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PubMed2005

Structures and properties of self-assembled monolayers of bistable [2]rotaxanes on Au (111) surfaces from molecular dynamics simulations validated with experiment.

Bistable [2]rotaxanes display controllable switching properties in solution, on surfaces, and in devices. These phenomena are based on the electrochemically and electrically driven mechanical shuttling motion of the ring-shaped component, cyclobis(paraquat-p-phenylene) (CBPQT(4+)) (denoted as the ring), between a tetrathiafulvalene (TTF) unit and a 1,5-dioxynaphthalene (DNP) ring system located along a dumbbell component. When the ring is encircling the TTF unit, this co-conformation of the rotaxane is the most stable and thus designated the ground-state co-conformer (GSCC), whereas the other co-conformation with the ring surrounding the DNP ring system is less favored and so designated the metastable-state co-conformer (MSCC). We report here the structure and properties of self-assembled monolayers (SAMs) of a bistable [2]rotaxane on Au (111) surfaces as a function of surface coverage based on atomistic molecular dynamics (MD) studies with a force field optimized from DFT calculations and we report several experiments that validate the predictions. On the basis of both the total energy per rotaxane and the calculated stress that is parallel to the surface, we find that the optimal packing density of the SAM corresponds to a surface coverage of 115 A(2)/molecule (one molecule per 4 x 4 grid of surface Au atoms) for both the GSCC and MSCC, and that the former is more stable than the latter by 14 kcal/mol at the optimum packing density. We find that the SAM retains hexagonal packing, except for the case at twice the optimum packing density (65 A(2)/molecule, the 3 x 3 grid). For the GSCC and MSCC, investigated at the optimum coverage, the tilt of the ring with respect to the normal is theta = 39 degrees and 61 degrees, respectively, while the tilt angle of the entire rotaxane is psi = 41 degrees and 46 degrees , respectively. Although the tilt angle of the ring decreases with decreasing surface coverage, the tilt angle of the rotaxane has a maximum at 144 A(2)/molecule (the 4 x 5 grid/molecule) of 50 degrees and 51 degrees for the GSCC and MSCC, respectively. The hexafluorophosphate counterions (PF(6)(-)) stay localized around the ring during the 2 ns MD simulation. On the basis of the calculated density profile, we find that the thickness of the SAM is 40.5 A at the optimum coverage for the GSCC and 40.0 A for MSCC, and that the thicknesses become less with decreasing surface coverage. The calculated surface tension at the optimal packing density is 45 and 65 dyn/cm for the GSCC and MSCC, respectively. This difference suggests that the water contact angle for the GSCC is larger than for the MSCC, a prediction that is verified by experiments on Langmuir-Blodgett monolayers of amphiphilic [2]rotaxanes.

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PubMed2007

Design and optimization of molecular nanovalves based on redox-switchable bistable rotaxanes.

Redox-controllable molecular nanovalves based on mesoporous silica nanoparticles have been fabricated, using two bistable [2]rotaxanes with different spacer lengths between their recognition sites as the gatekeepers. Three different linkers with varying chain lengths have been employed to attach the bistable [2]rotaxane molecules covalently to the silica substrate. These nanovalves can be classified as having IN or OUT locations, based on the positions of the tethered bistable [2]rotaxanes with respect to the entrances to the nanopores. The nanovalves are more efficient when the bistable [2]rotaxane-based gatekeepers are anchored deep within (IN) the pores than when they are attached closer to (OUT) the pores' orifices. The silica nanopores can be closed and opened by moving the mechanically interlocked ring component of the bistable [2]rotaxane closer to and away from the pores' orifices, respectively, a process which allows luminescent probe molecules, such as coumarins, tris(2-phenylpyridine)iridium, and rhodamine B, to be loaded into or released from the mesoporous silica substrate on demand. The lengths of the linkers between the surface and the rotaxane molecules also play a critical role in determining the effectiveness of the nanovalves. The shorter the linkers, the less leaky are the nanovalves. However, the distance between the recognition units on the rod section of the rotaxane molecules does not have any significant influence on the nanovalves' leakiness. The controlled release of the probe molecules was investigated by measuring their luminescence intensities in response to ascorbic acid, which induces the ring's movement away from the pores' orifices, and consequently opens the nanovalves.

