Diarylethene Molecules on a Ag(111) Surface: Stability and Electron

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Diarylethene Molecules on a Ag(111) Surface: Stability and Electron-Induced Switching Jonas Wirth, Nino Hatter, Robert Drost, Tobias Reinhard Umbach, Sara Barja, Marc Zastrow, Karola Rueck-Braun, Jose I. Pascual, Peter Saalfrank, and Katharina J Franke J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/jp5122036 • Publication Date (Web): 09 Feb 2015 Downloaded from http://pubs.acs.org on February 18, 2015

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The Journal of Physical Chemistry

Diarylethene Molecules on a Ag(111) Surface: Stability and Electron-Induced Switching J. Wirth,† N. Hatter,‡ R. Drost,‡ T. R. Umbach,‡ S. Barja,‡ M. Zastrow,§ K. Rück-Braun,§ J. I. Pascual,k P. Saalfrank,∗,† and K. J. Franke∗,‡ Universität Potsdam, Institut für Chemie, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany, Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany, Universidad Autonoma de Madrid, Departamento Fisica de la Materia Condensada, Cantoblanco 28049, Madrid, Spain, Technische Universität Berlin, Institut für Chemie, Straße des 17. Juni 135, 10623 Berlin, Germany, and CIC nanoGUNE, 20018 Donostia-San Sebastian, Spain, and Ikerbasque Basque Foundation for Science, 48013 Bilbao, Spain E-mail: [email protected]; [email protected]

Abstract

electric-field dependent switching process is interpreted on the basis of a simple electrostatic model, which suggests that the reaction proceeds via an “upright” intermediate state. This pathway thus strongly differs from the switching reaction in solution.

Diarylethene derivatives are photochromic molecular switches, undergoing a ring-opening/-closing reaction by illumination with light. The symmetry of the closed form is determined by the Woodward-Hoffmann rules according to which the reaction proceeds by conrotatory rotation in that case. Here, we show by a combined approach of scanning tunneling microscopy (STM) and density functional theory (DFT) calculations that the open isomer of 4,4’-(4,4’-(Perfluorocyclopent-1-ene-1,2-diyl)bis(5-methylthiophene4,2-diyl)dipyridine) (PDTE) retains its open form upon adsorption on a Ag(111) surface. It can be switched into a closed form, which we identify as the disrotatory cyclization product, by controlled manipulation with the STM tip. Evidence of an

Keywords molecular switch, isomerization, scanning tunneling microscopy (STM), density functional theory (DFT), first principles kinetics

Introduction An important challenge for the development of functional nanomaterials and nanoscale devices is the switching of organic molecules on metallic substrates. Ideally, the physical properties of hybrid materials, such as electrical conductance or optical absorption bands, could be controlled by the isomeric state of the molecular coating. 1 Whereas many classes of molecular switches have been designed and successfully employed as functional entities in solution or in molecular crystals, 2,3 their functionality on metal surfaces is yet very limited. 4,5 The change in electronic properties upon adsorption is typically accompanied by a modification of potential energy landscapes

∗ To

whom correspondence should be addressed Potsdam, Institut für Chemie, KarlLiebknecht-Straße 24-25, 14476 Potsdam, Germany ‡ Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany ¶ Universidad Autonoma de Madrid, Departamento Fisica de la Materia Condensada, Cantoblanco 28049, Madrid, Spain § Technische Universität Berlin, Institut für Chemie, Straße des 17. Juni 135, 10623 Berlin, Germany k CIC nanoGUNE, 20018 Donostia-San Sebastian, Spain, and Ikerbasque Basque Foundation for Science, 48013 Bilbao, Spain † Universität

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Table 1: Adsorption energies Eads and Gibbs free energies Gads (T = 5 K) of potential PDTE species on the Ag(111) surface; as a reference, values without dispersion interaction are given in parentheses. See “Methods” section for computational details.

