C-Au Covalently Bonded Molecular Junctions Using Nonprotected Alkynyl Anchoring Groups

Article abstract of DOI:10.1021/jacs.6b03383

We report on an approach to realize carbon-gold (C-Au) bonded molecular junctions without the need for an additive to deprotect the alkynyl carbon as endstanding anchor group. Using the mechanically controlled break junction (MCBJ) technique, we determine the most probable conductance value of a family of alkynyl terminated oligophenylenes (OPA(n)) connected to gold electrodes through such an akynyl moiety in ambient conditions. The molecules bind to the gold leads through an sp-hybridized carbon atom at each side. Comparing our results with other families of molecules that present organometallic C-Au bonds, we conclude that the conductance of molecules contacted via an sp-hybridized carbon atom is lower than the ones using sp³ hybridization due to strong differences in the coupling of the conducting orbitals with the gold leads.

Full text of DOI:10.1021/jacs.6b03383

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Article
C-Au covalently bonded molecular junctions
using non-protected alkynyl anchoring groups
Ignacio Jose Olavarria-Contreras, Mickael L Perrin, Zhi Chen,
Svetlana Klyatskaya, Mario Ruben, and Herre S. J. van der Zant
J. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.6b03383 • Publication Date (Web): 07 Jun 2016
Downloaded from http://pubs.acs.org on June 8, 2016
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C-Au covalently bonded molecular junctions using
non-protected alkynyl anchoring groups
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†
†
‡
Ignacio José Olavarria-Contreras, Mickael L. Perrin, Zhi Chen, Svetlana
‡
‡,¶
∗,†
Klyatskaya, Mario Ruben, and Herre S.J. van der Zant
Kavli Institute of Nanoscience, Delft University of Technology, Institute of Nanotechnology
(
INT), Karlsruhe Institute of Technology (KIT), and IPCMS-CNRS, Université de
Strasbourg
E-mail: H.S.J.vanderZant@tudelft.nl
Abstract
We report on an approach to realize carbon-gold (C-Au) bonded molecular junc-
tions without the need of an additive to deprotect the alkynyl carbon as endstanding
anchor group. Using the mechanically controlled break junction (MCBJ) technique
we determine the most probable conductance value of a family of alkynyl terminated
oligophenylenes (OPA(n)) connected to gold electrodes through such a akynyl moiety
in ambient conditions. The molecules bind to the gold leads through a sp-hybridized
carbon atom at each side. Comparing our results with other families of molecules that
present organometallic C-Au bonds, we conclude that the conductance of molecules
∗
†
To whom correspondence should be addressed
Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, Delft 2628 CJ, The Nether-
lands
‡
Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-
Leopoldshafen, Germany
¶
IPCMS-CNRS, Université de Strasbourg, 23 rue de Loess, 67034 Strasbourg, France
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contacted via an sp-hybridized carbon atom is lower than the ones using sp hybridiza-
tion due to strong differences in the coupling of the conducting orbitals with the gold
leads.
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Introduction
Recent developments in break-junction measuring techniques1–4 have allowed researchers
to investigate charge transport through individual molecules. Strategies for contacting
molecules to metallic electrodes usually rely on the use of anchoring groups such as thiols,5
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8–10
and systematic comparisons have been carried out.11–14 Re-
cyano, pyridines or amines
cently, new methods have been developed to contact molecules based on a direct carbon-gold
bond.15–22 These methods employ protection groups at the extremities of the molecule that,
by applying different external stimuli, are removed in the solvent leaving the endstanding
carbon-atoms free to coordinate directly to the gold atoms of the electrodes. It has been
shown that direct a carbon-gold bond can give rise to a high molecular conductance.17
Molecules composed of a series of phenyl rings, such as oligphenylenes (OP), oligophenylethylenes
OPE) or oligophenylvinylenes (OPV) are interesting systems because they posses delocal-
(
ized orbitals allowing for efficient charge transport. Several research groups have reported
on transport through single-molecule junctions with a direct C-Au bond using these conju-
gated molecular backbones.16–21 W. Chen et. al. have studied a family of highly conductive
17
OP(n=1-4) molecules which form a covalent C-Au bond by cleaving SnMe protecting groups,
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exposing a methylene (sp -hybridized carbon). The same research group also reported on
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the conductance of a para-phenyl (OP1) molecule connected by a sp -hybridized carbon to
the gold using the same SnMe leaving groups.16 Hong et. al.18 performed measurements
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on a trimethylsilyl oligophenylethylene (TMS-OPEn, n=1,2,3) family of molecules. Using
tetrabutylammonium fluoride (TBAF) as a de-protecting agent the TMS end group was
cleaved from the oligophenylethylene backbone leaving a sp-hybridized carbon free to form a
Au-C σ-bond. Despite the advantages of the C-Au bonding, there are also drawbacks to the
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reported approaches, including the rapid formation of dimers, the need of a de-protecting
agent and/or rather toxic precursors as leaving groups.
