Stimuli-controlled self-assembly of diverse tubular aggregates from one single small monomer

The design and synthesis of new stimuli-responsive hydrogen-bonding monomers that display a diversity of self-assembly pathways is of central importance in supramolecular chemistry. Here we describe the aggregation properties of a simple, intrinsically C2-symmetric enantiopure bicyclic cavity compound bearing a terminally unsubstituted ureidopyrimidinone fragment fused with a pyrrole moiety in different solvents and in the absence and presence of C60 and C70 guests. The tetrameric cyclic aggregate is selectively obtained in chlorinated solvents, where only part of the available hydrogen bonding sites are utilized, whereas in toluene or upon addition of C70 guests, further aggregation into tubular supramolecular polymers is achieved. The open-end cyclic assemblies rearrange into a closed-shell capsule upon introduction of C60 with an accompanied symmetry breaking of the monomer. Our study demonstrates that a C60 switch can be used to simultaneously control the topology and occupancy of tubular assemblies resulting from the aggregation of small monomers.


Synthesis
Supplemetary Figure 1. Synthesis of compounds 1-4. The synthesis of the target compounds 1-4 is based on the Fischer indolization reaction between corresponding bicyclic ketones and pyrimidine hydrazines . The starting enantiopure diketone (+)-(1R,5R)-10 was obtained in multigram quantities by kinetic resolution of racemic 10 with bakers yeast [3] . Diketone 10 was converted into dienone 11 either via one-pot selenation-selenoxide elimination using Barton conditions [1] (milligram scale) or via two step procedure based on sulfoxide elimination (multigram scale). Dienone 11 was further used for the synthesis of diketones having the required solubilizing group. For compound 5 having bulky bis(decyloxy)benzyl groups tin-lithium exchange was used to obtain, first benzylic organolithium intermediate, which was then transmetalated to corresponding cuprate using soluble CuCN·2LiCl salt. Direct synthesis of benzyllithium or benzylmagnesium derivative was not possible due to extensive Wurtz coupling. On the other hand, p-bromobenzyl derivative 5b was obtained without problems using direct oxidative insertion of zinc followed by transmetalation with copper (I). Diketones 5a,b were treated with hydrazine derivatives 6 and 14 containing isocytosine moeity at rt in AcOH to provide corresponding bis-hydrazones, which were used directly in the next step. The acid catalysed low-temperature Fischer indolization is not efficient with heteroaromatic hydrazones, therefore thermal conditions were utilized [4] . The heating mantle was used to provide high temperature (>300 º C) and argon stream was constantly passed through the reaction mixture throughout the course of the reaction ( Supplemetary Fig. 2). The amino group of the pyrrolo-isocytosine derivatives 8a-c obtained were activated with phenyl chloroformate before the addition of ammonia (for compounds [1][2][3] or diethylamine (for compound 4). In the first version of this transformation, the temporal protection of OH-groups with TMSCl was used (see synthetic procedure for compound 4), however, later it was found that redundant phenyloxycarbonyl functionalities on isocytosine oxygen atoms were readily cleaved with an excess of ammonia or amine used for urea synthesis.   Under nitrogen, to a stirred suspension of sodium hydride (7.85 g, 0.20 mol, 60 % dispersion in mineral oil) in dry THF (30 mL) was added methyl benzenesulphinate (11.3 g, 9.50 mL, 77.0 mmol) at once. A solution of (+)-(1R,5R)-10 (5.00 g, 32.9 mmol) in dry THF (40 mL) was added dropwise and the reaction mixture was stirred at rt overnight. The green-yellow suspension was quenched with 4% phosphoric acid until pH 3-4. After addition of water (50 mL), the aqueous phase was extracted with ethyl acetate. The combined organic fractions were washed with brine, dried with Na2SO4 and concentrated under reduced pressure yielding 18.1 g of a crude yellow oil, which was subjected to flash chromatography (ethyl acetate). Besides unreacted methylbenzene sulfinate (Rf 0.84), two other fractions, consisting of the compounds 3,7-bis(phenylsulfinyl)bicyclo[3.3.1]nonane-2,6-dione (Rf 0.28) and 7-(phenylsulfinyl)bicyclo[3.3.1]non-3-ene-2,6-dione (Rf 0.45) were obtained. To the mixture of above compounds in toluene (80 mL), sodium carbonate (17.4 g, 0.16 mol) was added and the reaction mixture was brought to reflux. After 10 min., TLC (petrol ether/ethyl acetate-6:1) showed complete conversion and the reaction mixture was cooled to rt and filtered. The filter cake was washed with toluene (60 mL) and the green clear filtrate was evaporated. The residue was purified by flash chromatography (petrol ether/ ethyl acetate-6:1), yielding 3.90 g (80 %) of (+)-(1R,5R)-11 as an yellowish solid, which was stored in the fridge under nitrogen, protected from ambient light.
