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Conductance of Junctions with Acetyl-functionalized Thiols: A first-principles based analysis Atsushi Yamada, Qingguo Feng, Qi Zhou, Austin Hoskins, Kim M. Lewis, and Barry D. Dunietz J. Phys. Chem. C, Just Accepted Manuscript • Publication Date (Web): 26 Apr 2017 Downloaded from http://pubs.acs.org on May 1, 2017

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The Journal of Physical Chemistry

Conductance of Junctions with Acetyl-functionalized Thiols: A first-principles based analysis Atsushi Yamada,† Qingguo Feng,† Qi Zhou,‡ Austin Hoskins,† Kim M. Lewis,∗,‡ and Barry D. Dunietz∗,† Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA, and Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, NY 12180, USA Received April 25, 2017; E-mail: [email protected]; [email protected]

Abstract: Thiol-based contacts are widely used in fabrication of molecular junctions, but are associated with several drawbacks due to their chemical reactivity. In particular, their tendency to dimerize by forming sulfur-sulfur bonds is viewed as a barrier for large scale bridge fabrication. Instead, the use of functionalized sulfur end groups in the fabrication of the junctions is promoted. We analyze the effects of thiol functionalization by acetyl on the transport properties of porphyrin based bridges. In scanning tunneling microscopy (STM) experiments, where the conductance is measured as the tip is retracted, we observe molecular conductance steps due to junctions with acetyl protected thiols that are significantly lower than observed for junctions with deprotected thiols (by a factor of ≈ 5). Using a first-principles based computational approach, we explain the lower conductance of junctions with acetyl functionalized thiol and associate it to chemical changes of the sulfur, where essentially a tunneling barrier in the transport pathway is enforced. The acetyl protected thiol lowers the transmission mainly through its direct effect on the electronic structure. We show that the geometrical relaxation upon acetylation where the Au-S bond is elongated plays a smaller role in determining the conductance trends. Interestingly, we find that in a hypothetical deprotected case with an imposed longer Au-S bond distance to that of the protected thiol bond length the transmission is slightly increased.

Introduction Molecular junctions, where molecules bridge two electrodes, are at the focus of intense research. An important feature of the junctions stems from the potential to tune their properties at the molecular level and employ them in electrical or energy conversion applications. 1–12 Computational modeling complements the conductance measurements of such junctions by providing insight into the electron transport mechanism at the molecular level and therefore contributes to material design and device fabrication efforts. 13–21 In molecular electronics thiol end groups are frequently used to contact the bridges to the electrodes. 22,23 However, while the fabrication of these junctions is relatively easy, the thiol based contacting scheme is also associated with several limitations. For example, the tendency of the thiol to dimer† Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA ‡ Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, NY 12180, USA

ize 24,25 by forming direct sulfur-sulfur bonds has been associated with the observed deterioration of the junctions. 26,27 A recent review describes in detail a variety of ways that sulfur groups can bond to gold surfaces. 28 Thiol functionalization by acetyl group is considered as a means to control the chemistry of the molecules attached to the surface and the conductance. In this paper we analyze computationally the effect of the acetylation on the conductance. We show that the acetyl protection adversely affects the molecular junction conductance. We relate the substantial change in the measured conductance upon deprotection to the direct effect of acetylated thiols on the electronic structure of the junction, 29 while its effect on the geometry, as to increase the Au-S bond length, affects only to a lesser extent the transmission trends. Importantly the conductance of deprotected forms are substantially higher than those of the protected forms. The Au-S bonding is weakened in the case of the protected systems. Below, thiolated molecules with sulfurs functionalized by acetyl groups are addressed as protected and where the sulfurs remain reactive even after forming strong ligand bonds with the electrode are addressed as deprotected. While, here we follow up on our recent reports on the conductance in thiolated tetraphenyl-meso-porphyrin molecules, 29,30 we show below that the effect of acetylation of the thiol contacts (protection) on the junction transmission is not limited to porphyrin junctions. Porphyrins are widely used as building blocks in molecular electronics 31–35 as they achieve high conductance 32 and can be chemically tuned to adversely affect the conductance. 14,36–40 In a previous study acetyl functionalized thiols were used to bridge porphyrins between gold electrodes. 33 To assert the role of acetyl protection of the thiol contacts we calculate the transmission using a series of models that incorporate the same thiolated phenyl based contacts in either acetyl protected or deprotected forms (see Figure 1). Importantly, in all the cases the protected form is associated with a transmission function that is lower by over one order of magnitude than that of the deprotected based junction. The same conductance ratio as for the free base porphyrin (FBP) due to deprotection is found for the case where Zn is ligated by the porphyrin ring (ZnP) as well as in the case where the porphyrin is completely removed and a bi-phenyl junction (BPh) is considered. (As defined above, we refer to the protected and deprotected forms of the ZnP system, for example, as P-ZnP and U-ZnP.) The three pairs of protected and deprotected molecules: (a) U-FBP and PFBP, (b) U-ZnP and P-ZnP, and (c) U-BPh and P-BPh are shown in Figure 2. We show computationally that the acetyl functionalization of the thiols main effect is to directly alter