Here, we report on the measurement of the low-bias conductance on a family of oligopheny-
lene ethylene OPA(n) molecules, displayed in Figure 1a, in which the alkynyl end-group
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(
R −C ≡ C −H) acts as anchoring group. These molecules directly form a C-Au bond
to the leads by the in-situ de-protonation of the acidic C-H proton (pKa ∼ 26) of the
alkynyl groups.23–25 This approach avoids the need of de-protecting agents or toxic leaving
groups. Moreover, the molecules do not exhibit bulky protective groups. Measurements are
performed using the mechanically controlled break junction (MCBJ) technique in ambient
conditions and show the formation of molecular junctions even after several hours after de-
position; the conductance values are of the same order of magnitude as similar molecules
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with sp- or sp -hybridized Au-C bonds while being an order of magnitude lower than those
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using sp Au-C hybridization.
Results and discussion
Figure 2 displays the conductance vs. electrode displacement histograms of three oligo py-
henylene ethynylene molecules: a) OPA2, b) OPA3 and c) OPA4. In each of these diagrams
we identify two characteristics. First, an exponential conductance decay is present between
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0 and 0.5 nm covering the conductance range from about 10 G to the noise level (marked
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with thin black lines); these breaking traces are attributed to empty junctions. The color
scale indicates that in most of the cases no molecule has been trapped between the elec-
trodes. The second characteristic is a region where the conductance decreases slower with
stretching. Examples of individual traces in this regime are displayed in the insets of Fig-
ure 2. OPA3 (Figure 2b) exhibits this region between displacements ranging from 0 to 1
−3
nm with a conductance around 10 G . For OPA4 (Figure 2c) the same behavior is ob-
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served between 0 and 1.5 nm with a conductance around 10 G . OPA2 needs a closer look,
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because it presents two of such regions; the first one, around 10 G , is characterized by
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displacements shorter than 0.6 nm and a second high-count region is present near 10 G
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for traces between 0.5 and 2.5 nm. An interesting feature is that most of the traces show
slanted plateaus rather than flat ones as is usually seen in molecular wires.
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We have also performed the same experiment on a phenyl ethylene (OPA1) molecule but
we did not observe clear molecular signatures in that case; see the molecular structure and
histograms in Figure S3 in the SI. In reference [1 8] a similar single phenyl ring with an unpro-
tected alkynyl anchoring group was measured: Junction formation was not observed there
either while the same backbone with a TMS protecting group showed molecular features.
To determine the conductance value of the OPA(n) molecules we construct one-dimensional
conductance histograms without any data selection (Figure 3a). By fitting a log-normal dis-
tribution to the conductance regions with molecular features (dotted lines in Figure 3a),
we extract the most probable molecular conductance value for the three molecules; for each
molecule two samples were measured. The values of the obtained conductance are summa-
rized in Table 1 and the average values are plotted with blue diamonds as a function of
molecular length in Figure 3b. For OPA2, two values of conductance are listed; one at high
conductance and one at low conductance, corresponding to the two features appearing in
the two-dimensional histogram. We attribute the highest one to the molecular conductance
of the molecule itself, whereas the lower value with plateau lengths exceeding the length of
the molecule can be associated to the presence of dimers of the molecule18,19 or to π −π
stacking of two molecules each attached to one electrode.26 For this molecule, we have ana-
lyzed the time evolution of the conductance vs. displacement curves in time to investigate
whether the dimer formation occurs more frequently as times progresses. We have not found
a clear indication for such a trend (see Figure S4): after four hours of measurements high
and low-conductance traces are still present.