Racemic 11 was obtained using the same procedure starting from racemic 10.
The reaction mixture was directly loaded on the silica gel column and diphenyl ether was removed by using petroleum ether as eluent. Then, the eluent was changed to CH2Cl2/MeOH (10/1) to afford 2.34 g of partially purified product. The crude product was further purified by flash chromatography with gradient eluent system (CH2Cl2, then CH2Cl2/  11.0 eq.) was added dropwise. After 10 min, the ice bath was removed and the reaction mixture was stirred at rt for 22h. Then it was cooled to 0 o C again and 25% NH3·H2O (2.8 mL) was added dropwise.
The result mixture was allowed to reach rt and was stirred at rt overnight. The suspension was quenched with excess of 10% HCl and extracted with CH2Cl2. The combined organic phase was washed with sat. NaHCO3, dried with Na2SO4 and evaporated. The residue was triturated with MeOH (300 mL) and sonicated for several minutes. The suspension was filtered to give 0.43 g (77% yield) of compound 1 as an off-white solid.
A suspension of 7b (288 mg) in diphenylether (8 ml) was refluxed for 10.5 h. with argon gas passing through the reaction mixture via long cannula (see Supplementary Fig. 2). After cooling to r.t., the crude product was precipitated with hexane (40 ml). Column chromatography on silica gel using gradient eluent system CH2Cl2/MeOH (20:1 -10:
7c (150 mg) in diphenyl ether (8 ml) was refluxed for 6 h. with argon gas passing through the reaction mixture via long cannula (see Supplementary Fig. 2). After cooling to rt, the reaction mixture was directly loaded on the silica gel column and diphenyl ether was removed by using petroleum ether as eluent. Then, the eluent was changed to CH2Cl2/MeOH (50/1) and elution was continued to afford 8c (59 mg, 40%) as a yellowish glass.   Supplementary Figure 6. DEPT spectrum of 5a in CDCl3.       Figure 33. COSY spectrum of 1-DAN (X1) in CDCl3.In order to additionally confirm that all previous NMR assignments made for 1 in CDCl3 corresponds to a proposed conformer and tautomeric form of the isocytosine unit in 1, we prepared H-bonded 1:2 heterocomplex of 1 with 2,7diamido-1,8-naphthyridine derivative (DAN). It is well established that DAN forms 4H-bonded heterocomplex with ureidopyrimidinone derivatives using ADDA-DAAD H-bonding mode with remarkable fidelity [6] . The same correlations as in 14 aggregate where found within complexed PUPY unit, corroborating the assignment of the conformer of 1.   Figure 35. DOSY spectrum of 1 in CDCl3. The spectrum indicates the presence of a single aggregate and the value of diffusion coefficient obtained D= 2.39×10 -10 m 2 s -1 agrees well with proposed cyclic tetramer as compared with related systems [5] .   Fig. 43).
Please note, the calibration curve obtained was used for the calculation of Mw and polydispersity index (PDI). The hydrodynamic properties of polystyrene chain and mass density along the chain is very different from the hollow supramolecular polymer 1n.
