Physisorption Controls the Conformation and. Density of States of an Adsorbed Porphyrin

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1 Physisorption Controls the Conformation and Density of States of an Adsorbed Porphyrin S.P. Jarvis, S. Taylor, J. D. Baran, D. Thompson, A. Saywell, B. Mangham, N. R. Champness, J. A. Larsson, and P. Moriarty Supplementary Material Simulation Methods Dispersion-Corrected Density Functional Theory Density functional theory calculations (DFT) were performed using the generalized gradient approximation (GGA) parametrization by Perdew Burke Ernzerhof (PBE) 1 implemented within the projector-augmented wave method 2,3 in the VASP software package. 4 6 The VASP plane-wave basis set energy cutoff was 400 ev, and a Gaussian smearing of 0.1 ev was used for the initial electronic occupations. To account for the missing dispersion forces in the standard implementation of DFT, we describe the vdw forces using three approaches in conjunction with PBE exchange-correlation functional: the semiempirical corrections proposed by Grimme (PBE-D3), 7 and the Tkatchenko-Scheffler (PBE-TS), 8 as well as the van der Waals density functional method with optimized exchange term (optb86b-vdwdf). 9 To calculate the Cu bulk structure, a (14x14x14) Monkhorst-Pack 10 k-point mesh was used and the resulting lattice constant for Cu was found to be 3.593/3.591/3.605 Å for the PBE-D3/PBE-TS/optB86b-vdwDF methods, respectively, all in good agreement with the 1

2 experimental lattice constant of Å. To model the surface structure, a 12x12 hexagonal three-layer-thick slab of Cu(111) was used. The resulting Cu(111) surface model contains in total 432 Cu atoms. The Br 4 TPP (H22C44N4Br4) molecule was placed parallel to the surface and a thick vacuum level of 20.0 Å was set up to ensure that there was no spurious interaction between periodically repeated slabs in the direction normal to the surface. Geometry optimization of the Br4TPP/Cu(111) system was performed with the Brillouin zone sampling at the Γ-point. The first two layers of the surface and the molecule are fully relaxed until the force acting on each atom is less than 0.05 ev/å, whereas the bottom surface layer was kept fixed in the bulk position. To check the effect of the fixed bottom layer on the adsorption geometry, the constraints on the bottom layer were removed and the further optimization was carried out relaxing all atoms in the cell. No differences were found in the calculated properties when all three layers of the Cu(111) where allowed to relax. On top of the optimized system, the single point calculations with the (2x2x1) k-point mesh were performed, but these calculations brought negligible difference from these at the Γ- point. The density of states have been analysed using p4vasp, 11 whereas the charge density difference and electron localization functions were visualised using VESTA. 12 Molecular Dynamics The Cu(111) surface slab was cut from the Cu bulk crystal and its geometry was optimised using VASP electronic structure calculations as described above. The porphyrin molecule was placed on the surface and a variety of molecular positions were generated over ten nanoseconds of room temperature molecular dynamics. We used an artificially softened Cu van der Waals potential in this initial simulation, by quartering the force constant of the potential 13 to ensure that a wide variety of conformations were sampled within the fewnanosecond time-scale of the simulation. Planar, half-saddle and saddle conformations were identified by monitoring the elevation of the C=C carbon atoms in the core. Four starting planar conformations, four saddle conformations (two bent along the N-H H-N direction 2

3 and two bent along the N N direction), and four half-saddle conformations (two with one bent pyrrole moiety and two with one bent deprotonated pyrrole) were extracted. The full Cu van der Waals potential was then switched on and the twelve complexes were each subjected to a further ten nanoseconds of dynamics. Force field parameters for the Br 4 TPP molecules were generated from existing force field data for pyrrole 16 and 1-bromobenzene. 15 We used Gaussian09 17 electronic structure calculations to generate atomic charges for deprotonated pyrrole, 2,3-dimethyl-pyrrole and 1-bromo- 4-methyl-benzene, and then mapped the natural population analysis (NPA) charge differences relative to pyrrole and 1-bromobenzene to parameterise the full porphyrin molecule. The structure generated gave negligible penalties in the CGenFF program 18 and the charge distributions are similar in overall topology to Bader charges 19 calculated in the VASP calculations, but with lower magnitudes on the atom-centered charges. 20 Time- and structure-averaged values for molecule conformations, dynamics, and surface adsorption energies were calculated by sampling every twenty picoseconds over ten nanoseconds of dynamics, to provide 200 statistically independent structures for each complex. Image generation and Tcl script-based trajectory analysis was performed using the VMD program. 21 Additional Experimental Results Experimental results detailing the distribution of Type I and II molecules and their relative orientations, following 77K deposition, on the Cu(111) crystal are shown in Figure S1. As shown in Figure S1(a) Br 4 TPP molecules adsorb in one of three unique orientations relative to the crystal directions of the Cu(111) surface. For ease of interpretation we have labelled these directions as -15,-75 and +45 with respect to the horizontal axis of the STM image shown in (a). Analysis across a greater number of images for a total of N=262 Br 4 TPP molecules results in the distribution shown in Figure S1(b), where we not only find an equal number of Type I and II conformers, but also an equal number of molecules adopting each 3