A striking characteristic of Figure 3b is the non-exponential decay of the conductance
with molecular length (open blue diamonds) for the OPA(n=2,3,4) series. The fact that
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the conductance of OPA2 has approximately the same value as OPA3 is an unexpected
result, especially because measurements on the same molecular backbone (oligophenylene)
have shown an exponential decay for different anchoring groups and measurement tech-
niques,17,27–29 with β ≈ 0.45 Å . An interesting observation is that the de-protonated
OPA1 has the same structure as the de-protected TMS-OPE1 in reference [18]. If we take
into account this conductance value an exponential decay among OPE1, OPA3 and OPA4
−1
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(
black dashed line in Figure 3b) is found.
To put our results in a broader context we compare our data with other molecules that
also form a direct Au-C bonds to the leads. The conductance vs. length dependence of
these molecular families is displayed in Figure 3b as well. We observe that the conductance
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of molecular chains which are connected via sp -hybridized carbon atoms is higher than the
corresponding chain connected by sp-hybridized carbon atoms. For the single benzene ring
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case this observation was already discussed in reference [17] when comparing sp - and sp
hybridization.
We have also performed density functional theory (DFT) calculations to compute the
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molecular geometries and electronic structures for sp- and sp hybridization of the anchor-
ing carbon atoms, corresponding to the OPA(n) and SnMe-OP structure inside the junction,
respectively. These calculations were combined with the non-equilibrium Green’s function
NEGF) formalism to obtain the transmissions, were self-energies corrected using DFT+Σ,8
(
of the OP(n=1-4) molecules. Figure 4 (a,b) shows the iso-surface of the highest occupied
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molecular orbital (HOMO) for OP3 with an sp- and sp -hybridized anchoring carbon, respec-
tively. The lower panels display the same orbitals in the region where the molecule contacts
the gold. We note two important differences. First, the amplitude of the wave functions
around the linking gold is smaller in the case of sp and second, the symmetry of the atomic
orbital of the gold atom that is involved in the wave function, is different in the two cases.
In the case of sp hybridization the main contribution of the gold to the wave function comes
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from the 5d orbital while in the case of the sp -hybridized carbon, the main contribution
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comes from the 6s orbital of the gold.
Focusing on the transmission function of OP3 as displayed in Figure 4c, one notes that
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in the case of sp (green drawn line) the shape of the resonance peaks is broader, indicating
a higher coupling between the electrodes and the molecule, in agreement with the wave-
function overlap discussion earlier. The calculations further support our findings that the
conductance of molecules with the same number of benzene rings differs greatly depending
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on the hybridization of the end-standing carbon atoms: sp -hybridization gives a higher
conductance, mainly because the favorable coupling between the gold electrodes and the
molecule.
We also analyzed the dependence of the conductance on the molecule length and found
that the transmission function decays exponentially with molecular length for the sp-hybridized
OPA(n) series as can be seen in Figure S7. The odd behavior of the OPA2 conductance,
therefore, may be associated with degrees of freedom not captured in the calculation. For
example, a non-exponential decay of conductance has also been observed for oligo-thiophene
molecules,30,31 and in that case it was attributed to the ability of a 4-thiophene to rotate
toward a more conjugated configuration compare to the 3-tiophene that cannot rotate. An-
other explanation may originate from the binding configuration itself. In the literature it has
been proposed that alkynyl groups in contact with gold may form a rather “undetermined”
binding configuration displaying a more sp like character;23,32–34the smaller the molecule,
the more likely this is expected to occur.35 This suggestion is in line with the results dis-
played in Fig.3 which show that a line parallel to the black and red drawn lines through the
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sp -hybridized OP1 and diazonium terminated OP2 data points (open square and the green
x respectively) interestingly is close to the OPA2 conductance value from our study.
