Conductance of 'bare-bones' tripodal molecular wires

Article abstract of DOI:10.1039/c8ra01257a

Controlling the orientation of molecular conductors on the electrode surfaces is a critical factor in the development of single-molecule conductors. In the current study, we used the scanning tunnelling microscopy-based break junction (STM-BJ) technique t

Full text of DOI:10.1039/c8ra01257a

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Conductance of ‘bare-bones’ tripodal molecular
wires†
Cite this: RSC Adv., 2018, 8, 23585
a
*
Ross J. Davidson,
David C. Milan,b Oday A. Al-Owaedi,cd Ali K. Ismael,ce
b
b
c
Dmitry S. Yufita
*
Richard J. Nichols, Simon J. Higgins,
Colin J. Lambert,
a
*
and Andrew Beeby
Controlling the orientation of molecular conductors on the electrode surfaces is a critical factor in the
development of single-molecule conductors. In the current study, we used the scanning tunnelling
microscopy-based break junction (STM-BJ) technique to explore ‘bare-bones’ tripodal molecular wires,
employing different anchor groups (AGs) at the ‘top’ and ‘bottom’ of the tripod. The triarylphosphine
tris(4-(methylthio)phenyl)phosphine and its corresponding phosphine sulfide showed only a single high
conductance feature in the resulting 1- and 2-dimensional conductance histograms, whereas analogous
molecules with fewer than three thiomethyl AGs did not show clear conductance features. Thus, by
systematic molecular modifications and with the aid of supporting DFT calculations, the binding
geometry, with respect to the surface, was elucidated.
Received 9th February 2018
Accepted 18th June 2018
DOI: 10.1039/c8ra01257a
rsc.li/rsc-advances
example, two or more AGs were attached to the central conju-
gated unit via sp3 hybridised carbon or silicon atoms (by the use
of a carbon atom, spirouorene, or adamantane motif),5,7–9
Introduction
The eld of single molecule conductance has almost exclusively
involved the study of one-dimensional molecular wires, with
one anchor group (AG), e.g. pyridine, thiol or amine, attached at
each end.1,2 This motif has been favoured as it provides the
least-complicated example for examining structure-property
relationships and conductance mechanisms. However, to
afford greater spatial control relative to the substrate it is
necessary to increase the number of AGs to give tripodal
conductors. Increasing the number of AGs signicantly
enhances the strength of attachment of the molecule to the
surface(s), thereby increasing the mechanical stability of the
metal|molecule|metal junction.3,4 Recent studies demonstrated
the use of tripodal molecules consisting of three monodentate
AGs (e.g., pyridine, thiophene) attached to a central carbon or
silicon atom, bridged by a conductor such as phenylene or
phenylene ethynylene, to give conductance values of 2 ꢀ 10ꢁ5
and 5 ꢂ 1 ꢀ 10ꢁ4 G0 respectively.3,5,6 However, in each reported
reducing the degree of conjugation between each of the AGs.
To examine the electrical conductance of a tripodal molec-
ular wire in its simplest form, we examined a ‘bare-bones’
structure consisting a triaryl phosphine with AGs on each of the
aryl groups. Ragaini demonstrated that 4,40,400-phosphanetriyl-
tribenzenethiol can simultaneously coordinate to metal
complexes such as Ni(CO)3 via the phosphine, and chemisorb to
a gold surface via the thiols to give a trigonal pyramidal struc-
ture on the surface.10
Parameswaran et al. has previously demonstrated that
diphenylphosphine moieties can function as mechanically and
chemically stable AGs with a tendency to bind to under-
coordinated gold atoms on the surface.11 In addition to
enhanced stability compared with corresponding dia-
lkylphosphines, diphenylphosphines couple well to the s-
system of alkanes resulting in relatively high conductances for
Ph2P(CH2)nPPh2 junctions. Additionally, phosphines can also
be readily oxidised by sulfur to give the corresponding phos-
phine sulde. Fukazara demonstrated that dibenzophosphole-
suldes act as strong AGs and when bridged by 1,4-phenylene
and biphenyl-4,40-diyl groups, give conductance values of 5 ꢀ
10ꢁ4 and 5 ꢀ 10ꢁ5 G0 respectively and favour conductance via
the LUMO.12
aDepartment of Chemistry, Durham University, South Rd, Durham, DH1 3LE, UK.