PDTE isomers adsorbed on the Ag(111) surface. From these simulations we determine the relative thermodynamic and kinetic stabilities of the isomers, as well as their electronic structure, that can be used to interpret the measured differential conductance spectra. Four PDTE isomers (see Figure 4) were studied here as potential adsorbate species (for convenience a shorthand notation is given in parentheses): a) The open form, outstretched on the surface (o-flat), b) the open isomer in an upright position (o-upright), allowing for a parallel conformation of the methyl groups at the central hexatriene unit, c) the closed form resulting from conrotatory cyclization with the methyl groups being arranged in trans configuration (c-trans), and d) the respective disrotatory cyclization product with the methyl groups in cis configuration (c-cis). The surface supercell used in this study contains one molecule. It is chosen such that the adsorbate spacing and orientation resembles the structure within the molecular rows as in Figure 2. Geometry optimizations were started from molecular orientations allowing for bond formation between the N atoms of the pyridine units and surface Ag atoms; for comparison, also the gas phase structures of all four isomers were optimized. Table 1 compiles the obtained adsorption energies and Gibbs free energies (at 5 K), both with and without considering dispersion interaction. Being in line with prior studies concerning the adsorption of organic molecules (featuring a conjugated π -electron system) on transition metal surfaces, 31,32 we find fairly small adsorption energies for all isomers if dispersion interaction is neglected. This small non-dispersion contribution to the adsorption energy originates from the bonding interaction between the N atoms of the pyridine units and Ag substrate atoms, ranging from about 0.5 eV for the o-upright isomer, exhibiting a beneficial steep orientation of the pyridine rings relative to the surface, to effectively 0 for the c-trans isomer, where steric hindering due to one methyl group pointing towards the surface seems to counterbalance the N-Ag bonding energy. Considering zero-point energies and vibrational finite-temperature contributions does not change this picture significantly. The largest contribution to the adsorption energy

open flat open upright closed trans closed cis

Eads /eV

Gads /eV

(−0.11) −2.32 (−0.53) −1.39 (+0.01) −1.99 (−0.32) −2.97

−2.31 −1.55 −2.01 −3.02

originates from dispersion interaction and amounts up to 2.65 eV for the c-cis isomer. The total adsorption energy is only 0.3 eV higher in this case, and the free energy adds an additional 0.05 eV. The dispersion contribution directly correlates with the adsorbate’s capability to nestle up against the surface (especially because the sulfur atoms exhibit a very large dispersion coefficient). Therefore, its contribution to the adsorption energy is smallest for the o-upright and largest for the c-cis isomer which, in addition, is able to form weak covalent bonds between the thienyl sulfur atoms and the silver substrate (bond lengths: 2.6 and 2.7 Å, respectively). In conclusion, the c-cis isomer shows the strongest adsorption on Ag(111), followed by the o-flat isomer. More relevant to the question which isomer actually forms the monolayer adsorbate islands observed in experiment is the relative thermodynamic stability of the different PDTE species. This quantity is given in Table 2 for gas phase and adsorbed state, plus the intermediate case of an adsorbate layer without the substrate (see Methods section for details). The comparison of results for the different states allows to disentangle effects of dispersion, as well as interadsorbate and substrate-adsorbate interaction on the energetic order of the PDTE isomers. We note that going from real gas phase to a free layer case, i. e. including lateral interaction between the molecules, the energetic order does not change significantly: The o-flat isomer is most stable, closely followed by the o-upright configuration, while c-trans and ccis are less stable by approximately 0.6 and 1.2 eV, respectively (∆E values). Including zero-point en-


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(a) open flat (o-flat)

(b) open upright (o-upright)

(c) closed trans (c-trans)

(d) closed cis (c-cis)

Figure 4: Optimized adsorption structures of the four PDTE isomers on Ag(111) considered in this study (including dispersion interaction). The different colors denote: carbon (black), hydrogen (white), fluorine (green), sulfur (yellow), nitrogen (blue), and silver (grey). ergies and vibrational finite-temperature contributions does not modify the resulting energy balance between isomers considerably (∆G values). Bringing adsorbate layer and Ag(111) substrate together seems to enhance the stability of the o-upright isomer over the flat configurations (see discussion above). However, the flat lying molecules gain significant stability by dispersion interaction, rendering the upright configuration the least stable. Dispersion interaction also leads to a substantial reordering of the stability of the flat forms: the o-flat isomer is now the most stable but c-cis comes second by approximately 0.6 eV, followed by c-trans (≈ 0.8 eV). The larger stability of the closed cis form with respect to the trans isomer can be ascribed to the closer proximity of the molecule’s backbone, and especially of its thienyl S atoms, to the surface in the former case, leading to stronger dispersion forces. For the present experiment we can conclude that, judging purely from thermodynamics, the observed PDTE isomer before manipulation by STM is most probably the o-flat form, with c-cis being a candidate for the product state of the switching process.

