Controlling Single Molecule Conductance by a Locally Induced Chemical Reaction on Individual Thiophene Units

Article abstract of DOI:10.1002/anie.201915200

Among the prerequisites for the progress of single-molecule-based electronic devices are a better understanding of the electronic properties at the individual molecular level and the development of methods to tune the charge transport through molecular junctions. Scanning tunneling microscopy (STM) is an ideal tool not only for the characterization, but also for the manipulation of single atoms and molecules on surfaces. The conductance through a single molecule can be measured by contacting the molecule with atomic precision and forming a molecular bridge between the metallic STM tip electrode and the metallic surface electrode. The parameters affecting the conductance are mainly related to their electronic structure and to the coupling to the metallic electrodes. Here, the experimental and theoretical analyses are focused on single tetracenothiophene molecules and demonstrate that an in situ-induced direct desulfurization reaction of the thiophene moiety strongly improves the molecular anchoring by forming covalent bonds between molecular carbon and copper surface atoms. This bond formation leads to an increase of the conductance by about 50 % compared to the initial state.

Full text of DOI:10.1002/anie.201915200

A Journal of the Gesellschaft Deutscher Chemiker
Angewandte
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Accepted Article
Title: Controlling Single Molecule Conductance by Chemical Reaction
Authors: Tomasz Michnowicz, Bogdana Borca, Rémi Pétuya, Verena
Schendel, Marcel Pristl, Ivan Pentegov, Ulrike Kraft, Hagen
Klauk, Peter Wahl, Pingo Mutombo, Pavel Jelínek, Andrés
Arnau, Uta Schlickum, and Klaus Kern
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To be cited as: Angew. Chem. Int. Ed. 10.1002/anie.201915200
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Controlling Single Molecule Conductance by a Locally Induced
Chemical Reaction on Individual Thiophene Units
Tomasz Michnowicz[a]‡, Bogdana Borca*[a,b]‡§,Rémi Pétuya[c]‡#, Verena Schendel[a], Marcel Pristl[a], Ivan
Pentegov[a], Ulrike Kraft[a]┴, Hagen Klauk[a], Peter Wahl[a,d], Pingo Mutombo[e], Pavel Jelínek[e], Andrés
Arnau[c,f], Uta Schlickum*[a,g] and Klaus Kern[a,h]
Abstract: Among the prerequisites for the progress of single-
molecule-based electronic devices are a better understanding of the
electronic properties at the individual molecular level and the
development of methods to tune the charge transport through
molecular junctions. Scanning Tunneling Microscopy (STM) is
an ideal tool not only for the characterization, but also for
the manipulation of single atoms and molecules on surfaces.
The conductance through a single molecule can be measured by
contacting the molecule with atomic precision and forming
a molecular bridge between the metallic STM tip electrode and
the metallic surface electrode. The parameters affecting
the conductance are mainly related to their electronic structure and to
the coupling to the metallic electrodes. Here, the experimental and
theoretical analyses are focused on single tetracenothiophene
molecules and demonstrate that an in-situ-induced direct
desulfurization reaction of the thiophene moiety strongly improves the
molecular anchoring by forming covalent bonds between molecular
carbon and copper surface atoms. This bond formation leads to an
increase of the conductance by about 50% compared to the initial
state.