E-mail: ross.davidson@durham.ac.uk; andrew.beeby@durham.ac.uk
bDepartment of Chemistry, University of Liverpool, Crown St, Liverpool, L69 7ZD, UK.
E-mail: nichols@liv.ac.uk
cDepartment of Physics, University of Lancaster, Lancaster LA1 4YB, UK
dDepartment of Laser Physics, Women Faculty of Science, Babylon University, Hilla,
Iraq
Here we report conductance measurements and calculations
on ‘bare-bones’ tripodal molecular wires based on triaryl-
phosphines, -phosphine suldes, -phosphine oxides and -sele-
nides using scanning tunnelling microscopy (STM)-based
techniques and we examine how conductance is affected by
eDepartment of Physics, College of Education for Pure Science, Tikrit University, Tikrit,
Iraq
† Electronic supplementary information (ESI) available. CCDC 1578844–1578846.
For ESI and crystallographic data in CIF or other electronic format see DOI:
10.1039/c8ra01257a
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the number of available AGs in the tripods making contact with produce the phosphine selenides 1¼Se, 2¼Se and 3¼Se). The
the single apex terminal group. The triarylphosphines and their phosphine oxides 2¼O and 3¼O were prepared by reaction of (4-
P(V) derivatives are a good test case for this due to their (methylthio)phenyl)lithium with phenylphosphinic dichloride
simplicity and the fact that they can be easily modied in or phosphoryl bromide respectively, to avoid complications
a modular fashion.
from oxidation of thiomethyl groups that arose upon attempted
H2O2 oxidation of 2 and 3. To aid control experiments (q.v.), the
methylphosphonium iodide salt of 3 ([3-Me]+) was synthesised
using the standard techniques of reacting 3 with methyl iodide
(Chart 1).
Experimental methods
Synthetic work
Compound 3 was prepared by the literature methods,10 the
synthesis of compounds 1, 2, 1–3¼S, 1–3¼Se, 2¼O, 3¼O, and
[3-Me]+ are given in the ESI.†
Molecular conductance
The single-molecule conductances of tripodal compounds were
determined using the STM-BJ method.17 Conductance values
and break-off distances (95th percentile) are summarized in
Table 1. Conductance histograms for the compounds (2, 3, 3¼S,
and 3¼O) are shown in Fig. 1. Representative conductance
traces with current plateaus, two-dimensional (2D) histograms;
conductance values and break-off distances (95th percentile)
are shown in the ESI.†
Each of the three phosphine selenide compounds (1¼Se–
3¼Se) showed a complete absence of molecular conductance
peaks. In addition, in experiments with the phosphine sele-
nides, the G0 peaks in the histograms were signicantly altered,
with much-diminished peak heights, indicating that the gold
surface had been chemically altered. The most likely cause of
this alteration is ‘selenium poisoning’ resulting from the
surface-induced decomposition of the phosphine selenide. In
fact, in the present study, we examined the stability of these
compounds by a 1H and 31P NMR study in CDCl3; see ESI.† This
analysis shows that the compounds decayed over a number of
hours, primarily to the corresponding phosphine oxide liber-
ating the selenium.
Conductance measurements
All measurements were performed at room temperature and
under ambient conditions with an Agilent (Keysight) STM
running Picoscan 5.3.3. soware. The STM-BJ setup used to
perform all the measurements consists of a home-made
scanner13 controlled by an Agilent Picoscan 5500 controller
with a N9503A modied scanner and a multichannel current
amplier. Samples were prepared by adsorption onto
commercially-obtained gold-on-glass Au(111) substrates
prepared with a chromium adhesion layer (Arrandee). The gold
slides were ame annealed with a butane torch. The process
involved heating the gold-on-glass slide in a dark room until it
shows an orange glow, then allowing the slide to cool; this
process is repeated as many times as necessary to obtain the
desired Au(111) at surface.14 Sample solutions were prepared
by dissolving the amount of compound (a few milligrams) in
10 mL of mesitylene needed to achieve a 10ꢁ4 M concentration.
