Controlling destructive quantum interference in tunneling junctions comprising self-assembled monolayers: Via bond topology and functional groups

Article abstract of DOI:10.1039/c8sc00165k

Quantum interference effects (QI) are of interest in nano-scale devices based on molecular tunneling junctions because they can affect conductance exponentially through minor structural changes. However, their utilization requires the prediction and deterministic control over the position and magnitude of QI features, which remains a significant challenge. In this context, we designed and synthesized three benzodithiophenes based molecular wires; one linearly-conjugated, one cross-conjugated and one cross-conjugated quinone. Using eutectic Ga-In (EGaIn) and CP-AFM, we compared them to a well-known anthraquinone in molecular junctions comprising self-assembled monolayers (SAMs). By combining density functional theory and transition voltage spectroscopy, we show that the presence of an interference feature and its position can be controlled independently by manipulating bond topology and electronegativity. This is the first study to separate these two parameters experimentally, demonstrating that the conductance of a tunneling junction depends on the position and depth of a QI feature, both of which can be controlled synthetically.

Full text of DOI:10.1039/c8sc00165k

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Controlling Destructive Quantum Interference in
Tunneling Junctions Comprising Self-assembled
Monolayers via Bond Topology and Functional
Groups
†
,‡,¶
†,‡,¶ †,‡ †,‡
Saurabh Soni, Xinkai Qiu, Theodorus L.
Yanxi Zhang,
Gang Ye,
†
,‡
‡
†,‡
§
Krijger, Harry T. Jonkman, Marco Carlotti, Eric Sauter, Michael
§
∗,†,‡
Zharnikov, and Ryan C. Chiechi
†
Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG
Groningen, The Netherlands
‡
Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The
Netherlands
¶
These authors contributed equally to this work.
Applied Physical Chemistry, Heidelberg University, Im Neuenheier Feld 253, Heidelberg
9120, Germany
§
6
E-mail: r.c.chiechi@rug.nl
1

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ABSTRACT
Quantum interference effects (QI) are of interest in nano-scale devices based on molecular
tunneling junctions because they can affect conductance exponentially through minor
structural changes. However, their utilization requires the prediction and deterministic
control over the position and magnitude of QI features, which remains a significant
challenge. In this context, we designed and synthesized three benzodithiophenes based
molecular wires; one linearly-conjugated, one cross-conjugated and one cross-conjugated
quinone. Using eutectic Ga-In (EGaIn) and CP-AFM, we compared them to a well-known
anthraquinone in molecular junctions comprising self-assembled monolayers. By combining
density functional theory and transition voltage spectroscopy, we show that the presence of
an interference feature and its position can be controlled independently by manipulating
bond topology and electronegativity. This is the first study to separate these two
parameters experimentally, demonstrating that the conductance of a tunneling junction
depends on the position and depth of a QI feature, both of which can be controlled
synthetically.
2

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INTRODUCTION
Molecular electronics is concerned with the transport of charge through molecules spanning
two electrodes,[1] the fabrication of which is a challenging area of nanotechnology.[2–4] In
such junctions, π-conjugated molecules influence transport more than a simple, rectangular
tunneling barrier; when a tunneling electron traverses the region of space occupied by or-
bitals localized on these molecules, its wave function can undergo constructive or destructive
interference, enhancing or suppressing conductance. When the presence of different path-
ways in molecular system affects conductance, it is typically described as quantum interfer-
ence (QI),[5] which was originally adapted from the Aharonov-Bohm effect[6] to substituted
benzenes.[7,8] The concept “quantum interference effect transistor” was also proposed using
meta-benzene structures for device application.[9] Solomon et al. further refined the concept
in the context of Molecular Electronics where it is now well established that destructive QI
leads to lower conductance in tunneling junctions.[10–15] We previously demonstrated QI in
SAM-based junctions using a series of compounds based on an anthracene core; AC, which is
linearly-conjugated; AQ, which is cross-conjugated via a quinone moiety; and AH, in which
the conjugation is interrupted by saturated methylene bridges (Figure S1).[16] Subsequent
studies verified these findings in a variety of experimental platforms and a consensus emerged
that, provided the destructive QI feature (anti-resonances in transmission) is sufficiently close
to the Fermi level, E , cross-conjugation leads to QI.[
17–24]
However, experimental studies
F
on conjugation patterns other than AC/AQ are currently limited to ring substitutions such
as meta-substituted phenyl rings,[25–32] or varied connectivities in azulene,[33–35] which differ
fundamentally[5,11,36–38] from cross-conjugated bond topologies[23,39,40] because they change
tunneling pathways, molecular-lengths and bond topology simultaneously (Table S1). Isolat-
ing these variables is however important because the only primary observable is conductance,
which varies exponentially with molecular length. More recent work has focused on “gating”
QI effects by controlling the alignment of π-systems through-space[37,41,42] and affecting the
orbital symmetry of aromatic rings with heteratoms.[43–45] These studies exclusively study
3

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the effects of the presence and absence of QI features; to date—and despite recent efforts[46]
—
the specific effects of bond topology and electronegativity on the depth and position of QI
features have not been isolated experimentally.