To corroborate this implication by spectroscopic means, we also calculated the site-projected density of states (PDOS) for the four isomers adsorbed on the surface. The resulting graphs are shown in Figure 5 and can be compared with the measured differential conductance spectra of Figure 3 (c, d). First of all, we note that, in contrast to the closed forms, both open isomers possess an electronic energy gap of nearly 3 eV, with the LUMO being located close to the Fermi level (EF ). Taking into account the well-known DFT-typical underestimation of electronic band gaps, 33 the large gap coincides with the spectrum of Figure 3 (c), obtained for the adsorbate monolayer before manipulation by STM. Considering the above analysis of isomer stabilities that virtually rules out the o-upright form in thermodynamic equilibrium, we therefore conclude that the initial PDTE isomer observed in experiment is the o-flat form. The closed forms, on the other hand, only show very small or even vanishing energy gaps; the ctrans isomer exhibits a strong weight of PDOS at the Fermi level, while the c-cis isomer only features very small PDOS around EF in combination with a distinct HOMO peak at -0.8 eV. This


5


Table 2: Relative stabilities of potential PDTE species in the gas phase and on the Ag(111) surface, taking the o-flat isomer as a reference point (for comparison, values without dispersion interaction are given in parentheses); finite-temperature contributions to the Gibbs free energies were calculated for T = 5 K, all energies are given in eV. closed trans ∆E ∆G

closed cis ∆E ∆G

gas phase

0.03

0.02

0.57

0.69

1.17

1.31

gas phase layer

0.23

0.15

0.50

0.59

1.24

1.34

(−0.27) 0.93

0.97

(0.71) 0.84

0.83

(1.06) 0.59

0.57

surface layer

difference is a result of enhanced charge transfer from the substrate to the adsorbed c-cis molecule, since a parallel calculation for this species without the substrate reveals a similar electronic structure as for the adsorbed c-trans isomer with the two peaks corresponding to HOMO and LUMO of the molecule. The PDOS pattern of the adsorbed c-cis isomer reflects the characteristic features of the measured dI/dV spectrum (Figure 3 (d)). It exhibits a smaller energy gap than the open forms and a resonance at -1 eV. Deviations are most probably also due to the model necessarily describing a uniform monolayer of the c-cis isomer instead of a single switched PDTE unit embedded in a monolayer of o-flat molecules as this is the case in experiment. Based on this and also considering its high thermodynamic stability, we identify the observed PDTE species after manipulation by STM as the closed cis isomer, formally arising from a disrotatory ring closure. To be conclusive on this point, we investigate the switching mechanism and its implications for the stability of the product state.

(a) 10

(b) switching voltage (V)

open upright ∆E ∆G

dI/dV (a.u.)

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5

0

0

1 2 3 Sample Bias (V)

4

2

approach 0

5 ¨Z (Å)

10

Figure 6: (a) Constant-current differential conductance spectrum at positive bias. The differential conductance in the forward scan (black curve, increasing bias) is substantially different from the backward scan (red curve, decreasing bias). This change results from the switching of the molecular state of PDTE at roughly 2.9 V marked with a blue circle. There the differential conductance increases abruptly (I = 200 pA). (b) Distance dependence of the switching bias as extracted from constant height spectra at positive bias (reference point ∆Z = 0 Å at I = 50 pA, V = 300 mV, speed of voltage ramps dV /dt = 20 mV/s). nances of the open and closed PDTE isomer, respectively. STM images recorded after such manipulation reveal a brighter molecular appearance. Sometimes, we also observe switched molecules in the vicinity of a few nanometers from the tip. Ramping the bias voltage again with the tip located on top of these switched isomers has never restored the initial state. The backreaction thus does not seem possible by manipulation with the STM tip. Voltage sweeps at negative bias do not yield a systematic change of the initial molecule either. Ramping the bias voltage while keeping the tipmolecule distance constant allows to obtain a set

The switching process Experimental Findings Some insight into the switching mechanism can be gained from a detailed analysis of the voltage at which the switching process occurs. A typical fingerprint of a switching event is a sudden jump in the conductance while ramping the bias voltage (Figure 6 (a)). As a result, forward and backward scans of the bias voltage reveal the distinct reso-


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12 10 8 6 4 2 0

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PDOS (norm.)

PDOS (norm.)

(a) open flat 12 10 8 6 4 2 0

12 10 8 6 4 2 0

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(d) closed cis PDOS (norm.)

síPDOS píPDOS sum

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síPDOS píPDOS sum

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(c) closed trans PDOS (norm.)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


2.0

12 10 8 6 4 2 0

síPDOS píPDOS sum

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Figure 5: Site-projected density of states (PDOS) of the four PDTE isomers on the Ag(111) surface considered in this study. s-PDOS/p-PDOS denotes the “s-/p-like” contribution (by projection onto the corresponding spherical harmonics) to the total PDOS (sum) of the adsorbate molecule. of switching voltages at a specific tip height. A statistical analysis of the switching voltages as a function of tip relative distance is shown in Figure 6 (b). 1 With larger tip-molecule distance this switching voltage increases linearly. This linear increase suggests an influence of the electric field in the tunneling junction, 34 which scales as E = Vd with distance d in the simplified model of a parallel plate capacitor. However, a purely electric field-induced switching mechanism can be excluded, because we could not observe switching at voltages below ∼ 1.4 eV (marking the tail of the o-PDTE LUMO resonance) even at very close tipmolecule distances.