Gold STM tips were fabricated from 0.25 mm Au wire (99.99%)
that was freshly mechanically cut for each STM experiment.
Conductance experiment were carried out adding 100 mL of the
10ꢁ4 M solution into the STM-BJ liquid cell, then the STM-BJ tip
was repeatedly approached into contact and then withdrawn
from the Au(111) surface. A current set point of 100 mA was used
to achieve a good gold contact with the surface, and the tip was
In contrast, the 3 and 3¼S compounds showed single, well-
dened conductance peaks, at 10ꢁ2.36 and 10ꢁ2.91 G0 respec-
tively, similar in value to 1,4-bis(methylthio)benzene (10ꢁ2.15
G0).18 However, replacement of a single thiomethyl group with
a hydrogen resulted in two conductance peaks being observed
for compound 2 (10ꢁ3.23 and 10ꢁ4.46 G0), and no conductance
peaks being observed for compound 2¼S.
then retracted 4 nm away from the surface at a rate of 20 nm sꢁ1
.
A bias voltage of 100 mV was applied between the sample and
tip; current–distance traces were recorded during the approach
to contact and the withdrawal process.
Further replacement of the thiomethyl groups with hydro-
gens (i.e., 1 and 1¼S) resulted in no molecular conductance
peak being observed, suggesting that the conductance path is
not simply that between one single thiomethyl group and the
central donor group (either phosphorus or phosphorus sulde).
To further elucidate the nature of the central atom involvement
Results and discussion
Synthesis
A family of triaryl phosphines and their oxidised derivatives in junction formation, we performed STM-BJ studies on the
were chosen as the tripods with aryl groups consisting of corresponding phosphine oxides (compounds 2¼O and 3¼O)
combinations of either thioanisole or phenyl groups. Thio- and on the methylphosphonium iodide compound [3-Me]I.
methyl AGs have been chosen due to their chemical stability Compound 3¼O displayed conductance peaks at 10ꢁ2.96 and
and their proven record as contact groups in molecular junc- 10ꢁ4.35, while compound 2¼O displayed no conductance peak,
tions.15 Each of the phosphines were synthesised by carrying out as for the sulde 2¼S. The presence of a second peak for 3¼O
halogen-lithium exchange on (4-bromophenyl)(methyl)sulfane, suggests that the phosphine oxide does not bind to the surface
followed by reaction with PCl3, dichlorophenylphosphine or as strongly as the sulde, allowing the formation of other
chlorodiphenylphosphine.10,16 The phosphines (1–3) were then contact geometries, possibly consisting of
a thiomethyl-
heated in the presence of either sulfur (to produce the respec- molecule-thiomethyl contacted arrangement based on the
tive phosphine suldes 1¼S, 2¼S and 3¼S) or selenium (to increased break-off distance for the low conductance band.
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Chart 1 Triaryl phosphines and their derivatives used in this investigation.
Finally, [3-Me]+ showed no detectable conductance peak, which which one P–C6H4–SMe lies at on the gold surface, allowing
suggests that junction formation via thiomethyl groups at each the lone pair in conjunction with the p-orbitals of the thio-
contact does not contribute signicantly to the conductance anisole to make contact with the surface. This arrangement
peaks in these molecules. Rather, for the highest conductance would leave a single thioanisole raised perpendicular to the
mode to be reached, the central atom (P or P]S) must be able to surface, providing a contact for the second electrode. In fact,
act as a contact for one electrode, and all three thiomethyl similar behaviour has been observed by Su et al.,19 whereby the
groups must be available to make contact with the surface, 1,1-bis(4-(methylthio)phenyl)siletane system displayed two
giving the tripodal shape of the molecule. Indeed, previous conductance peaks, which were an order of magnitude
work by Ragaini demonstrated that on a similar compound different. The low conductance peak corresponded to the end-
(4,40,400-phosphanetriyltribenzenethiol),10 contact occurs via the to-end thiomethyl–thiomethyl contact mode, while the high
aryl thiols leaving the central donor phosphorus atom available
to act as a binding site able to coordinate to metal carbonyls.