ACS Paragon Plus Environment 1

The Journal of Physical Chemistry 10-0 U-FBP P-FBP

Transmission (E)

(a) -2

10

U-FBP

(a) U-FBP Au

2.66

Au

2.30

P-FBP S S

U-ZnP P-ZnP

(b) Transmission (E)

P-FBP

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(b) U-ZnP

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P-ZnP 2.66

2.30 P-ZnP

10-6 10-0

1

(c) Transmission (E)

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U-BPh P-BPh

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-8

-6

-4

(c) U-BPh

U-BPh

P-BPh 2.30

-4

10

P-BPh

2.65 S

electrode

10-6 -6.5

-6

-5.5

-5 Energy (eV)

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Figure 1. (Color online) Transmission plots of (a) the U-FBP and P-FBP, (b) the U-ZnP and P-ZnP, and (c) the U-BPh, PBPh. The transmission has the same trend among the three systems, which is enhanced for the junctions basd on the unprotected form in comparison to those with the protected form.

Figure 2. (Color online) Three molecular systems are investigated: (a) free base porphyrin [U-FBP and P-FBP] (b) zincporphyrin (with Zn [U-ZnP and P-ZnP]), and (c) bi-phenyl models (porphyrin ring removed [U-BPh and P-BPh]). The inset in (c) illustrates the electrode model used in the junction calculations. Au-S bond lengths are also shown.

the effectiveness of the electronic transport path while it also affects substantially the junction geometry.

Models and Methods The molecular models are obtained through geometry optimizations of the molecular junction with a single gold atom contacting each sulfur atom at the B3LYP functional level with a mixed large basis set (6-31+G* for S, O atoms, 631G* for H, C, N atoms, the Los Alamos triple zeta with core potential (LANL2TZ) for Au, 41 the Los Alamos double zeta with core potential (LANL2DZ) for Zn). 42–44 To address steric effects to the acetyl group near the gold surface, the protected molecule optimizations include a second layer of gold atoms (three gold atoms with fixed positions). The Au-S bond length is found to be 2.30˚ A in the unprotected form and to be ∼0.35˚ A longer in the protected case for all the systems (see Figure 2). We confirm that the same trend of the Au-S bond lengths of FBP is obtained with different basis sets (see SI Table S1). At the equilibrium geometry we find that all four phenyl rings are tilted in relation to the porphyrin ring at an angle of about 70◦ . (A list of the atomic coordinates for all the optimized structures is provided in the SI.) A similar level have been used recently in successfully addressing the experimental measurements. 29 The conductance of the molecular junctions is described using the scattering free Landauer picture of electron transport, where the current is obtained by integrating the electron transmission function (T(E)) over energy within the potential bias window around the Fermi energy: I(V ) = R T (E) f v+ (E) − f v− (E) dE. 13,45–47 Here the f v (E) is

Figure 3. (Color online) Representative conductancedisplacement (G-S) curves for the deprotected free base porphyrin samples. These G-S curves are categorized into 3 groups: Low Conductance plateau ( 41%, green), High Conductance plateau ( 28%, red), and both Low and High conductance plateau ( 31%, cyan). 29


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Figure 4. (Color online) Current-bias relationships for the three systems. Measured conductances are noted by circles.