To address this issue, we designed and synthesized the series of benzodithiophene deriva-
tives (BDT-n); benzo[1,2-b:4,5-b’]dithiophene (BDT-1, linearly conjugated), benzo[1,2-
b:4,5-b’]dithiophene-4,8-dione (BDT-2, cross-conjugated with quinone), and benzo[1,2-b:5,4-
b’]dithiophene (BDT-3, cross-conjugated and an isomer of BDT-1). These compounds sep-
arate the influence of cross-conjugation (bond topology) from that of the electron-withdrawing
effects of the quinone functionality while controlling for molecular formula and length. We in-
vestigated the charge transport properties of these molecules in tunneling junctions compris-
ing self-assembled monolayers (SAMs), which are relevant for solid-state molecular-electronic
devices.[47–49] Through a combination of density functional theory (DFT) and transition volt-
age spectroscopy (TVS) we show that cross-conjugation produces QI features near occupied
molecular states and that the position and depth of the QI feature is strongly influenced by
the strongly electron-withdrawing quinone functionality, which places these features near un-
occupied states while simultaneously bringing those states close to E . Thus, by controlling
F
bond topology and electronegativity separately, the conductance can be tuned independently
of length and connectivity via the relative positions of the QI features and molecular states
and not just the presence or absence of such features.
RESULTS AND DISCUSSION
To isolate molecular effects on transport, it is important to control for changes to the width
of the tunneling barrier which, in SAMs, is typically defined by the end-to-end lengths of
the molecules. Conductance G generally varies exponentially with the barrier-width d such
that G = G exp(−βd), where G is the theoretical value of G when d = 0, and β is the
0
0
tunneling decay coefficient. Since β depends on the positions of molecular states relative to
4

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E and we are comparing compounds with very different redox potentials (orbital energies)
F
we can only ascribe changes to G if d is invariant across the series. Furthermore, to isolate
the variable of bond topology experimentally, the electronic properties of the linear- and
cross-conjugated compounds must be nearly identical. Figure 1a shows the structures of the
BDT-n series and AQ; the “arms” are linearly-conjugated phenylacetylenes (highlighted
in the light blue background) and the cores (Ar, highlighted in the brown background)
are substituted by the structures indicated. The variation in the end-to-end lengths of
˚
these compounds is within 1 A and the linear- and cross-conjugated compounds BDT-1 and
BDT-3 differ only by the relative position of sulfur atoms; they have the same molecular
formula. The synthesis, full characterization and a detailed discussion of their properties
are provided in the Supplementary Information. Note that we include AQ in the series as a
benchmark for destructive QI effects.
We measured tunneling charge transport through metal-molecule-metal junctions com-
prising BDT-1, BDT-2, BDT-3 and AQ using conformal eutectic Ga-In (EGaIn) contacts
as top electrodes.[50] We utilized an established procedure of the in situ deprotection of
thioacetates[41,51] to form well-defined SAMs on Au substrates; these substrates served then
as bottom electrodes. We refer to the assembled junctions as Au/SAM//EGaIn where “/”
and “//” denote a covalent and van der Waals interfaces, respectively. The geometry of
the junctions is shown in Figure 1b. To verify that the structural similarities of the com-
pounds carry over into the self-assembly process, we characterized the SAMs of BDT-n
by several complementary techniques, including (high-resolution) X-ray photoelectron spec-
troscopy (HRXPS/XPS) and angle-resolved near-edge X-ray absorption fine structure spec-
troscopy (NEXAFS). These data are discussed in detail in the Supplementary Information
and summarized in Table 1. The characterization of SAMs of AQ is reported elsewhere.[16,41]
The XPS and NEXAFS data suggest that the molecules in the BDT-n SAMs are assembled
◦
upright with the tilt angle of approximately 35 . The molecules are packed densely on the
1
4
2
[41]
order of 10 molecules per cm as are similar conjugated molecular-wire compounds.
