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1 Simultaneous and coordinated rotational switching of all molecular rotors in a network Y. Zhang, H. Kersell, R. Stefak, J. Echeverria, V. Iancu, U. G. E. Perera, Y. Li, A. Deshpande, K.-F. Braun, C. Joachim, G. Rapenne, & S.-W. Hla S1. Molecular Structure and Adsorption Geometries When the molecular rotors are deposited on an atomically cleaned Au(111) and Cu(111) surfaces, the stator (lower deck) binds to the surface through 8 sulfur (S) atoms positioning at three-fold surface hollow sites (Fig. S1). The calculated structure shows that both upper and lower decks (stator and rotator) are bent to opposite directions (see Fig. 1e) thereby it reduces the coupling of the central Eu atom to the surface, and the dipole in the rotator arms at the upper deck maintains. The two opposite π-rings of the rotator arms are positioned almost vertical due to the internal steric repulsion (see Fig. 1e in the main article). These two vertical π-rings produce as two lobes of the rotator arm in STM images. Supplementary Figure 1. a, Adsorption geometry of the stator part of the molecular rotor on Cu(111). Adsorption sites of individual rotors on Au(111) are similar to the structure except that the rotors do not self-assemble. b, Adsorption structure of complete rotors in hexagonal assembly formed on Cu(111). On Au(111) surface, individual rotors are found and the rotors do not self-assemble probably due to a weak surface-molecule binding and/or Herringbone surface reconstruction. The ESQC calculations of rotor on Au(111) surface also reveal their physisorbed status. Adsorption sites of individual rotors on Au(111) are similar to the ones on Cu(111) structure (Fig. S1a) where two of the stator legs position along surface close-packed row directions, i.e [110] directions, while the other two legs position along [211] directions of the surface. On Cu(111) surface, the rotors are aligned along [110] surface directions and form a hexagonal network. The alternate rows of stators are 30 rotated (Supplementary Fig. 1a and NATURE NANOTECHNOLOGY 1

2 1b), which reduces the lateral space between the neighboring rotors, and enhances dipolar interactions among the rotator arms. S2. di/dv Spectroscopy of Rotor di/dv tunneling spectroscopy measurements of rotors in the network on Cu(111) surface show that the highest occupied and lowest unoccupied molecular states are located at V and V. These states are so called the spin-orbit molecular orbitals (SOMO) derived from the Eu atom. The measured gap of 1.1 ev is in excellent agreement with the calculated gap of 1.05 ev using DFT for a free standing rotor. Moreover, the di/dv spectroscopic data clearly reveal a cogent Shockley surface state (SS) of Cu(111) within the gap (indicated with a red arrow in Supplementary Fig. 2a) at ev. Supplementary Fig. 2a presents three di/dv curves shown for comparison. Supplementary Figure 2. a, di/dv spectra of rotors on Cu(111). The red arrows in the top and middle curves indicate the change in signal due to rotational switching. b and c : Characteristics SOMO s with a large MO weight on the central Eu. During the di/dv data acquisition, rotational switching of the rotator can occur due to the electric field from the STM tip. For instance, the top and middle di/dv curves in Supplementary Fig. 2a contain signatures originated from the rotational switching (indicated with red arrows). A slight shoulder at ~-6V in the bottom di/dv curve (indicated with a dashed oval) is not observed in the top and middle curves. Thus it is not a common feature associated with the electronic states. We attribute this as caused by a slight reorientation of rotator arms, which can occur frequently at the low biases (see Fig. 4e in the main article). From these findings, we can conclude the followings: The Cu(111) surface state (SS) is well within the energy gap of the rotor and it remains intact. SS is the key for the molecule surface interactions, and the frontier molecular states are energetically the most possible to interact with SS. But the donor and acceptor units from the rotator arm do not contribute to the observed molecular states (Supplementary Fig. 2b, and 2c). Thus, even if there are negligible interactions between the SS and the closest frontier orbitals, the donor and acceptor of the rotator arm will still be electronically isolated. Moreover, the excellent agreement between the measured energy gap of the rotors on Cu(111) with that of the free standing rotor further indicates that the electronic structure of the rotor does not alter significantly upon adsorption on the surface. Thus, the molecule-surface interaction is 2 NATURE NANOTECHNOLOGY

