Self-assembly of polycyclic supramolecules using linear metal-organic ligands

Coordination-driven self-assembly as a bottom-up approach has witnessed a rapid growth in building giant structures in the past few decades. Challenges still remain, however, within the construction of giant architectures in terms of high efficiency and complexity from simple building blocks. Inspired by the features of DNA and protein, which both have specific sequences, we herein design a series of linear building blocks with specific sequences through the coordination between terpyridine ligands and Ru(II). Different generations of polycyclic supramolecules (C1 to C5) with increasing complexity are obtained through the self-assembly with Cd(II), Fe(II) or Zn(II). The assembled structures are characterized via multi-dimensional mass spectrometry analysis as well as multi-dimensional and multinuclear NMR (1H, COSY, NOESY) analysis. Moreover, the largest two cycles C4 and C5 hierarchically assemble into ordered nanoscale structures on a graphite based on their precisely-controlled shapes and sizes with high shape-persistence.

(Accelrys Software, Inc.). All counterions were omitted. An initially energy-minimized structure was subjected to 80 -100 annealing cycles with initial and mid-cycle temperatures of 300 and 1500 K, respectively, twenty heating ramps per cycle, one thousand dynamic steps per ramp, and one femtosecond per dynamic step. A constant volume/constant energy (NVE) ensemble was used and the geometry was optimized after each cycle. Geometry optimization used a universal force field with atom-based summation and cubic spline truncation for both the electrostatic and Van der Waals parameters. 75-80 energy-minimized structures were used for the calculation of theoretical collision cross-sections using MOBCAL program 3 .

TEM.
The sample was drop-casted on to a lacey carbon coated Cu grid (300 mesh, purchased from Ted Pella Inc.) or carbon-coated Cu grid (400 mesh, purchased from SPI supplies), and the extra solution was absorbed by filter paper to avoid aggregation. The TEM images of the drop casted samples were taken with a FEI Morgagni transmission electron microscope, AFM. AFM imaging was carried out with a Digital Instrument Nanoscope Dimension 3000 system.
The sample was diluted to a concentration of 10 -6 M using acetonitrile, then dropped on freshly cleaved mica surface and dried in the air. Silicon cantilevers tip with spring constant of around 0.1N/m was used for the experiments.
STM. The sample was dissolved in DMF at a concentration of 5.0 mg/mL. Sample Solution (5 uL) was dropped on HOPG surface. After 30 seconds, surface was washed slightly with water for three times and acetone for once, then dried at room temperature in air. The STM images were taken with a PicoPlus SPM system with a PicoScan 3000 Controller. The 3D STM images were processed using a free Scanning Probe Microscope (SPM) image analysis software (Gwyddion 2.4). chloroform, and the organic layer was dried over anhydrous Na2SO4 and filtered through celite.
After the evaporation of solvent under vacuum, 30 mL of chloroform and 30 mL of methanol was added, followed by the addition of K2CO3 (1.38 g, 10 mmol) in one portion. The suspension was then stirred at room temperature for 2h, and another 100 mL of water was added. With the extraction using chloroform, the organic layer was dried over anhydrous Na2SO4 and the solvent was evaporated under vacuum. The crude product was purified via column chromatography on silica gel (CHCl3/MeOH = 100/1) to give compound 3 as a pale yellow solid (653 mg, 87% yield). mol/L in THF), the mixture was stirred at 70 °C for 16h. After that the reaction was cooled down to room temperature and 100 mL of water was added. The mixture was extracted with chloroform, and the organic layer was collected, dried over anhydrous sodium sulfate and the solvent was evaporated under vacuum. The crude product was purified via column chromatography on silica gel (CHCl3/MeOH = 100/2) to give L1 as a white solid (374 mg, 52.3% yield). 1  mg, 0.08 mmol) were mixed in a 100 mL Schlenk flask. After degassing and backfill with nitrogen for three times, 30 mL of THF and 30 mL of Et3N were added under nitrogen atmosphere. After the addition of TMSA (400 µL, 2.8 mmol), the mixture was stirred at 60 °C for 16h. After cooling down to room temperature, 100 mL of water was added. The mixture was extracted with chloroform, and the organic layer was collected, dried over anhydrous sodium sulfate and the solvent was evaporated under vacuum. The crude product was purified via column chromatography on silica gel (CHCl3/MeOH = 100/1) to give 3 as a pale yellow solid (600.1 mg, 71% yield). 1 H NMR (400 MHz, CDCl3, 300K) δ 8.72 (dt, J = 3.9, 0.9 Hz, 2H, tpy-H 6,6'' ), 8 18 . To an aqueous solution of NaOH (25%, 50 mL) containing p-bromophenol (17.3 g, 0.1 mol) and methanol (25 mL) was added formaldehyde (38%, 90 mL) and the mixture was stirred for 12 days at room temperature. Then, a mixture of water (50 mL) and acetic acid (15 mL) was added. The reaction mixture was stirred for 8 h at room temperature to give a yellow precipitate, which was collected via filtration. The precipitate was then dissolved in 10% aqueous NaOH, followed by acidify with 2 M HCl until pH = 1. The crystals formed was collected via filtration and washed with water, dried to give a pale yellow solid (10.9 g, 47% yield).
The white residue was dissolved using 200 mL of DCM, after which PCC (11.8 g, 75 mmol) and celite (20 g) was added. The mixture was stirred at room temperature for 5h with TLC analysis until disappearance of the material. After that the mixture was directly poured onto silica gel column with DCM as eluent to afford compound 11 as a white solid (6.98 g, 86% yield  20 . To a solution of NaOH powder (6.24 g, 156.0 mmol) in EtOH (350 mL), 5-bromo-2-(hexyloxy)benzene-1,3-dialdehyde (4.0 g, 13.0 mmol) and 2-acetylpyridine (7.5 g, 62 mmol) were added. After stirring at room temperature for 20 h, aqueous NH3•H2O (150 mL) was added and the mixture was refluxed for 40 h. Upon cooling to room temperature, the precipitate was filtered and washed with cold ethanol, dried and recrystallized using CHCl3/EtOH to give 6 as a white solid    were added. After degassing and backfill with nitrogen for three times, 30 mL of THF and 30 mL of Et3N were added under nitrogen atmosphere. After the addition of TBAF (0.98 mL, 0.98 mmol, 1 mol/L in THF), the mixture was stirred at 70 °C for 16h. After that the reaction was cooled down to room temperature and 100 mL of water was added. The mixture was extracted with chloroform, and the organic layer was collected, dried over anhydrous sodium sulfate and the solvent was  13     6H, H t ). 13 13 13  With the addition of 100 mL chloroform and 100 mL methanol, the brown slurry was stirred under reflux for 24h. Afterwards the solvent was removed under vacuum, and the residue was washed with methanol for three times. The solid was collected and dried under vacuum to give compound 18 as a brown solid (2.8g, 83.6% yield). Due to the extremely poor solubility, compound 18 was directly used for the following steps without further characterization.  13                                       is the van der Waals radius of the solvent, which is far less than the hydrodynamic radius of the supramolecules being investigated. Thus, ≈ 6. . rh(ob)/r(cal) is the ratio of the hydrodynamic radius generated from the oblate model and the equivalent radius generated by the volume of the spheroid; this ratio was used to guide the adjustment of a and b until the volume generated by them matches the volume generated by rh(ob) (rh(ob)/r(cal) ≈ 1). Figure 113. Screenshot of Microsoft Excel spreadsheet used to fit C1 in CD3CN using oblate spheroid model.