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Figure 2a shows the current-density versus voltage (J/V ) curves for the BDT-n series and
AQ using EGaIn top contacts. BDT-1 is the most conductive across the entire bias window.
The conductance of linearly-conjugated BDT-1 and AC (Figure S1; a linearly-conjugated
analog of AQ), are almost identical (Figure S21), meaning that the low-bias conductivity
and/or values of J are directly comparable between the AC/AQ and BDT-n series. As
expected, the cross-conjugated BDT-2, BDT-3 and AQ are all less conductive than BDT-
1
(and AC). The low-bias conductivity (from the Ohmic region, −0.1 V to 0.1 V) of the
quinones (BDT-2 and AQ), however, is even more suppressed than the cross-conjugated
BDT-3, while the magnitudes of J for BDT-2, BDT-3 and AQ are similar beyond −0.5 V.
We observed similar behavior in QI mediated by through-space conjugation in which the
compound with an interference feature very close to E exhibited a sharp rise in J, eventually
F
crossing J/V curve of the compound with a feature further from E .[ This observation
41]
F
suggests that, as the junction is biased, the transmission probability “climbs” the interference
feature rapidly, bringing highly transmissive conduction channels into the bias window at
sufficiently low values of V to meet and exceed the total transmission of the compound
for which the interference feature is far from E at zero bias. Further discussion on the
F
asymmetry of J/V curves is included in the Supplementary Information.
To better compare the conductance of the molecules, we calculated the low-bias conduc-
tivities and normalized them to BDT-1. These values are plotted in Figure 2b, showing
that cross-conjugation lowers the conductance of BDT-3 by an order of magnitude com-
pared to BDT-1 and the quinone functionality of BDT-2 and AQ lowers it by two orders
of magnitude, in agreement with the analogous behavior of AC and AQ.[20] To control
for large-area effects (e.g., if there are defects in the SAM), we measured BDT-n series
by conducting-probe atomic force microscopy (CP-AFM) with Au electrodes and found the
same trend: BDT-1 > BDT-3 > BDT-2, however, a direct comparison of low-bias con-
ductivities was precluded by the extremely high resistance of BDT-2 and AQ at low bias.
These data are discussed in detail in the Supplementary Information. Thus, we conclude
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that quinones suppress conductance more than cross-conjugation alone, irrespective of the
measurement/device platform.
For insight into the shapes of the J/V curves and the conductance, we simulated the
transmission spectra, T(E) vs. E−E (E value of −4.3 eV, see Experimental Section), of
F
F
the BDT-n series using density functional theory (DFT) and compared the resulting curves
with AQ (Figure 3). These calculations, which are discussed in more detail in the Compu-
tational Methodology section of the Supplementary Information, simulate the transmission
spectra through isolated molecules in vacuum at zero bias and are useful for predicting
trends in conductance. There are three important features of these curves: 1) Only the com-
pounds with cross-conjugation (including quinones) show sharp dips (anti-resonances or QI
features)[13,18] in the frontier orbital gap; 2) the dips occur near E only for the two quinones;
F
and 3) the QI features are more pronounced for the molecules in which the cross-conjugation
is caused by a quinone moiety as opposed to the carbon-carbon bond topology. When bias
is applied to a junction, the x-axis of the transmission plot shifts and E broadens such that
F
an integral starting at E − E = 0 eV and widening to larger ranges of E − E is a rough
F
F
approximation of how T(E) translates into current, I(V ). This relationship is apparent in
the slightly lower conductance of AQ compared to BDT-2 (Figure 2b) and the slightly
lower values of T(E) for AQ compared to BDT-2 across the entire range of E − E . The
F
proximities of the QI features to E is also apparent in the J/V curves (Figure 2a). As the
F
junction is biased, the minimum of the QI feature shifts such that, by 0.5 V, the transmission
probabilities are roughly equal for BDT-n and AQ.
The shape of T(E) near E − E = 0 eV is roughly traced by differential conductance
F
dJ
[18,41,52]
plots of log |dV | vs. V , allowing QI features near E to be resolved experimentally.
