Chemical Physics Letters 517 (2011) 204–210

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Chemical Physics Letters

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Behavior of a chemisorbed azobenzene derivative in an STM environment:A DFT study of charged states and electric fields

Chris Chapman, Irina Paci ⇑Department of Chemistry, University of Victoria, P.O. Box 3065, Victoria, BC, Canada V8W 3V6

a r t i c l e i n f o

Article history:Received 8 July 2011In final form 21 October 2011Available online 28 October 2011

0009-2614/$ - see front matter � 2011 Elsevier B.V. Adoi:10.1016/j.cplett.2011.10.047

⇑ Corresponding author. Fax: +1 250 721 7147.E-mail address: ipaci@uvic.ca (I. Paci).

a b s t r a c t

The cis–trans isomerization of azobenzene has many uses in materials technologies. Among forecastedapplications are molecular switches for nanoscale devices. Chemisorbed and physisorbed azobenzenescan switch between their two isomers, with different charge-conduction properties. Here, we examinethe switching behavior of N-(2-mercaptoethyl)-4-phenylazobenzamide, chemisorbed on Au (111) inan upright conformation. We considered the effects of electric fields and charging processes on the isom-erization process. Cationic and anionic isomerization mechanisms presented lower barriers than neutralground state isomerization. This effect was moderated on metallic substrates, due to charge delocaliza-tion into the surface. The relationships between observed barriers and frontier orbitals are also discussed.

� 2011 Elsevier B.V. All rights reserved.

1. Introduction

Molecular switches are bistable molecules that can reversiblyconvert from one state to another as a result of changes in theirexternal environment. Such environmental stimuli include light,temperature and electric fields, to name a few. In biological sys-tems, molecular switches play a role in genetic regulation [1] andsignal transduction pathways [2,3]. Molecular switches are alsobeing investigated as potential components in nanotechnology de-vices: electrical switches in nanoelectronics [4–6], optical storagedevices [7,8], and molecular motors [9,10]. Many such applications,however, require that these physical changes occur while the mol-ecules are adsorbed onto a solid surface. Depending on the re-quired stability of the adsorbate–substrate complex, chemisorbedor physisorbed species may be used. The presence of the surface it-self complicates our understanding of the switching process, asequilibrium geometries, energetics and transition barriers arestrongly changed in the overall surface potential field.

The photoinduced cis–trans isomerization of azobenzene andits derivatives has long been used in a number of applications: asan alignment modulator in liquid crystals [11], in molecular sen-sors [12–14], in nonlinear optics [15,16] and as a photobiologicalswitch [17–19]. The process occurs in the excited state, throughone of three mechanisms: inversion of one of the CNN bond angles,rotation around the CNNC dihedral or concerted inversion of bothCNN bond angles [20–22]. Upon isomerization of the more thermo-dynamically-stable trans isomer to the cis isomer, there is a largechange in geometry. The trans isomer has its two phenyl rings inthe same plane, whereas the cis isomer has its rings twisted out

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of plane, due to the steric hindrance between hydrogen atoms onneighboring phenyl rings. Consequently, there is a break in theconjugation along the N@N bond. Cis azobenzene occupies a largervolume than the trans isomer and has a non-zero dipole moment.

In surface-bound states, large conformational changes uponisomerization can lead to very different properties. For instance,azobenzene derivatives chemisorbed in high coverage monolayerson gold surfaces have been shown to exhibit two distinct conduc-tance states when exposed to light. The high-conducting and low-conducting states were presumed to be determined by the transand cis isomer, respectively [4,23]. In contrast, scanning tunnelingmicroscopy (STM) studies of several physisorbed azobenzenederivatives, in conjunction with quantum chemistry calculations,suggest that the cis isomer corresponds to the high-conductingstate, where one phenyl ring is pointed away from the surface,and the trans form lies parallel to the surface [24,25]. In many ofthese experimental studies isomerization was photoinduced. How-ever, several studies showed that isomerization in adsorbed statesmay occur without UV light, in the ground electronic state, wherethe high barrier to isomerization is changed under the influence ofan STM electric field or tunneling electrons [26–29].