sentially providing information about thermally driven processes and the kinetic stability of the different isomers, as well as ground-state dominated dynamics following transient population of excited states. In this context, we note that a switching process solely as a consequence of electronphonon coupling in the adsorbate molecule, can be practically ruled out by a rough estimate: At a tunneling current of 200 pA electron injection should, on average, take place every 0.8 ns so that, compared to a realistic, electronic-friction governed vibrational lifetime on a metallic substrate of only a few ps, 35 vibrational relaxation between two tunneling events would be ensured in any case. Lifetimes of electronically excited states are similarly short-lived such that the switching process is likely to effectively happen on the ground state potential energy surface after gaining momentum in an ionic resonance state (cf. Menzel-Gomer-Redhead 36,37 or Antoniewicz model 38 of desorption upon electronic excitation). Three distinct reactions starting from the thermodynamically most stable o-flat isomer were investigated by means of the nudged elastic band

Theoretical Findings To better understand the switching process of PDTE on Ag(111), we first studied the ground state potential energy surface of the system, es1 We

have investigated the switching behavior in single rows, double rows, both within and at the edge of the island. The behavior of the switching voltage is similar for all molecules, i.e. within the error bars of Figure 6 (b).


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Table 3: Activation energies ∆E ‡ , Gibbs free energies ∆G‡ (at 300 K) and rate constants k (at 300 K) for possible thermal forward/back reactions from/to the open flat form (values without dispersion are given in parentheses). process

direction

∆E ‡ /eV

∆G‡ /eV

k/s−1

erection/reclining

forward back

(0.28) 1.21 (0.56) 0.28

1.27 0.37

3.5 × 10−9 3.5 × 106

conrotatory reaction

forward back

(2.09) 1.48 (1.38) 0.64

1.52 0.65

2.1 × 10−13 6.2 × 101

disrotatory reaction

forward back

(1.34) 2.44 (0.28) 1.85

2.57 1.89

3.5 × 10−31 1.1 × 10−19

(a) erection/reclining

(b) conrotatory reaction

(c) disrotatory reaction

Figure 7: Transition state geometries for possible thermal reactions involving the o-flat isomer. All calculations were performed including dispersion interaction. (NEB) method: a) Erection of the PDTE molecule into o-upright conformation, b) conrotatory cyclization leading to the c-trans, and c) disrotatory cyclization leading to the c-cis isomer. The resulting transition state (TS) geometries determined by a climbing-image NEB procedure (see Methods section for details) are shown in Figure 7. The typical conformation of the central switching unit, allowing for bonding interaction between the carbon pz orbitals at opposite sites of the hexatriene unit, is clearly visible in case of the electrocyclic reactions. Here, again, the different interaction strength between adsorbate and surface becomes obvious: While in case of the conrotatory TS structure the methyl group pointing towards the surface constitutes a strong steric hinderance, in the disrotatory TS geometry, the S atoms and pyridine unit can nestle up against the surface and are subject to strong dispersion forces. This stabilizing effect on the transition state, however, is generously overcompensated by the even stronger interaction of the final cis prod-

uct with the Ag substrate as can be seen from the activation (Gibbs free) energy for the thermal back reaction given in Table 3 which is by far the highest of the three studied processes. The large barrier presumably results from the need to buckle the molecule’s central backbone (including the “dispersion-intensive” sulfur atoms) away from the surface in order to implement the TS conformation. While under the experimental lowtemperature conditions any thermal back reaction is quantitatively suppressed, the corresponding rate constant for disrotatory ring-opening at 300 K amounts to a mere 1.1 × 10−19 s−1 according to Eyring transition state theory, rendering the process highly improbable and hardly observable within reasonable timescales even at room temperature. This is in line with the irreversibility of STM-induced switching and our conclusion that the observed product state on Ag(111) is indeed the PDTE cis isomer. We note that the energetic order of dis- and conrotatory transition state is inverted on the surface


8

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as compared to the gas phase (not shown) which constitutes a violation of the Woodward-Hoffmann rules predicting the thermally driven process to almost exclusively follow the disrotatory pathway. Although this steric and electronic influence of the surface is not particularly surprising, it definitely suggests a revisit of the model for substrateadsorbate situations which is, however, not in the scope of the present article. In order to understand the experimentally observed field-dependence of the switching process, in a next step we modeled the influence of the electric field in the vicinity of the STM tip on the ground state potential energy surface. For this purpose a simple and very approximate point charge approach was chosen (see “Methods” section for details), considering only the electrostatic interaction of the vertical electric field Ez of a hypothetical parallel-plate capacitor between tip and sample with the permanent dipole moment between a charged adsorbate molecule (charge Q, distance dz ) and its image charge in the metal substrate, leading to an energy correction of Vel = −2dz QEz