F
Figure 4 shows heatmap plots of differential conductance of Au/SAM//EGaIn constructed
dJ
from histograms binned to log |dV | for each value of V . (Note that these are histograms
of J/V curves with no data-selection, thus, brighter colors correspond to mean values of
J and are not related to conductance histograms of single-molecule break-junctions; see
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Supplementary Information for details.) Both BDT-1 and BDT-3 exhibit ordinary, U-
shaped plots characteristic of non-resonant tunneling. By contrast, both AQ and BDT-
2
—the two compounds bearing quinone functionality—show V-shaped plots with negative
curvature. These results are in agreement with Figure 3, which places the QI features for
the quinone moieties, AQ and BDT-2, much closer to E than for BDT-3. The positions
F
of these features are related to the positions of highest-occupied and lowest-unoccupied
π-states (HOPS and LUPS), which are in good agreement between DFT and experiment
(
(
Tables S2 and S3). Thus, the differential conductance heatmaps (experiment) and DFT
simulation) both indicate that cross-conjugation suppresses conductance because it creates
a dip in T(E) in the frontier orbital gap, but that the electron-withdrawing nature of the
quinone functionality simultaneously pulls the LUPS and the interference features close to
E such that the J/V characteristics and transmission plots of AQ and BDT-2 are nearly
F
indistinguishable despite the presence of two thienyl groups in BDT-2. These results also
suggest that tunneling transport is mediated by the HOPS (hole-assisted tunneling) for
BDT-1 and BDT-3 and by the LUPS (electron-assisted tunneling) for BDT-2 and AQ
because tunneling current is dominated by the resonance(s) closest to EF.
To further investigate the mechanism of transport, we measured transition voltages,
Vtrans (Table S3, Figures S17 and S18), which provide information about the energy offset
between E and the dominant frontier orbital.[53,54] Figure 5a shows the levels for the BDT-
F
n series calculated by DFT with respect to E (−4.3 eV), clearly predicting LUPS-mediated
F
tunneling for BDT-2 and AQ. Figure 5b compares the experimental values of Vtrans to
the energy differences between E and the frontier orbitals. The salient feature of Figure
F
5
b is that the trend in |EHOPS − E | opposes the trend in V
such that the trend in
trans
F
experimental values of Vtrans agrees with DFT only when we compare Vtrans with |EHOPS−EF|
for BDT-1 and BDT-3, and with |ELUPS−E | for BDT-2 and AQ. Thus, DFT calculations
F
combined with experimental values of Vtrans predict electron-assisted tunneling for BDT-2
and AQ. This degree of internal consistency between the experiment and theory is important
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because, ultimately, the only primary observable is conductance, which we plot as J/V
curves, differential conductance heatmaps and Fowler-Nordheim plots (from which we extract
Vtrans). And we find remarkable agreement between these direct and indirect observations
and DFT calculations on model junctions comprising single molecules.
CONCLUSION
The key question of this work is how cross-conjugation and electronegativity affect QI fea-
tures.[11,20,52,55,56] Based on our experimental observations and calculations, we assert that
destructive QI induced by cross-conjugation is highly sensitive to the functional groups that
induce the cross-conjugation and that quinones are, therefore, a poor testbed for tuning
QI effects (beyond switching them on and off[57]) because their strong electron-withdrawing
nature places a deep, destructive feature near E irrespective of other functional groups (in
F
our case, two fused thiophene rings barely make a difference). Comparing a quinone to a hy-
drocarbon also compares HOPS-mediated tunneling to LUPS-mediated tunneling between
molecules with significantly different band-gaps and absolute frontier orbital energies. In
contrast, BDT-1 and BDT-3 are heterocyclic isomers with no functional groups, identi-
cal molecular formulas, nearly-identical HOPS, identical lengths that translate into SAMs
of identical thicknesses, and transport is dominated by the HOPS. They isolate the single
variable of conjugation patterns, allowing us to separate bond topology (cross-conjugation)
from electronic properties (functional groups), giving experimental and theoretical insight
into the relationship between bond topology and QI. Our results suggest that there is a lot of
room to tune the conductance of moieties derived from BDT-3 by including pendant groups
(
e.g., halogens, CF groups or acidic/basic sites) that shift the QI feature gradually towards
3
E synthetically and/or in response to chemical signals.
F
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Experimental
Synthesis
Reagents. All reagents and solvents were commercial and were used as received. Benzo[1,2-
b;4,5-b’]dithiophene was purchased from TCI. 2,6-dibromobenzo[1,2-b:4,5-b’]dithiophene-
4
,8-dione[58], 2,6-dibromobenzo[1,2-b:5,4-b’]dithiophene[59], 4-ethynyl-1-thioacetylbenzene[60]
and 1-tert-butylthio-4-ethynylbenzene[61] were synthesized according to literature proce-
dures.
NMR and Mass Spectra. 1HNMR and 13CNMR were performed on a Varian Unity
◦
Plus (400 MHz) instrument at 25 C, using tetramethylsilane (TMS) as an internal standard.
