Modification of Molecular Conductance by in Situ ... - ACS Publications

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Modification of Molecular Conductance by in Situ Deprotection of Thiol-Based Porphyrin Qi Zhou,*,†,‡ Atsushi Yamada,†,§ Qingguo Feng,†,§ Austin Hoskins,§ Barry D. Dunietz,*,§ and Kim M. Lewis*,‡ ‡

Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York 12180, United States Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States

§

S Supporting Information *

ABSTRACT: Acetylthio-protected free base porphyrins are used to form scanning tunneling microscope-molecular break junctions. The porphyrin molecules are deprotected in situ, before the self-assembly. Two types of molecular junctions are formed in the junctions: Au-S-Por-SAc-Au and Au-S-Por-S-Au. Lower conductance values and higher conductance values are observed. Computational modeling attributes the lower conductance to the Au-S-Por-SAc-Au junctions and the higher conductance to the Au-S-Por-S-Au junctions. First-principles calculation suggests that the reduced conductance in the protected porphyrin originates from the presence of the acetyl end groups (−COCH3), rather than from the elongation of the sulfur−gold (S−Au) bonds at the tip-molecule interface. KEYWORDS: porphyrin, in situ deprotection, molecular conductance, scanning tunneling microscope, molecular break junctions, Green’s function density functional theory

M

We investigate the conductance of molecular junctions formed using a gold STM tip and a self-assembled monolayer (SAM) of free base porphyrin (FBP) molecules on a gold substrate. We start with the protected free base porphyrin 5, 15di-4 (S-acetylphenyl) 10, 20-diphenyl porphine (henceforth denoted as AcS-Por-SAc) shown in Figure 1a. The in situ deprotection20 of the AcS-Por-SAc is described in Figure 1b. The detail of the deprotection procedure is described in the Supporting Information. The composition of the deprotected solution is confirmed by Matrix-assisted laser desorption/ionization (MALDI) with Bruker Ultraflex IIIMALDI TOF/TOF Mass Spectrometer (Figure 1c). Three porphyrin species are indicated, with protonated (MH+) molecular masses of 763, 721 and 679, corresponding to AcS-Por-SAc, AcS-Por-SH, and HS-Por-SH, respectively. After deprotection, the molecules are self-assembled onto a gold (111)/mica (Au/mica) substrate (see Figure 1d, e and the Supporting Information). As a control experiment, a protected SAM sample is prepared by submerging a gold (111)/mica substrate (Figure S1) into a diluted solution (∼1 mM) of AcS-Por-SAc in dichloromethane/ethanol (2:1) overnight, under a nitrogen purge. The thicknesses d of the SAMs are determined by Angle

etal−molecule−metal (MMM) junctions are fundamental units in molecular electronics, and are promoted as a means for the fabrication of inexpensive, functional, and atomically precise1 electronic components and devices. Conductance measurements of molecular junctions are achieved using a conductive atomic force microscope (CAFM),2,3 mechanical break junctions,4,5 and scanning tunneling microscope (STM) break junctions.6 Thiol-based contacts are widely used in molecular junctions because of the relatively strong thiol-metal bonds on the order of 100 kJ/mol.7 However, unprotected thiols tend to degrade by oxidation forming sulfonate or disulfide that are relatively weakly bound to the surface. In order to overcome these disadvantages, thiols are usually protected by functional groups such as acetyl.8,9 Acetylthio is also known to self-cleave upon contacting to a gold surface,10,11 and to form covalent bonds at the molecule−substrate interface even without deprotection.12,13 In this work, we study the effect of the tip−molecule interface on the conductance by deprotecting the acetylthio end groups. Porphyrins form a highly π-conjugated ring of delocalized electrons associated with ultralow attenuation of electron transport over molecular length (β ≈ 0.04 Å−1, compared to a typical β ≈ 0.1−0.6 Å−1 of alternative π-conjugated organic bridges).14 This makes porphyrins eligible for efficient electron transport through molecular wires. For the past decade, porphyrins have been used in molecular electronic applications as rectifiers,15,16 transistors,17 sensors,18 and memory units.17,19 © XXXX American Chemical Society

