Hydroxyl Group as the ‘Bridge’ to Enhance the Single-Molecule Conductance by Hyperconjugation

For designing single-molecule devices that have both conjugation systems and structural flexibility, a hyperconjugated molecule with a σ–π bond interaction is considered an ideal candidate. In the investigation of conductance at the single-molecule level, since few hyperconjugation systems have been involved, the strategy of building hyperconjugation systems and the mechanism of electron transport within this system remain unexplored. Based on the skipped-conjugated structure, we present a rational approach to construct a hyperconjugation molecule using a hydroxyl group, which serves as a bridge to interact with the conjugated fragments. The measurement of single-molecule conductance reveals a two-fold conductance enhancement of the hyperconjugation system having the ‘bridging’ hydroxyl group compared to hydroxyl-free derivatives. Theoretical studies demonstrate that the hydroxyl group in the hyperconjugation system connects the LUMO of the two conjugated fragments and opens a through-space channel for electron transport to enhance the conductance.


Introduction
Aiming at the miniaturization of electric devices, the development of molecular electronics depends on fabricating molecular devices with highly conductive molecules [1][2][3][4].Since the π orbital has the energetic advantages in electron transport, the strategies to design molecules performing high conductance are usually based on the fully conjugated structures, including the introduction of constructive quantum interference [5][6][7], the construction of self-gating systems [8][9][10] and the 'topological insulator' built by the radical system [11,12].However, despite the good performance in electric properties, the conjugated structures which bring in high structural rigidity prevent the conformational transition that offers the opportunities to modulate the conductance through folded structures, for instance, intramolecular π-π stacking [13][14][15].Thus, exploring a strategy to design molecules having the feature of conjugation and structural flexibility synchronously is of great significance.
Hyperconjugation, which refers to the interaction between σand π-orbital, introduces the delocalized molecular orbitals in non-conjugated structures [16][17][18][19][20].Although it is a promising candidate for combining structural flexibility with conjugated backbones in designing single-molecule devices, the molecular structures containing a hyperconjugation system are rarely investigated [21,22].In particular, the mechanism of electron transport in a hyperconjugation system is still unclear.Therefore, designing a molecule with π-σ hyperconjugation to explore the mechanism of electron transport in this system is of great importance in developing high-performance single-molecule devices.
Here we report a hyperconjugation system based on a skipped-conjugation structure [23] with a non-conjugated hydroxyl group as a 'bridge' to connect the conjugated fragments.The distinct enhancement of conductance for the hydroxyl-contained hyperconjugation systems was confirmed by comparison with that for the corresponding hydroxylfree derivatives.Theoretical studies demonstrated that hyperconjugation, in which the anti-bonding orbital (σ*) of the C-O (hydroxyl group) bond interacts with the anti-bonding orbital (π*) of the adjacent conjugated structure, builds the interaction between the hydroxyl group and the two conjugated fragments and connects the two fragments, thus opening a new through-space channel for the transmission of electrons to enhance the conductance.