NMR shifts are reported in ppm, relative to the residual protonated solvent signals of CDCl3
(
δ = 7.26 ppm) or at the carbon absorption in CDCl (δ = 77.0 ppm). Multiplicities are
3
denoted as: singlet (s), doublet (d), triplet (t) and multiplet (m). High Resolution Mass
Spectroscopy (HRMS) was performed on a JEOL JMS 600 spectrometer.
UV-Vis and Cyclic Voltammetry UV-Vis measurements were carried out on a Jasco
V-630 spectrometer. Cyclic voltammetry (CV) was carried out with a Autolab PGSTAT100
potentiostat in a three-electrode configuration.
General. Unless stated otherwise, all crude compounds were isolated by bringing the reac-
tion to room temperature, extracting with CH Cl , washing with saturated NaHCO , water
2
2
3
and then brine. The organic phase was then collected and dried over Na SO and the sol-
2
4
vents removed by rotary evaporation. Synthetic schemes and NMR spectra are provided in
the Supplementary Information.
2
,6-dibromobenzo[1,2-b:4,5-b’]dithiophene (1). Benzo[1,2-b;4,5-b’]dithiophene (540
mg, 2.84 mmol) were dissolved in 70 mL anhydrous THF under an atmosphere of N , cooled
2
◦
to −78 C and n-butyllithium (8.5 mmol, 5.3 mL, 1.6 m in hexane) was added drop-wise. The
solution was stirred for 30 min in the cold bath before being warmed to room temperature
◦
and stirred for and additional 20 min. The mixture was cooled to −78 C again and a solution
1
0

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of CBr (2.8 g, 8.5 mmol) in 5 mL anhydrous THF was added. The solution was stirred for
4
3
0 min in the cold bath before being quenched with concentrated sodium bicarbonate solution
◦
(
(
2
10 mL) at −78 C. The crude solid was purified by recrystallization from CHCl to give 1
3
1
890 mg, 90 %) as colorless platelets. HNMR (400 MHz, CDCl ) δ: 8.03 (s, 2H); 7.33 (s,
3
1
3
H). CNMR (100 MHz, CDCl ) δ: 138.36, 136.88, 125.63, 116.00, 115.10.
3
2
,6-Bis[(4-acetylthiophenyl)ethynyl]benzo[1,2-b:4,5-b’]dithiophene (BDT-1). 2,6-
dibromobenzo[1,2-b:4,5-b’]dithiophene (125 mg, 0.36 mmol) and 4-ethynyl-1-thioacetylbenzene
176 mg, 1 mmol) were dissolved in mixture of fresh distilled Et N (5 mL) and anhydrous
(
3
THF (10 mL). After degassing with dry N , the catalysts Pd(PPh ) (58 mg, 0.05 mmol)
2
3 4
and CuI (10 mg, 0.05 mmol) were added. The reaction mixture was refluxed overnight un-
der N . The crude solid was purified by column chromatography to give BDT-1 (78 mg,
2
1
4
0 %). HNMR (400 MHz, CDCl ) δ: 8.17 (s, 2H), 7.59 (d, J=8.2, 4H), 7.55 (s, 2H), 7.43
3
1
3
(
d, J=8.2, 4H), 2.45 (s, 6H). CNMR (100 MHz, CDCl ) δ: 195.88, 140.66, 140.46, 136.90,
3
1
34.76, 131.51, 130.89, 126.53, 126.25, 119.27, 97.57, 87.31, 32.97. HRMS(ESI) calcd. for
+
C H O S [M+H] : 539,02624, found: 539.02457.
3
0
18
2 4
2
,6-Bis[(4-tert-butylthiophenyl)ethynyl]benzo[1,2-b:4,5-b’]dithiophene-4,8-dione (5).
2
4
,6-dibromobenzo[1,2-b:4,5-b’]dithiophene-4,8-dione (3; 200 mg, 0.53 mmol) and 1-tert-butylthio-
-ethynylbenzene (4; 230 mg, 1.21 mmol) were dissolved in mixture of fresh distilled Et N
3
(
5 mL) and anhydrous THF (10 mL). After degassing, the catalysts Pd(PPh ) (30 mg,
3 4
0
.03 mmol) and CuI (5 mg, 0.03 mmol) were added. The reaction mixture was refluxed for
overnight under N . The crude solid was purified by column chromatography to give 5
2
1
(
100 mg, 32 %). HNMR (400 MHz, CDCl ) δ: 7.71 (s, 2H), 7.55 (d, J=8.2, 4H), 7.50 (d,
3
J=8.2, 4H), 1.31 (s, 18H). 13CNMR (100 MHz, CDCl ) δ: 173.33, 143.91, 142.55, 137.24,
3
1
35.17, 131.73, 131.56, 130.31, 121.70, 98.14, 82.55, 46.81, 31.02.