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PubMed2001

Self-assembly of novel [3]- and [2]rotaxanes with two different ring components: donor-acceptor and hydrogen bonding interactions and molecular-shuttling behavior.

Three of the first kind of hetero[3]rotaxanes, which comprise one linear component and one neutral and one tetracationic ring component, have been assembled by using the intermolecular hydrogen bonding and donor-acceptor interactions. Three neutral [2]rotaxanes and three tetracationic [2]rotaxanes have also been synthesized as intermediate products or for the sake of property comparison. The linear molecules are incorporated with two glycine subunits, for templating the formation of the neutral tetraamide cyclophane, and one or two hydroquinone subunits, for inducing the formation of the tetracationic cyclophane. Variable-temperature (1)H NMR investigation reveals that the shuttling behavior of the tetracationic ring component along the linear component is substantially influenced by the existence of the neutral ring component. The spatial repelling interaction of the neutral ring on the electron-deficient tetracationic ring simultaneously weakens the latter's "positioning" tendency at both electron-rich hydroquinone sites of the linear component. As a result, the activation energy associated with the shuttling process of the tetracationic ring between the two hydroquinone sites is remarkably reduced in comparison to that of the shuttling process of the corresponding neutral ring-free [2]rotaxanes. For the first time, the rotation of the dipyridinium subunit around the axis formed by the two methylene groups connecting them within the tetracationic cyclophane has been investigated by variable-temperature (1)H NMR spectroscopy and the associated kinetic data have also been successfully obtained. Furthermore, the UV-vis and fluorescent properties of the new [2]- and [3]rotaxanes have been studied. The results demonstrate that [3]rotaxanes with different ring components possess unique kinetic features that are not available in [3]rotaxanes with identical ring components.

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PubMed2006

Unidirectional threading synthesis of isomer-free [2]rotaxanes.

The threading of an alpha-cyclodextrin (alpha-CyD) by an unsymmetrical dumbbell generally results in two isomeric [2]rotaxanes differing in the orientation of the alpha-CyD. In this work, two methods have been developed for the unidirectionally threading an alpha-CyD to obtain isomer-free [2]rotaxanes. These methods use the Suzuki coupling of a boronic acid derivative and a halide in aqueous alkaline solution. The conformations of the two unidirectional [2]rotaxanes-R3 and R4 were determined by 2D 1H ROESY NMR spectra. The optical spectral studies revealed that each of the two [2]rotaxanes can proceed with E/Z photoisomerization and shuttling motions of the alpha-CyD ring on the thread under alternating irradiation at 330 and 275 nm, accompanied by fluorescence intensity changes at 530 nm. The induced circular dichroism (ICD) spectra of another two analogous [2]rotaxanes R1 and R2 were also studied. Distinctive ICD signal changes resulting from the photoisomerization with respect to the movements of alpha-CyD were detected. This demonstrates that, besides the fluorescence, ICD signal is another way to identify the shuttling motions of alpha-CyD in these [2]rotaxanes.

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PubMed2006

Wire-type ruthenium(II) complexes with terpyridine-containing [2]rotaxanes as ligands: Synthesis, characterization, and photophysical properties.

[2]Rotaxanes based on the 1,2-bis(pyridinium)ethane subset[24]crown-8 ether motif were prepared that contain a terminal terpyridine group for coordination to a transition-metal ion. These rotaxane ligands were utilized in the preparation of a series of heteroleptic [Ru(terpy)(terpy-rotaxane)]2+ complexes. The compounds were characterized by 1D and 2D 1H NMR spectroscopy, X-ray crystallography, and high-resolution electrospray ionization mass spectrometry. The effect of using a rotaxane as a ligand was probed by UV/Vis/NIR absorption and emission spectroscopy of the Ru(II) complexes. In contrast with the parent [Ru(terpy)(2)]2+ complex, at room temperature the examined complexes exhibit a luminescence band in the near infrared region and a relatively long lived triplet metal-to-ligand charge-transfer (3MLCT) excited state, owing to the presence of strong-electron-acceptor pyridinium substituents on one of the two terpy ligands. Visible-light excitation of the Ru-based chromophore in acetonitrile at room temperature causes an electron transfer to the covalently linked 4,4'-bipyridinium unit and the quenching of the MLCT luminescence. The 3MLCT excited state, however, is not quenched at all in rigid matrix at 77 K. The rotaxane structure was found to affect the absorption and luminescence properties of the complexes. In particular, when a crown ether surrounds the cationic axle, the photoinduced electron-transfer process is slowed down by a factor from 2 to 3. Such features, together with the synthetic and structural advantages offered by [Ru(terpy)2]2+-type complexes compared to, for example, [Ru(bpy)3]2+-type compounds, render these rotaxane-metal complexes promising candidates for the construction of photochemical molecular devices with a wire-type structure.