.

this seems to contradict the experiment, in which a positve electric field favors the STM-induced switching. Erection of the open PDTE isomer into the oupright position, however, is clearly favoured by the electric field at positive sample bias due to its positive (or at least less negative) charge and large vertical distances dz , leading to a large dipole moment. This behaviour would be consistent with the observed increase of the energy required for switching with growing tip-sample distance, i. e. with decreasing field strength. Hence, it suggests that the erected TS plays a role during STMinduced ring closure. This in fact allows to draw a modified picture for the switching process: Since a major prerequisite for disrotatory cyclization is the rotation of the methyl groups at both ends of the hexatriene unit into an anti-parallel conformation, the erection of the PDTE molecule into oupright position featuring this rotation can in fact be imagined as the first step of an effective threestep process. In this case, the calculated disrotatory TS might not be relevant anymore in favour of a respective TS in the upright conformation, followed by the rapprochement of the now-cyclic PDTE molecule. To be conclusive on this point, however, further inspection of the PES, e. g. by means of additional NEB calculations for the transformation between o-upright and c-cis state (including a possible “ccis-upright” intermediate), is needed. Also an explicit description of electric-field effects such as charge transfer and polarization seems crucial for a comprehensive picture.

(1)

This correction was done for all stationary points describing the three processes discussed above. The calculated molecular charges can be slightly positive or negative, respectively (Table 4), again reflecting both components of substrate-adsorbate interaction: On the one hand, this is the weak covalent bond between surface and pyridyl nitrogen atoms which constitutes the dominant interaction in case of the o-upright configuration and its corresponding transition state; it has an electrondonating character and leads to a small positive charge on the adsorbate. On the other hand, the molecule tends to accept more charge from the substrate the closer its molecular backbone lies to the surface. This is consistent with the above discussion of the c-cis isomer’s PDOS. The relative shift of the ground state potential energy surface (PES) with respect to the o-flat isomer resulting from Equation (6) with an estimate of Ez = ±0.2 V/Å is shown in Figure 8. Both cyclization reactions only show insignificant TS shifts and a destabilization of the respective product state at positive bias Ez = +0.2 V. At first sight,

Conclusions We studied the adsorption and switching behaviour of PDTE molecules on a Ag(111) surface by means of scanning tunneling microscopy and spectroscopy as well as density functional theory calculations. It was found that PDTE molecules remain in their open state upon adsorption on the Ag surface and self-assemble in highly ordered islands. Controlled manipulation with the STM tip can be utilized to induce a disrotatory ringclosing reaction into the cis product (with both methyl groups on the same side of the molecu-


9


Table 4: Total molecular charges Q and vertical positions dz of the respective center of charge entering Equation (1); absolute level shifts Vel and level shifts with respect to the shifted energy of the o-flat isomer ∆Vel = Vel −Vel,o−flat (see also Figure 8) under the influence of a homogenous electric field with E = +0.2 V/Å. erection TS

Q/e −0.16 dz /Å 3.59 Vel /eV +0.24 ∆Vel /eV 0.00

o-upright conrotatory TS

+0.03 6.11 −0.08 −0.31

+0.11 7.29 −0.31 −0.55

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2.0

1.5 1.0

1.5 1.0

0.5

0.5

0.0

0.0

0.0

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Page 10 of 19

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TS

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Figure 8: Energy diagrams for three possible switching processes of PDTE on the Ag(111) surface. Level shifts (relative to the o-flat isomer) due to interaction with the electric field in the vicinity of the STM tip are indicated for a homogeneous field of Ez = ±0.2 V/Å. The stabilization of transition and product state at positive sample bias found for reaction (a) is consistent with the experimentally observed fielddependence of the switching process.

Acknowledgements

lar backbone). Inspection of the ground state energy surface by means of DFT, reveals that this state is metastable and, due to a prohibitive reaction barrier, cannot be the product of a thermal process. This situation clearly disagrees with the symmetry selection rules according to Woodward and Hoffmann, emphasizing the importance of substrate-adsorbate interaction. The switching process was found to be induced by a combination of electron attachment and its coupling to an external electric field, whereas the switching most probably takes place on the ground state PES in a non-thermal reaction. Based on a simple electrostatic model we propose a stepwise mechanism of field-assisted lifting of the open PDTE isomer, followed by the disrotatory cyclization. Our findings highlight the importance of surface interactions on both the adsorption and dynamics of molecules in contact with a (metallic) substrate.