,6-Bis[(4-acetylthiophenyl)ethynyl]benzo[1,2-b:4,5-b’]dithiophene-4,8-dione (BDT-
2
2
0
).[62] TiCl (0.04 mL, 0.364 mmol) was added drop-wise to a solution of compound 5 (100 mg,
4
◦
.167 mmol) and CH C(O)Cl (0.03 mL, 0.377 mmol) in CH Cl at 0 C. The resulting mix-
3
2
2
1
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ture was stirred at room temperature for 1 h and the conversion was monitored by TLC
hexanes/CH Cl , 2:1). Upon completion, the reaction was quenched with water (10 mL).
(
2
2
The crude solid was purified by column chromatography to give BDT-2 (50 mg, 53 %).
1
HNMR (400 MHz, CDCl ) δ: 7.73 (s, 2H), 7.59 (d, J=8.2, 4H), 7.45 (d, J=8.2, 4H), 2.46 (s,
3
6
1
5
H). 13CNMR (100 MHz, CDCl ) δ: 195.59, 175.96, 145.20, 136.95, 134.87, 134.20, 133.15,
3
+
32.57, 132.50, 125.24, 100.42, 85.49, 33.01. HRMS(ESI) calcd. for C H O S [M+H] :
3
0
17
4 4
69,00042, found: 568.99887.
,6-Bis[(4-tert-butylthiophenyl)ethynyl]benzo[1,2-b:5,4-b’]dithiophene (7). 2,6-
dibromobenzo[1,2-b:5,4-b’]dithiophene (6; 50 mg, 0.143 mmol) and 1-tert-butylthio-4-ethynylbenzene
4; 68 mg, 0.358 mmol) were dissolved in mixture of fresh distilled Et N (5 mL) and anhy-
2
(
3
drous THF (10 mL). After degassing, the catalysts Pd(PPh ) (16 mg, 0.014 mmol) and CuI
3
4
(
2.7 mg, 0.014 mmol) were added. The reaction mixture was refluxed overnight under N2.
1
The crude solid was purified by column chromatography to give 7 (40 mg, 49 %). HNMR
(
400 MHz, CDCl ) δ: 8.16 (s, 1H), 8.14 (s, 1H), 7.56 (s, 2H), 7.54 (d, J=4, 4H), 7.51 (d, J=4,
3
4
1
H), 1.31 (s, 18H). 13CNMR (100 MHz, CDCl ) δ: 141.35, 140.05, 139.89, 136.77, 134.10,
3
31.29, 125.64, 125.38, 120.85, 117.39, 97.51, 86.99, 49.30, 33.67.
2
,6-Bis[(4-acetylthiophenyl)ethynyl]benzo[1,2-b:5,4-b’] dithiophene (BDT-3).[62]
TiCl (0.042 mL, 0.388 mmol) was added drop-wise to a solution of compound (7) (100 mg,
4
◦
0
.176 mmol) and CH C(O)Cl (0.03 mL, 0.397 mmol) in CH Cl at 0 C. The resulting mix-
3
2
2
ture was stirred at room temperature for 10 min and the conversion was monitored by TLC
hexanes/CH Cl 2:1). Upon completion the reaction was quenched with water (10 mL). The
(
2
2
1
crude solid was purified by column chromatography to give BDT-3 (25 mg, 26 %). HNMR
(
(
400 MHz, CDCl ) δ: 8.17 (s, 1H), 8.15 (s, 1H), 7.59 (d, J=7.2, 4H), 7.58 (s, 2H), 7.43
3
1
3
d, J=8.2, 4H), 2.45 (s, 3H). CNMR (100 MHz, CDCl ) δ: 195.88, 141.43, 140.03, 136.90,
3
1
34.76, 131.51, 131.48, 126.27, 126.50, 120.94, 117.42, 97.22, 87.15, 32.97. HRMS(ESI) calcd.
+
for C H O S [M+H] : 539,02624, found: 539.02476.
3
0
18
2 4
1
2

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DOI: 10.1039/C8SC00165K
Self-assembled monolayers
The SAMs of BDT-n were formed via in situ deprotection[41,51] on template-stripped Au
substrates.[63] Freshly template-stripped substrates were immersed into 3 mL of 50 µm solu-
tions of the thioacetate precursors in freshly distilled toluene inside a nitrogen-filled glovebox
and sealed under a nitrogen atmosphere. The sealed vessels were kept inside a nitrogen flow
box[64] (O below 3 %, RH below 15 %) overnight; all subsequent handling and EGaIn mea-
2
surements were performed inside the flowbox. 1.5 h prior to measurement, 0.05 mL of 17 mm
diazabicycloundec-7-ene(DBU) in toluene was added to the precursor/substrate solution.