the Fermi distribution function with either a positive or negative shift due to the potential bias. The transmission function is calculated using the density functional theory (DFT)based models and Green’s function (GF) based expressions. The GF treatment is performed at the DFT level with the Baer-Neuhauser-Livshits (BNL) functional. 48,49 We design the computational models to avoid artificially enhanced transmission 21,50 and following recent benchmark study based on the BNL functional. 51 We point out the well established success of our BNL-based protocol in reproducing measured conductances. 51 However, we emphasize that in this work we use a larger basis set than employed in the previous benchmark study, since here we consider relatively weak intermolecular bonding in the protected form. 29 For the electrode part, the LANL2TZ is used for the first two layers and LANL2DZ for all other layers. The range separated hybrid (RSH) parameter is obtained for the various junctions, where only a single gold layer is included. In this way we guarantee proper treatment of the frontier molecular junction orbitals that are key for the low voltage conductance. The junction models used in transport calculations include a total of seven layers of gold atoms at each side of the optimized structure (see inset of Figure 2 (c)). In calculating the transport, the central region in the transmission calculation includes the molecule and four gold layers on each side. The electrode model is of hexagonal close packed (hcp) Au structure representing an idealized tip structure that is shown in the inset of Figure 2 (c). Gold self-energies are calculated using a wide band limit of a tight binding calculation at the gold Fermi energy (-5.1eV). The repeating unit is fixed to that of the fifth layer. We implement the electronic structure calculations and geometry optimizations using Q-Chem 4.4 package. 52 The quantum transport utility within Q-Chem, T-Chem, is used to calculate the transport properties of the molecular junctions. 14,18,19,53–55,55–57

Results and Discussion In a recent report we associated the higher conductance steps in STM based measurement of molecular conductance of thiolated FBP to the fully unprotected form (U-FBP), and the lower conductance junctions to the asymmetric form where the thiol retains the acetyl protection at the moleculetip interface (UP-FBP). 29 In the case of protected-based molecules spontanous cleavage is expected to occur on the self assemblied monolayer side. 58–60 Measured conductance-

displacement curves of the deprotected junctions exhibit typically higher conductances than those in the case of protected junctions. Representative plots are shown in Fig. 3, where three types of junctions are indicated: Protected junctions of low conductance, deprotected junctions with high conductance and deprotected junctions where both conductance steps are apparent (presumably due to limited yield of the deprotection procedure, where both forms of junctions may be present). We reported in detail the experimental setup to study the conductance of the junctions upon chemically deprotecting the FBP molecules. 29 Our calculated current-voltage plots are provided in Figure 4, where we indicate by full circles measured currents at 0.4V. 29 We base our computational approach on on our recent reported protocol that was shown to achieve excellent agreement with the measured values. 51 We also list the conductance of the protected and deprotected forms of the three junctions in Table 1, where we compare to measured values when available. Our results agree quantitatively with the measured values for the three systems: The calculated conductance of the deprotected form of FBP (U-FBP) 4.2 × 10−4 G0 is in excellent agreement with the measured conductance step 2.0 × 10−4 G0 . For the protected untreated form that is assigned to UPFBP we achieve a similar level of agreement of 5.0 × 10−5 G0 with the measured value of 4.4 × 10−5 G0 . 29 We also achieve agreement for the UP-ZnP junction, where our calculated value of 2.9 × 10−5 G0 agrees with the measured values of 2 − 3 × 10−5 G0 . Finally our calculated values compare well with the measured conductance of the unprotected BPh junction where the measured 61,62 and our calculated conductances are at 1 × 10−3 G0 . Importantly, the calculated ratio between the deprotected and protected symmetric forms for the three systems varies only slightly: It remains about 80 for the porphyrinic systems (FBP and ZnP) and drops slightly to about 60 for the BPh system. We proceed by analyzing the effect of thiol protection on the transport channels of the three pairs of junctions. In all three cases the main transporting channel is based on the central region highest occupied molecular orbitals (HOMOs) that are either delocalized across the whole molecular bridge region as in the deprotected cases of higher conductance, or localized towards one of the Au-S bonding regions as in the protected cases of lower conductance. These transporting orbitals involve a Au-S bonding character in the unprotected forms, and a Au-S anti-bonding character in the unprotected forms as illustrated in Figure 5. Indeed, natural bond orbital (NBO) 63 analysis reveals reduced Au-S bonding in the case of P-FBP compared to that of U-FBP: In calculations involving a single Au on each side we find that the Au-S bond is associated with a pair of electrons in the case of the acetyl-free molecules, but with a single electron in the case that acetyl is also attached to the sulfur atom. The decisive role of the Au-S coupling on the transmission is next unmasked by following the transmission of the P-FBP and Ul-FBP where the Hamiltonian Au-S coupling elements are copied across the two systems, resulting with P-FBP’ and Ul-FBP’, respectively. (Ul-FBP has the Au-S bond distance set to that of P-FBP; for comparison sake, and Ul-FBP’ Au-S elements are set to those of the P-FBP junction). We find that the P-FBP transmission rises significantly in P-FBP’ and that of Ul-FBP drops significantly in Ul-FBP’, see these trends in Figure 6. This confirms our hypothesis on the pivotal effect of Au-S coupling in affecting