To account for the low conductance mode that occurs when
only two thiomethyl groups are attached, we propose a model in
Table 1 Conductance values and break-off distances (95th percentile)
for 2, 3, 3¼S and 3¼O
Molecule
Conductance (G0)
Break-off distance (nm)
1
2
No peak
3.46 ꢀ 10ꢁ5
5.88 ꢀ 10ꢁ4
4.36 ꢀ 10ꢁ3
No peak
0.76
0.94
0.76
3
1¼S
2¼S
3¼S
3¼O
No peak
1.23 ꢀ 10ꢁ3
4.46 ꢀ 10ꢁ5
1.09 ꢀ 10ꢁ3
No peak
0.87
0.91
0.76
2¼O
[3-Me]+
No peak
Fig. 1 Conductance histograms for the compounds 2, 3, 3¼S and
3¼O.
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ꢁ1
0.05 eV A . A double-zeta plus polarization orbital basis set,20,21
norm-conserving pseudopotentials, an energy cut-off of 250
Rydbergs dened the real space grid. Transmission functions
were computed using and the local density approximation
(LDA),22 a generalized gradient approximations (GGA),23 and
using a van der Waals24 functional and were found to be qual-
itatively similar in all cases,25 (see Fig. S45 in the ESI†).
The use of DFT to compute the ground state energy of
various molecular junctions permits us to calculate binding
energies to gold electrodes and optimal geometries. To avoid
basis set superposition errors (BSSE)26 we use the counterpoise
correction27 in which the binding energy of a molecule denoted
a to an electrode b is expressed as:
˚
Table 2 The binding energies DE(ab) of molecules to the Au(111)
surface, calculated using a vdW functional. For comparison the cor-
responding binding energies obtained using GGA are shown. To obtain
these results, we started from 252 different initial conditions for each
molecule and allowed each to fully relax to a minimum energy. Then
from these 252 different simulations, we chose the relaxed structure
corresponding to the lowest energy. Fig. S41–S44 in the ESI show the
various local energy minima obtained from this procedure
DE(ab)
DE(ab)
System
(eV) GGA
(eV) vdW
2-A
2-B
2-C
3
ꢁ0.57
ꢁ0.76
ꢁ0.82
ꢁ0.94
ꢁ0.61
ꢁ0.79
ꢁ0.85
ꢁ1.02
DEðabÞ ¼ E ꢁ Eaab ꢁ Ebab
ab
(1)
ab
conductance peak corresponded to attachment formed between
the thiomethyl group at one gold contact and the central silicon
at the other gold contact.
In this expression, the total energy of the combined a and
b system is Eaabb, while the total energies of isolated systems
a and b are Eaab and Ebab respectively, maintaining identical basis
sets (a,b) for the three energies.
The DFT calculations predicted three possible geometries for
the system involving two thiomethyl AGs (compound 2). Based
on the binding energy calculations shown in Table 2, the most
probable geometry was shown to be 2-C (Fig. 2), since the order
Theoretical calculations
Using the density functional code SIESTA4 the optimum
geometries of the isolated molecules were obtained by relaxing
the molecules until all forces on the atoms were less than
Fig. 2 The relaxed geometries of all possible structures for 2, 3, 3¼S and 3¼O; where atoms are indicated by grey (carbon), white (hydrogen),
yellow (sulfur), red (oxygen) and orange (phosphorus).
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Fig. 3 The relaxed geometries of all molecular junctions; where atoms are indicated by grey (carbon), white (hydrogen), yellow (sulfur), red
(oxygen) and orange (phosphorus).