The substrates were then rinsed with toluene and allowed to dry for 30 min before perform-
ing the measurements.
Characterization
The SAMs of BDT-n were characterized by XPS (laboratory and synchrotron), NEXAFS
spectroscopy, UPS and water contact angles. In some cases, SAMs of CH (CH ) SH or
3
2 15
CH (CH ) SH on Au were used as a reference. See Supplementary Information for details.
3
2 17
Transport measurements
EGaIn. For each SAM, at least 10 junctions were measured on each of three different
substrates by applying a bias from 0.00 V → 1.00 V → −1.00 V → 0.00 V with steps of
0
.05 V. At least 20 trace/re-trace cycles were measured for each junction; only junctions
that did not short over all 20 cycles were counted as “working junction” for computing
yields.
CP-AFM. I-V measurements were performed on a Bruker AFM Multimode MMAFM-2
equipped with a Peak Force TUNA Application Module. The Au on mica substrates were
removed from the flowbox immediately prior to measurement, which occurred under ambient
conditions by contacting the SAM with a Au-coated Si N tip with a nominal radius of 30 nm
3
4
1
3

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(
NPG-10, Bruker; resonant frequency: 65 kHz, spring constant: 0.35 N/m). The AFM tip
Mica
was grounded and the samples were biased from −1.0 V → 1.0 V → −1.0 V on Au
. 11
trace/re-trace cycles per junction were performed and the top electrode was removed from
SAMs between junctions.
Processing. All raw data were processed algorithmically using Scientific Python to generate
histograms, Gaussian fits, extract transition voltages and construct differential conductance
heatmap plots.
DFT calculations
Calculation were performed using the Orca 4 software package[65,66] and the Artaios-
0
30417 software package.[67,68] The molecules terminating with thiols were first minimized
to find the gas-phase geometry and then attached to two 18-atom Au(111) clusters via the
˚
terminal sulfur atoms with a distance of 1.75 A at hexagonal close-pack hollow sites (hydro-
gen atom from the thiol was deleted before attaching the electrodes). Single-point energy
calculations were performed on this model junction using B3LYP/G and LANL2DZ basis
sets according to literature procedures to compute the energy levels.[67] Transmission curves
and isoplots of the central molecular orbitals, for isolated molecules without electrodes and
terminal hydrogen atoms, were generated using the Artaios-030417 software package and
the energy axis was scaled using the E of −4.3 eV. The use of this E value for comparing
F
F
transmission trends to the experimental tunneling conduction in Au/SAM//EGaIn junction
is supported by the UPS measurements that also give a similar E value (see Supplemen-
F
tary Information section 1.3.3). It is has also been established experimentally that SAMs
of aliphatic and conjugated molecules on Au shift the E values by 0.85 and 0.98 eV, re-
F
[
69–71]
spectively, (i.e., to −4.2 eV to −4.4 eV) from −5.2 eV for a clean gold surface.
This
value of E was used for all DFT calculations. Further rational for choosing this value of EF
F
and the detailed step-wise procedure for all the calculations involved is further described in
Supplementary Information.
1
4

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ACKNOWLEDGMENTS
R.C.C., Y.Z. and M.C. acknowledge the European Research Council for the ERC Starting
Grant 335473 (MOLECSYNCON). G.Y. acknowledges financial support from the China
Scholarship Council (CSC):NO.201408440247. X.Q. acknowledges the Zernike Institute for
Advanced Materials “Dieptestrategie.” E.S. and M.Z. thank the Helmholtz Zentrum Berlin
for the allocation of synchrotron radiation beamtime at BESSY II and A. Nefedov and Ch.
W o¨ ll for the technical cooperation during the experiments there; a financial support of the
German Research Society (Deutsche Forschungsgemeinschaft; DFG) within the grant ZH
6
3/22-1 is appreciated. We thank the Center for Information Technology of the University
of Groningen for their support and for providing access to the Peregrine high performance
computing cluster.