The Journal of Physical Chemistry Protected (P-)

Unprotected (U-) (a) FBP HOMO (α-5.605 eV)

(β-5.605 eV)

HOMO (α-5.769 eV)

(β-5.769 eV)

Au Au

S Au S

S

(b) ZnP HOMO (α-5.714 eV)

HOMO (α-5.850eV)

(β-5.714 eV)

(β-5.850 eV)

Au Au

S

S

(β-5.877 eV)

HOMO-1 (α-5.877eV)

HOMO-2 (α-5.905 eV)

(β-5.905 eV)

(c) BPh HOMO-7 (α-6.884 eV)

(β-6.884 eV)

S

HOMO-10 (α-7.646 eV)

Au

(β-7.646 eV)

Au S

S

S Au

Au

HOMO-11 (α-7.673 eV)

S

(β-7.673 eV) S

Au

FBP (see Figure 5[a] and Figure 7). Therefore, we find that the acetyl effect on the transporting orbitals is due to two mechanisms that significantly lower the transmission: The first effect is reflected by the transporting HOMOs. The HOMOs in the case of the P-FBP present spin symmetry breaking, where the α orbital is localized onto one Au-S region and the β orbital is localized towards the second AuS bond. (The spin orbitals remain at the same energy level ). The second effect is due to acetylation inducing (semi) degeneracy of Au-S localized orbitals at the level of the key transporting orbitals. Such degeneracy of occupied orbitals carries reduced transmission, and only if avoided, as in the case of the U-FBP, achieved is significant transmission. (See detailed analysis of orbital degeneracies and transmission trends in ref. 50). In short, the acetylation appears to break orbital spin symmetry resulting with localized orbitals which present (semi) degeneracy. (We find that the spin orbital energies remain the same while with different spatial symmetry.) Both electronic structure effects of orbital localization and degeneracy explain the significantly lower transmission seen upon acetylation!

Au

P-FBP-Au2

U-FBP-Au2

Figure 5. (Color online) The key orbitals involved in transmission channels, which are delocalized on the junctions, for (a) UFBP and P-FBP, (b) U-ZnP and P-ZnP, and (c) U-BPh and PBPh. The insets shows the orbitals with smaller isosurface value. Bonding and anti-bonding transporting orbitals are indicated for the unprotected and protected forms, respectively.

10-0 10

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Au

S

Au

HOMO-1 (alpha) (-5.955eV)

HOMO-1 (beta) (-5.955eV)




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Figure 6. (Color online) Transmission plots of Ul-FBP, Ul-FBP’, P-FBP and P-FBP’, where dash indicate that the switched Fock matrix elements for Au-S relevant part are used (see main text)

reduced transmission upon acetylation. We now consider closely the relationship of the acetylation to the key transporting orbitals and therefore to the ways it reduces the transmission. Overall, the primary effect of the acetylation is to localize the electronic structure, which also affects the spin symmetry. As shown in the central panel of Figure 5 for ZnP, the α spin HOMO orbital is of a large right electrode region and the β spin orbital bears a large left electrode region contribution. A similar trend is apparent for the BPh (see Figure 5[c]). For the FBP we present this trend, for clairty, using a junction with only a single Au atoms on each side (see Figure 7). As reflected in all the cases, the acetylation lowers the transmission also by inducing energy-degeneracy (or close to degeneracy) of the transporting orbitals. Consider the degenerate pairs of HOMO and HOMO-1 in the case of PZnP (see Figure 5[b]), HOMO-10 and HOMO-11 in the PBPh case (see Figure 5[c]), and HOMO-1 and HOMO-2 in P-

Figure 7. (Color online) The key orbitals of U-FBP and P-FBP with single gold atom attached to each thiol, which are corresponding to the two transmission peaks in the fully junction system. The relationship of the orbitals with the transmission is explained in the main text.