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PubMed2003

Synthesis of a copper [3]rotaxane able to function as an electrochemically driven oscillatory machine in solution, and to form SAMs on a metal surface.

Two new copper [3]rotaxanes have been synthesized. The axes are identical for both compounds and incorporate two bidentate chelates joined together by a disulfide bridge. The rings contain either the single phen (phen = 1,10-phenanthroline) chelate or two different chelates (phen and terpy; terpy = 2,2',6',2' '-terpyridine, a tridentate chelate). The key intermediates for both synthetic routes are semi-rotaxanes obtained in high yields using the three-dimensional effect of copper(I). In the case where the wheels are heterobischelating macrocycles, large molecular motions, namely rotation or oscillation of the wheels around the axle, have been induced electrochemically. Anchoring of these two copper [3]rotaxanes on a gold electrode was carried out by standard procedures. Cleavage of the disulfide bridge and formation of monolayers of rotaxanes were evidenced by cyclic voltammetry. The adsorbed rotaxanes can be viewed as copper [2]rotaxanes for which the gold electrode surface acts as a stopper linked to one end of their axes.

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PubMed2002

Reversing a rotaxane recognition motif: threading oligoethylene glycol derivatives through a dicationic cyclophane.

An already well-established recognition motif-namely one in which the NH2+ centers in the rod sections of the dumbbell components of rotaxanes are encircled by macrocyclic polyether components-has been turned simultaneously outside-in and inside-out, a fact that has been proved beyond any doubt by the stoppering of both ends of a [2]pseudorotaxane to give a stable [2]rotaxane. The [2]pseudorotaxane is formed in nitromethane when a benzylic dibromide, obtained after reacting an excess of 1,4-bis(bromomethyl)benzene with hexaethylene glycol, is added to an equimolar amount of a dicationic cyclophane in which two -CH2OCH2- chains link a pair of dibenzylammonium ions through the para positions on their phenyl rings. When the [2]pseudorotaxane is reacted in nitromethane with triphenylphosphine, a [2]rotaxane and the corresponding free dumbbell compound are isolated in 58 and 31% yields, respectively. The structure of the [2]rotaxane is established by using mass spectrometry (FABMS and ESMS) and NMR (1H and 13C) spectroscopy in nitromethane-d3. The [2]rotaxane exhibits quite dramatic changes in the 1H chemical shifts of the signals for its CH2N+ and CH2O protons compared with those in the free dumbbell compound. The 1H NMR spectrum of the [2]pseudorotaxane shows many similar features. Titration experiments with three of the six different CH2O probes give an average Ka value of 2900 +/- 750 M-1 in nitromethane-d3. The new recognition motif for the template-directed synthesis of rotaxanes can now be exploited at both the molecular and macromolecular levels of structure with numerous potential applications in sight.

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PubMed2003

Assembly of an electronically switchable rotaxane on the surface of a titanium dioxide nanoparticle.

This paper describes the self-assembly of a heterosupramolecular system consisting of a tripodal [2]rotaxane adsorbed at the surface of a titanium dioxide nanoparticle. The tripodal [2]rotaxane consists of a dumbbell-shaped molecule, incorporating two electron-poor viologens, threading an electron-rich crown ether. The [2]rotaxane also incorporates a bulky tripodal linker group at one end and a bulky stopper group at the other end. The [2]rotaxane is adsorbed, via the tripodal linker group, at the surface of a titanium dioxide nanoparticle. The structure and function of the resulting hetero[2]rotaxane have been studied in detail by (1)H NMR spectroscopy and cyclic voltammetry. A key finding is that it is possible to electronically address and switch the above hetero[2]rotaxane.