We gratefully acknowledge fruitful discussions with B.W. Heinrich, and funding by the Deutsche Forschungsgemeinschaft through Sonderforschungsbereich 658 and grant FR2726/4. S. B. acknowledges funding for her research stay at FU Berlin by FPU Grant AP-2007-001157.

Methods Experiment The PDTE compound was synthesized according to the literature and its stability upon vaporization has been checked by mass spectrometry. 39,40 The molecules were evaporated from a Knudsen cell at 375 K onto an atomically clean Ag(111) surface held at room temperature in ultra-high vacuum. The sample was then cooled down and transferred into a custom-made scanning tunneling mi-


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the D2 level of correction sufficient. The lattice constant of the cubic close-packed ¯ Ag bulk structure (space group Fm3m) was optimized (neglecting dispersion interaction) as a = b = c = 4.157 Å, exceeding experimental values 52 by GGA-typical 1.8%. The corresponding (111) surface was then modelled by a (6 × 5) supercell, providing enough space for one PDTE molecule and at the same time mimicking the adsorbate periodicity observed in STM experiments. Approximately 30 Å of vacuum were introduced to separate repeating slabs, each consisting of three atomic layers, of which the lowermost was fixed at its bulk position during geometry optimization and vibrational analysis. Pairwise dispersion interactions were limited to distances smaller than 20 Å to avoid interference between adjacent slabs; additionally, for the D2 set of calculations only the uppermost atomic layer was included in the list of pair interactions to account for the method-specific overbinding on metallic substrates as proposed in ref. 31. For comparison, also the gas phase structures of all four isomers were optimized using the same computational protocol as for the adsorbed species to ensure error cancellation for energy differences. In consideration of the limited supercell size, however, this situation rather resembles a gas phase “layer” of adsorbate molecules than a real gas phase situation. Therefore, additional gas phase DFT calculations were performed on the PW91/cc-pVQZ level of theory 53–55 (ensuring convergence with respect to the size of the basis set), using the Gaussian 09 program package. 56 This procedure also allows to disentangle possible effects on the isomers’ energetic order due to adsorbate-adsorbate and adsorbate-substrate interaction.

croscope at a temperature of 4.8 K. All STM images were recorded in constant-current mode. Differential conductance spectra were acquired with fixed tip-sample distance or activated feedbackloop as indicated in the respective figures, and using a lock-in amplifier with a modulation voltage of Vrms = 10 − 15 mV at 833 Hz.

Theory First-principles calculations Periodic first-principles total energy calculations were performed within the framework of KohnSham density functional theory 41 applying the projector augmented wave method 42,43 as implemented in the Vienna ab initio simulation package (VASP). 44–46 Electron exchange and correlation were treated according to the generalized gradient approximation (GGA) using the PW91 functional. 47 Total energies and vibrational frequencies were found to be sufficiently accurate using a planewave basis set truncated at a kinetic energy cutoff of 400 eV and a Γ-point centered (3 × 3 × 1) Monkhorst-Pack grid 48 (resulting in a set of 5 irreducible k-points) for sampling the Brillouin zone of the hexagonal supercell. Self-consistent field convergence was considered sufficient for a total energy difference of less than 10−4 eV between iterations; ionic relaxation was stopped when the forces acting on ions dropped below 0.01 eV/Å. Since dispersion interaction is known to play an important role for the adsorption of organic molecules on metal substrates, especially if featuring a conjugated π -electron system, 31,32 its impact on adsorption energies and geometries was studied in some detail here. Therefore, two sets of calculations were performed in this study, one without considering dispersion interaction, opposed to another one applying Grimme’s semiempirical D2 correction scheme. 49 In order to rule out a strong methodic bias, also Grimme’s more recent D3 method 50 with the damping function for short interatomic distances according to Becke and Johnson (see ref. 51 and references therein) was applied for selected test cases. The largest effect found, however, was a mere 0.1 eV difference in the relative stability of the c-cis isomer, rendering

Thermodynamic quantities Free energies G(T ) = E + Gvib (T ) = E + H(T ) − T S(T ), with E denoting the self-consistent field energy for a given species, were calculated including finite temperature vibrational contributions to enthalpy H(T ) and entropy S(T ),


11


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

"

Gvib (T ) = ∑i hνi 

  −kB T   

1 2

hν  hνi i kB T e kB T −1

+

1 hνi e kB T

−1

projected density of states (PDOS) was calculated for the different isomers. This was done using the built-in VASP routine, based on the projection N |φ i of the orbitals φ hYlm nk nk onto spherical harN monics Ylm centered at the ionic positions (index N).