4 (a) (b) % of Total Average orientation (N= 262) o -75 o +45 o Type 1 Avg Type 2 Avg Figure S1: Distribution of conformers and adsorption orientation. (a) Representative STM image showing the three unique orientations adopted by each Br 4 TPP molecule. (b) Analysis across N=262 molecules shows an equal distribution between the number of molecules in each conformation, and the orientations they adopt with respect to the surface. orientation with respect to the surface. The equal distribution of conformers is consistent with the similar values of adsorption energy calculated in Table 1 of the main text. The full sequence of Br 4 TPP manipulation on Cu(111) is shown in Figure S2. The native Type I conformer is laterally translated and rotated across the surface (Figure S2(a-c)). Subsequent imaging of the local Cu(111) surface shows that the Type I conformer adopts the same adsorption site in each orientation. In Figure S2(d) an intermediate structure is shown adopting a mixed Type I and II arrangement obtained from the same lateral manipulation protocol. After successful translation of the mixed conformer (Figure S2(e)) the molecule spontaneously switched to the complete Type II conformation during continued scanning (Figure S2(f)). Subsequent manipulations show translation and rotation of the Type II conformer (Figure S2(g-i)). In this case many more attempts were required for successful manipulation, suggesting a stronger binding (or larger diffusion barrier) for the Type II conformer. We also note the reduction in tip quality over the Cu(111) region in Figure S2(h and i) and apparent shift of the step edge, suggesting subtle changes to the tip structure during manipulation. 4

5 a) e) c) b) f) d) h) g) i) Figure S2: Full manipulation sequence of Br4 TPP imaged with constant height STM. (a-c) Images of the Type I conformer in different orientations, (b,c) are taken following lateral manipulation with the STM/NC-AFM tip with zero tunnelling current. (d,e) Images taken after half the molecule has been changed to the Type II conformation. (f) The Br4 TPP molecule spontaneously switching to the fully Type II conformation during a downwards scan at the position marked by the arrow. (g,h,i) Images taken following lateral manipulation of the Type II conformer. Scan parameters: 50mV, a0=300pm; Cu(111) image height -520pm relative to that over Br4 TPP. Additional Theoretical Results Twelve types of starting structures were identified during the initial phase of 10 nanoseconds of molecular dynamics using the artificially weakened Cu van der Waals potential. Four starting planar conformations, four half-saddle conformations (two with one bent pyrrole moiety and two with one bent deprotonated pyrrole), and four saddle conformations (two bent along the N-H H-N direction and two bent along the N N direction) were extracted. The corresponding final structures are shown in Figure S3, obtained after 10 nanoseconds of equilibrated room temperature dynamics on each of the twelve starting orientations using the full Cu van der Waals potential. The predominant conformation observed in the simulaitons is a saddle structure with the legs either side of a bent pyrrole titled away from each 5

6 other to improve leg:cu(111) vdw contacts, which elongates the molecule in the direction perpendicular to the N N direction of the bent pyrroles Figure S3: Ball-and-stick diagrams of the twelve final structures obtained from MD simulations using the full Cu vdw potential shown with an example top-down view with and without semi-transparent vdw spheres. As discussed in the main manuscript, standard DFT calculations in the absence of dispersion corrections show only small changes to the calculated DOS (green and red) compared to the gas-phase molecule (grey), as shown in Figure S4. When dispersion corrections are switched on, however, much larger shifts are observed. Additional calculations of the DOS of the adsorbed molecule, using a variety of exchangecorrelation and vdw descriptions, is shown in Figure S5 for each conformer. Specifically, we test the PBE-D3, PBE-TS and optb86b-vdw functionals as described above. Regardless of the description used we observe extremely similar structure in the DOS, suggesting that the choice of functional has negligible effect on the results we describe. The calculated adsorption energies for each functional are shown in Table S1. In addition, the calculated DOS obtained using the standard PBE (DFT) and corrected optb86b-vdw (vdw-dft) exchange-correlation functionals for the isolated Br 4 TPP and 6

7 Figure S4: Calculated structures and DOS for non-vdw corrected calculations using the PBE functional. (a) and (c) show side and top views of the structure obtained using the vdw optimised Type I coordinates as the starting geometry for calculation and (b) and (d) using the Type II coordinates. Both calculations using the PBE functional result in very similar molecular structures, with a planar macrocycle and a core position centred over a surface hollow site in both cases. (e) Calculated density of states for the free gas-phase molecule (grey), and the structures shown in (a) and (c) (green) and (b) and (d) (red). Table 1: Calcualted adsorption energies for each Br4 TPP conformer on Cu(111) with optb86b-vdwdf, PBE-D3 and PBE-TS functionals. Eads Type I optb86b-vdwdf PBE-D PBE-TS (ev) Type II