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PubMed2006

Homo- and hetero-[3]rotaxanes with two pi-systems clasped in a single macrocycle.

Here we present the first synthesis of a [3]rotaxane with two dumbbell components threaded through a single gamma-cyclodextrin macrocycle. This synthesis is carried out in two steps: first one dumbbell is synthesized threaded through the macrocycle to give a [2]rotaxane, then a second dumbbell is synthesized through the remaining cavity of the [2]rotaxane. We have synthesized a hetero- [3]rotaxane with one stilbene and one cyanine dye threaded through gamma-cyclodextrin, which exhibits quantitative energy transfer between the two encapsulated dyes. The stilbene [2]rotaxane intermediate in this synthesis has a remarkably high affinity for suitably shaped hydrophobic guests in aqueous solution, facilitating the synthesis of [3]rotaxanes and suggesting possible applications in sensors.

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PubMed2003

Self-assembly of novel [3]- and [2]rotaxanes based on donor-acceptor and hydrogen-bonding interactions. Intensified inter-ring repulsion interaction and shuttling behavior.

Three novel hetero[3]rotaxanes, which comprise one neutral tetraamide cyclophane, one tetracationic cyclophane, and one linear component, have been assembled by utilizing hydrogen-bonding and donor-acceptor interactions, through three neutral [2]rotaxanes as intermediates. Three tetracationic [2]rotaxanes are also prepared for property comparison. For all three linear components, diamide subunits, the hydrogen-bonding templating moieties, are introduced at the center of the molecules, while the electron-rich hydrogquinone subunits, the donor-acceptor interaction templates, are incorporated between the diamides and the triphenylmethyl stoppers. Compared with the reported [3]rotaxanes, the novel hetero[3]rotaxanes exhibit remarkably intensified spatial interaction between the two ring components, which had been proved by (1)H NMR and UV study. For the first time, inter-ring NOEs are observed for interlocked [3]rotaxanes.

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PubMed2006

Squaraine-derived rotaxanes: highly stable, fluorescent near-IR dyes.

Squaraines are fluorescent, near-IR dyes with promising photophysical properties for biomedical applications. A limitation with these dyes is their inherent reactivity with nucleophiles, which leads to loss of the chromophore. Another drawback is their tendency to form nonfluorescent aggregates in water. Both problems can be greatly attenuated by encapsulating the dye inside an amide-containing macrocycle. In other words, the squaraine becomes the thread component in a Leigh-type rotaxane, a permanently interlocked molecule. Two new rotaxanes are described: an analogue with four tri(ethyleneoxy) chains on the squaraine to enhance water solubility, and a rotaxane that has an encapsulating macrocycle with transposed carbonyl groups. An X-ray crystal structure of the latter rotaxane shows that the macrocycle provides only partial protection of the electrophilic cyclobutene core of the squaraine thread. The stabilities of each compound in various solvents, including serum, were compared with a commercially available cyanine dye. The squaraine rotaxane architecture is remarkably resistant to chemical and photochemical degradation, and likely to be very useful as a versatile fluorescent scaffold for constructing various types of highly stable, near-IR imaging probes.

Animals↗

PubMed2003

Host-[2]rotaxanes as cellular transport agents.

Host-[2]rotaxanes, containing a diarginine-derivatized dibenzo-24-crown-8 (DB24C8) ether as the ring and a cyclophane pocket or an aromatic cleft as one blocking group, are cell transport agents. These hosts strongly associate with a variety of amino acids, dipeptides, and fluorophores in water (1 mM phosphate buffer, pH 7.0), DMSO, and a 75/25 (v/v) buffer to DMSO solution. All peptidic guests in all solvent systems have association constants (K(A)'s) in the range of 1 x 10(4) to 5 x 10(4) M(-)(1), whereas the K(A) range for the fluorophores is 1 x 10(4) to 9 x 10(5) M(-)(1). Association constants for the cyclophane itself, cyclophane 3, are smaller. These values are in the 1 x 10(3) to 5 x 10(3) M(-)(1) range, which shows that the rotaxane architecture is advantageous for guest binding. Cyclophane-[2]rotaxane 1 efficiently transports fluorescein and a fluorescein-protein kinase C (PKC) inhibitor into eukaryotic COS-7 cells, including the nucleus. Interestingly, cleft-[2]rotaxane 2 does not transport fluorescein as efficiently, even though the results from the fluorescence assays show that both [2]rotaxanes bind fluorescein with the same ability.