Results
To clarify the role of hyperconjugation playing in single-molecule conductance, we elaborately designed two groups of directly comparable molecules in this work, as depicted in Figure 1.Molecule 1, containing one hydroxyl group as the 'bridge' to link the two conjugated fragments (phenylethenyl groups), was designed and synthesized according to the reported methods [24][25][26][27].As a structural reference, the hydroxyl group was replaced by the carbonyl group to link the two conjugated fragments in molecule 2 [28].Upon the removal of the hydroxyl group, we obtained molecule 3 with methylene to space the conjugated fragments.Molecules 4-6 were designed as the structural derivatives of molecules 1-3 with the ethenyl groups in the former replaced by the ethynyl groups in the latters, respectively.The single-molecule conductance was measured using the scanning tunneling microscopy break junction (STM-BJ) technique in the 1,2,4-Trichlorobenzene (TCB) solution containing 0.1 mM of the prepared molecules.
As shown in Figure 1, the most probable conductance of molecule 1 is 10 −4.85 G 0 (1.09 nS, G 0 represents the quantum conductance and equals 77,500 nS) [23], which is lower than the conductance of molecule 2 (10 −4.29 G 0 , 3.97 nS) and higher than the conductance of molecule 3 (10 −5.10 G 0 , 0.62 nS).This implies that, compared to the fully conjugated molecule 2, breaking the conjugated system with a saturated carbon atom at the central site of molecule 1 suppresses the conductance effectively.However, compared with molecule 3, the existence of the hydroxyl group enhances the conductance as the conductance of molecule 1 is about two times as high as that of molecule 3 [29].This conductance modulation is observed not only in ethenyl-connected molecules 1-3, but also characterized in ethynyl-connected molecules 4-6.The conductance of hydroxyl group-bridged molecule 4 (10 −5.05 G 0 , 0.69 nS) is also lower than that of fully conjugated molecule 5 (10 −4.42 G 0 , 2.95 nS), but higher than that of hydroxyl-free molecule 6 (10 −5.40 G 0 , 0.31 nS).
To find the origin of the conductance enhancement by the hydroxyl group in skippedconjugated structures, the junction length was investigated because the conductance is very sensitive to a change in the junction length.Since the conductive backbone of molecules 1-6 are almost the same, the variation of the statistical junction lengths of molecules 1-6 is relatively small, and are 1.04, 0.87, 1.03, 0.90, 1.02 and 0.88 nm, respectively.The measured junction lengths (1.54, 1.37, 1.53, 1.40, 1.52 and 1.38 nm for molecules 1-6, Figure S17) match well with the simulated S-S distances (1.51, 1.59, 1.40, 1.43, 1.48 and 1.46 nm for molecules 1-6) after correcting the junction length using a 0.5 nm 'snap-back' length [30].With such as small length fluctuation, the contribution of the junction length is negligible in the conductance enhancement by the hydroxyl group.The transmission coefficients (T(E)) and the transmission pathway for the electron, which investigated the relationship between the electronic structure and the conductance, were calculated by combining density functional theory (DFT) with non-equilibrium Green's functions (NEGF), where the Green's function estimates the behavior of the electron wave in a single molecule and yields the T(E) [12,[33][34][35].The molecular junctions of 1-5 were simulated while the junction of molecule 6 was reported in previous work [29].As shown in Figure 3, the transmission coefficients, which closely correspond with the single-molecule conductance, at a Fermi energy of (E − EF = 0 eV), decrease following the sequence of 2 > 5 > 1 > 4 > 3, which matches well with the sequence of the measured singlemolecule conductance.More importantly, in the curves of the transmission coefficient for these molecules, the peaks representing LUMO are closer to EF than the peaks of HOMO.This indicates that, for the corresponding molecules, the conductance is dominated by LUMO, which is also found in molecule 6 in the previous study.Hence, since the hydroxyl group connects the two conjugated fragments forming a delocalized system, the LUMO provides a continuous channel for the electron to transport from the source to the drain, which is explicitly demonstrated in the transmission pathway [36].As shown in Figure 3b, a broad arrow between the two carbon atoms connecting the central carbon atom, which indicates the strong through-space transmission of electrons between the end atom of the two conjugated fragments, is observed in molecules 1, 2, 4 and 5, while no such a Molecular orbitals, especially the frontier molecular orbitals (FMOs) such as the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) are crucial to the conductance magnitude [29].To investigate the influence of the hydroxyl group on the FMOs, the theoretical studies were conducted using density functional theory (DFT).The geometry optimization and orbital calculations of molecules 1-5 are performed by the Gaussian16 package [31], while the theoretical study of molecule 6 was reported in the previous research [29].The electronic structure of the FMOs, which is highly correlated to the conductive property, was analyzed by simulating the distribution of HOMO and LUMO.In molecules 3 and 6, the reported study shows an imbalanced