-n). Kinetically stable nonequilibrium co-conformations have also been observed in cyclodextrin-based shuttles; see refs 13l and 16d.
169. Since the method of operation of 5 involves varying the relative heights of energy minima and maxima irrespective of the position of the macrocycle, this is a partial "energy ratchet" mechanism (ref 25b). Other types of mechanisms are known (see ref 22), for example, an "information ratchet" which achieves directional transport of a Brownian substrate by varying the relative heights of energy maxima using information provided by the position of the substrate (ref 25b).
170. Chatterjee, M. N.; Goldup, S.; Kay, E. R.; Leigh, D. A. Manuscript in preparation.
171. Indeed, their branched topologies rule out rotaxanes as architectures for the particular examples of compartmentalized machines shown in Figure 5d (i) and (ii).