SUPPLEMENTARY INFORMATION

Transcription

1 In the format provided by the authors and unedited. SUPPLEMENTARY INFORMATION DOI: /NCHEM.2824 Supramolecular heterostructures formed by sequential epitaxial deposition of two-dimensional hydrogen-bonded arrays Vladimir V. Korolkov 1, Matteo Baldoni 2, Kenji Watanabe 3, Takashi Taniguchi 3, Elena Besley 2 and Peter H. Beton 1 * 1 School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, UK 2 School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK 3 National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki , Japan *elena.besley@nottingham.ac.uk; peter.beton@nottingham.ac.uk Supplementary Information 1. Additional AFM Images 2 2. Simulations : Methods and Additional Results 4 NATURE CHEMISTRY Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

2 1. Additional AFM images hbn 1.2nm 2.0nm Supplementary Figure 1 Contact mode image of CA.M network and underlying hbn lattice showing a misalignment of principal axes by 3 ± 1 o. Both image were acquired in contact mode from the same area of sample. The scan of hbn lattice was taken at a slightly elevated setpoint (typical value 2-3 nn) allowing a punch-through of the CA.M layer to reveal the hbn lattice. 200 Z[nm] µm X[µm] Supplementary Figure 2 An AFM image showing multilayers of CA.M network on a 102nm thick hbn flake. The corresponding cross-section provides height information for the thicknesses of these layers which ranges between 16 nm to 50 nm. Multilayers were grown from 240 μm aqueous solution with a depositon time of 10 minute. 2

3 a 400nm b 400nm Supplementary Figure 3 AFM scans showing surface coverage of TMA on CA.M. Samples were prepared via 100 sec (a) and 300 sec (b-d) immersion of a CA.M/BN sample into a TMA solution in EtOH (0.04mg/ml). Scans were acquired in AC mode. 2.4nm Supplementary Figure 4 AFM showing lattice resolution of a TMA overlayer and CA.M underlayer. The dotted lines highlight the misalignment of pores of TMA and pores CA.M; note that the pores are not coincident. 3

4 2. Simulations: methods and additional results 2.1 General Description of the Methods Molecular mechanics (MM) calculations have been performed using the LAMMPS simulation package 1. The OPLS potential 2 has been employed, which was previously used to model the self-assembly of CA molecules 3 and molecular adsorption on 2D materials 4. The OPLS parameters for TPA and TMA can be found in the general OPLS database, however for CA and M molecules these parameters are not included. To describe CA and M molecules, the parameters for the Lennard-Jones (LJ) potential and bonding terms (bonds, angles dihedrals and impropers) were inferred from uracil and 1,3,5-triazine/aniline molecules, respectively. The atomic charges were calculated using the restrained electrostatic potential (RESP) scheme 5 based on density functional theory (DFT) as implemented in the CP2K program package 6. Identical types of atoms were constrained to have the same charge. DFT calculations were performed at the gradient-corrected level by applying the BLYP 7,8 exchange-correlation functional within the GPW approach 9,10. Electronic states were expanded by a double-ζ plus polarization basis set, DZVP, 11 with norm-conserving pseudopotentials for the description of core levels and a plane-wave representation of the charge density with a cut-off of 500 Ry. The Martyna-Tuckerman Poisson solver 15 was used in combination with a relatively large simulation box (up to 3.0 nm in the main dimension) to avoid computational artefacts. Long-range electrostatic interactions were treated by the particle-particle particle-mesh method 16 with the relative error in electrostatic forces of A cut-off distance of 1.4 nm was used for both Coulomb and van der Waals (vdw) interactions. Energy minimisation, using the conjugate gradient algorithm with tight convergence criteria, was used to locate the minimum potential energy structures. During energy minimisation, the LJ potential was shifted at the cut-off value to 0. Molecular dynamics (MD) simulations have been performed with a time step of 1 fs. The Nosé Hoover thermostat was used for simulations in the canonical NVT ensemble with a time constant of 1.0 ps. Periodic boundary conditions (PBC) in 3 dimensions were used for the simulation of the 2D systems, by inserting a vacuum region of about 4.0 nm along the z-direction. The structures and potential were built using VMD 20 and Moltemplate 21. 4

5 Supplementary Figure 5 (a) CA.M (in red and blue respectively) on hbn (in white) model shown as a snapshot from an MD at 300 K;(b) 2D radial distribution function and coordination number of CA+M (bin size 0.01 nm) 5