Several theoretical studies examined the ground state isomeri-zation of azobenzene and its derivatives [30–34]. In particular,Füchsel et al. [35] and Henningsen et al. [36] discussed the isomer-ization of surface-bound azobenzene species in ground and excitedstates. The authors used density functional theory to examine neu-tral and charged isomerization pathways, and examined the effectof a surface represented by a work function. In the gas phase,energy barriers for the isomerization of neutral azobenzenes werebetween 1.6 and 2 eV, depending on the substituents attached tothe phenyl rings. Barriers for both non-concerted inversion androtation pathways were lowered when cationic species were

C. Chapman, I. Paci / Chemical Physics Letters 517 (2011) 204–210 205

zconsidered. For anionic azobenzene derivatives, only the rota-tional barrier decreased significantly. It was also found that anelectric field alone could not induce the cis–trans isomerization[35], though the rotation of one of the phenyl rings around theCAN bond may be achieved in charged azobenzene derivatives un-der strong STM fields [36].

Chemisorbed N-(2-mercaptoethyl)-4-phenylazobenzamide(named hereafter AB) has been shown experimentally to undergofield induced switching when coadsorbed in a dodecanethiolmonolayer on gold [29]. Changes in brightness, induced by changesin the applied STM field, were observed when individual AB mole-cules were adsorbed at pit sites of the dodecanethiol monolayer.The conductance changes were attributed to either isomerizationof trans-AB to cis-AB at negative sample bias [29], or to rotationaround the sp3-hybridized linking group [37].

We have previously modeled the adsorbed states of cis- andtrans-AB in the zero-density (single molecule) regime [38]. Bothisomers were found to lie parallel to the surface in their most sta-ble conformations. Changes to upright configurations had a 3 eVenthalpic penalty for trans-AB, and either 1 or 1.5 eV for cis-AB,depending on whether one or both benzene rings were desorbed.The enthalpic cost of trans–cis isomerization itself was 1.7 eV.Thus, either isomerization or the desorption of the ‘parallel’ azo-benzene moiety were found to be unlikely mechanisms for thepit-site switching, leading to the assumption that upright struc-tures could be involved in the switching process, stabilized bythe partial monolayer at the edge of the pit site.

In this study we examine the isomerization of AB chemisorbed ona gold surface, in its upright configuration. The upright structure,rather than the parallel structure, is present within single- andmulti-component monolayers, as well as in monolayer boundarysites. Furthermore, upright structures can interact with an STM tipmore effectively due to a larger molecular height. Field-inducedswitching is discussed, as is the isomerization of gas phase andadsorbed AB, in both neutral and ionic states. Rotation about theCNNC dihedral and non-concerted inversion of the CNN bond angleare examined as possible switching mechanisms. Because ofchemical attachment to the surface, the two ends of the azobenzenemoiety are unequal, and the concerted pathway is unlikely.

2. Methods and models

2.1. Computational details

For all calculations, we employed the spin-polarized PBE/DZPformalism in the SIESTA [39,40] (Spanish Initiative for ElectronicSimulations with Thousands of Atoms) 2.02 code. Core electronsfor all atoms were treated using norm-conserving nonlocal Troul-lier–Martins [41] pseudopotentials. SIESTA uses periodic boundaryconditions (PBC). In order to simulate a single-molecule environ-ment and minimize lateral interactions between cells, a cubic peri-odic box with 50 Å edges was used. Wavefunction plots wereobtained using the DENCHAR utility program.

The gold surface was represented by a two-layer, 61 atomAu (111) slab. This surface was large enough to support theprojection of an upright AB conformation. A two-layer surfacewas chosen, as the surface atom binding energy remains approxi-mately constant for surfaces comprised of more than one layer[38,42]. Using more than two layers would be computationallyexpensive without a marked improvement in accuracy [38]. Toeliminate spurious forces acting on surface atoms, the surfacewas optimized in bulk conditions, at the PBE/DZP level of theory,with PBC, without an adsorbed AB molecule. For all AB calculationsafterwards, the Au (111) surface was frozen. Surface reconstruc-tion likely has an important effect on electronic structure, and thus

energy balance in experiments. However, its incorporation, and,more importantly, the incorporation of its associated timescale, isbeyond the scope and computational capability of this study.

