Molecular Seesaw: Intricate Dynamics and Versatile Chemistry of

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Molecular Seesaw: Intricate Dynamics and Versatile Chemistry of Heteroaromatics on Metal Surfaces Sergey N. Filimonov, Wei Liu, and Alexandre Tkatchenko J. Phys. Chem. Lett., Just Accepted Manuscript • DOI: 10.1021/acs.jpclett.7b00071 • Publication Date (Web): 23 Feb 2017 Downloaded from http://pubs.acs.org on March 3, 2017

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The Journal of Physical Chemistry Letters

Molecular Seesaw: Intricate Dynamics and Versatile Chemistry of Heteroaromatics on Metal Surfaces Sergey N. Filimonov,∗,† Wei Liu,‡ and Alexandre Tkatchenko¶ †Department of Physics, Tomsk State University, 634050 Tomsk, Russia ‡Nano Structural Materials Center, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China ¶Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg E-mail: [email protected]

Abstract

Graphical TOC Entry

The design of novel elementary surface processes is important for applications in catalysis, single-molecule junctions, molecular sensors, switches and surface mounted molecular machines. Here we demonstrate by van der Waals inclusive density functional theory calculations that a small and relatively simple heteroaromatic compound s-triazine (C3 H3 N3 ) unexpectedly possesses five metastable states when adsorbed on the Pt(111) surface. This diversity of the adsorption states stems from an interplay between versatile molecule/surface chemical bonding and van der Waals interactions and from “softening” of the aromatic ring by nitrogen substitution, which makes folding of the aromatic ring energetically much less demanding as compared to benzene. The intricate seesaw-like surface dynamics and tunable electronic structure of s-triazine show promise for applications in molecular sensors and switches. The broad implications of our findings are demonstrated for triazine- and pyrimidinebased heteroaromatic compounds and other metal surfaces.

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e.g. pyridine. 21,22 In the case of bonding solely through the delocalized π-electrons one would expect the aromatic ring to be parallel to the surface, while bonding via the N lone pair favors upright standing orientation of the adsorbed molecule. In a mixed case of bonding involving both delocalized π-electrons and lone electron pairs of N atoms one expects the adsorbed molecule to be tilted relatively to the surface. Remarkably, the mixed case renders different possible configurations at the same adsorption location, as will be presented below. To explore possible adsorption configurations of s-triazine on Pt(111) we performed structural optimization of the molecule at four highsymmetry adsorption positions (atop, bridge, hollow fcc and hollow hcp), starting from two different adsorption heights (2 and 3 ˚ A) and four tilt angles of the molecule to the surface: −30◦ (left), 0◦ (parallel), 30◦ (right), and 90◦ (normal). Our calculations were carried out using the van der Waals (vdW) inclusive DFT+vdWsurf method 23 (see Methods section for computational details), which enables accurate prediction of structure and stability of organic molecules on metal surfaces as has been demonstrated for a range of different adsorption systems. 24,25 The adsorption energy was calculated as Ead = Emol/metal − Emetal − Emol , where Emol/metal is the total energy of the complete adsorption system, Emetal and Emol are the energies of the clean Pt slab and isolated molecule, respectively. According to this definition more negative adsorption energies correspond to a stronger binding of the molecule to the substrate. Relaxed geometry, calculated adsorption energies and simulated constant-current scanning tunneling microscopy (STM) images of the revealed adsorption configurations are shown in Fig. 1. Similar to benzene 26–28 and to some other benzene derivatives, 29–31 s-triazine on Pt(111) preferentially occupies the bri30 position. However, in contrast to benzene, striazine does not lie parallel to the surface in its energetically most favorable adsorption configuration but shows considerable folding of the aromatic ring (Fig. 1(a)). This is originated