6 2.2 Interaction between CA.M and hbn The hexagonal BN layer (hbn) was treated as rigid with atoms fixed at their crystallographic positions. The LJ parameters were taken from Ref. 22. The values for atomic charges of B and N, ranging from 0 to ±0.6 e, were initially tested leading to the same qualitative results; hence B and N atoms were kept neutral in all simulations. A square hbn model with dimensions of 61 nm x 61 nm with PBC was used to represent an infinite hbn plane. A layer of alternating CA and M molecules with a hexagonal motif was placed on top of hbn (Supplementary Figure 5a). The CA.M layer was made a bit smaller in dimensions than hbn in order to remove any bias due to the registry mismatch at the edges of the simulation cell. In MD simulations, the CA.M layer has been equilibrated in an NVT ensemble at 300 K for 5 ns and then propagated for a further 2 ns in an NVE ensemble. The effect of relative orientation of the CA.M and hbn lattices has been extensively studied by performing a lateral slide analysis of the potential energy surface (PES) (followed by relaxation of the CA.M layer) for different orientations over a range of 30 o, i.e. ranging from armchair to zigzag direction in the hbn lattice. The minimum value for the interaction energy between the layers was found to be around ±1-3, in good agreement with the experimental results, although the difference in the interaction energy remains below kt/molecule at all angles. For the CA.M layer, the optimised value of the average lattice vector at 0K is found to be nm and the angle between lattice vectors is 120. The stability of the CA.M layer has also been probed by MD simulations at 300K, which confirmed that the adsorbed molecular layer remains stable at room temperature. The lattice constant of CA.M layer at 300K has been estimated through the 2D radial distribution function between equivalent atoms in molecules, which peaks at nm (Supplementary Figure 5b), in excellent agreement with experiment. 2.3 Interaction between TMA, TPA and CA.M/hBN The interaction between TPA and TMA arrangements and CA.M has been investigated by the lateral slide analysis of PES. A CA.M hexagonal arrangement consisting of 8024 molecules has been prepared with a periodicity of 9.75 Å (the lattice constant predicted by 6

7 MD simulations at 300K) and minimised in vacuum keeping the central ring of each molecule fixed at its original position. PBCs applied to the simulation box were chosen to be an exact multiple of the CA.M lattice vector in the xy-directions, namely nm x nm. A row of TPA containing 40 molecules (Supplementary Figure 6a) was optimised in vacuum producing an intermolecular distance of nm. The energy of a single hydrogen bond, defined as ( ) ( ), where n is the number of TPA molecules in a row, is ( ) calculated to be 0.27 ev. The optimised TPA row has been placed onto the CA.M layer, separated by 0.35 nm. The TPA row is then moved as a rigid body along x and y with a step size of 0.01 nm. At each step, the adsorption energy was calculated as ) ( ) (. ). This gives a pure adsorption contribution to the total energy excluding the energy required to form hydrogen bonds. The adsorption energy as a function of the displacement along the XY plane for different angles between the principal axis of the row and the CA.M lattice vector has been calculated (see Supplementary Fig 6). PES profiles for the rotation angles of 0, 10, 20, and 30 are presented in Supplementary Figures 6b-e. The lowest energy corresponds to orientations where a TPA row is aligned with the CA.M lattice vector, i.e. at the rotation angles of 0, 60 and 120 ; the adsorption process at these angles is favoured by about 0.09 ev per molecule (see Supplementary Figure 10). After full relaxation of TPA molecules on the CA.M layer, the adsorption energy at 0 is ev/molecule. The energy decomposition, shown in Supplementary Figure 6b, indicates that although the van der Waals interactions account for the largest contribution to the total energy of adsorption, the exact position of the minimum is strongly influenced by the Coulombic energy. Except for preferred orientations, the PES is fairly flat representing an average of inregistry and out-of-registry positions of the interacting layers. The low energy regions near the minima extend to 0.2 to 0.4 nm in each direction allowing for some flexibility in the positioning of TPA molecules on CA.M layer, which is important in the multi-row systems. 7

8 Supplementary Figure 6: a) set-up of the model and the minimum energy configuration. CA, M and TPA molecules are colored in red, blue and green, repsectively; Lateral sliding analysis of PES at 0 rotation, including Lennard-Jones and Coulombic contributions (b); at 10 (c); at 20 (d); at 30 (e) 8

9 Supplementary Figure 7: a) the interaction potential energy for 14 TPA rows as function of MD simulation time calculated for different initial rotation angles between the TPA bundle and CA.M lattice. b) a snapshot of MD simulation showing that for the initial rotation angle of 10 the ends of TPA bundle spontaneously align along the preferred orientation of 0 during equilibration time. CA, M and TPA molecules are colored in red, blue and green, respectively. The underlying hbn layer was removed for sake of clarity. In MD simulations, the three-layered system (as shown in Figure 5a of the main text) was equilibrated for 4 ns in an NVT ensemble and then propagated for a further 2 ns with an NVE integrator. For the initial rotation angle of 0 o, 10 o, 20 o and 30 o between the TPA row bundle and CA.M lattice vector, the interaction potential energy of TPA rows was recorded every 10 fs and averaged every 100 fs (Supplementary Figure 7a). MD simulations show that the orientation at 0 is the most stable, by about 0.04 ev/molecule. This energy value is somewhat smaller than that found for the rigid body scan because the increased flexibility allows the assembly in the non-optimal orientations accommodated through local distortions. It is also interesting to note that in simulations with the initial angle of 10, both ends of the TPA bundle rotated to the preferred orientation of 0 during the equilibration time, thus lowering the potential energy of interaction (Supplementary Figure 7b) and demonstrating a tendency for the rows to align along the CA.M lattice vector. A complete rotation of the whole assembly is difficult to observe in a short time scale of MD simulation as it implies simultaneous rotations of all the rows, which are strongly interacting with one another. These simulations merely provide a comparison between different orientations of the TPA bundle on CA.M/hBN support, and are not an attempt to model a direct assembly of TPA rows. 9