The effects of charging on the isomerization pathway are dis-cussed below. Both cationic and anionic pathways were consid-ered. While the cationic pathway can be well treated with thePBE/DZP methodology implemented in SIESTA, anionic species of-ten require diffuse basis set functions to treat the more weaklybound charge. Calculations involving diffuse basis sets were com-putationally prohibitive for systems of the size considered here,especially for late transition metal elements such as gold. However,for completeness, we included anionic calculations in the discus-sion. The gas phase results discussed in Section 3 reproduced wellliterature data which considered large, diffuse basis sets. Becausethe anionic charge inhabited the extended AB conjugated system,it was delocalized, closer to the relevant nuclei and could be welltreated without diffuse functions. When a surface was included,the MO’s involved in charging also included the surface atoms,which further delocalized the charge.

Calculations of isomerization pathways were performed usingrelaxed scans: in the inversion channel, the AB geometry was opti-mized while holding the CNN bond angle frozen. The rotationchannel calculations were optimized with the CNNC dihedral fro-zen in place. Initial configurations for the two pathways werebased on the trans isomer for CNN bond angles of 120–175� andCNNC dihedrals of 105–180�. For the remainder of the inversionand rotation optimizations, the cis isomer was used as the initialgeometry. Equilibration of points at and near the transition statethat had difficulties in reaching their optimized geometries and en-ergy minima were equilibrated again, with initial structures basedon their neighboring points along the reaction path. Transitionstates obtained with these relaxed scans were confirmed at thesame level of theory, using the QST3 transition state search meth-ods implemented in GAUSSIAN09 [43].

2.2. Calculation of dipole moments

The electric field of an STM can provide the necessary energy toinduce molecular switching, even when the tip is far enough fromthe molecule that tunneling is unlikely [28]. The field may stabilizeone isomer of the molecular switch through coupling with the di-pole moment. The energetic contribution of this coupling variesproportionally to the field strength and the dipole moment. If theSTM field is considered to be a uniform field applied along the sur-face normal, which can be chosen as the lab-frame z direction, thenonly the z component of the permanent dipole moment, and the zzcomponent of the polarizability are involved in this coupling.

The induced dipole moment of the entire unit cell is reported inSIESTA. However, most of the charge organization in an appliedfield appears within the metal surface, which is not well repre-sented for such a purpose by a 61-atom slab. To estimate the dipolemoment of the adsorbed molecular entity solely, on-surface geo-metrical optimizations, with or without an applied field, were fol-lowed by off-surface single-point calculations of the moleculardipole with the same applied field strength.

We present in Table 1 the z components of the permanent di-pole moments, the chemisorbed AB molecule and the (hydrogencapped) gas-phase thiol, along with the difference in dipole mo-ments between the cis and trans isomers. The energetic contribu-tion of the coupling between permanent dipole moments and thefield, DEfield ¼ Vðlz;cis � lz;transÞ is, as seen in the table, independentof capping. In the formula, V is the applied field. Capping is essen-tial in molecular polarizability calculations, however, as even asmall surface can contribute many highly polarizable electrons tothe response properties of the entire system.

Table 1Permanent dipole moments for upright chemisorbed trans and cis AB ðlz;S�AuÞ and inthe gas phase, with a thiol group ðlz;S�HÞ.

Isomer lz;S�Au (D) lz;S�H (D)

Trans 0.60 1.66

Cis �1.44 �0.35

lz;cis � lz;trans �2.04 �2.01

Figure 1. System schematic and field effects. A sketch of the trans-to-cis isomeri-zation of AB chemisorbed on a Au (111) is drawn in panel a. The effects of anelectric field normal to the surface on the relative energy of chemisorbed AB and themolecular height of AB are given in b and c, respectively. Black circles and redsquares represent trans and cis AB, respectively. In b, the insert presents thedifference between the two curves: DE ¼ Ecis � Etrans ðeVÞ, as a function of appliedfield. (For interpretation of the references to colour in this figure legend, the readeris referred to the web version of this article.)

206 C. Chapman, I. Paci / Chemical Physics Letters 517 (2011) 204–210

2.3. Modeling chemisorbed ionic states

To investigate changes in the switching mechanism occurringunder tunneling conditions, we examined cationic and anionic spe-

cies of adsorbed and gas phase AB isomers and pathways. Eitherspecies may arise as the electron transits through the molecule,or as it is pulled into the surface or the tip from the molecule itself.Barriers on the charged isomerization pathways may present loweractivation energies, thus facilitating the switching process.