!

 !  hν  − k Ti  B  −ln 1−e   

,

(2)

Transition state calculations Minimum-energy paths (MEP) and transition state (TS) geometries were found using the nudged elastic band method (NEB) 58,59 as implemented in the modified VASP version of Jónsson and coworkers. The latter includes an improved tangent estimate 60 and a climbing image (CI) scheme for finding the transition state on the MEP. 61 The CINEB procedure was carried out as follows: After construction of an initial guess MEP consisting of two intermediate images by linear interpolation between educt and product structure, a first NEB calculation was performed. Following up convergence of the initial band, two subsequent linearinterpolation and NEB steps were performed to end up with 13 images along the band (including starting and terminating image). Since the transition states in question (for the cyclization reactions) turned out to emerge rather “late” during the reactions, i. e. very close to the end of the MEP, after convergence of the thirteen-image band a fiveimage detail, presumably embracing the TS, was constructed out of this band by linear interpolation and brought to convergence as well. If necessery, this procedure was repeated until the central image was found to resemble a plausible TS structure for an electrocyclic reaction. Finally, this central image (highest in energy) was driven up to the saddle point using the implemented CI scheme. The respective bands were considered converged when forces acting on the individual images dropped below 0.01 eV/Å. Corresponding rate constants for relevant processes were calculated using the transition state theory (TST) expression 62

with temperature T , Planck constant h, Boltzmann constant kB , and the vibrational frequencies νi of the system. The latter were obtained by normal mode analysis at stationary points for all atoms allowed to move during geometry optimizations. To reduce the computational effort, frequencies were obtained at the Γ-point only. This approximation is justified by the large unit cell on the one hand, on the other hand enthalpy contributions due to phonon dispersion will cancel out by a large extent, since we are mainly interested in free energy differences. All stationary points were characterized by means of normal mode analysis, yielding, however, up to four imaginary frequencies (not considered in Equation (2)) on the order of a few tens of cm−1 at most. In fact, this is a well-known and purely numerical problem arising with shallow potential energy landscapes as they are very common for substrate-adsorbate interactions, especially if dominated by dispersion (cf. ref. 57 and references therein). Small errors, potentially resulting for the vibrational contributions to Gibbs free energies (especially in the entropy term), are likely to cancel out by a large extent as long as energy differences are concerned. The adsorption free energy for any adsorbate species A was evaluated as the free energy difference ∆Gads = G⋆A − (G⋆ + GA ) ,

Page 12 of 19

(3)

with ⋆ denoting the bare surface and ⋆A indicating adsorption of species A on the surface. To ensure error cancellation, equal computational settings were applied to all species involved.

kB T − ∆Gk ‡ T(T ) k(T ) = e B h

Projected density of states

,

(4)

with the activation Gibbs free energy ∆G‡ , i. e. the barrier height for the reaction.

To help identify the adsorbed PDTE species by means of differential conductance spectra, the site-


12

Page 13 of 19

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Electric field effect

Metal Surfaces. J. Phys. Cond. Matt. 2012, 24, 394001.

Finally, in order to investigate the role of the electric field in the vicinity of the STM tip for the switching process, a simple model following ref. 63,64 was set up by introducing a shift, V = V0 +Vel

(6) Choi, B.Y., Kahng, S.J.; Kim, S.; Kim, H.; Kim, H.W.; Song, Y.J.; Ihm, J.; Kuk, Y. Conformational Molecular Switch of the Azobenzene Molecule: A Scanning Tunneling Microscopy Study. Phys. Rev. Lett. 2006, 96, 156106.

(5)

,

of the ground state potential energy surface V0 due to the electrostatic interaction of the electric field Ez (approximated as being homogenous) between STM tip and sample with a vertical dipole µz between the charged adsorbate molecule and its image charge in the metallic substrate. Neglecting higher electric moments, this interaction energy is given by Vel = −µz Ez = −2dz QEz

,

(7) Comstock, M. J.; Levy, N.; Kirakosian, A.; Cho, J.; Lauterwasser, F.; Harvey, J. H.; Strubbe, D. A.; Frechet, J. M.; Trauner, D.; Louie, S. G.; Crommie, M. F. Reversible Photomechanical Switching of Individual Engineered Molecules at a Metallic Surface. Phys. Rev. Lett. 2007, 99, 038301.