Chemical reactivity and physical properties of organic molecules deposited on inorganic surfaces depend crucially on the geometrical structure adopted by the molecule upon adsorption. This behavior is of paramount importance for selective organic catalysis 1–5 and also has important practical implications in material science and molecular electronics, where controlled transitions between different metastable configurations of adsorbed molecules are utilized to design novel molecular devices from simple molecular switches 6–9 to complex molecular machines mounted on surfaces. 10,11 The diversity of adsorption configurations usually stems from conformational changes of large and flexible molecules, 12–16 whereas the smallest aromatic compounds, like benzene and its simplest derivatives, are commonly considered to be rigid and to be unable to switch the adsorption state by a conformational change. In dense molecular arrays the change of the adsorption configurations of rigid molecules can occur by changing orientation of the molecule with respect to the surface. 17–19 For single adsorbed molecules such orientational transitions are much less anticipated due to the absence of intermolecular interactions, which might stabilize or destabilize different adsorption structures. However, in the present paper we show by using van der Waals-inclusive density functional theory calculations that reduced aromaticity of triazine and pyrimidine compounds combined with subtle interplay of the chemical bonding and dispersive forces can result in both the conformational and orientational transformations of the adsorbed molecules on reactive metal surfaces. The emergence of multiple states of adsorption at the single molecule level offers new perspectives for the smallest heteroaromatic compounds in catalysis and molecular electronics. We begin with the adsorption of the symmetric 1,3,5-triazine (C3 H3 N3 ), also called striazine, on Pt(111). When deposited on a metal surface s-triazine can form chemical bonds with the substrate atoms either via delocalized π electrons of the C-N ring or using lone pairs of electrons of nitrogen atoms, 19 similar to other N-substituted benzene derivatives,


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Figure 1: Relaxed geometry and simulated constant-current STM images of five representative adsorption configurations of s-triazine on Pt(111): (a) bri30-left, (b) bri30-par, (c) bri30-right, (d) atop30 and (e) hcp30. STM images were calculated using the Tersoff-Hamann approach 20 at a positive bias voltage of 0.05 V. Red lines at the top and right sides of the STM images are the vertical and horizontal line scans across the molecule. from breaking the aromaticity of the C-N ring in the adsorbate. The folding helps to minimize the Pauli repulsion between the molecule and the substrate by lifting up two of three hydrogen atoms to a distance of 2.92 ˚ A from the surface. Thereby two of three nitrogen atoms and one carbon atom are brought very close to the surface. The adsorption height of 1.95 ˚ A of the lowermost N and C atoms suggests formation of chemical bonds with the metal. In the parallel arrangement s-triazine also adsorbs preferentially at the bridge site position. Relaxed geometry of the bri30-par state is characterized by an upward tilt of the C-H bonds and a slight nonplanarity of the aromatic ring with C atoms lying 0.02 ˚ A closer to the surface than N atoms (Fig. 1(b)). The adsorption height of 2.05–2.07 ˚ A in the bri30-par state is typical for chemisorption of small benzene derivatives on Pt(111). 29 The bri30-par state is energetically less favorable by 0.35 eV than the tilted bri30-left state. Another possible configuration of s-triazine, adsorbed at the bridge site, is bri30-right. Here the aromatic ring of the molecule is only slightly deformed, but the relaxed molecule is tilted by 24◦ relative to the substrate surface (Fig. 1(c)). Thereby one nitrogen atom and two carbon atoms reside close enough to the surface to form chemical bonds with the underlying Pt atoms.

The bri30-right state is energetically less favorable by 0.23 eV than the bri30-left state, but it is more favorable by 0.12 eV than the bri30-par state. For s-triazine oriented normal to the surface the preferential adsorption position is the atop site. In the optimal atop30 configuration the plane of the molecule is rotated by 30◦ with respect to the rows of surface atoms and the lowermost N atom of the molecule is located 2.19 ˚ A above Pt (Fig. 1(d)). With the adsorption energy of −1.11 eV, the atop30 state is the second energetically most favorable adsorption state, with bri30-left being the first. Apart from the four chemisorbed states our calculations reveal the existence of a physisorbed state of s-triazine on Pt(111). Among possible physisorbed configurations the most favorable one is hcp30 with the adsorption energy of −0.76 eV and the adsorption height of 2.89 ˚ A (Fig. 1(e)). However, as will be shown below, the energy barriers separating physisorbed and chemisorbed states of s-triazine on Pt(111) are very low, so that the molecule can easily transfer from the physisorbed state to one of the energetically more favorable chemisorbed states. All the revealed adsorption configurations of s-triazine on Pt(111) are strongly stabilized by vdW interactions. In particular, the vdW en-