Examination of the relevant electronic states of ionic AB mole-cules chemisorbed on a gold surface provides a computationalchallenge. The molecular highest occupied molecular orbital(HOMO) and the lowest unoccupied molecular orbital (LUMO)are involved in the charging (or conduction, if two electrodes wereconsidered) process. Experimentally, these orbitals mediate tun-neling between the tip and the surface. Depending on whetherthe HOMO or the LUMO are involved in conduction, cationic or an-ionic states may appear transiently, respectively. This is a dynamicprocess, while the optimization of the entire system’s electronicstructure leads to an equilibrium charge distribution. In electronicstructure calculations of surface-supported molecules, the metallicsubstrate contributes many electrons and states to the system. Inour case, the HOMO and LUMO for the entire system were locatedwithin the conduction band of the gold surface, with no compo-nent located on the AB moiety. Also, when removing an electronor adding one to the system, the charge localized in the surface,not the molecule.

To correct for this effect, an electric field of +1 V/nm along thesurface normal was necessary in cationic studies, to produce aHOMO partly localized on the adsorbed AB molecule, without sig-nificantly altering the molecular conformation. Similarly, to exam-ine the behavior of adsorbed AB in the anionic state we applied an�1 V/nm electric field along the surface normal. In the STM setupitself, a field is applied, producing a difference in the electrochem-ical potential of the two electrodes that leads to charge movementwhen molecular orbitals are available in the gap. For comparisons,a + 1 V/nm electric field was also added for neutral, adsorbed AB.To distinguish these molecular orbitals from the field-free frontierorbitals, fully localized on the surface, we denote them in thefollowing pages as pseudo-HOMO (p-HOMO) and pseudo-LUMO(p-LUMO).

3. Results and discussion

In our previous work [38], stable single-molecule conformationsof Au (111)-supported isomers of N-(2-mercaptoethyl)-4-phenylazobenzamide were parallel to the surface. These conforma-tions were strongly stabilized by the dispersive interactionsbetween the conjugated azobenzene moiety and the ‘free’ electronsin the metal surface. Switching processes, either through isomeri-zation or through parallel-upright conformational changes werethus unlikely. However, upright molecular conformations(Figure 1a) can be stabilized by lateral interactions at higherdensities, and can form when embedded within a monolayer orat monolayer boundary sites (e.g., as seen in STM pictures inRef. [29]). Because upright structures are higher, they can interactwith an electric field (applied in the direction of the surfacenormal) more effectively than parallel geometries.

3.1. The adsorbed molecule in the external STM field

In an STM field, the energy of the chemisorbed moleculechanges both due to the total dipole–field coupling, and due tosubtle changes in molecular conformation. To account for theseconformational changes, we allowed adsorbed AB to equilibratewhile applying static electric fields of varying strengths andpolarities. The dependence of the relative energy of trans and cisAB on the applied field is shown in Figure 1b. The reported energiesinclude contributions from field–surface coupling, through a

Table 2Energy barriers for the inversion and rotation channels of the gas phase and adsorbedAB structures (in eV).

Channel DEzneutral DEzcation DEzanion

Gas phaseInversion 1.51 0.67 1.37Rotation 1.56 0.62 0.72

Adsorbeda

Inversion 1.45 1.18 1.41Rotation 1.37 1.03 0.96

a Barriers calculated in the presence of an applied field of +1 V/nm for the neutraland cationic mechanisms, and �1 V/nm for the anionic mechanism.

Table 3Geometrical features and isomerization energy cost for neutral and charged trans-and cis-AB.