[a]
[b]
Dr. T. Michnowicz, Dr. B. Borca, Dr. V. Schendel, Mr. M. Pristl, Dr. I. Pentegov, Prof. P. Wahl, Prof. U. Schlickum and Prof. K. Kern
Department: Nanoscale Science
Dr. U. Kraft, Dr. H. Klauk,
Department: Organic Electronics
Institution: Max Planck Institute for Solid State Research
Address 1: Heisenbergstrasse 1, D-70569, Stuttgart, Germany
Dr. B. Borca
Institution: National Institute of Materials Physics
Address 2: Atomistilor Str., No. 405A, 077125, Magurele, Romania
Email: bogdana.borca@infim.ro
[c]
[d]
Dr. R. Pétuya, Prof. A. Arnau
Institution: Donostia International Physics Centre
Address 3: Paseo Manuel de Lardizabal 4, E-20018 Donostia - San Sebastián, Spain
Prof. P. Wahl
Department: SUPA, School of Physics and Astronomy
Institution: University of St Andrews
Address 4: North Haugh, St Andrews, KY16 9SS, United Kingdom
Dr. P. Mutombo, Dr. Ing. P. Jelínek
[e]
Department: Nanosurf Lab
Institution: Institute of Physics of the Czech Academy of Science
Address 5: Cukrovarnicka 10, CZ-16253, Praha 6, Czech Republic
Prof. A. Arnau
[f]
Institution: UPV/EHU and Material Physics Center (MPC), Centro Mixto CSIC-UPV/EHU
Address 6: Paseo Manuel de Lardizabal 5, E-20018 Donostia - San Sebastián, Spain
Prof. U. Schlickum
[g]
Institution: Institute of Applied Physics, Technische Universität Braunschweig,
Address 7: Mendelssohnstraße 2, 38106 Braunschweig, Germany
Email: u.schlickum@tu-bs.de
[h]
Prof. K. Kern
Institution : Institut de Physique, École Polytechnique Fédérale de Lausanne (EPFL)
Address 8: EPFL SB IPHYS-Direction Bâtiment PH, Station 3, CH-1015 Lausanne, Switzerland
Present addresses:
# University of Liverpool, Department of Chemistry, Crown Street, Liverpool L69 7ZD, United Kingdom
┴ University of Cambridge, Cavendish Laboratory, J J Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
§ Institute of Applied Physics, Technische Universität Braunschweig, Mendelssohnstraße 2, 38106 Braunschweig, Germany
Author Contributions
‡ Tomasz Michnowicz, Bogdana Borca, and Rémi Pétuya contributed equally.
Supporting information for this article is given via a link at the end of the document.
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Figure 1. Controlled desulfurization reaction. a,b) AFM frequency-shift images of tetracenothiophene (TCT) and tetraceno-derivative (TC-D) molecules respectively.
c,d) simulated AFM images based on DFT calculations. e,f) adsorption geometry of the surface-molecule structure obtained from DFT calculations in a ball-and-
stick representation. g) schematic representation of the experiment; the reaction produces a step-like feature in the I(V) trace recorded at a constant height above
the thiophene unit.
greater overlap of metal and molecular wave functions. The most
One of the challenges associated with reducing electronic circuits
to single-molecule components is the formation of reliable, low-
resistance contacts between the molecule and the metallic
electrodes to enable an efficient charge transport across the
metal-organic interface [1,2]. While π-conjugated systems with a
delocalized electronic structure are typically characterized by a
high electronic conductance through the molecules [3,4], they are
usually equipped with non-conjugated end groups designed to
selectively couple the molecules to specific metallic electrodes [5-
7]. Moreover, the ability to control the junction’s geometry with the
spatial overlap of orbitals is an important prerequisite for the
optimization of the electronic device properties, such as the
charge-injection efficiency and the charge mobility [8-11]. To this
end, covalent bonds between the molecule and the metal
electrodes are advantageous to ensure a robust mechanical and
electronic connection. In the ideal case, the organo-metallic
contacts of the molecular electronic element are established
through a chemical reaction between the molecule and the metal.
The most popular examples are systems with covalent bonds
formed between sulfur-containing molecular end groups and gold
electrodes [4]. When the anchoring is realized through direct
covalent bonds between the carbon atoms and the metal, a higher
electronic conductance is obtained [4,12] due to a stronger
coupling between the metal and the molecular π-system and a
common methods used to measure the electronic properties of
organic molecules are based on the formation of break junctions
[13] by trapping the molecules between contacts. This technique
can be realized in mechanically controlled break junctions, and in
a more controlled way in Scanning Tunneling Microscopes (STM)
[14] or in conductive Atomic Force Microscopes (AFM) [15].