Table 3 The experimental (Exp. G/G0) and calculated conductance
values (Th. G/G0) at EF ꢁ EFDFT ¼ 0 eV. Z* is the experimental break-off
distance. The calculated electrode separation in relaxed junctions (Z);
Z ¼ dAu–Au ꢁ 0.25 nm, where 0.25 nm is the calculated centre-to-
centre distance of the apex atoms of the two opposing gold electrodes
when conductance ¼ G0 in the absence of a molecule. dAu–Au is the
calculated centre-to-centre distance of the apex atoms of the two
opposing gold electrodes in relaxed junctions
Molecule Exp. G/G0
Th. G/G0
Z* (nm) Z (nm) dAu–Au (nm)
3
3-S
3-O
4.36 ꢀ 10ꢁ3 5.5 ꢀ 10ꢁ3 0.76
1.23 ꢀ 10ꢁ3 2.8 ꢀ 10ꢁ3 0.87
1.09 ꢀ 10ꢁ3 2.5 ꢀ 10ꢁ3 0.76
0.27
0.39
0.26
0.52
0.64
0.51
Fig. 4 The calculated conductance as a function of Fermi energy for
all molecular junctions, with molecules bound to Au (111) surfaces, Conclusions
obtained using a van der Waals functional.20,21
In conclusion we have investigated the molecular conductance
of a ‘bare-bones’ tripodal structure, consisting of either tris(4-
(methylthio)phenyl)phosphine (3) or phosphine sulde (3¼S),
and with both the thiomethyl and phosphorus/phosphine
sulde acting as surface binding groups. Using STM-BJ, we
determined that both 3 and 3¼S are highly conductive, with
only a single conductance peak.
of binding energies between the molecule and gold electrode
follows the trend |E2-C| > |E2-B| > |E2-A|. For the structures with
three thiomethyl anchor groups, our model shows one possible
geometry for compounds 3, 3¼S and 3¼O (Fig. 3). The highest
binding energy value is presented by compound 3 (DE ¼ ꢁ1.02
eV).
Through the systematic substitution of thiomethyl groups
with hydrogens, it was determined that three thiomethyl groups
were required to achieve the single conductance mode, inferring
that molecules bind to the surface via the thiomethyl groups,
leaving the phosphorus (3) or phosphine sulde (3¼S) available
to act as a ‘top’ contact for the molecular bridge. This was sup-
ported by DFT calculations, which showed that this geometry was
the only stable geometry for the 3, 3¼S and 3¼O. The calculations
also indicate the Fermi-energy level lies in the vicinity of the
middle of the HOMO–LUMO gap slightly closer to the LUMO.
To further explain the conductance behaviour we employed
DFT-based transport code GOLLUM28 to compute the trans-
mission coefficient T(E) for each relaxed junction geometry (see
Fig. 3). This was achieved by rst obtaining the corresponding
Hamiltonian and overlap matrices with SIESTA, using a double-
zeta polarized basis set. The optimized junction geometries as
shown in Fig. 3 conrm well that the thiomethyl-contacted
compounds are not oriented normal to the electrode surface
within the molecular junction. Rather, they are tilted within
molecular junctions to accommodate the directionality of the
lone pairs of electrons on the sulfur atoms that bind to the gold
electrodes.3,4 From T(E), the electrical conductance G was ob-
tained using the Landauer formula.
Conflicts of interest
The authors declare no competing nancial interest.
Fig. 4 indicates that in all cases the Fermi level lies near the
centre of the HOMO–LUMO gap, but shied slightly towards the
LUMO resonance, and therefore a LUMO-mediated electron
tunnelling mechanism is anticipated. These results are
consistent with our previous studies.1,2 The order of the calcu-
lated conductances is G3 > G3-S > G3-O (Table 3).
Acknowledgements
A. B. and R. J. D. also gratefully acknowledge the EPSRC (EP/
K007785/1; EP/K007548/1) for funding this work. D. C. M., R.
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J. N., C. J. L. and S. J. H. also gratefully acknowledge the EPSRC 12 A. Fukazawa, M. Kiguchi, S. Tange, Y. Ichihashi, Q. Zhao,
(EP/M029522/1; EP/M005046/1; EP/M014169/1; EP/N017188/1;
EP/M014452/1) for funding this work. This work support from
the European Commission is provided by the FET Open project
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