Isomera State rNN \CNN \CNNC DE

Gas phaseTrans Neutral 1.28 113.5 177.0

Cation 1.24 123.4 167.6Anion 1.33 112.2 176.6

Cis Neutral 1.26 122.6 12.6 0.51Cation 1.23 130.2 30.5 0.38Anion 1.32 121.8 39.7 0.58

Adsorbed phase (upright)b

Trans Neutral 1.28 113.8 178.0Cation 1.27 116.5 177.1Anion 1.29 112.7 177.5

Cis Neutral 1.26 122.7 14.3 0.62Cation 1.24 124.8 15.3 0.59Anion 1.27 122.4 16.3 0.60

a N@N bond lengths (Å), CNN bond angles (�), CNNC dihedrals (�), and trans ? cisisomerization energies DE ¼ Ecis � Etrans ðeVÞ are shown.

b Geometries determined in the presence of and applied field of +1 V/nm for theneutral and cationic mechanisms, and �1 V/nm for the anionic mechanism.

Figure 2. PBE/DZP frontier orbital diagrams for gas phase trans (panels (a) and (c))and cis (panels (b) and (d)) AB. C, H, N, O and S atoms are gray, white, blue, red andyellow, respectively. (For interpretation of the references to colour in this figurelegend, the reader is referred to the web version of this article.)

Figure 3. PBE/DZP frontier orbital diagrams of the transition state structures for gasphase AB. Panels (a) and (c) show the inversion transition state and panels (b) and(d) show the rotation transition state. C, H, N, O and S atoms are gray, white, blue,red and yellow, respectively. (For interpretation of the references to colour in thisfigure legend, the reader is referred to the web version of this article.)

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significant reorganization of the surface’s electron density in theapplied field. The polarizability of the surface contributed to a large

degree to the field-induced energy changes in the two isomers. Italso led to lower energies in negative fields than in positive fields,for both isomers, when the reverse was expected, because theinteractions between the permanent molecular dipoles and theexternal field are favorable at positive fields. Single point energycalculations performed without the surface, and with cappedmolecule, restored the expected dependence on field polarity.Regardless, the contribution of the field–surface coupling largelycancels out when assessing the energy difference between ABisomers (see, e.g., inset in Figure 1b), and the full-surface calcula-tions are reported in the figure.

Regardless of the strength of the applied field, the trans isomerwas more stable than the cis isomer. A relative stabilization of thecis isomer occurred at low negative fields. At these fields, the totaldipole–field coupling contribution was destabilizing for trans-AB.However, dipole–field coupling became favorable in the trans iso-mer again at stronger negative fields, because of the higher polar-izability of trans-AB. This effect was discussed in further detail inthe context of classical calculations in our previous work [44].

The conformations of AB isomers also changed, particularly instrong applied fields. As shown in Figure 1c, both cis- and trans-AB adopted more upright structures in these fields, with tilt anglechanges of 5–7�. Although these tilt angle changes were mediatedthrough rotations within the linking groups, changes in the eleva-tion of the O atom were minimal. This confirmed that the gain inmolecular height occurs through rotational adjustments, ratherthan through stretching of the ethylamide linker.

3.2. Gas phase evaluation of trans–cis isomerization and energyconsiderations

To understand the impact of the surface on the isomerizationprocess, and to establish the relative position of the PBE/DZP calcu-lations in the broader literature context, we examined neutral andcharged isomerization pathways for the free (gas phase) ABmolecule. The effect of charging on the energies involved in the

208 C. Chapman, I. Paci / Chemical Physics Letters 517 (2011) 204–210

isomerization process is discussed below, in addition to geometricand electronic effects in neutral and charged pathways.

3.2.1. Isomerization pathwaysBarrier energies calculated for non-concerted inversion and

rotation pathways in neutral, anionic and cationic mechanisms,are presented in Table 2. As shown in the table, the inversionand rotation pathways presented comparable activation energiesfor the neutral state, which suggests that isomerization could pro-ceed through either mechanism in the ground state, provided thatsufficient energy is supplied. The two cationic mechanisms werealso mostly isoenergetic, though presenting significantly loweractivation energies than the neutral pathways. When the electrontransfer process was such that AB was transiently anionic, the rota-tion path was more favorable than the inversion path. These resultsare in good agreement with other azobenzene derivatives studiedby Füchsel et al. [35], in which anionic systems were treated withdiffuse basis sets.

3.2.2. Geometries and frontier orbitalsRelevant geometric parameters and energies for gas phase and

adsorbed AB are presented in Table 3. When the molecule waseither positively or negatively charged, its geometry changed mostsignificantly around the azo group, because the frontier orbitals in-volved in the charging process had high density in this molecularregion.