Variations of the molecular geometry and the number of
molecules in the junction as well as the significant effects of the
local environment may lead to very different signatures in the
conductance even for the same molecular species. To avoid
these uncertainties, we use an STM operating under ultra-high
vacuum conditions and at low temperature. The instrument is
particularly suitable for performing accurate conductance
measurements through single molecules, as it allows us to
characterize the structure at the submolecular level [16-19] and to
atomically precisely contact one specific end of the molecular unit
with the tip apex [20-25].
Here we explore a new class of covalent bond formation between
a chemically reacted thiophene molecular end group and Cu
electrodes. We investigate the molecule-metal-electrode
anchoring and the conductance across a tetracenothiophene
(TCT) molecule, a pentacene analogue, by controlling the
formation of covalent C-Cu bonds between the molecule and the
metal substrate on the submolecular scale. We demonstrate in
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this work that the resulting tetraceno derivative (TC-D) shows a
significant increase in the conductance, as a result of a better
contact formation between the bifurcated end of the remaining
thiophene part and the metal surface, whose fingerprint is an
intramolecular enhancement of the local density of states close to
the Fermi energy.
Previously we have shown [26] an in-situ-induced direct
desulfurization reaction on single thiophene units on Cu (111)
surfaces driven by the electric field confined in the tunnel junction
(Fig. 1). This desulfurization reaction of the TCT molecules can
also be induced thermally (see SI-2 for details). We now included
high-resolution non-contact AFM (nc-AFM) images clearly
revealing the opening of the thiophene ring and the split-off of the
S-atom. Using a CO-functionalized tip for non-contact AFM, we
are sensitive to the potential energy basins produced by the Pauli
repulsion between the CO-terminated tip apex and specific atomic
positions within adsorbed molecules [27]. This methodology gives
rise to an extremely high resolution of intermolecular structures
[28]. The high-resolution nc-AFM images of TCT and TC-D as well
as simulated nc-AFM images obtained from DFT calculations
clearly uncover the inter-molecular structure before and after the
chemical surface reaction (Figure 1).
As a consequence of this reaction, the two carbon atoms formerly
connected to the S atom in the thiophene group bind covalently
to Cu surface atoms, while the S atom is irreversibly detached
from the molecule. The resulting molecule, a tetraceno derivative
(TC-D) is therefore anchored to the surface by two covalent bonds.
To probe the effect of the strong anchoring of one of the
molecule’s end groups to the metal electrode, we performed
conductance measurements through single TCT and TC-D
molecules. The geometry of the measurement is sketched
schematically in Fig. 2. Before each conductance measurement,
the molecule is first imaged by STM. Then, the tip is placed on top
of the acene termination of the molecule, the feedback loop is
switched off and the tip is moved towards the molecule while the
current is recorded as a function of the tip-sample displacement
(z). At the jump-to-contact position we obtain the conductance in
units of the conductance quantum G0 = 2e2/h = 77.5 µS. Figure
2a shows an example of such a G(z) curve. The exponential
increase of the conductance corresponding to the tunneling
regime is due to the reduction of the width of the tunneling barrier.