In conclusion, we have demonstrated that it is possible to contact single molecules through
a covalent σ-C-Au bond formation directly from de-protonating alkynyl anchoring groups.
This method avoids the need of cleavage off bulky protecting groups and the use of de-
protection by an external agent. In our approach, the molecules connect to the gold leads
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through a sp-hybridized carbon atoms in a way that it mainly couples to the 5d orbital of
the gold. The involvement of the 5d orbital leads to a lower electronic coupling than for
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Methods
Synthesis
The molecules OPA2 and OPA3 were synthesized following reported procedures.36,37 For the
synthesis of OPA4 a novel procedure was developed. The detailed description and charac-
terization of OPA4 can be found in the SI.
Conductance Measurements
Single-molecule conductance measurements were performed in a mechanically controllable
break junction (MCBJ) set up.38 The devices consist of a phosphorus bronze flexible sub-
strate coated with a polyimide insulation layer, on top of which a lithographically defined
gold wire with a constriction is patterned. The narrower part of the wire is suspended by
reactive ion etching of the polyimide. The substrate is then clamped at both ends and
bent by the action of a pushing rod beneath the center of the substrate (Figure 2b) until
the gold wire breaks leaving two atomically sharp electrodes separated by a nano-scale gap.
The electrodes are fused and broken thousands of times at a rate of 10 nm/s. During this
process, the conductance (G = I/V ) is recorded using a logarithmic amplifier with a bias
voltage of 0.1 V. During each breaking process the conductance is recorded as a function
of the electrode displacement. Before the gold wire breaks, the conductance of the junction
drops in a stepwise manner due to atomic rearrangements in the contact. When the metallic
contact breaks, the conductance sharply drops below 1 G , where G is the conductance
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quantum (G = 2e /h with h the Planck’s constant and e the charge of an electron). This
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sharp decrease in conductance is used to set the zero displacement of each trace. In the
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case no molecule bridges the gap, the breaking traces show a featureless exponential conduc-
tance decrease, indicative of single-barrier tunneling. If a molecule contacts both electrodes,
the conductance no longer follows this behavior. Instead, a slower conductance decay with
plateau-like features is observed.
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We present our data in the form of two-dimensional conductance versus displacement
histograms built from 2000 consecutive traces. To check the presence of spurious contam-
inants in the MCBJ devices, 1000 traces are first recorded on the bare Au devices before
exposing them to the solvent with the molecules. Only if a clean junction was formed as
indicated by clear single-barrier tunneling traces (see SI Figure S3), the molecules are de-
posited by pipetting a 2 µL drop of solution onto the sample. Subsequently, the solvent
(dichloromethane) is let to evaporate. The molecules in this study consist of a n-phenylene
backbone (n=2,3,4) with alkynyl moieties at both sides (see Figure 1a). On each junction
calibration of the electrode displacement is done using the length of single-gold atom chains
obtained from the 1000 traces on bare junctions before molecular deposition.38,39
Theoretical calculations
The electronic ground-state properties were calculated using density functional theory (DFT)
as implemented in the ADF package,40,41 using the GGA-PBE functional,42 and the triple-
ζ plus polarization (TZP) Slater-type basis set. All electrons were considered, expect for
the gold atoms were the frozen core approximation was used. The zero-th order regular
approximation (ZORA) to the Dirac equation was used to account for relativistic effects due
to the presence of the Au electrodes. Each molecule was connected to two pyramidal gold
electrodes consisting of 30 atoms each. The geometries were converged to energy changes
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of less than 10 hartree, energy gradients of less than 10 hartree/Å maximum and 6.7 ·
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hartree/Å RMS. We calculated the transmission through the molecular junction using
the non-equilibrium Green’s function (NEGF) formalism by connecting the outer gold layer
to wide-band limit electrodes,43 with a coupling strength of 1 eV. To correct for electron
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correlation errors upon addition/removal of a charge on the molecule, the DFT + Σ method
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was used, implemented as follows. First, a correction to the ionisation potential and electron
affinity is calculated based on the anion and cation charge states of the molecule in gas phase.