Received: November 18, 2016 Accepted: March 23, 2017 Published: March 23, 2017 A

DOI: 10.1021/acsami.6b14841 ACS Appl. Mater. Interfaces XXXX, XXX, XXX−XXX

Letter

ACS Applied Materials & Interfaces

Figure 1. (a) Chemical structure of a protected free base porphyrin (AcS-Por-SAc) molecule. (b) In situ deprotection scheme for the free base porphyrin. By adding sulfuric acid into the AcS-Por-SAc solution, two additional porphyrin species (AcS-Por-SH and HS-Por-SH) are formed by deprotection. (c) Matrix-assisted laser desorption/ionization (MALDI) confirms three types of molecules in the solution: AcS-Por-SAc, AcS-Por-SH, and HS-Por-SH. (d, e) Self-assembly of the porphyrin species from the in situ deprotected solution on a gold surface.

Resolved X-ray photoelectron spectroscopy (ARXPS) to be ∼1.7 nm for the deprotected sample and ∼1.5 nm for the protected sample (Figure S2).

The STM-molecular break junctions and conductance measurements are performed using an Agilent 5500 SPM (Keysight Technologies, formerly Agilent Technologies). B


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Figure 2. (a−c) Representative G−S curves from SAM samples prepared by in situ deprotection. These G−S curves can be grouped into 3 categories: curves with steps only at mid-10−5 G0 range (black), curves with steps only at mid-10−4 G0 range (green), and curves that show steps at both 1 × 10−5 G0 and 1 × 10−4 G0 range (blue). (d, e) Histograms from 50 representative G−S curves from in situ deprotected samples in the range of 1.00 × 10−6 G0 − 2.00 × 10−4 G0 with a bin size of 2.00 × 10−6 G0; and in the range of 1.00 × 10−5 G0 − 2.00 × 10−3 G0 with a bin size of 2.00 × 10−5 G0, respectively. The histograms are constructed from the same set of G−S curves. Insets show the Gauss peak fit for the net histograms (with the backgrounds subtracted).

as well as higher conductance values at (1.97 ± 0.05) × 10−4 G0, (4.31 ± 0.26) × 10−4 G0, and (9.34 ± 0.40) × 10−4 G0 are observed for the in situ deprotected sample. From the control sample, about 1000 G−S curves are obtained, of which ∼58% are from empty contacts, ∼24% are noisy, and ∼18% show molecular conductance steps. Representative G−S curves with the molecular steps are shown in Figure 3a. The curves with molecular conductance steps are shown in the histograms in the ranges of 1.00 × 10−6 G0 to 2.00 × 10−4 G0 and 1.00 × 10−5 G0 to 2.00 × 10−3 G0. As shown in Figure 3b, in the lower conductance range there is a maximum count around (4.73 ± 0.03) × 10−5 G0. However, in the higher conductance range the histogram is a good fit to an exponential decay (Figure 3c) similar to an empty junction. Both the in situ deprotected sample and the protected control sample show molecular conductances in the lower conductance range (4.39 × 10−5 G0 for the deprotected sample and 4.73 × 10−5 G0 for the control sample), while only the deprotected samples show conductances in the higher conductance range at 1.97 × 10−4 G0, 4.31 × 10−4 G0, and 9.34 × 10−4 G0. For the in situ deprotected sample, two types of substratemolecule-tip junctions are formed: The Au-S-Por-SAc-Au junction and the Au-S-Por-S-Au junction, where the difference occurs at the molecule-tip interface depending on whether the deprotection affects both or only one of the acetyl group (see Figure 1d, e). No self-cleaving of acetyl occurs at the tipmolecule interface as the tip and the molecule is in contact for