At a certain distance of the tip above the molecule, an abrupt
increase in conductance is observed with a step-like feature
(Figure 2a). This corresponds to the jump-to-contact of the
molecular moiety to the tip apex and indicates lifting-up of this part
of the molecule from the surface. We speculate that the contact
of the terminal acene ring to the tip is formed through the
molecular π-orbitals. The conductance through the molecular
system (GM) is extracted from the step height in the jump-to-
contact regime (Figure 2a). Each conductance measurement was
performed on a different molecule. The jump-to-contact behavior
can occur at different tip-sample distances. To reduce the
influence of the geometry of the junction with the molecule lifted
from the surface on the conductance comparison, we only
considered data obtained within a small tip-distance window of 50
pm (see SI-4 for details). All these conductance values GM for TCT
and TC-D are summarized in the histograms in Figure 2b. Since
TCT is a pentacene analogue, we also added as a reference the
values measured for pure pentacene. The average conductance
Figure 2. Conductance measurements through single molecules. a) G(z) curves
acquired after switching the feedback loop off at a set point: I = 100 pA, V = 100
mV and approaching the tip 400 pm towards the molecule (only last 150 pm of
the approach depicted). Initially, the measured conductance corresponds to the
tunneling current (tunneling regime). Upon the approach, a tip-molecule contact
is realized and the recorded conductance corresponds to the sum of direct
current passing through the molecule and a tunneling current between tip and
Cu-surface (contact regime). The conductance through the molecular system
GM is obtained by subtracting the tunneling conductance measured just before
the jump-to-contact from the value measured just after the jump-to-contact. The
curve shown was acquired on a TC-D molecule contacted on the acene side. b)
Conductance histograms (with a binning of ±0.01 G0; all data points are obtained
at the same bias voltage (V = 100 mV) and at small snap-to-contact window (z
distance between 315 and 365 pm. We show the data of pentacene analogues
TCT and TC-D and added for comparison pure pentacene. The error bar
corresponds to the standard deviation extracted from the Gaussian fit. Insets:
Schematic representation of the measurement configuration.
values for TC-D are significantly larger; they are more than 45%
higher compared with TCT and 130% compared to pentacene.
The broad conductance distributions reflect the variation in the
bonding geometries at the contact with the tip and different tip
geometries encountered in different experiments.
We attribute the differences between the conductance through
the different types of molecules (TCT, TC-D, pentacene) to
variations of the molecule-metal interaction strength together with
changes in the molecular electronic structure. These effects are
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Figure 3. Calculated electronic structure and adsorption conformation of pentacene, TCT and TC-D molecules on Cu(111). a) Side views of the electronic
partial charge densities after an energy integration in the interval [-0.5;0.5] eV around the Fermi level. The corresponding isocontour value is 0.004 e/Bohr3 for
the converged molecular structures represented on ball-and-stick models of the pentacene, TCT and TC-D molecules. b) Ball-and-stick representation of the
molecules considering different moieties for the calculation of the projected density of states (PDOS). c) PDOS on different sides of the molecules summing
over 8 carbon atoms for pentacene, TCT and TC-D, respectively.
further analyzed using DFT calculations, in particular by
comparing the electronic structure and the degree of the
hybridization of the molecules to the Cu surface atoms (Figure 3).
The conduction of the molecular junction is mainly determined by
the electronic structure close to the Fermi level and by the
transmission eigenchannels through the calculated molecular
structures (ensuring a low molecular resistance).
In Figure 3a we show the partial charge densities of each type of
molecule, as defined in the figure caption by energy integration
around the Fermi level. For all three molecules the spatial
distribution of the electronic charge shown in Figure 3a is rather
uniform along the tetracene part. However, there is a significant
difference on the reacted thiophene side of the TC-D molecule.
The locally driven desulfurization reaction leads to the formation
of covalent bonds between the bifurcated termination and the
copper surface. The covalent bond formation results in a strong
increase in the overlap of the wave functions between the metal
electrode and the molecular end group, thus inducing a strong
anchoring process that may also induce a reduction of the contact
resistance (for details see SI-5). The strong coupling between the
molecular end group and the surface atoms is also evidenced in
the experiments by the fact that the reacted molecule cannot be
picked up completely with the STM tip apex by STM manipulation,
whereas this is possible for TCT and pentacene molecules.
In order to correlate the changes of the conductance to the
intrinsic molecular properties, we calculated the projected density
of states (PDOS) by summing over the atoms on different parts of
the molecules (Figure 3b, c). An overall enhancement of the
PDOS close to the Fermi level (EF) of the metal is observed on
the entire TC-D molecule, which is related to the electronic-
density delocalization of the aromatic system, but it is most
significant at the thiophene side (side 2) compared to pentacene
and TCT. The enhancement of the PDOS close to EF for TC-D is
responsible for the higher transmission, especially at the contact
formation at side 2.