distribution in both HOMO and LUMO (Figure S16) [32].In particular, the central carbon atom, which skips the conjugated system, plays the role of a node to divide the structure into two conjugated fragments with no orbital distributed on it.Despite there being still no orbital distribution on this atom in HOMO, the orbital distribution of the two conjugated fragments in molecules 1-2 and 4-5 is connected through it in LUMO when a hydroxyl group is substituted.This results in orbital distribution in the skipped-conjugated molecules 1 and 4 is visually the same as that of fully conjugated molecules 2 and 5, respectively (Figure 2).The transmission coefficients (T(E)) and the transmission pathway for the electron, which investigated the relationship between the electronic structure and the conductance, were calculated by combining density functional theory (DFT) with non-equilibrium Green's functions (NEGF), where the Green's function estimates the behavior of the electron wave in a single molecule and yields the T(E) [12,[33][34][35].The molecular junctions of 1-5 were simulated while the junction of molecule 6 was reported in previous work [29].As shown in Figure 3, the transmission coefficients, which closely correspond with the single-molecule conductance, at a Fermi energy of (E − EF = 0 eV), decrease following the sequence of 2 > 5 > 1 > 4 > 3, which matches well with the sequence of the measured singlemolecule conductance.More importantly, in the curves of the transmission coefficient for these molecules, the peaks representing LUMO are closer to EF than the peaks of HOMO.This indicates that, for the corresponding molecules, the conductance is dominated by LUMO, which is also found in molecule 6 in the previous study.Hence, since the hydroxyl group connects the two conjugated fragments forming a delocalized system, the LUMO provides a continuous channel for the electron to transport from the source to the drain, which is explicitly demonstrated in the transmission pathway [36].As shown in Figure 3b, a broad arrow between the two carbon atoms connecting the central carbon atom, which indicates the strong through-space transmission of electrons between the end atom of the two conjugated fragments, is observed in molecules 1, 2, 4 and 5, while no such a through-space transmission is characterized in molecules 3 and 6.The strong throughspace transmission reveals that the connection of the two conjugated fragments in LUMO opens an extra transmission channel for the electron, enhancing the conductance.The transmission coefficients (T(E)) and the transmission pathway for the electron, which investigated the relationship between the electronic structure and the conductance, were calculated by combining density functional theory (DFT) with non-equilibrium Green's functions (NEGF), where the Green's function estimates the behavior of the electron wave in a single molecule and yields the T(E) [12,[33][34][35].The molecular junctions of 1-5 were simulated while the junction of molecule 6 was reported in previous work [29].As shown in Figure 3, the transmission coefficients, which closely correspond with the single-molecule conductance, at a Fermi energy of (E − E F = 0 eV), decrease following the sequence of 2 > 5 > 1 > 4 > 3, which matches well with the sequence of the measured single-molecule conductance.More importantly, in the curves of the transmission coefficient for these molecules, the peaks representing LUMO are closer to E F than the peaks of HOMO.This indicates that, for the corresponding molecules, the conductance is dominated by LUMO, which is also found in molecule 6 in the previous study.Hence, since the hydroxyl group connects the two conjugated fragments forming a delocalized system, the LUMO provides a continuous channel for the electron to transport from the source to the drain, which is explicitly demonstrated in the transmission pathway [36].As shown in Figure 3b, a broad arrow between the two carbon atoms connecting the central carbon atom, which indicates the strong through-space transmission of electrons between the end atom of the two conjugated fragments, is observed in molecules 1, 2, 4 and 5, while no such a through-space transmission is characterized in molecules 3 and 6.The strong through-space transmission reveals that the connection of the two conjugated fragments in LUMO opens an extra transmission channel for the electron, enhancing the conductance.
Finally, the hyperconjugation effect was employed to elucidate the origin of the enhanced conductance facilitated by the hydroxyl group connecting the two conjugated systems [17,18,37].Hyperconjugation refers to the interaction between the σand πorbital [19].In molecules 1 and 4  Finally, the hyperconjugation effect was employed to elucidate the origin of the enhanced conductance facilitated by the hydroxyl group connecting the two conjugated systems [17,18,37].Hyperconjugation refers to the interaction between the σ− and π−orbital   General Procedures and Reagents.All the manipulations were carried out using Schlenk techniques and vacuum-line systems under a dry argon atmosphere unless otherwise specified.All reagents were of commercial origin and were used as received.The triethylamine (TEA) was distilled over CaH 2 .Silica gel (100-200 mesh) was used for the column chromatography.