The most notable geometrical changes upon charging of thetrans isomer were seen in the N@N bond length, which decreased(strengthened) slightly in the cation and increased (was weakened)in the anion, from the neutral state value. These changes were re-

Figure 4. PBE/DZP frontier orbital diagrams for adsorbed trans (panels (a) and (c)) and cpresence of a +1 V/nm and �1 V/nm electric field, respectively, normal to the surfaceinterpretation of the references to colour in this figure legend, the reader is referred to

lated to the relevant molecular orbitals in each case. The electronwas removed from the HOMO of the neutral molecule in the cat-ionic case, and added to the LUMO in the anion. The trans-ABHOMO (Figure 2a), from which an electron is removed in the cat-ionic form, was overall non-bonding, although there was a smallamount of antibonding character in the N@N region: this orbitalwas stabilized by removing an electron. The trans-AB LUMO (Fig-ure 2c), which hosted the additional electron in the anion, was lar-gely antibonding, particularly in the azo region. Adding an electronto the LUMO weakened, thus lengthened, the N@N bond. As in pre-vious works [45], the cationic trans-AB presented an out-of planetwist of the two phenyl rings.

The cis isomer underwent similar changes upon charging. Itshould be noted that the large change of the CNNC dihedral angleupon charging of the cis isomer was accompanied by complemen-tary changes in the adjacent NNCC dihedrals, such that the relativeorientation of the two phenyl rings in cis-AB was relativelyunchanged.

3.2.3. Transition statesTo understand the differences between the inversion and rota-

tional pathways to isomerization, we examined transition state(TS) geometries and frontier orbitals (see Figure 3). Regardless ofthe charging state, the azo group was more strongly bound tothe inner (para-substituted) phenyl ring in the rotation channeland to the outer (free) phenyl ring in the inversion channel. N@Nbonds were significantly shorter in cationic mechanisms (1.21 Å)than in anionic mechanisms (1.28 Å for the inversion and 1.33 Åfor the rotation channel).

is (panels (b) and (d)) AB. The p-HOMO and p-LUMO plots were determined in the. C, H, N, O and S atoms are gray, white, blue, red and yellow, respectively. (Forthe web version of this article.)

Figure 5. Energy profile of trans–cis isomerization of the (a) inversion and (b)rotation pathway for adsorbed AB. Black circles, red squares and blue trianglesrepresent neutral, anionic and cationic species, respectively. All energies are relativeto the energy of the optimized trans geometry for that species. The anionic andcationic plots are translated up and down, respectively, such that the trans isomerhad zero energy. Energies were calculated in the presence of an electric field normalto the surface, with a value of +1 V/nm for neutral and cationic AB, and �1 V/nm foranionic AB. (For interpretation of the references to colour in this figure legend, thereader is referred to the web version of this article.)

C. Chapman, I. Paci / Chemical Physics Letters 517 (2011) 204–210 209

Both the inversion and rotation TS HOMO’s resembled more clo-sely the cis-AB than trans-AB HOMO, and had some CAN bondingand N@N antibonding character (see Figure 3a and b). For the cat-ionic mechanism, removing an electron from the TS HOMO prefer-entially stabilized the transition state of each isomerizationchannel, thereby lowering the activation energy. The similarity ofthe HOMO’s in the azo region for the two pathways led to similarcationic activation energies, as well.

TS LUMO’s were however different in the inversion and rotationpathways. The inversion TS LUMO was antibonding, and localizedon the azo bond. The rotation TS LUMO was more evenly distrib-uted along the azo bond and the outer ring, also manifesting anantibonding character. The outer electron in the anionic rotationTS was more delocalized than in anionic inversion. This led to lessrepulsion in the azo region, thus a lower TS energy and a lower bar-rier along this pathway.

3.3. Isomerization of chemisorbed trans-AB

3.3.1. Geometries and frontier orbitalsConformational changes were less extensive upon charging of

upright chemisorbed AB than in gas phase AB (see Table 3). Bondlengths, angles and dihedrals in the azo region of neutral chemi-sorbed AB were similar to gas phase values, and changed littleupon charging. The isomerization energies were also relatively un-changed upon charging. This relative independence on the charg-ing state was due to the fact that significant portions of thefrontier orbitals p-HOMO and p-LUMO, and thus the relevant outercharge population, resided within the gold surface in these chem-isorbed ABs, as shown in Figure 4.