In conclusion, we have demonstrated a significant increase in the
conductance (about 50%) through a single molecular junction by
a
controlled direct desulfurization reaction on one single
thiophene unit. As a consequence of the chemical reaction,
covalent bonds are formed between the bifurcated end of the
reacted thiophene part and Cu surface atoms. This strongly
enhances the electronic and mechanical anchoring to the
substrate and reduces the contact resistance between the
molecular end group and the metal substrate. The augmented
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der-Waals dispersion forces were included using the vdW-DF-cx method
[34, 35]. It is worth mentioning that with this functional we obtained a 2.38
Å adsorption distance of pentacene on Cu(111), in good agreement with
experimental findings of 2.34 +/- 0.02 Å [36]. We considered a 500 eV
energy cutoff in the plane-wave expansion, with a 2 × 3 k-point mesh in
the 1 × 1 unit cell as sampling of the Brillouin zone reciprocal space. The
electronic convergence criterion was 1 × 10-4 for all static calculations, and
the convergence on forces in the relaxations was 0.05 eV/Å. The VESTA
software [37] was employed for the ball-and-stick and charge density
representations.
overlap of the wave functions results in an overall increase of the
density of states close to the Fermi level, in particular at the
thiophene side, and in an increase of the conductivity through
single TC-D molecules. These results pave the way toward a new
approach for an efficient molecule-metal-electrode anchoring
resulting in a drastic increase in conductance essential for single-
molecule electronic device elements.
Experimental Section
From the DFT-vdW optimized adsorptions geometries, AFM image
simulations were performed using the probe-particle model [27,38], which
is based on the van-der-Waals (vdW) and electrostatic interactions
between the sample and the tip. The electrostatic interaction between tip
and sample was calculated from the surface Hartree potential obtained
from DFT calculations, while the classic pairwise potential (Lenard-Jones)
was used to describe the Van-der-Waals attraction and the Pauli repulsion.
The AFM calculations were carried out with different values of the effective
charge of the probe particle in order to obtain AFM images that show a
good agreement with the experimental results. It was found that a
quadrupole (dz2) distribution of the effective charge was more appropriate
to describe the CO-terminated tip [39]. Note that all theoretical simulations
were performed with a fixed lateral stiffness of (k) = 0.25 N/m and by
approximating the CO-functionalized tip by an effective atomic radius Rc =
1.661 Å. The agreement between the theoretical findings and the
experiments enables us to understand and interpret the origin of the
chemical contrast.
Experimental Details
Experiments were performed under ultrahigh-vacuum (UHV) conditions.
The substrate is a Cu(111) surface, which was cleaned by repeated cycles
of Ar+ ion bombardment and subsequent annealing at 800 K. Pentacene
was purchased from Sigma-Aldrich. TCT molecules were synthesized
following the methodology described in reference [29]. The spectroscopic
investigations of the identity and purity of tetracenothiophene and the
precursors is presented in the SI-1. The pentacene and TCT molecules
were thermally sublimated separately and in different experiments from
ceramic crucibles at 445 K and 485 K, respectively. The molecular
coverage in different experiments was between 7 to 15% of a monolayer.