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ergy accounts for more than 50% of the total binding energy in the two energetically most stable bri30-left and atop30 states (see Supporting Information for more details). Moreover, the contribution of vdW interactions determines relative stability of different adsorption configurations of s-triazine on Pt(111). Indeed, the atop30 state becomes equally stable with the bri30-left state when vdW interactions are not taken into account. This finding is in accord with our recent results revealed the critical role of vdW interactions in determining relative stability of the reactive intermediates of complex molecules on surfaces. 32 To check whether the choice of the method for vdW interactions could affect any of the revealed adsorption states of s-triazine on Pt(111) we have performed test calculations with the optimized optB88-vdW functional, 33 which represents a conceptually different approach to treatment of dispersive interactions. Using the PBE+vdWsurf relaxed geometry as an input we have observed only slight changes in the adsorption geometry when the optB88vdW method was utilized. That is all five metastable states of adsorption of s-triazine on Pt(111) were well reproduced when using the optB88-vdW functional. Selection of a particular adsorption configuration upon adsorption is determined by the orientation of the molecule with respect to the surface. Our calculations show that s-triazine can directly adsorb into the chemisorbed atop30 state when the molecule approaches the surface standing upright. In other cases the molecule can be temporary trapped in the physisorbed hcp30 state, from which it can transfer to one of the energetically more favorable chemisorbed states. The states which can be directly occupied by impinging molecules are marked by red arrows in Fig. 2(a). Possible transitions between the physisorbed and chemisorbed states and corresponding activation barriers are shown in Fig. 2(a). As can be seen the activation barrier for the transition from the physisorbed hcp30 state to the bri30-left state is substantially higher than the barriers for the transitions from the physisorbed hcp30 state to the chemisorbed bri30-right and

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Figure 2: (a) Adsorption mechanisms of striazine on Pt(111). Red arrows mark channels for direct (barrierless) adsorption from the gas phase, black arrows mark transitions between the physisorbed and chemisorbed states. (b) Potential energy diagram of the transitions between different chemisorbed states of s-triazine on Pt(111). Numbers in (a) and (b) indicate corresponding activation barriers in eV.


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bri30-par states. That is, the energetically most favorable bri30-left state is the most difficult one to reach from the physisorbed state, suggesting that filling up this state occurs via transient adsorption into less favorable but more accessible chemisorbed configurations. Bearing in mind the possibility of the direct (barrierless) adsorption into the chemisorbed atop30 state and a close to zero barrier for the transition from the physisorbed hcp30 state to the chemisorbed bri30-right state, we conclude that the most plausible scenario for s-triazine arriving at the Pt(111) surface is immediate chemisorption either into the tilted bri30-right state or into the upright standing atop30 state. We further consider the possibility of striazine trapped in a certain chemisorbed state to change its adsorption configuration and reach the energetically most favorable bri30left state. The potential energy landscape associated with the transitions between different chemisorbed states of s-triazine on Pt(111) is shown in Fig. 2(b). From the atop30 state s-triazine can switch to the bri30-right state via a 30◦ rotation around the N-Pt bond, followed by a 66◦ tilt of the aromatic ring toward the surface. From the bri30-right state the molecule can further switch to the bri30-par state and then from the bri30-par state it can finally reach the energetically most favorable bri30-left configuration. Since the molecule has to pass through a sequence of energetically less favorable states, the overall energy barrier for the atop30→bri30-left transition is 0.36 eV. The activation barrier for the reverse transition from the bri30-left to atop30 state is 0.50 eV. We also searched for possible diffusion pathways of s-triazine on Pt(111). We found that the barrier for surface diffusion of s-triazine in the physisorbed state (0.02 eV) is higher than the barrier for transition from the physisorbed hcp30 state to the chemisorbed bri30-right state. This excludes any long range lateral mobility of physisorbed molecules and rules out the possibility of diffusion of chemisorbed molecules via a transient physisorbed state. The lowest energy diffusion path for chemisorbed s-triazine involves transitions between two neighboring atop30 states. The energy barrier of 0.55 eV