Synthesis and Characterizations
= doublet of doublets.
1,5-bis(4-(methylthio)phenyl)penta-1,4-diyne (3) Compound 3a (1.831 g, 2.52 mmol) was added to 50 mL of anhydrous THF under nitrogen.The contents were cooled to −78 °C with an ice bath and n-BuLi was added dropwise (1.6 M in hexanes, 5.04 mmol).After stirring at this temperature for 1 h, the ice bath was removed and it slowly warmed to room temperature.After 15 min at room temperature, 4-(methylthio)benzaldehyde (0.355 g, 2.33 mol) was added in 10 mL of anhydrous THF dropwise.A reflux condenser was added and the system was heated to 80 °C.It was heated for 1.5 h and then cooled and quenched with 50 mL of water.The aqueous was 1,3-bis(triphenylphosphino)propane dibromide (3a) A mixture of the triphenylphosphine (6.557 g, 25 mmol) and 1,3-dibromopropane (2.019 g, 10 mmol) in DMF (30 mL) was stirred and refluxed for 4 h.After reaction was complete, the reaction mixture was cooled and the crude white precipitate was filtered and washed with DMF (3 × 10 mL).The white powder was dried under stream of air and recrystallized in water as cubic shape crystals 3a (white solid, 6.901 g, 95%) [38].
1,5-bis(4-(methylthio)phenyl)penta-1,4-diyne (3) Compound 3a (1.831 g, 2.52 mmol) was added to 50 mL of anhydrous THF under nitrogen.The contents were cooled to −78 • C with an ice bath and n-BuLi was added dropwise (1.6 M in hexanes, 5.04 mmol).After stirring at this temperature for 1 h, the ice bath was removed and it slowly warmed to room temperature.After 15 min at room temperature, 4-(methylthio)benzaldehyde (0.355 g, 2.33 mol) was added in 10 mL of anhydrous THF dropwise.A reflux condenser was added and the system was heated to 80 • C. It was heated for 1.5 h and then cooled and quenched with 50 mL of water.The aqueous was extracted with diethyl ether (3 × 100 mL) and organic layer was washed with water (2 × 150 mL) and brine (1 × 100 mL) and dried over MgSO4.The solvents were removed under vacuum yielded a crude orange oil that slowly solidified.The crude product was purified by flash chromatography to obtain compound 3 (white solid,0.201g, 28%) [39]. 1  (2.019 g, 10 mmol) in DMF (30 mL) was stirred and refluxed for 4 h.After reaction was complete, the reaction mixture was cooled and the crude white precipitate was filtered and washed with DMF (3 × 10 mL).The white powder was dried under stream of air and recrystallized in water as cubic shape crystals 3a (white solid, 6.901 g, 95%) [38].
1,5-bis(4-(methylthio)phenyl)penta-1,4-diyne (3) Compound 3a (1.831 g, 2.52 mmol) was added to 50 mL of anhydrous THF under nitrogen.The contents were cooled to −78 °C with an ice bath and n-BuLi was added dropwise (1.6 M in hexanes, 5.04 mmol).After stirring at this temperature for 1 h, the ice bath was removed and it slowly warmed to room temperature.After 15 min at room temperature, 4-(methylthio)benzaldehyde (0.355 g, 2.33 mol) was added in 10 mL of anhydrous THF dropwise.A reflux condenser was added and the system was heated to 80 °C.It was heated for 1.5 h and then cooled and quenched with 50 mL of water.The aqueous was extracted with diethyl ether (3 × 100 mL) and organic layer was washed with water (2 × 150 mL) and brine (1 × 100 mL) and dried over MgSO4.The solvents were removed under vacuum yielded a crude orange oil that slowly solidified.The crude product was purified by flash chromatography to obtain compound 3 (white solid,0.201g, 28%) [39]. 1  A mixture of 1-iodo-4-methylsulfanylbenzene (3.751 g, 15.00 mmol), 3,3-diethoxyprop-1-yne (3.01 mL, 21.00 mmol), triethylamine (9 mL) and Pd(PPh 3 ) 2 Cl 2 (1.052 g, 10 mol%), CuI (0.286 g, 10 mol%) in 45 mL of THF was stirred in nitrogen at room temperature for 5 h.The solvent was removed in vacuo.The residue was extracted with water and dichloromethane, followed by the organic phase being washed with saturated brine, dried over anhydrous sodium sulfate and concentrated under reduced pressure.The crude product was purified by flash chromatography to obtain compound 4a (yellow oily liquid, 3.470 g, 92.4%). 1  3-(4-(methylthio)phenyl)propiolaldehyde (4b) Compound 4a (3.470 g, 13.86 mmol) was dissolved in a mixed solvent (60 mL) of acetone and water (v:v = 1:1), then 5% HCl (45 mL) was added to the solution and the mixture was allowed to stand overnight at room temperature.Upon completion of the reaction, acetone was removed in vacuum.The residue was extracted with water and dichloromethane, washed with saturated brine, dried over anhydrous sodium sulfate and concentrated under reduced pressure.The crude product was purified by flash chromatography to obtain compound 4b (yellow solid, 2.390 g, 97.8%). 1  To a solution of the 4-ethynylthioanisole (0.815 g, 5.50 mmol) in anhydrous THF (20 mL), n-BuLi (1.6 M, 3.44 mL, 5.50 mmol) was added slowly at −78 • C. The resulting mixture was stirred at −78 • C for 1 h, then compound 4b (0.872 g, 4.95 mmol) was added and the reaction temperature was raised to room temperature until completion of the reaction.The resulting mixture was quenched with a saturated solution of NH 4 Cl and extracted with ethyl acetate.The combined organic layers were washed with brine, dried over anhydrous Na 2 SO 4 and concentrated under reduced pressure.The crude product was purified by flash chromatography to obtain compound 4 (yellow solid, 624 mg, 35.0%) [24,25]. 1 H NMR (400 MHz, CDCl 3 ): δ 7.39 (d, J = 8.7 Hz, 4H), 7.17 (d, J = 8.5 Hz, 4H), 5.57 (s, 1H), 2.48 (s, 6H). 13