Therefore, the molecular weight calculated in this way is a very rough estimate and can be used for qualitative discussion only.  was assigned to C=O stretching vibration, ν(C=O) [8] . Downshift of this band due to 15 N-isotope labeling indicates considerable coupling of C=O stretching and NH2 deformation vibrational modes. [9] The bands at 1635 and 1421 cm −1 also exhibit red shift upon 14 N/ 15 N exchange and was assigned to NH2 deformation, δ(NH2), and C−N antisymmetric stretching, νa(C−N), vibrations, respectively. [9][10][11] In the high frequency spectral region the band at 3353 cm  Table 1). In addition, the 14 N/ 15 N-isotope substitution sensitive ν(N−H) band downshifts from 3353 to 3317 cm −1 . All these changes are consistent with involvement of both C=O and NH2 groups of urea linkage in hydrogen bonding interaction; it is well-known that such interaction results in decreased frequencies of ν(C=O) and ν(N−H) modes, while opposite shift is expected for the νa(C−N) band [8,9,[11][12][13][14] .     Supplementary Figure 55. Variable temperature 1 H NMR spectra of C60@14 in CDCl3. The resonances labelled * correspond to protons 7' which are too broad to observe at higher temperature as a result of the facile rotation around C-N bond.

5'
inter-unit NOE Supplementary Figure 61. 1 H NMR titration of C 60 with 1 in CDCl 3 . Sample preparation: to a carefully weighted mixture of 1 and C 60 CDCl 3 was added and the mixture was stirred for one week at rt 1 H NMR titration experiment showed that resonances of the free 14 disappears when the fraction of C60 reaches 0.25 equiv. Mixing of C60 with an excess of 14 and integrating the resulting 1 H NMR spectra confirmed the 4:1 stoichiometry of the inclusion complex. For instance, 1 H NMR spectrum of 6.7:1 -1:C60 mixture (top) gave the integral ratio of the free 1 and C60@14 equal to 1/0.77 = 1.3 which translated into the ratio 1:C60 = 6.6 (after taking into account the C2-symmetry of 1 in free 14). The good agreement between the actual ratio and the one calculated from monomer-tetrameric complex equilibrium confirms the 1:4 stoichiometry of the inclusion complex. C 60 @1 4 C 60 @1 4 Molecular modeling. The geometry of monomer 1 having two different conformers of PUPY unit was first calculated at semi-empirical quantum chemistry level of theory (AM1 within Spartan 10 [15] ). The optimized monomers were then used to construct D2-symmetric tetramer with an alternating arrangement of H-bonded conformers at the poles of capsule-like aggregate with C60 molecule inside. Solubilizing groups were replaced with H to save computational time. However, simple geometry optimization of complete tetrameric structure showed that solubilizing groups do not interact significantly and can be easily accommodated around the capsule without significant steric interference. All attempts to assemble analogous supramolecular complex with C70 failed.

Standard Curve
Supplementary Table 2. Liquid-solid extraction of C60/C70 with 1. The solid-liquid extraction of fullerenes with 1 showed no significant selectivity and the affinities of 1n and 14 toward C70 and C60, respectively, were very similar. The large increase of the solubility of fullerenes in CDCl3 was observed in the presence of 1. a The preparation of sample: a mixture of solid C60, C70 and 1 was put into a small vial followed by 0.8 mL of dried CDCl3. The suspension was stirred at rt for at least one week. Then, it was filtered by syringe filter for removing the excess of solid fullerene. For standard solution, known amount of C60 or C70 were stirred in CDCl3 until full dissolution and then diluted to obtain required concentration b The preparation of sample for HPLC: 50 µl of filtered solution, were diluted with 950 µl of toluene and then 10 µl TFA were added; c TFA was added before dilution; d Additional 10 µl of TFA were added to 3B; e The data were corrected by subtracting HPLC area of the blank sample.
Self-sorting experiments. Sample preparation. A mixture of monomers 1 (10.0 mg, 7.78 µmol) and 9 (10.0 mg, 7.78 µmol ) were dissolved in CDCl3 (600 µL) in NMR tube. After 24 hr, 1 H NMR spectrum was acquired and then, C60 (1.4 mg, 1.95 µmol) was added as a solid. The mixture was kept at room temperature until homogenous solution is obtained and no further changes in 1 H NMR spectrum was observed. The solution was evaporated and dried in vacuo before toluene-d8 was added. After 24 hr, the 1 H NMR spectrum was recorded and the solvent was again removed in vacuo. Redissolving the sample in CDCl3 and aging the solution for 48 hr resulted in the recovery of the original spectrum.