Animals↗

PubMed2005

Squaraine-derived rotaxanes: sterically protected fluorescent near-IR dyes.

A squaraine dye with bulky end groups is employed as the thread component in two Leigh-type amide rotaxanes. The rotaxanes are synthesized in a simple two-step process. X-ray crystal structures of the rotaxanes show that the pyridyl-containing macrocycle is more rigid and wraps more tightly around the cyclobutene core of the squaraine thread compared to the isophthalamide-containing macrocycle. The rotaxanes exhibit photophysical properties that are similar to the precursor squaraine. The encapsulating macrocycle greatly increases the chemical stability of the squaraine thread and inhibits aggregation-induced broadening of its absorption spectrum. It should be possible to prepare squaraine-derived rotaxanes with improved properties for a wide range of photophysical, photochemical, and biomedical applications.

Crystallography, X-Ray↗

PubMed2003

Kinetic versus thermodynamic control during the formation of [2]rotaxanes by a dynamic template-directed clipping process.

A template-directed dynamic clipping procedure has generated a library of nine [2]rotaxanes that have been formed from three dialkylammonium salts-acting as the dumbbell-shaped components-and three dynamic, imino bond-containing, [24]crown-8-like macrocycles-acting as the ring-shaped components-which are themselves assembled from three dialdehydes and one diamine. The rates of formation of these [2]rotaxanes differ dramatically, from minutes to days depending on the choice of dialkylammonium ion and dialdehyde, as do their thermodynamic stabilities. Generally, [2]rotaxanes formed by using 2,6-diformylpyridine as the dialdehyde component, or bis(3,5-bis(trifluoromethyl)benzyl)ammonium hexafluorophosphate as the dumbbell-shaped component, assembled the most rapidly. Those rotaxanes containing this particular electron-deficient dumbbell-shaped unit, or 2,5-diformylfuran units in the macroring, were the most stable thermodynamically. The relative thermodynamic stabilities of all nine of the [2]rotaxanes were determined by competition experiments that were monitored by (1)H NMR spectroscopy.

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PubMed2005

A [3]rotaxane with three stable states that responds to multiple-inputs and displays dual fluorescence addresses.

A [3]rotaxane molecular shuttle containing two alpha-cyclodextrin (alpha-CD) macrocycles, an azobenzene unit, a stilbene unit, and two different fluorescent naphthalimide units has been investigated. The azobenzene unit and the stilbene unit can be E/Z-photoisomerized separately by light excited at different wavelengths. Irradiation at 380 nm resulted in the photoisomerization of the azobenzene unit, leading to the formation of one stable state of the [3]rotaxane (Z1-NNAS-2CD); irradiation at 313 nm resulted in the photoisomerization of the stilbene unit, leading to the formation of another stable state of the [3]rotaxane (Z2-NNAS-2CD). The reversible conversion of the Z1 and Z2 isomers back to the E isomer by irradiation at 450 nm and 280 nm, respectively, is accompanied by recovery of the absorption and fluorescence spectra of the [3]rotaxane. The E isomer and the two Z isomers have been characterized by 1H NMR spectroscopy and by two-dimensional NMR spectroscopy. The light stimuli can induce shuttling motions of the two alpha-CD macrocycles on the molecular thread; concomitantly, the absorption and fluorescence spectra of the [3]rotaxane change in a regular way. When the alpha-CD macrocycle stays close to the fluorescent moiety, the fluorescence of the moiety become stronger due to the rigidity of the alpha-CD ring. As the photoisomerization processes are fully reversible, the photo-induced shuttling motions of the alpha-CD rings can be repeated, accompanied by dual reversible fluorescence signal outputs. The potential application of such light-induced mechanical motions at the molecular level could provide some insight into the workings of a molecular machine with entirely optical signals, and could provide a cheap, convenient interface for communication between micro- and macroworlds.

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PubMed2000

alpha- and beta-cyclodextrin rotaxanes of mu-bis(4-pyridyl)bis[pentacyanoferrate(II)] complexes.