10 In Supplementary Fig. 8a and b two example of snapshots from MD runs with different relative displacement in neighboring rows are shown. The configuration in Supplementary Fig. 8b has the correct inter-row separation, but not the right displacement. The configuration in Supplementary Fig. 8a shows a displacement closer to the experimental results, but the inter-row separation is slightly broader. In both cases we can observe defect formation in terms of row dislocations. As mentioned in the main text, this could be due to a an intrinsic limitation of the classical potential. We tried to improve it by recalculating the TPA charges from DFT-based RESP calculations. In the Standard OPLS set of charges all the atoms in the phenyl ring have the same negative charge ( e). In our new set those attached to the carboxylic group are slightly positive (0.095 e). This make sense from a chemical perspective given the electron-withdrawing nature of the COOH group. The C atom of the COOH group becomes less positive (0.532 e instead of e) while all the other atom types remain very close to the original OPLS values (the largest difference is e). With this new set of charges we can obtain a perfect match with the experimental results for both inter-row separation and displacement as shown in Supplementary Fig 8c and d. 10

11 Supplementary Figure 8: a-b) two examples of different configurations of TPA rows taken from different MD simulations of the three-layered system at 300 K using the standard OPLS set of charges for TPA. CA, M and TPA molecules are colored in red, blue and green, respectively. The underlying hbn layer was removed for sake of clarity. c) and d) show contact mode images of the same area showing rows of TPA molecules (d). At higher deflection setpoint (c) the underlying CA.M is revealed and shows that every sixth TPA row is positioned over every fourth CA.M row. The angle between the CA.M and TPA lattice direction is highlited. e) a snaphost taken from MD simulations with new set of RESP charges for TPA. Highlighted angle show the perfect match with experimental results. Similarly, a TMA molecular network was studied. A hexagonal arrangement of 486 TMA molecules was formed and optimised in vacuum. The gain in energy corresponding to hydrogen bond formation is the same as in the case of TPA (0.27 ev). The TMA molecular arrangement was placed 0.35 nm above the CA.M layer (Supplementary Figure 9a). Lateral 11

12 sliding analysis of the PES clearly identified the preferred angle of 30 between the CA.M and TMA lattices, for which the total energy and different contributions to it are shown in Supplementary Figure 9c. The energy profiles at 0, 10 and 20 are shown in Supplementary Figure 9d-f. The adsorption energy profile (see below) indicates a minor secondary minimum at 0. In all other orientations, the PES is essentially flat. As in the case of TPA, most of the adsorption energy in the preferred orientation comes from the vdw interaction (Supplementary Figure 9c). However, for TMA two distinct minima in the total energy profile are present: one is due to the vdw interaction and corresponds to a TMA molecule positioned on-top of M, while the other is driven by Coulombic interaction and corresponds to TMA being on-top of CA. Geometry optimisation in the two positions gives an almost identical adsorption energy of about ev/molecule in both cases. To investigate further these two positions, the three-layer system with TMA on-top of CA and on top of M was studied using MD simulations. The potential energy of TMA molecules in both cases was recorded, as described above for the case of TPA, and is shown in Supplementary Figure 10a. The configuration with TMA on-top M is slightly more stable, but the difference in energy is comparable to kt. 12

13 Supplementary Figure 9 a-b) set-up of the model and the minimum energy configuration. CA, M and TPA molecules are colored in red, blue and green, repsectively; Lateral sliding analysis of PES at 30 rotation, including Lennard-Jones and coulombic contributions (c); at 0 (d); at 10 (e); at 20 (f) 13

14 Supplementary Figure 10: a) the interaction potential energy as function of MD simulation time, calculated for TMA on top of CA and on top of M; (b) snapshot from the equilibrated MD run of the full three-layered system with TMA on-top of M. CA, M and TPA molecules are colored in red, blue and green, respectively. Underlaying hbn layer was removed for sake of clarity. Supplementary Figure 11: the adsorption energy as a function of the angle between the the CA.M lattice vector and principal axis of the TPA row (a) or the TMA lattice vector (b). 14

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