Electronic Conductance and Thermopower of Single-molecule Junctions of Oligo(phenyleneethynylene) Derivatives

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I) Experimental details for the synthesis of the OPE3 molecules
General procedure for the Sonogashira coupling reactions A solution containing the diiodide (1 eq.) in a THF/iPr2NH mixture (5/1 v/v, 4 mL per 0.1 mmol eq.) was degased by bubbling argon for 20-30 min. Catalytic amounts of Pd(PPh3)2Cl2 (0.05 eq.) and CuI (0.05 eq.) were added, followed by 4-acetynyl-dihydrobenzo[b]thiophene (2.2 eq.). The mixture was then stirred at room temperature for 2 h and the solvents were evaporated under reduced pressure in the presence of a few spatulas of silica. The resulting residue was then chromatographed using CH2Cl2/n-hexane on silica to extract the desired products. After removal of the solvents, the compounds were precipitated from a CH2Cl2 solution and dried under vaccum after filtration and washing with n-hexane.

Synthesis of OPE3-An
Starting from 9,10-diiodoanthracene I2-An (67 mg, 156 mol), OPE3-An was obtained (37 mg, 75 mol, 48 %) following the general procedure. Eluent for column chromatography: n-hexane /CH2Cl2 (1.5: 1 v/v). Special care was taken to perform all the reaction and purification steps in the absence of day-and UV-light.    Mass spectrum and high-resolution profile obtained for OPE3-Ph(OMe)2 (ASAP) ; Signals above and below the compound peaks are attributed to degradation products (reaction with ambient air and O-demethylation, respectively).

Figure 9.
Mass spectrum and high-resolution profile obtained for OPE3-An (ASAP).
Normalised UV-vis absorption spectra of OPE3-Ph (blue), OPE3-Ph(OMe)2 (red) and OPE-An (black) recorded in dichloromethane at 298 K. The concentration of the samples was in the range of 0.01-0.0025 mg/mL. The absorption onsets are at 371, 395 and 489 nm for OPE3-Ph, OPE3-Ph(OMe)2 and OPE-An, which correspond to energies of 3.342, 3.038 and 2.454 eV respectively according to the formula E = 1240/(nm).

Figure 11.
TD-DFTB absorption spectra of OPE3 derivatives in the gas phase. Absorption peaks have been Lorentzian broadened by 0.1 eV. Structures are optimized at the DFTB level.
As a further characterisation we recorded the UV-Vis absorption spectra of OPE3-Ph, OPE3-Ph(OMe)2 and OPE3-An in dichloromethane solution (Fig. 10) and compared them to simulated spectra (Fig. 11). The position of the absorption maxima are following a similar trend in both cases. Better agreement over the full wavelength range can be obtained, but requires more sophisticated exchange-correlation functionals in the DFTB treatment. Please note that due to electron-hole interactions, the optical gap generally differs strongly from the frontier orbital (HOMO-LUMO) gap that is relevant for transport. OPE3-An Figure 13. a) dimeric structure adopted by OPE3-An in its crystal unit cell and b) packing view IV) Structural investigations by DFT Figure 14.

OPE3-Ph
Structure of OPE3-Ph with atom labels.

Geometrical parameter
Exp. crystal structure  We performed additional transport simulations for OPE3-Ph to investigate the influence of the metal-molecule binding. The computational parameters are the same as detailed in the main article. There, the junction was constructed by first optimizing a Au20-molecule-Au20 complex in the gas phase which was then embedded in the junction. We refer to this conformer as Au20tilted (main article Fig. 6). Four additional structures are considered here: the first one is based on the top conformer obtained in the periodic DFT calculations (see main article Fig 5a)), where OPE3-Ph binds directly to a flat gold surface. Due to limited computational resources, the second electrode is manually placed in a symmetrical fashion with respect to the first electrode without additional geometry relaxations (flat surface -tilted, Fig. 15a)). The periodic DFT calculations also predict another stable conformer in a top position which is higher in energy, where the molecule is oriented perpendicular to the surface. The corresponding junction model is named (flat surface -straight, Fig. 15c)). We also consider binding through adatoms. Both hcp and fcc positioning of the adatom were considered, but since the resulting transmission differs only very slightly, only fcc results are shown. Calculations for straight (adatom -straight, Fig. 15d)) and tilted orientations of OPE3-Ph with respect to the adatom have been performed (adatom -tilted, Fig. 15b)).

Isolated gas phase
The resulting transmission (Fig. 16) is found to be rather noisy around the Fermi energy, which is related to manual construction of the junctions without proper geometry relaxation. Some general trends can nevertheless be found. The straight conformers feature HOMO/LUMO resonances that are considerably shifted to higher energies with respect to Au20-tilted and therefore lead to positive Seebeck coefficients. The adatoms have an opposite effect, such that the adatom -tilted conformer comes closest to the fully relaxed Au20-tilted conformer that is discussed in the main article. DFTB transmission for OPE3-Ph junction models depicted in Fig. 15 and the Au20-tilted structure of the main article VI) Electrical and thermal schematic for Seebeck measurement As the STM-tip is connected to the voltage source through a copper wire that experiences an opposite temperature gradient, the Seebeck coefficient of the whole junction is given by: Smeasured = Smolecule + SCu-lead , with SCu-lead =1.8 mV/K 1,2 Figure 17.
Electrical circuit and equivalent thermal circuit when Vbias is set to zero. The molecular junction (marked in green) is electrically equivalent to a conductance G and a thermovoltage (battery) in series. It is also necessary to include the thermovoltage that develops across the connecting copper lead (marked in yellow), due to the uncompensated temperature gradient.