Finally, we consider the effect on the conductance of the Au-S bond elongation in the protected thiol contacts. Upon thiol acetylation, the Au-S bond length increases from about 2.30˚ A to about 2.66˚ A. We compare the transmission of the deprotected U-FBP to a modified P-FBP junction, where the acetyls are removed without further optimization. In this way we consider a variant of the U-FBP with stretched Au-S bond lengths (Ul-FBP). The transmission functions are plotted in the SI Figure S1. While the S-Au bond lengths of Ul-FBP and P-FBP are the same, the transmission of the Ul-FBP remains similar to that of the U-FBP. (Reflecting this trend we show the bond strength of these systems in SI Table S2, where the bonding energy of the Ul-FBP is still closer to the optimal energy in the U-FBP in spite of the stretching). In fact, the conductance of the Ul-FBP (2.3×10−3 G0 ) becomes larger (by a factor of over three) than calculated for the U-FBP (4.2 × 10−4 G0 ). This is somewhat surprising, as extending the tunnel distance appears to increase the conductance. More precisely this trend reflects the changes at the electronic structure level upon bond activatation that affect the transmission channels. 64 Indeed, in a series of calculated transmission of geometries obtained by


HOMO (beta) (-5.538eV)

HOMO (alpha) (-5.538eV) Au

S

Au

Ul-FBP Ul-FBP‡ P-FBP P-FBP‡

-2

HOMO (beta) (-5.538eV)

HOMO (alpha) (-5.538eV)


Transmission (E)

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The Journal of Physical Chemistry Table 1. Calculated and measured (where available) conductances (in G0 ) of the U, UP and P forms of the three considered molecular junctions (FBP, ZnP and BPh).

U Calc. Exp.

4.2 × 10−4 2.0 × 10−4

UP FBP 29

5.0 × 10−5 4.4 × 10−5 1.8 × 10−5 ZnP

P 5.2 × 10−6 29 65

Calc. Exp. 65

2.2 × 10−4

2.9 × 10−5 2.7 × 10−5 2.0 × 10−5 BPh

2.8 × 10−6

Calc. Exp. 61,62

1.1 × 10−3 1 × 10−3

1.4 × 10−4

1.8 × 10−5

puter and the Kent state university for access to computing resources. Q. Z. and K. M. L. would like to acknowledge partial support from the National Science Foundation DMR #1150866 and the New York State’s Empire State Development’s Division of Science, Technology, Innovation (NYSTAR) Contract # C100117 and # C130117. Q. Z. and K. M. L. would also like to acknowledge Dr. Peter Dinolfo for advice on the chemistry procedure, and Dr. Guoguang Qian for suggestions related to equipment setup. Supporting Information Available: Transmission of UFBP, Ul-FBP and P-FBP (Fig. S1), conductance vs. S-Au distance for U-FBP (Fig. S2), optimized S-Au bond distance for UFBP and P-FBP with various basis sets (Table S1), S-Au bonding energy for U-FBP, Ul-FBP and P-FBP (Table S2), and coordinates of U-FBP and P-FBP (Table S3). This material is available free of charge via the Internet at http://pubs.acs.org/.

References symmetrically stretching the Au-S bonds, we find that the transmission reaches a maximum when the Au-S bond is stretched to 2.65˚ A (that is the bond length in the protected form). Further stretching leads to the expected trend of decaying conductance due to an increasing tunneling barrier. (See SI Figure S2 for the stretch dependence of the conductance). It therefore appears that upon acetylation the effect of the (small enough) bond stretch to increase the conductance is more than mitigated by the acetyl groups effect to decrease the conductance. Namely, the protected systems are associated with weaker transmission due to the direct impact of the acetyl groups on the electronic structure of the junction.

Conclusions To conclude we investigate the transport properties of porphyrin-based molecular junctions that are contacted to gold electrodes through sulfur end groups. We focus on the effect of chemically protecting the thiol on the electron transport properties of the junctions. The acetyl protected thiol group upon contacting to gold is found to affect the junction electronic structure resulting with reduced transmission in comparison to the deprotected case. We therefore relate the observence of high conductance steps in related measurements only with deprotected junctions. We confirm the role of the thiol end group functionalization in affecting the conductance by following the ratio of conductance in deprotected versus protected in a series of pairs of molecular models involving the same thiol contacts. The series adds to the FBP junctions, a bi-phenyl dithiolated junction, where porphyrin is removed, and a ZnP junction, where Zn ligates the porphyrin ring. Finally, we find that for all considered junctions sufficiently small Au-S bond stretching of the deprotected form results in increased conductance. We therefore isolate the electronic structure effect of the acetyl group on the electron transport channels and find it as responsible to the reduced transmission in the protected forms. Acknowledgement B.D.D acknowledge the financial support by a DOE-BES award through the Chemical Sciences Geosciences and Biosciences Division (Grant Nos. DE-SC0004924 and DE-FG02-10ER16174 and No. DESC0016501), as well as the support from the Ohio supercom-

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