3 SUPPLEMENTARY INFORMATION weak. This is further supported by the ESQC calculations of the molecule image including its tunneling junction (Fig. 1d in main article). Since both upper and lower decks (stator and rotator) are bent away from the surface, the interaction between the molecule and surface is greatly reduced. Similar case has been reported for YPc 2 double-decker on Au(111) [s1] where both the upper and lower decks are bent, thereby reducing interactions of the molecule with the surface, and the charge state of the doubledeckers maintain. In fact, the charged state of molecules or individual metal atoms can be maintained on metallic surfaces even when they are directly adsorbed on the surface as proven by the donoracceptor charge transfer molecular systems showing superconductivity [s2] and Kondo effect [s3] as well as a recent study of polar molecules directly adsorbed on Au(111) surface [s4] where a charged metal adatom can be maintained on Au(111) surface. In the present work, we used electric field, not inelastic electron excitation, to rotate the rotors, and therefore the influence on the electronic states of the molecules in the rotation process is minimal. References: [s1]. R. Robles et al. Spin doping of individual molecules by using single-atom manipulation. Nano Lett. 12, (2012). [s2]. K. Clark et al. Superconductivity in just four pairs of (BETS)2-GaCl4 molecules. Nature Nanotechnology 5, (2010). [s3]. I. Fernandez-Torrente et al. Vibrational Kondo effect in pure organic charge-transfer assemblies. Phys. Rev. Lett. 101, (2008). [s4]. Z. Feng et al., Trapping of charged gold adatoms by dimethyl sulfoxide on a gold surface. ACS Nano 9, (2015). S3. Parallel Rotor Network In addition to the hexagonal network, a parallel network of molecular rotors can be formed on both Cu(111) and Ag(111) surfaces using long alkyl chains (-C 10 H 21 ) attached to the stator as spacers (Supplementary Fig. 3a). An example image of a parallel network of dipolar rotors is shown in Supplementary Fig. 3b together with the corresponding adsorption geometry (Supplementary Fig. 3c) on Ag(111). An axis of the parallel rotor network aligns along a surface close packed row direction and the molecular packing here is less dense then the hexagonal network. We have not observed rotational switching of the rotors in the parallel networks on both Cu(111) and Ag(111) surfaces when scanning at different biases exceeding ± 2.2 V. Repeated attempts of STM tip induced switching such as the ones demonstrated in the hexagonal network (see Fig. 2d to 2e in the main article) were not successful for parallel networks. An example of STM tip manipulation sequence for rotors in a parallel network is presented in Supplementary Fig. 3d to 3f. Here the STM tip is positioned above a rotator arm (Supplementary Fig. 3d) and the then tunneling bias is ramped from 0 to 2.5 V while the corresponding tunneling current is recorded. A sudden change occurs in tunneling current around 2.3 V (Supplementary Fig. 3e), which is associated with the destruction of the rotor under the tip. However, there is no rotation as shown in the subsequent STM image after this event (Supplementary Fig. 3f). NATURE NANOTECHNOLOGY 3

4 Supplementary Figure 3. a, A model showing the dipolar rotor with long alkyl chains (-C 10 H 21 ) attached to its stator unit. b, An STM image of a parallel rotor network on Ag(111). The oval indicates the top rotator arm. [V t = 0.5 V, I t = 3.6 x10-11 A]. c, Adsorption geometry of the rotor on Ag(111). d, For the manipulation, the STM tip is positioned above the red oval location and then the voltage is ramped. e, Corresponding I-V spectroscopy curve shows an abrupt decrease in current at ~ 2.3V (indicated with a blue arrow). f, The STM image recorded after this event shows destruction of the rotor in this area while the rest of the rotator arms remain in their initial position. [V t = 1.8 V, I t = 3.6 x A, 8.8 x 5.3 nm 2 scan area] S4. Rotor Dipoles The calculated STM image of a rotor (Fig. 1d in the main article) shows that the top rotator part appears as two lobes with a height difference. In agreement with the calculation, the experimental STM image also shows two different height lobes for each rotator arm (Supplementary Fig. 4, and Fig. 3a in the main article). The STM line profile in Supplementary Fig. 4b reveals a height difference between the two opposite ends of the rotator as 0.03 nm. This is in agreement with the theoretical height profile from the calculated STM image (Fig. 1d in the main article). The higher protrusion here is the acceptor while the 4 NATURE NANOTECHNOLOGY

5 SUPPLEMENTARY INFORMATION other is the donor. This height difference allows us to distinguish the dipole direction as pointing toward the lower height lobe. Supplementary Figure 4. a, An STM image showing a hexagonal pattern of ordered rotors. Here, one end of the rotator appears slightly higher than the other. b, Corresponding line profile of a rotor indicated with a circle in a. S5. Synchronized Rotation in Parallel Rotor Network The synchronized rotation in the hexagonal network does not change the net dipolar energy (see Supplementary Fig. 6, and Fig. 3c in the main article). However, for the parallel dipolar network, the net dipolar energy is not flat but it fluctuates (Supplementary Fig. 5). Therefore a synchronized rotation is not favorable in the parallel network. Supplementary Figure 5. The net dipolar energy fluctuates for synchronized rotation of all dipoles in a parallel network. The two energy minima positions here are for the opposite dipole orientations. The red straight line is for the synchronized rotation of all dipoles in the hexagonal symmetry. NATURE NANOTECHNOLOGY 5