STM-BJ Method
The single-molecule conductance was measured by scanning tunneling microscopy break junction (STM-BJ) technique using commercially available STM-BJ equipment provided by VR (Xiamen) Technology Co., Ltd.(Xiamen, China) in the 1,2,4-Trichlorobenzene (TCB) solution containing 0.1 mM of synthesized molecule [40].The bias voltage applied between electrodes was 100 mV [33,41].The retraction rate of electrodes was calibrated using the reported method in pure TCB solvent as a blank experiment (Figure S13) [42].

Computational Details
Geometry optimizations and orbital simulations of molecules were carried out by the Gaussian 16 software [31] based on the density functional theory (DFT) method employing the function of B3LYP with a 6-311+g (d,p) basis set and the vibrational frequencies were also calculated simultaneously with the same theoretical level to make sure that all the optimized configurations had the lowest energies.The DFT combined with nonequilibrium Green's functions (NEGF) was used to simulate the transmission coefficient that corresponded to the transport properties.
The curves of the transmission coefficient were calculated by first-principles calculations using the Quantum Atomistix ToolKit software package, U-2022.12version.The two electrodes, which were constructed from gold (111) surfaces, consisted of a unit cell of 5 × 5 with an extension region thickness of five layers to avoid strong interactions with electrodes.A pyramid-shaped gold tip was built to simulate the stable contact with anchors on both gold electrode sides.The above optimized molecular structures were then transformed between two electrodes to construct the single-molecule devices.For the initial configuration of the device, the distances between the sulfur atom and the top gold atom were controlled at ~2.5 Å.In the following optimized process, the coordinates of the gold tip atoms were frozen and molecular skeletons were kept rigid to save the computational cost and maintain the optimal conformation of the molecular structure.The exchange-correlation Generalized Gradient Approximation (GGA) with Perdew-Burke-Ernzerh (PBE) parameterization was employed in the simulations of the molecular device.In the simulation, the double-ζ basis set was adopted for gold atoms while the double-ζ polarization basis functions were applied to the other atoms.To meet the requirement of estimating the Au electrode system, the energy cutoff was set to 200 Ry.At zero bias voltage, the geometry optimization was optimized to meet the convergence criterion of 0.02 eV/A.The k point with a grid of (4 × 3 × 200) was set and a bias energy range from −3 eV to 3 eV was adopt in the transmission spectrum calculation.