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a
b
Figure 1: (a) Structures of BDT-1, BDT-2 and BDT-3 with linearly and cross-conjugated
pathways of the cores drawn in blue and red, respectively. The phenylacetylene arms (high-
lighted in blue) are linearly conjugated. BDT-1 is linearly-conjugated, BDT-2 contains
a cross-conjugation imposed by the central quinone ring analogous to AQ and BDT-3 is
similarly cross-conjugated, but the cross-conjugation separating the two linearly-conjugated
pathways arises from the positions of the sulfur atoms relative to the central phenyl ring
(
there are no exocyclic bonds). (b) Schematic of Au/SAM//EGaIn junction (“/” and “//”
denote a covalent and van der Waals interfaces, respectively).
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a
-2
-3
-4
-5
-6
BDT-1
BDT-2
BDT-3
AQ
-1,0
-0,5
0,0
0,5
1,0
Potential (V)
b
1
Linear-conjugation
0
,1
Cross-conjugation
Quinone
0
,01
0
,001
BDT-1
BDT-2
BDT-3
AQ
Molecule
−
2
Figure 2: (a) Plots of log |J(Acm )| versus V of Au/SAM//EGaIn junctions comprising
SAMs of BDT-1 (salmon up-triangles), BDT-2 (purple down-triangles), BDT-3 (pink
diamonds) and AQ (grey circles). Each datum is the peak position of a Gaussian fit of
log |J| for that voltage. The error bars are 95 % confidence intervals taking each junction
as a degree of freedom. (b) Normalized low bias conductance, linearly conjugated BDT-1
(
salmon ball) features the highest values, the quinone BDT-2 (purple ball) and AQ (grey
ball) the lowest and cross conjugated BDT-3 (pink ball) is in between.
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0
1
2
3
4
5
1
0
-
10
-
-
-
-
10
10
10
10
BDT-1
BDT-3
BDT-2
AQ
-
2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0
E-E (eV)
F
Figure 3: Transmission spectra for isolated molecules of BDT-n and AQ. The spectrum of
BDT-1 (salmon) is featureless between the resonances (T(E) → 1) near the frontier orbitals.
The sharp dips in the spectra of BDT-2 (purple), BDT-3 (pink) and AQ (grey) indicated
with arrows are destructive QI features. The energies on the bottom axis are with respect
to the E value of −4.3 eV.
F
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!
"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
!' %
!' $
!% #
!& ꢀ
!& "
!# %
!# $
!ꢁ #
!" ꢀ
!' %
!' $
!% #
!& ꢀ
!& "
!# %
!# $
!ꢁ #
!" ꢀ
BDT-1
BDT-2
()*+,*-./ 012
()*+,*-./ 012
!' %
!' $
!% #
!& ꢀ
!& "
!# %
!# $
!ꢁ #
!" ꢀ
!' %
!' $
!% #
!& ꢀ
!& "
!# %
!# $
!ꢁ #
!" ꢀ
BDT-3
AQ
()*+,*-./ 012
()*+,*-./ 012
Figure 4: Differential conductance heatmap plots of Au/SAM//EGaIn junctions comprising
BDT-1 (top-left), BDT-2 (top-right), BDT-3 (bottom-left) and AQ (bottom-left) showing
dJ
dV
histograms binned to log | | (differential conductance, Y-axis) versus potential (V , X-axis).
The colors correspond to the frequencies of the histograms and lighter (more yellow) colors
indicate higher frequencies. The bright spots near ±1 V are due to the doubling of data that
occurs in the forward/return J/V traces. The plots for both BDT-2 and AQ, which contain
quinones, are V-shaped at low bias and exhibit negative curvature, indicating a destructive
QI feature near E , while the plots of BDT-1 and BDT-3 are U-shaped.
F
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a
2
1
0
1
2
LUPS
HOPS
-
-
BDT1
BDT2
BDT3
AQ
Molecule
b
0,7
0,6
0,5
0,4
0,3
0,2
0,1
2,2
2
,0
,8
1
1,6
1
,4
,2
1
1,0
Vtrans
EHOPS-Efermi
0
,8
,6
|
|
0
|EMO-Efermi
|
0,4
BDT1
BDT2
BDT3
AQ
Molecule
Figure 5: (a) Energy offsets of the frontier orbitals calculated using DFT with respect to EF
value of −4.3 eV. (b) The energy offsets (salmon and purple lines, right axis) plotted with
the measured values of Vtrans (black line, left axis). The salmon line plots the energy offsets
of the HOPS. The purple line plots the smallest energy difference (purple arrows in Figure
5
a); |E
− E
| for BDT-1 and BDT-3, |E
− E
| for BDT-2 and AQ. The
HOPS
Fermi
LUPS
Fermi
exact values of V
and the orbital energies are shown in Table S3 and S5.
trans
2
9