(6)

(8) Comstock, M. J.; Levy, N.; Cho, J.; Berbil-Bautista, L.; Crommie, M. F.; Poulsen, D. A.; Frechet, J. M. J. Measuring Reversible Photomechanical Switching Rates for a Molecule at a Surface. Appl. Phys. Lett. 2008, 92, 123107.

with total charge Q of the adsorbate molecule, evaluated by summation over atomic charges qi at positions zi obtained from Bader analysis; 65–67 dz denotes the vertical distance of the center of charge 1 modulus zcoc = |Q| ∑i |qi | zi from the surface mirror plane, the latter being defined as the average zcoordinate of Ag atoms in the uppermost substrate layer. In order to arrive at numerical values, Ez was assumed to equal ±0.2 V/Å, e. g. corresponding to a tip-sample distance of 10 Å and a potential bias of ±2 V.

(9) Pechenezhskiy, I. V.; Cho, J.; Nguyen, G. D.; Berbil-Bautista, L.; Giles, B. L.; Frechet, J. M. J.; Crommie, M. F. Self-Assembly and Photomechanical Switching of an Azobenzene Derivative on GaAs(110): Scanning Tunneling Microscopy Study. J. Phys. Chem. C 2012, 116, 1052-1055.

References (1) Feringa, B. L. The Art of Building Small: From Molecular Switches to Molecular Motors. J. Org. Chem. 2007, 72, 66356652.

(10) Schulze, G; Koch, M.; Franke, K.; Pascual, J.I. Induction of a Photostationary Ring-Opening-Ring-Closing State of Spiropyran Monolayers on the Semimetallic Bi(110) Surface. Phys. Rev. Lett. 2012, 109, 026102.

(2) Irie, M. Diarylethenes for Memories and Switches. Chem. Rev. 2000, 100, 16851716.

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(3) Feringa, B. Molecular Switches; WileyVCH: Weinheim, 2001. (4) van der Molen, S. J.; Liljeroth, P. Charge Transport Through Molecular Switches. J. Phys. Cond. Matt. 2010, 22, 133001. (5) Tegeder, P., Optically and Thermally Induced Molecular Switching Processes at


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(12) Mielke, J.; Leyssner, F.; Koch, M.; Meyer, S.; Luo, Y.; Selvanathan, S.; Haag, R.; Tegeder, P.; Grill, L. Imine Derivatives on Au(111): Evidence for "Inverted" Thermal Isomerization. ACS Nano 2011, 5, 20902097.

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(25) Arramel; Pijper, T.C.; Kudernac, T.; Katsonis, N.; van der Maas, M.; Feringa, B.L.; van Wees, B.J. Reversible Light Induced Conductance Switching of Asymmetric Diarylethenes on Gold: Surface and Electronic Studies. Nanoscale 2013,, 5, 9277.

(17) Piantek, M.; Miguel, J.; Krüger, A.; Navío, C.; Bernien, M.; Ball, D. K.; Hermann, K.; Kuch, W. Temperature, Surface, and Coverage-Induced Conformational Changes of Azobenzene Derivatives on Cu(001). J. Phys. Chem. C 2009, 113, 20307-20315.

(26) Dulic,D.; van der Molen, S.J.; Kudernac, T.; Jonkman,H.T.; de Jong, J.J.D.; Bowden, T.N.; van Esch, J.; Feringa, B.L.; van Wees, B. One-Way Optoelectronic Switching of Photochromic Molecules on Gold. Phys. Rev. Lett. 2003, 91, 207402.

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Molecules from Metal Surfaces. International Journal of Quantum Chemistry 2000, 80, 210-219. (64) Füchsel, G.; Klamroth, T.; Doki´c, J.; Saalfrank, P. On the Electronic Structure of Neutral and Ionic Azobenzenes and Their Possible Role as Surface Mounted Molecular Switches. J. Phys. Chem. B 2006, 110, 16337-16345. (65) Tang, W.; Sanville, E.; Henkelman, G. A Grid-Based Bader Analysis Algorithm without Lattice Bias. J. Phys.: Condens. Matter 2009, 21, 084204. (66) Sanville, E.; Kenny, S. D.; Smith, R.; Henkelman G. Improved Grid-Based Algorithm for Bader Charge Allocation. J. Comp. Chem. 2007, 28, 899-908. (67) Henkelman, G.; Arnaldsson, A.; Jónsson, H. A Fast and Robust Algorithm for Bader Decomposition of Charge Density. Comput. Mater. Sci. 2006, 36, 354-360.


17



Page 18 of 19

F

F

F F Page 19 The of Journal 19 of Physical Chemistry F F

current (nA)

10

1 2 3 4 5 6 7

N

S

S

N

STM tip

5 F

F

F

F F

F


0 0

1 sample bias (V)

2

S N

S N

Diarylethene Molecules on a Ag(111) Surface: Stability and Electron

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