6 S6. Synchronized Rotation in Hexagonal Network Supplementary Figure 6. a, A cluster of dipole rotors containing up to 8 th near-neighbor used for the dipole energy calculation. b, The calculated dipole energy as a function of rotation angle. The three large sinusoidal rotational energy barriers are (blue, green and red) induced by the first nearest neighbor dipoles while the smaller sinusoidal barriers are from the higher order neighbors. Total energy of the system appears flat (black line at the bottom). The dipolar energy barrier for the synchronized rotation of a rotor cluster containing up to 8 th nearneighbours (Supplementary Fig. 6a) are calculated. The rotator dipoles are rotated clockwise for 360 in a synchronized manner, i.e. in the same direction, the same speed, and in phase rotation. As soon as the rotations start, the dipolar energies of individual pair of rotators fluctuate however, the total dipolar energy barrier for the rotation remains constant (Supplementary Fig. 6b). This situation is valid only when all the rotators in the network are rotated at the same speed and the same rotational direction either clockwise or anticlockwise. As soon as one of the dipole becomes out of phase during rotation, then the total energy is no longer constant (see the next section). Because of 1/r 3 dependence of the 6 NATURE NANOTECHNOLOGY

7 SUPPLEMENTARY INFORMATION dipolar energy on the distance, the dipole energy rapidly attenuates, and only the first near neighbour rotators mainly contribute to the energy barrier (Supplementary Fig. 6b). S7. Antiparallel and Unsynchronized Rotation Previous analysis (section S6) shows that the synchronized rotation of all rotors in a hexagonal dipole network produces a constant dipole energy barrier. Simulated results for antiparallel and unsynchronized rotations are described in this section. In Supplementary Fig. 7a, the rotation speed and starting time of all the rotors are the same except that the neighbouring rotators rotate in opposite directions (anti-parallel or antiferroelectric rotation). Here the dipolar energy barrier continues to vary indicating that such rotation is energetically not favorable. Supplementary Fig. 7b presents an unsynchronized rotation process. The rotators here are allowed to rotate with different speeds and rotation directions, i.e. anticlockwise or clockwise. The net dipolar energy barrier for rotation here is found to vary randomly in a noise-like fashion. Thus, it is not favorable condition for rotation. Supplementary Figure 7. a, anti-parallel rotation; and b, random rotation sequence (ω = rotational speed). The rotations are restricted in the x-y plane only to reflect the experimental conditions. The plots are for 2 complete turns (2 x 360 ). S8. Electric Field Energy (U el ) and Torque The electric field energy, U el, supplied by the scanning tip is estimated by using a spherical charge model and a point charge model. In the spherical charge model, the STM tip apex is considered as a part of a sphere with a radius R (Supplementary Fig. 8a). Here, z and d are the distances between the center of the sphere and the surface, and the rotator, respectively. The net electric field direction is along the path d however only the electric field in the x-y plane influences on the rotation. Thus, the effective electric field here is ε cos δ, and the U el experienced by a rotator is ε cosδ cosγ (inset drawing). The tip scanning direction is along the electric field component, ε cosδ. For point charge model calculations, the tip is considered as a moving point charge above the rotor. Here the electric field energy is the same as before, i.e. ε cosδ cosγ but ε = V t /r where r is the distance between the point charge and the rotor, and V t is the tunneling bias. The plot in Supplementary Fig. 8b shows the maximum electric field energy provided by the STM tip as a function of distance from the defect site calculated for different tip radii using the spherical charge model. The electric field energy is largely dependent on the radius of the sphere, however, all the curves NATURE NANOTECHNOLOGY 7

8 calculated for the tip radius from 5 nm to 50 nm show a similar trend: The electrical energy gained is higher than the dipolar energy barrier for rotation after 1 to 3 rotor distance (~ 5 nm), and therefore most of the STM tips should produce similar results. Supplementary Figure 8. a, The spherical charge model for the tip. The dipole drawing at the upper right corner shows the electric field component and the dipole direction within the x-y plane. b, The torques as a function of distance for various tip radius, R. The dipolar energy plot as a function of distance (red curve) is included for the comparison. S9. Rotator Domains Supplementary Figure 9. a, An STM image of hexagonal network of molecular rotors showing unidirectional orientations of the rotator arms. b, The same area in the subsequent scan shows domain regions formed by reoriented rotators marked with B, C, D and E. c, In another subsequent scan, most of the rotators in the domain C remains the same orientation but a new domain region, D, is formed at the upper right area. [V t = 1 V, I t = 3.2 x A, 76 x 14 nm 2 scan area]. 8 NATURE NANOTECHNOLOGY