for this transition is higher than any of the barriers in Fig. 2(b), therefore lateral mobility of chemisorbed s-triazine molecules should be suppressed on the timescale of switching between the atop30 and bri30-left configurations. Suppressed lateral mobility of s-triazine on Pt(111) and relatively high barriers for switching between the bri30-left and atop30 states should make the switching dynamics accessible for direct experimental investigations e.g. by STM. An elementary surface process can be tracked by STM if its rate is lower than the STM scan rate. In the following we identify three different temperature regimes of the adsorbate dynamics by comparing the typical scan rate of 1 frame/min with the transition rates of s-triazine on Pt(111). At low temperatures (T < 50 K) preferential adsorption of s-triazine into the upright standing atop30 configuration is expected. This state can be either directly occupied by impinging molecules, or filled up after short transient adsorption into less favorable bri30-par and bri30right states. Very low barriers for transitions from the bri30-par to bri30-right state and from the bri30-right to atop30 state make these transitions the dominant types of molecular moves at low substrate temperatures. In the middle temperature range (50–125 K), transitions from the atop30 to bri30-right, from bri30-right to bri30-par and from bri30-par to bri30-left states become possible. However, at middle and high temperatures it would be difficult to detect the bri30-par and bri30-right states with conventional STM due to a very short residence time of the molecules in these states. Therefore, the transition to the energetically most favorable bri30-left configuration should be seen as a spontaneous swap between the atop30 and bri30-left states. As a result of such transitions, the atop30 population will decay with time in favor of the bri30-left states. At elevated temperatures (T > 125 K) the net rate of the atop30 to bri30-left transitions becomes higher than the typical STM scan rate of 1 frame/min. Therefore, only the bri30-left state could be imaged with STM at high T . When the the bri30-left to atop30 transitions (via bri30-par and bri30-right states) become


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Figure 3: Electronic properties of two most stable adsorption configurations of s-triazine on Pt(111): (a) bri30-left, and (b) atop30. Left panel: density of states of s-triazine on Pt(111) projected onto the HOMO and LUMO of a free s-triazine molecule. Middle panel: charge density difference isosurfaces of s-triazine/Pt(111). The isovalues are ±0.04 electron/˚ A3 . The regions of the electron accumulation (depletion) are colored blue (red). Right panel: adsorption induced charge density difference of s-triazine/Pt(111) integrated over the xy plane. activated, the STM image of the molecule might become blurred due to a seesaw-like motion of s-triazine switching back and forth between the bri30-left and atop30 states. Transitions between different adsorption states can be activated not only by thermal fluctuations, but also by some external stimuli. For instance, Borca et al. 34 and Schendel et al., 35 have demonstrated recently that transitions between chemisorbed and physisorbed states of individual organic molecules (anthradithiophene on Cu(111)) can be triggered by charge injection from a STM tip. One can expect that similar switching mechanism can be applied to s-triazine on Pt(111). Transitions between different adsorption states of s-triazine on Pt(111) cause changes in the electronic structure of the adsorbed molecule. The left column in Fig. 3 show the projected density of states (PDOS) of the adsorbed s-triazine onto the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the free molecule. 36 The HOMO and LUMO states of s-triazine broaden considerably and strongly overlap upon adsorption in the bri30-left state (Fig. 3(a), left). The former HOMO and LUMO

states of s-triazine in the bri30-left configuration are occupied by 1.7 and 0.98 electrons, respectively, indicating considerable charge redistribution between the metal and the molecule. This is confirmed by the electron density difference plots, shown in the middle and right columns of Fig. 3(a), where accumulation of electrons on the N-Pt and C-Pt bonds just below the N and C atoms and depletion of electrons above the metal surface are seen. Similar character of the charge redistribution along the N-Pt and C-Pt bonds suggests that in both cases bonding is primarily due to the delocalized π electrons of the molecule. The adsorption induced redistribution of charge between the molecule and the substrate, and deformation of the backbone of the adsorbed molecule, generate an interfacial dipole, which changes the work function of the metal surface. Interestingly, despite the apparent charge transfer from the substrate to the molecule, adsorption of s-triazine into the bri30-left state reduces the surface work function by 0.38 eV. We explain this by a significant polarization of the adsorbate (note considerable charge oscillations within the molecule), which overcompensates the charge transfer effect and contributes to the


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observed work function decrease. 37 In the vertical atop30 configuration the overlap of the former HOMO and LUMO states is negligible (Fig. 3(b)). Analysis of the projected orbitals occupation indicates that in the atop30 state there are 1.64 and 0.09 electrons in the former HOMO and former LUMO orbitals, respectively. The fact that the LUMO state is almost empty and a noticeable depletion of the HOMO state, suggest a net charge transfer from the molecule to the metal surface, in agreement with the integrated charge difference distribution showing considerable depletion of electrons below the molecule and accumulation of electrons close to the metal surface. The surface work function of Pt(111) is reduced by 0.8 eV due to adsorption of s-triazine in the vertical atop30 configuration. The key features responsible for appearance of multiple adsorption states and intricate dynamics of s-triazine on Pt(111) are (i) relatively high reactivity of the metal substrate, (ii) substantial role of dispersive interactions in the chemisorbed states, (iii) symmetry breaking between the molecule and the substrate and (iv) “softening” of the aromatic ring by nitrogen substitution. The (i) ensures chemical bonding of the molecule to the surface, (ii) and (iii) serve for enhanced stability of nonplanar adsorption configurations and (iv) makes deformation of the aromatic ring energetically much less demanding as compared to benzene. Evidently, neither of the aforementioned features is unique to s-triazine on Pt(111), therefore one would expect similar behavior for a wide range of different adsorption systems. To confirm this we have performed structural relaxation of s-triazine on different metal surfaces and checked out a number of other heterocyclic compounds on Pt(111). Multiple states of adsorption connected by seesaw-like transitions have been found for s-triazine on Pd(111) and Rh(111) and for a number of triazine and pyrimidine derivatives on Pt(111) (see Fig. 4 and Supporting Information for more details). The occurrence of multiple state of adsorption offers new perspectives for the smallest heteroaromatic compounds in catalysis and molecular electronics.