The shapes of the AB-based fraction of p-HOMO and p-LUMOwere similar to those of gas phase frontier orbitals, discussed inthe preceding section and presented in Figure 2. TS pseudo-frontierorbitals also followed closely those of the gas phase TS’s. The dis-cussion related to gas-phase MOs in the previous section is thusrelevant in upright chemisorbed AB, as well.

3.3.2. Isomerization pathwaysThe impact of charging on the activation energy of chemisorbed

AB isomerization was attenuated (see Table 2), but followed simi-lar trends as those presented for gas-phase processes. Energy pro-files of the inversion and rotation pathways in neutral and chargedadsorbed AB are shown in Figure 5. Both neutral isomerizationchannels presented comparable activation energies, just slightlylower in value than the corresponding gas phase barriers.

The TS stabilization upon charging was not as marked for ad-sorbed AB as for gas phase systems. Barriers for inversion and rota-tion of cationic AB decreased by 0.27 eV and 0.42 eV, respectively.Anionic charges did not affect the inversion pathway, but stabilizedthe rotation one. As was the case for the stable adsorbed cis andtrans isomers, p-HOMO and p-LUMO had significant populationsresident on the gold surface, leading to a moderation of energy sta-bilization upon charging, as discussed above for the stable isomers.

Molecular switching of chemisorbed AB was thus facilitated bythe addition of either a positive or a negative charge. The energiesrequired were still far greater than those available in experimentalsettings such as those of Ref. [29], where energies of up to 0.2 eVcan be provided from thermal energy at room temperature and di-pole–field coupling in fields up to 2 V/nm. Dispersive interactionswith the STM tip, not considered here, may also provide additionalenergy in the experiment, by stabilizing cis isomers and transitionstates. Another important aspect is that the resonance lifetimes ofa charged state for an adsorbed molecule are generally short-lived(on the order of fs up to ps) [46,47], meaning that the timescale ofthe isomerization pathway may be too long to allow the entiremechanism to proceed through an ionic state. The distance of the

azo group of upright AB from the surface, however, is expectedto modify charged state lifetimes over those of the adsorbed ben-zene and C60 molecules examined in those studies. Moreover,sequential single charge processes are normally a rough approxi-mation for nanoscale conduction, so that experimental time scalesand charging states are different from the single charge situationsconsidered here.

4. Conclusions

We examined here possible mechanisms for the trans–cis isom-erization of upright chemisorbed AB exposed to the field of an STMexperiment. Field-induced and electron-transfer induced mecha-nisms were investigated. Both reaction enthalpies and activationbarriers were lowered upon charging. The TS HOMO and LUMOhad antibonding character in the azo region, and were thus stabi-lized by a reduction in their occupation numbers. Cationic chargingstabilized equally both the rotation and the isomerization path-ways. Anionic charging favored the rotation pathways, which pre-sented a TS with a more delocalized LUMO. The effects of chargingwere more marked in gas phase than in chemisorbed calculations.

The behavior of chemisorbed ABs in their upright configurationsfollowed to a great extent that of the gas-phase system. Someparticular care was necessary as charging, a transient phenomenon

210 C. Chapman, I. Paci / Chemical Physics Letters 517 (2011) 204–210

in the STM process, was not well treated by the customary elec-tronic structure equilibration performed in SCF calculations thatincluded the surface. Sample bias fields were used to stabilizethe charge onto the molecule, however, the surface still contrib-uted greatly to the resulting frontier orbitals. Charging-inducedconformational and energetic changes were thus moderated bythe surface participation in adsorbed AB. Overall, upright chemi-sorbed AB can undergo isomerization when uncharged if providedroughly 1.4 eV activation energy, and when charged, with roughly1 eV. Because the transition state search was performed oversimple reaction coordinates, and also due to the many approxima-tions inherent to the setup of the computational model, these areupper bounds to the experimental energy barriers.

Acknowledgments

Funding was provided by the National Science and EngineeringResearch Council of Canada, the Canada Foundation for Innovation,the British Columbia Knowledge Development Fund and the Uni-versity of Victoria.

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