8 Cu(111) are shown in Figure S6 (a) and (b) respectively. The comparison of the DOS for the corrected and non-corrected functionals show that the electronic structure of the systems is virtually the same. Consequently, the variations in DOS we observe in the main text must arise from the coupled surface-molecule system. A complete map of the calculated bond lengths for the free molecule and each adsorbed conformation are shown in Figure S7. Figure S5: Calculated DOS of the (a) Type I and (b) Type II adsorbed conformers using the PBE-D3, PBE-TS and optb86b-vdw methods showing negligible difference. Figure S6: (a) Molecular DOS calculated for an isolated Br 4 TPP molecule obtained using the standard PBE and dispersion-corrected optb86b-vdw functionals. (b) DOS calculated for the isolated Cu(111) slab obtained using the standard PBE and dispersion-corrected optb86b-vdw functionals. 8

9 Figure S7: Bond distances in Å for the free Br 4 TPP and adsorbed conformers on Cu(111) as resulting from calculations using optb86b-vdwdf. 9

10 Figure S8: Electron localisation function plotted as a 2D slice through the iminic nitrogen atoms as shown in Figure5(a) of the main manuscript, plotted on a small scale. ELF is plotted as a unitless measure of probability. Figure S9: Example additional structures calculated for the Type II conformer, using DFT with dispersion, demonstrating poorer agreement with experiment. In both (a) and (b), the N-Cu distances are greater and the calculated total energy less favourable than the structures showing best agreement shown in Figure 3 of the main manuscript. 10

11 References (1) Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1996, 18, (2) Blochl, P.E. Projector Augmented-Wave Method. Phys. Rev. B 1994, 50, (3) Kresse, G.; Joubert, D. From Ultrasoft Pseudopotentials to the Projector Augmented- Wave Method. Phys. Rev. B 1999, 59, (4) Kresse, G.; Hafner, J. Ab Initio Molecular Dynamics for Liquid Metals. Phys. Rev. B 1993, 1, 558. (5) Kresse, G.; Hafner, J. Ab Initio Molecular-Dynamics Simulation of the Liquid-Metal- Amorphous-Semiconductor Transition in Germanium. Phys. Rev. B 1994, 49, (6) Kresse, G.; Furthmuller, J. Efficiency of Ab-Initio Total Energy Calculations For Metals and Semiconductors Using a Plane-Wave Basis Set. Comput. Mater. Sci. 1996, 6, 15. (7) Grimme. S. Semiempirical GGA-Type Density Functional Constructed With a Long- Range Dispersion Correction. J. Comput. Chem. 2006, 27, (8) Tkatchenko, A.; Scheffler, M. Accurate Molecular Van Der Waals Interactions from 11

12 Ground-State Electron Density and Free-Atom Reference Data. Phys. Rev. Lett. 2009, 102, (9) Klimes, J.; Bowler, D. R.; Michaelides, A. Van Der Waals Density Functionals Applied to Solids. Phys. Rev. B 2011, 83, (10) Monkhorst, H. J.; Pack, J. D. Special Points for Brillouin-Zone Integrations. Phys. Rev. B 1976, 13, (11) p4vasp available from: (12) Momma, K.; Izumi, F. VESTA 3 for Three-Dimensional Visualization of Crystal, Volumetric and Morphology Data. J. Appl. Crystallogr. 2011, 44, (13) Heinz, H.; Vaia, R.A.; Farmer, B.L.; Naik, R.R. Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6 Lennard-Jones Potentials. J. Phys. Chem. C 2008, 112, (14) Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D; Kal, L.; Schulten, K; Scalable Molecular Dynamics With NAMD. J. Comput. Chem. 2005, 26, (15) MacKerell, A. D.; Bashford, D.; Bellott, Dunbrack, R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S., et al. All-Atom Empirical Potential For Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 1998, 102, (16) Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I., et al. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010, 31, 671. (17) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, 12

13 J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A., et al. Gaussian 09, Revision A.1, Gaussian Inc., Wallingford CT, (18) We use version 2b8, the latest version posted in September Program and methodology is outlined at kenno/cgenff/ and in: (a) Vanommeslaeghe, K.; MacKerell Jr., A.D. Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing. J. Chem. Inf. Model. 2012, 52, 3144; (b) Vanommeslaeghe, K.; Prabhu Raman, E.; and MacKerell, Jr., A.D. Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges. J. Chem. Inf. Model. 2012, 52, (19) Henkelman, G.; Arnaldsson, A., Jnsson, H. A Fast and Robust Algorithm For Bader Decomposition of Charge Density. Comput. Mater. Sci. 2006, 36, 254. (20) Simulation input files and calculated porphyrin-cu(111) structures are available on request. (21) Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graphics 1996, 14,