Figure 4: Triazine and pyrimidine compounds with multiple adsorption states on Pt(111). In summary, the structure and electronic properties of s-triazine adsorbed on Pt(111) were investigated with density functional theory calculations. It is shown that being trapped at a certain adsorption position s-triazine on Pt(111) can adopt several distinct adsorption configurations, which differ considerably by the adsorption geometry, bonding configuration and electronic properties of the adsorbed molecule. Noticeably, reversible transitions between different adsorption configurations may occur without changing the location of the molecule on the surface, which makes s-triazine a strong candidate for molecular switch applications.

Methods Density-functional theory calculations with semilocal Perdew-Burke-Ernzerhof (PBE) functional 38 were performed using the FHI-aims all-electron code. 39 The dispersive interactions were treated with the DFT+vdWsurf method, 23 which combines the DFT+vdW method 40 for intermolecular interactions with the Lifshitz-Zaremba-Kohn theory 41,42 for the nonlocal Coulomb screening within the inorganic bulk. The Pt(111) surface was represented by a periodic slab with a (4 × 4) unit cell containing six layers of Pt and 29 ˚ A of vacuum. The molecule was placed on the top surface of the slab. Dipole correction was applied to compensate an artificial dipole field due to


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Supporting Information Available

non-equivalent slab surfaces. 43 For the geometry optimization, the molecule and the two uppermost metal layers were allowed to relax, while atoms of four bottommost Pt layers were constrained at their bulk positions employing the theoretical PBE+vdWsurf lattice constant of 3.979 ˚ A . 28 The structure was optimized until the maximum residual force component per atom was converged to 10−4 eV. The final single-point calculations of the relaxed structures were carried out with the “tight” settings including the “tier2” standard basis set for light elements and “tier1” for heavy metal atoms. Relativistic effects were treated using the scaled zero-order regular approximation. 44 Convergence criteria of 10−5 electrons per unit volume for the electron density and 10−4 eV for the total energy of the system were applied. The reciprocal space integration was performed with a MonkhorstPack grid of (6 × 6 × 1) kpoints. We also performed test calculations with the optB88-vdW functional, 33 to confirm that the presence of the revealed adsorption states of s-triazine on Pt(111) is not affected by the method for dispersive interactions. The optB88-vdW calculations were performed with the VASP code 45 using PBE-based projector augmented wave potentials 46 with a cut-off energy of 400 eV and a 2 × 2 × 1 MonkhorstPack grid of k-points. The activation energies for lateral diffusion of the adsorbed molecule and for transitions between different adsorption states were calculated using the string method 47 combined with the climbing image technique, 48 as implemented in the aimsChain code from the standard FHI-aims distribution. The rate constants of the surface processes were evaluated using the harmonic transition state theory 49 and the DFT-calculated activation energies and normal vibrational modes for the metastable and transition states. The structural models, simulated STM images and charge density maps are visualized with the VESTA software 50

The following files are available free of charge. Transition rates of s-triazine on Pt(111); adsorption energies of s-triazine on Pt(111), Pd(111) and Rh(111); adsorption energies of triazine and pyrimidine derivatives on Pt(111).

Author information Corresponding Author: [email protected] (S.N.F.) Notes: The authors declare no competing financial interests Acknowledgement S.N.F. gratefully acknowledges financial support from the Russian Science Foundation through the grant 14-1200813 and computational resources provided by the Supercomputing Center of Tomsk State University. W.L. acknowledges support from the National Natural Science Foundation of China (no. 21403113), and the Natural Science Foundation for Distinguished Young Scholars of Jiangsu Province (no. BK20150035).

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