Similar methods to study the conductance of single molecules were used by other groups.21−25 Details of the STM-molecular break junction and the conductance−displacement measurement are discussed in the Supporting Information. For the sample prepared from in situ deprotection, about 500 G-S curves are obtained, with about 38% of the curves representing empty junctions (i.e., Au−Au contacts), 23% are noisy, and the remaining 39% of the curves show molecular conductance steps. Representative G-S curves with molecular conductance steps are shown in Figure 2a−c. According to the conductance values of the junctions, these G−S curves can be grouped into 3 categories: Curves with steps only at mid-10−5 G0 range (Figure 2a, ∼16%), curves with steps only at mid-10−4 G0 (Figure 2b, ∼11%) range, and curves that show steps at both 1 × 10−5 G0 and 1 × 10−4 G0 range (Figure 2c, ∼12%). To understand the molecular conductance, we present histograms of the molecular conductance steps in the ranges of 1.00 × 10−6 to 2.00 × 10−4 G0 and 1.00 × 10−5 to 2.00 × 10−3 G0. We start by considering the 50 G−S curves with molecular conductance steps of the deprotected samples represented in the histograms shown in Figure 2d, e. The gray shaded areas are those of the molecular conductance steps. The red curves are of the background curves (those due to empty junctions). The background is subtracted to obtain the net histogram (blue curves) in Figure 2d, e and the Gauss fit of the peaks are shown in the insets. The peaks in the histogram indicate the most probable conductance values. The most probable lower conductance values at (4.39 ± 0.06) × 10−5 G0 C


Letter


Figure 3. (a) Representative G−S curves from the control sample. G−S curves show well-defined step-like signatures in the mid-10−5 G0 range only. (b, c) Histograms from 50 representative G−S curves from the control sample in the range of 1.00 × 10−6 G0 − 2.00 × 10−4 G0 with a bin size of 2.00 × 10−6 G0; and in the 1.00 × 10−5 G0 − 2.00 × 10−3 G0 range with a bin size of 2.00 × 10−5 G0, respectively. Panels b and c are made from the same set of G−S curves.

The S−Au bond length is found to be 2.30 Å for the Au-SPor-S-Au junction, and 0.36 Å longer on the protected side of the Au-S-Por-SAc-Au junction (Table S1). We find that the phenyl rings in all cases are tilted in relation to the porphyrin plane at an angle of about 70°. A full list of the atomic coordinates is provided in Table S2. Importantly, the Au-S-Por-SAc-Au junction is associated with transmission that is lower than that of the Au-S-Por-S-Au junction (see transmission plots in Figure 4a). The key transport channels are based on the highest occupied molecular orbital (HOMO) in both the Au-S-Por-SAc-Au junction and Au-S-Por−S-Au junction (see Figure 4b). These main transport channels are at −5.8 for the Au-S-Por-SAc-Au junction and −5.6 eV for Au-S-Por-S-Au junction, both near the Fermi level EF and are of a delocalized nature across the whole molecular bridge. The effect of the acetyl group is to introduce an antibonding character to the HOMO at the Au−S region (see the insets in Figure 4b). The calculated conductances are listed in Table 1. The calculated conductance of Au−S−Por−S-Au junction, 4.24 × 10−4 G0, is in good agreement with the three measured values listed in the table ((1.97 ± 0.05) × 10−4, (4.31 ± 0.26) × 10−4, and (9.34 ± 0.40) × 10−4). Similarly, the calculated conductance of the Au-S-Por-SAc-Au junction of 4.99 × 10−5 G0 is in agreement with the measured conductance of (4.39 ± 0.06) × 10−5 G0 and (4.73 ± 0.03) × 10−5 G0. It is also interesting to note that the calculated conductance of the AuSAc-Por-SAc-Au junction is 5.21 × 10−6 G0, which is smaller

less than 0.1 s in the conductance measurement. For the control sample, only Au-S-Por-SAc-Au junctions are formed. In the case of the deprotected junctions, the higher-valued conductances (1.97 × 10−4 G0, 4.31 × 10−4 G0, and 9.34 × 10−4 G0) may result from multiple molecules in the junction. Expectedly, molecules with deprotected thiol end groups (i.e., AcS-Por-SH or HS-Por-SH) are prone to form a SAM of high surface density upon strong Au−S binding. Therefore, it is likely that these end groups tend to involve more than a single molecule in the junction. In fact for the deprotected molecules, the S−Au covalent bond strength is comparable to the Au−Au bond strength.26 This also suggests a higher probability for surface reorganization at the atomic binding site. We may also relate the variance in the conductance per one molecule to the possibly varied binding sites on the gold surface. Indeed a deprotected thiol was shown to bond to different sites using computational models that are associated with conductance values that can vary by as much as a factor of 5.27 In the case of the protected junctions, the SAc−Au bond is the weakest bond and, therefore, is expected to break first upon stretching. To understand the deprotection effect, we calculate the conductance using a Green’s function−density functional theory (GF-DFT) approach utilizing the Baer−Neuhauser− Livshits (BNL) functional, a scheme that was recently benchmarked successfully against widely studied systems.28 Our computational scheme addresses fundamental deficiencies typically affecting charge transport studies.29 Calculation details are provided in the Supporting Information. D