9 SUPPLEMENTARY INFORMATION Rotational switching of an entire region of rotor network under the STM scan area can occur during scanning or by a static STM tip induced rotation with biases higher than ~±1.0 V. Such rotational switching and the formation of rotational domains generally occur in the proximity of defects. The defects are necessary to exert a net electric torque to the network as well as to maintain the rotated domains. Supplementary Fig. 9a shows a large area STM image acquired at +1 V bias. Here, two defects are indicated with yellow and green ovals, respectively. Step-edges are located at the lower left and right corners of the image. The exact scan area taken at the subsequent image (Supplementary Fig. 9b) reveals reoriented rotators in the area marked with B, C, D, and E. Interestingly, the defect indicated with the green oval disappears in this image and a sharp domain boundary appears. Moreover, the reoriented rotator regions do not perfuse toward the step-edges. Therefore the rotators near the stepedges remain as in the initial orientation, i.e. as in the region A. The domain boundary at the right side also includes frustrated dipole configurations indicated with cross-like dipoles produced by two different dipole orientations. In the next subsequent scan (Supplementary Fig. 9c), a new domain region, D, appears at the upper-right area while the defect at the left remains. S10. Rotational Statistics Supplementary Figure 10. a, Switching angle as a function of bias. b, The number of rotated rotors as a function of of defects. Supplementary Fig. 10a presents the rotational switching angles as a function of bias taken on rotators with initial alignment perpendicular (90 ) to the tip position. Here, the maximum switching angles appear to be not dependent on the bias. Supplementary Fig. 10b shows the number of rotations as a function of the defects at the vicinity of rotator network. The maximum number of switching rotors increases from 160 to over 500 with the increasing number of defects from 1 to 4. S11. Bias Dependent STM Images Supplementary Fig. 11 shows a sample sequence of bias dependent images acquired at the same surface area except a slight lateral shift due to the thermal drift. In all images, the top rotator parts are appeared as two lobes. The shapes of the rotors do not change by varying bias up to ±2 V. Some of the images contain noise like patterns caused by the rotational switching of rotators during the scanning. Within a single scan line, some of the rotator arms appear as expected shape but a sudden change to the noise-like region appears. The scan area here is away from the step-edges and there are a few NATURE NANOTECHNOLOGY 9

10 defects located at the proximity. At -1.5V bias scan, a defect site can be observed next to the fluctuating domain. Supplementary Figure 11. A sequence of STM images acquired at different biases. The ovals in +2.0V image indicate different rotor dipole directions. Noise-like regions are due to the fluctuating dipoles. [14 nm x 18.5 nm, I t = 3.2 x A]. S12. Tip Size Determination Supplementary Figure 12. a, A single atom deep hole formed by a controlled indentation with the STM-tip on Cu(111). b, A two-atom deep hole is formed next to the first hole. c, A three atom and one atom deep holes are formed in another surface area with the same tip. d, Tip height profiles measured along the red lines in b (blue) and c (green). 1,2, and 3 mark the profiles of one, two and three atom deep holes. The double atomic step at right (D) and the single atomic step (S) at the left part of the green profile are used for height calibrations. e, A three atom deep hole profile is used to determine the radius of a sphere (2.7 nm) representing the tip-apex for electric field energy calculations. Here, the cone part of the tip is neglected. 10 NATURE NANOTECHNOLOGY

11 SUPPLEMENTARY INFORMATION Initially, several tips were prepared by electrochemically etching a W wire. Then the tip with an ideal triangular cone shape is carefully selected by using scanning electron microscope imaging of the tipapex. After introducing the tip to our STM scanner, reshaping of the tip-apex is done by gently dipping it onto the surface [s5, s6]. At low temperatures and in an ultrahigh vacuum environment, the tip-height can be precisely controlled [s7], and therefore such reshaping of the tip-apex allow formation of a sharp and reliable tip-apex [s5, s6]. From the shape of the hole formed by these controlled tip-indentations, the size and shape of the tip-apex can be estimated as shown in the Supplementary Fig. 12. Some of the locally prepared tips can maintain the same condition for a long period if they are not crashed to the surface. A sequence of STM images (Supplementary Fig. 12a to 12c) show one, two, and three atom deep holes formed by a controlled tip-sample contact. The corresponding line profiles are illustrated in Supplementary Fig. 12d. The line profiles of all three holes appear similar except the depth of the holes indicating that the initial structure of the tip used in the experiment is rather stable. Using a hole profile, we estimate the radius of the sphere representing the tip-apex as ~2.7 nm. References: [s5] S.-W. Hla et al. Single-atom extraction by scanning tunneling microscope tip crash and nanoscale surface engineering. Nano Lett. 12, (2004). [s6]. S.-W. Hla. Atomic level assembly. Rep. Prog. Phys. 77, (2014). [s7]. A. Deshpande et al. Atom-by-atom extraction using tip-cluster interactions. Phys. Rev. Lett. 98, (2007). NATURE NANOTECHNOLOGY 11