We have always selected isolated molecules for the conductance
measurements which is one of the advantages using STM. For the
pentacene sublimation, the substrate was at room temperature, while for
TCT the Cu(111) surface was held at 200 - 250 K during deposition to
avoid the thermally induced desulfurization (see SI-2). After each
evaporation, the sample was transferred in-situ into the STM, operating at
low temperatures (6 K). The STM measurements were carried out by
applying the bias voltages to the sample. The TC-D molecules were
produced in the STM by the direct desulfurization reaction, performed by
placing the tip on top of the thiophene moiety of a TCT molecule, at a
height corresponding to the set point of 100 pA, 100 mV. Then, the
feedback loop was switched off and at constant height the voltage was
ramped. Changes in the I(V) curves were observed when the reaction
occurred. The high-resolution nc-AFM frequency-shift images were
acquired with a CO-terminated tip. The CO molecule was vertically
manipulated to the tip apex from the NaCl(100) islands. For the AFM image
acquisition, the tip was positioned over the thiophene group in the case of
the TCT molecule and over the tetracene termination in the case of the
TC-D molecule. At the feedback 150 pA and 10 mV, the STM Z-feedback
was switched off and the bias voltage was reduced to 1 mV. The images
were obtained with both amplitude and phase feedback of the AFM
enabled and using the oscillation amplitude of 40 pm. The conductance
measurements were performed by a vertical manipulation procedure. After
switching off the feedback loop at 100 pA, 100 mV and moving the tip
toward the molecules by 250 pm, the I(z) curves were recorded above the
acene-terminated end of each molecule, which were identified beforehand
locally by imaging the molecule in the STM mode. STM images of a TCT
molecule and of the produced TC-D molecules are shown in SI-3.
Acknowledgements
The authors acknowledge the Emmy-Noether-Program of the
Deutsche Forschungsgemeinschaft, the SFB 767, Core Program
PN19-03 (contract number 21 N/08.02.2019) founded by the
Romanian Ministry of Research and Innovation, Basque
Departamento de Universidades e Investigación (grant no. IT-
756-13), the Spanish Ministerio de Economía y Competitividad
(grant no. FIS2013-48286-C2-8752-P and FIS2016-75862-P) and
the Operational Programme Research, Development and
Education financed by European Structural and Investment
Funds and the Czech Ministry of Education, Youth and Sports
(Project No. SOLID21 CZ.02.1.01/0.0/0.0/16_019/0000760). P.M.
acknowledges access to computing and storage facilities owned
by parties and projects contributing to the Czech National Grid
Infrastructure MetaCentrum provided under the programme
"Projects of Large Research, Development, and Innovations
Infrastructures" (CESNET LM2015042).
Keywords: single-molecule conductance • covalent-bond
formation • strong anchoring • STM/AFM • DFT
Computational details
DFT-vdW calculations were performed using the Vienna Ab-initio
Simulation Package (VASP) [30, 31]. An (8x6) periodic supercell with a 4-
layer slab was employed to model the adsorption of each type of molecule
(TCT, TC-D, pentacene) on the Cu(111) surface. For each geometry
optimization, full relaxation of all degrees of freedom of the molecule’s
atoms was performed, and the projected densities of states (PDOS) over
the pz orbitals of the carbon atoms were computed for the equilibrium
geometries. Ion-electron interactions were described with the projector
augmented-wave (PAW) method [32], and the exchange correlation was
modelled within the generalized gradient approximation (GGA) [33]. Van-
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10.1002/anie.201915200
Angewandte Chemie International Edition
COMMUNICATION
Entry for the Table of Contents
COMMUNICATION
We control and increase the
Tomasz Michnowicz, Bogdana
Borca*, Rémi Pétuya, Verena
Schendel, Marcel Pristl, Ivan
Pentegov, Ulrike Kraft, Hagen Klauk,
Peter Wahl, Pingo Mutombo, Pavel
Jelínek, Andrés Arnau, Uta
conductance of single molecules
by a stimulated chemical reaction
forming covalent bonds between
the reacted molecular unit and
surface atoms. The reaction path
is determined on the atomic scale
by scanning tunneling and atomic
force microscopy. The results are
supported by density functional
theory calculations.
Schlickum* and Klaus Kern
Page No. – Page No.
Controlling Single Molecule
Conductance by a Locally
Induced Chemical Reaction on
Individual Thiophene Units
This article is protected by copyright. All rights reserved.