The kinetics and mechanism of the self-assemblies of alpha- and beta-cyclodextrin (CD) [2]rotaxanes, [(NC)5Fe-[pyRpy.CD]Fe(CN)5]6-, containing pentacyanoferrate(II)-stoppered 4,4'-bis(pyridyl) threads pyRpy (R = -CH = CH-, -N=N-, -CH=N-N=CH-, and -C(CH3)=N-N=C(CH3)-) have been investigated in aqueous solution by using visible and 1H NMR spectroscopy. The rotaxanes may be formed rapidly by the addition of the [Fe(CN)5OH2]3- ion to the CD-included pyRpy thread or slowly by the addition of an excess of CD to the dimeric [(NC)5Fe(pyRpy)Fe(CN)5]6- complex. In the latter method, the mechanism involves a rate-determining dissociation of a [Fe(CN)5]3- center to form the monomeric complex, which subsequently includes the coordinated pyRpy in the CD cavity to yield the semirotaxane, which is rapidly recomplexed by the [Fe(CN)5OH2]3- ion, generating the [2]rotaxane. Rate and activation parameters and CD inclusion stability constants have been determined for the ligand substitution reactions involving the formations and dissociations of the semirotaxanes and rotaxanes. The extents of the decreases in the formation (kf) and dissociation (kd) rate constants upon CD inclusions of the free and coordinated ligands, respectively, are related to the natures of the CD hosts and the R linkage on the pyRpy guests. The semirotaxanes and rotaxanes exhibit significant bathochromic shifts in their visible MLCT transitions compared with the corresponding monomeric and dimeric iron complexes. A correlation between the extent of the decrease in kd and the change in the MLCT energy upon alpha-CD inclusions of [Fe(CN)5L]3-, where L is an aromatic N-heterocyclic 4-Rpy or pyRpy ligand, has been observed.

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PubMed2005

Intramolecular photoinduced charge transfer in rotaxanes.

We report the synthesis and photophysical investigation of a series of rotaxanes in which the physical confinement of the donor and acceptor (DA) pair leads, in some cases, to emissive exciplexes. As a comparison, we examined the photoinduced charge-transfer processes in the same DA mixtures under intermolecular conditions. The interlocked configuration of the rotaxane facilitates pi orbital overlap of the excited state DA pair by keeping their center-to-center distance extremely small. This increased interaction between the DA pair significantly lowers the activation energy for exciplex formation (E(a)) and helps stabilize the highly polar charge-transfer complex. We find that the stabilizing effect of the rotaxane architecture compensates for the modest thermodynamic driving force for some charge-transfer interactions. In addition, we examined the temperature dependence on the rotaxanes' optical properties. Metal coordination to the tetrahedral cavity disrupts the cofacial conformation of the DA pair and quenches the fluorescence. Binding of alkali metal ions to the 3,4-ethylenedioxythiophene (EDOT)-based rotaxane, however, gives rise to the emergence of a new weak emission band at even lower energies, indicative of a new emissive exciplex.

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PubMed2005

Synthesis and photoinduced electron transfer processes of rotaxanes bearing [60]fullerene and zinc porphyrin: effects of interlocked structure and length of axle with porphyrins.

Three rotaxanes, with axles with two zinc porphyrins (ZnPs) at both ends penetrating into a necklace pending a C60 moiety, were synthesized with varying interlocked structures and axle lengths. The intra-rotaxane photoinduced electron transfer processes between the spatially positioned C60 and ZnP in rotaxanes were investigated. Charge-separated (CS) states (ZnP*+, C60*-)rotaxane are formed via the excited singlet state of ZnP (1ZnP*) to the C60 moiety in solvents such as benzonitrile, THF, and toluene. The rate constants and quantum yields of charge separation via 1ZnP decrease with axle length, but they are insensitive to solvent polarity. When the axle becomes long, charge separation takes place via the excited triplet state of ZnP (3ZnP*). The lifetime of the CS state increases with axle length from 180 to 650 ns at room temperature. The small activation energies of charge recombination were evaluated by temperature dependence of electron-transfer rate constants, probably reflecting through-space electron transfer in the rotaxane structures.

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