Letter


To conclude, in situ deprotection of an acetylthio-protected free base porphyrin is used to modify the tip−molecule interface, and therefore to modify the conductance of the molecular junction. Two forms of substrate-molecule-tip junctions are identified: an Au-S-Por-SAc-Au junction and an Au-S-Por-S-Au junction. The junctions correspond to conductance values in the mid-10−5 G0 and 1.97, 4.31, 9.34 × 10−4 G0, respectively. First-principles calculations report conductance values with good agreement (to the same order of magnitude) to these two types of junctions. The calculations find that the reduced conductance in the protected form (Au-SPor-SAc-Au junction) originates from the presence of the acetyl end group, whereas elongated S−Au bonds are associated with an effect of increasing the conductance.

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ASSOCIATED CONTENT

* Supporting Information S

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsami.6b14841. Supplementary data for angle-resolved (ARXPS) on SAMs, details on STM-molecular break junctions and conductance−displacement (G−S) measurements, and computational details (PDF)

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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. *E-mail: [email protected]. *E-mail: [email protected]. ORCID

Qi Zhou: 0000-0002-5700-6644 Barry D. Dunietz: 0000-0002-6982-8995 Kim M. Lewis: 0000-0002-8342-8699

Figure 4. (a) Transmission plots of the Au-S-Por-S-Au (red), Au-SPor-SAc-Au (blue), and Au-SAc-Por-SAc-Au (green). The dotted line shows the position of the Fermi level. (b, c) Frontier orbitals involved in electron transmission of the Au-S-Por-S-Au and the Au-SAc-PorSAc-Au.

Author Contributions †

Q.Z., A.Y., and Q.F. contributed equally. A.H. contributed through a dual enrollment program as a student at Green High School, OH. The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.

than the conductances of Au-S-Por-S-Au and Au-S-Por-SAc-Au junctions. This confirms the assertion that acetyl protecting group attached to the thiol reduces the conductance. To further understand the origin of the reduced conductance in the protected form, we calculated conductance of a deprotected Au-S-Por-S-Au structure obtained by removing both acetyls of the protected Au-SAc-Por-SAc-Au structure while maintaining the same longer Au−S bond length (2.66 Å). The calculated conductance 2.28 × 10−3 G0 is higher than calculated for the deprotected system as shown in Table 1. Namely, the reduced conductance of the protected junctions stems from the acetyl end groups, and not the longer bond length. In fact, the conductance appears to be slightly enhanced by the small stretch of the bond length.

Funding

Q.Z. and K.M.L. 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. A.Y., Q.F., and B.D.D. acknowledge the financial support by a DOEBES award through the Chemical Sciences Geosciences and Biosciences Division (Grants 357 DE-SC0004924 and DEFG02-10ER16174). Notes

The authors declare no competing financial interest.

Table 1. Calculated and Experimentally Measured Conductance (unit is G0)

calculation experiment: in situ deprotected

experiment: protected

Au-S-Por-S-Au

Au-S-Por-SAc-Au

Au-SAc-Por-SAc-Au

4.24 × 10−4 (1.97 ± 0.05) × 10−4 (4.31 ± 0.26) × 10−4 (9.34 ± 0.40) × 10−4 none

4.99 × 10−5 (4.39 ± 0.06) × 10−5

5.21 × 10−6 none

(4.73 ± 0.03) × 10−5

none

E


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ACKNOWLEDGMENTS Q.Z. and K.M.L. acknowledge Dr. Peter Dinolfo for advice on the chemistry procedure, Dr. Guoguang Qian for suggestions related to equipment setup, and Michael Giordano for AFM imaging. A.Y., Q.F. and B.D.D. acknowledge support from the Ohio supercomputer and Kent State University for access to computing resources.

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Modification of Molecular Conductance by in Situ ... - ACS Publications

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