Figure 2 .
Figure 2. Electronic structure of the central parts of the HOMOs and LUMOs for molecules 1-6 with isovalues of 0.05 for molecules 1-6 (Supplementary Material Figure S16).

Figure 1 .
Figure 1.(a) Diagram of the interaction between the σ* and π* in the hydroxyl-bridged structure; (b) structures of molecules 1-6; (c) one-dimensional (1D) histograms of the measured conductance (grey) compiled by 4180, 3830, 3664, 2171, 2035 and 2406 conductance-displacement traces for molecules 1-6, respectively.The dashed lines are the fitting curves and the colored peaks are the fitting peaks of the most probable conductance for each molecule, with insets showing the statistical junction length (Supplementary Material Figures S14 and S15).

Figure 2 .
Figure 2. Electronic structure of the central parts of the HOMOs and LUMOs for molecules 1-6 with isovalues of 0.05 for molecules 1-6 (Supplementary Material Figure S16).

Figure 2 .
Figure 2. Electronic structure of the central parts of the HOMOs and LUMOs for molecules 1-6 with isovalues of 0.05 for molecules 1-6 (Supplementary Material Figure S16).
, the simulated electronic structures demonstrate the formation of the extended LUMO.The unsaturated C-C bonds (ethenyl or ethynyl group) offer the anti-bonding orbital (π*) and the C-O (hydroxyl group) bond also provides the anti−bonding orbital (σ*).In molecular structure, as the unsaturated C-C bonds connect to the carbon atom of the C-O bond, the matched phase of the π* and σ* results in parts of the π* orbital hybridizing with parts of the σ* orbital, which eventually extended the conjugation system in the skipped-conjugated structure.

Figure 3 .
Figure 3. (a) Calculated transmission coefficients of molecules 1-5.(b) Transmission pathways (blue arrows: forward transmission from source to drain, red arrows: reverse transmission) of molecules 1, 3, 4 and 6 with the green arrows demonstrating the through−space transmission channel opened by the hyperconjugation (the scaling magnitude for the transmission threshold is 0.05) (Transmission pathways of molecules 2 and 5 in Supplementary Material Figure S19).(c) Demonstration of the hyperconjugation in which the anti−bonding orbital (σ*) of C−O bond interacts with the anti−bonding orbital (π*) of C−C bond.
[19].In molecules 1 and 4, the simulated electronic structures demonstrate the formation of the extended LUMO.The unsaturated C−C bonds (ethenyl or ethynyl group) offer the anti−bonding orbital (π*) and the C−O (hydroxyl group) bond also provides the anti−bonding orbital (σ*).In molecular structure, as the unsaturated C−C bonds connect to the carbon atom of the C−O bond, the matched phase of the π* and σ* results in parts of the π* orbital hybridizing with parts of the σ* orbital, which eventually extended the conjugation system in the skipped−conjugated structure.

Figure 3 .
Figure 3. (a) Calculated transmission coefficients of molecules 1-5.(b) Transmission pathways (blue arrows: forward transmission from source to drain, red arrows: reverse transmission) of molecules 1, 3, 4 and 6 with the green arrows demonstrating the through-space transmission channel opened by the hyperconjugation (the scaling magnitude for the transmission threshold is 0.05) (Transmission pathways of molecules 2 and 5 in Supplementary Material Figure S19).(c) Demonstration of the hyperconjugation in which the anti-bonding orbital (σ*) of C-O bond interacts with the anti-bonding orbital (π*) of C-C bond.

3 .
Materials and Methods 3.1.General Physical Measurement.The 1 H and 13 C NMR spectra were recorded on a Bruker AVANCE III 400 M NMR or ECZ 600R NMR spectrometer with SiMe 4 as the internal reference.All coupling constants are absolute values and the J values are expressed in hertz (Hz).The description of the signals includes s = singlet, d = doublet, m = multiplet and dd = doublet of doublets.