As gas phase geometry, the geometry of the molecule in the junction was chosen with the
apex gold atoms attached. Second, image-charge effects were calculated for the different
charge states (also in gas phase). This was done using the Hirschfeld charge distribution
between two parallel plates, similar to a classic image charge model.44,45 The image planes
were set at a distance of 1 Å outside the innermost gold atoms.8,46 Both contribution were
combined to a scissor operator value for occupied and unoccupied levels, and used to correct
the transmission.
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Acknowledgement
We acknowledge support from the Dutch organization for Fundamental Research (FOM),
OCW/NWO, an ERC advanced grant (Mols@Mols) and the China scholarship council (CSC).
We also acknowledge the Karlsruhe Nano Micro Facility (KNMF, www.kit.edu/knmf) of the
Forschungszentrum Karlsruhe for provision of access to instruments at their laboratories.
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R. M. ; Michel-Beyerle, M. E. ; Miller, J. R. ; Newton, M. D. ; Rolison, D. R. ;
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Nature Nanotechnology 2013, 8, 282–287.
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V
a)
b)
OPA2
OPA3
OPA4
A
H
H
H
molecules in
solution
H
clamping support
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ꢀexible substrate
pushing rod
Figure 1: a) Chemical structure of the molecules studied in this work. Phenylene hydrogen
atoms are omitted. b) Schematics of the mechanically controlled break junction (MCBJ)
set up.
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b)
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0 2 4
0 2 4
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low
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2
diplacement (nm)
diplacement (nm)
diplacement (nm)
Figure 2: Two-dimensional conductance vs. electrode displacement histograms constructed
from 2000 consecutive breaking traces measured at room temperature in air with a 0.1 V bias
voltage applied and a ramp rate of 10 nm/s. Junctions exposed to a 28 µM molecule solution
in dichloromethane for a) OPA2, b) OPA3 and c) OPA4. Insets show examples of individual
conductance traces with plateau-like features assigned to the presence of a molecule; traces
are offset in the displacement direction.
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Figure 3: a) One-dimensional conductance histograms using a logarithmically binning (solid
line) for OPA2 (blue), OPA3 (red) and OPA4 (green). Dotted lines represent log-normal
fittings around the regions of high counts in the histograms and are used to extract the most
probable conductance value. b) Conductance as a function of molecular length for OPA(n)
(
blue) compared to other molecules in the literature that form direct C-Au bonds. Differ-
ent families present different hybridization of the last carbon. Red open circles represent
molecules with direct sp C-Au bonding from reference [17]; the green square is a single
benzene ring connected to gold through a sp -hybridized carbon; the open blue circle cor-
responds to OPE1 connected to gold via a sp-hybridized carbon from the series in reference [
3
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16
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8]; the green x is a diazonium terminated OP2 which is electrochemically deprotected and
2
connected through an sp -hybridized carbon that was studied in [20]. The black dashed
line connects the OPA(n) series. Note, that the structure of OPE1 corresponds to the same
structure as OPA1 in this study when contacted to the gold electrodes.
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sp
sp3
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energy eV
−2
Figure 4: Diagram of the HOMO of a OP3 attached to gold atoms through a) sp- and
b) sp -hybridized carbon. Zoom ins (lower panels) show the same orbitals near the Au-C
interface. c) Transmissions calculated using DFT+NEGF for the OP3 molecule with sp-
(blue line) and sp -hybridized (green line) linking to the gold.
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Table 1: Most probable molecular conductance for the series of OPA(n) molecules extracted
from the one-dimensional conductance histograms. The first column contains the values
obtained with a concentration of 28 µM and the values in the second column were obtained
with a saturated concentration of molecules, meaning 4.95 mM for OPA2, 0.36 mM for
OPA3 and 28 µM for OPA4. The values plotted in Figure 3 are the average of the two
measurements of each molecule. For OPA2, two values are listed, one at high conductance
and one at low conductance (see text for a discussion on these values).
Molecule Conductance (G )
0
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7.8 · 10−6
OPA2
OPA3
OPA4
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5.7 · 10
1.0 · 10
4.1 · 10
4.4 · 10
3.9 · 10
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