ARTICLE IN PRESS

Physica E 40 (2008) 26062613

www.elsevier.com/locate/physe

Density functional non-equilibrium Greens function (DFT-NEGF)

study of the smallest nano-molecular switch
M.D. Ganjia,, F. Nourozib
a

Department of Chemistry, Azad University of Ghaemshahr, Ghaemshahr, Iran

Department of Physics, Science Campus, University of Ferdousi, Mashhad, Iran

Available online 29 September 2007

Abstract
We report a density functional non-equilibrium Greens function (DFT-NEGF) study of electrical transport and switching behavior in
a single molecular conductor consisting of a 1,4-benzene-dithiolate (BDT) molecular wire with one sulfur end group bonded to an
Au(1 1 1) substrate and the other to a monatomic Au-scanning tunneling microscope (STM) tip.
The IV characteristics of the various congurations of the BDT between gold electrodes are calculated. We nd that the conductance
of the molecule varies dramatically upon the lateral motion of the STM tip, which suggests that this system has potential application as a
molecular device.
The projection of the density of states (PDOS) and the transmission coefcients (T(E)) of the two-probe system at zero bias are
analyzed, and it suggests that the variation of the coupling between the molecule and the electrodes with external bias leads to switchingbehavior. Furthermore, the transmission coefcients of the system at various external voltage biases are also investigated. The results
show that, the broadening of the transmission coefcient spectrum with increasing of the external voltage bias indicates a strong coupling
between the molecular orbitals in the BDT and the incident states from the electrodes, thus the current increases with increase of the bias
voltage.
r 2007 Elsevier B.V. All rights reserved.
PACS: 85.65.+h; 31.15.Ar; 73.40.Gk
Keywords: Molecular electronics; DFT; Electron transport; Non-equilibrium Greens function; BDT; Nano-molecular switch

1. Introduction
The next generation of electronic devices will undoubtedly be constructed of molecules, or will have features of
molecular size. The results of recent experimental [13] and
theoretical studies [411] predict a brilliant future for
molecular electronics. Among various efforts and activities,
several schemes have been proposed to design and
construct molecular switches [3,811]. The basic idea is to
nd molecules that have two or more distinct states with
vastly different conductance. Switching between on and off
states can be performed by applying an external bias or by
using a scanning tunneling microscope tip to manipulate
the system [3,811].
Corresponding author. Tel.: +98 1113267840.

E-mail address: ganji_md@yahoo.com (M.D. Ganji).

1386-9477/$ - see front matter r 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.physe.2007.09.123

It has been suggested that this intriguing behavior may

be due to charging of the molecule and/or changes of the
molecular geometry (conformation) [1216], however, the
complexity of the experimental systems has so far
prevented the development of a quantitative explanation.
On the theoretical side, the possibility of making molecular-wire switches by introducing a third (gate) electrode
into the system has been explored [1719], as has the
possibility of designing two-terminal molecular wires
that switch due to electric eld-induced conformational
changes [15,19].
A popular model system to understand the electrical
transport properties of the metalmoleculemetal system is
the benzene molecule [2022]. More interestingly, switching
behavior has been reported in the 1,4-dithiole-benzene
(BDT) ring in Emberlys theoretical research [11], while the
mechanism governing switching behavior in it is not yet

ARTICLE IN PRESS
M.D. Ganji, F. Nourozi / Physica E 40 (2008) 26062613

clearly claried, furthermore, their investigation has been

performed via the semiempirical approximation method.
To contribute to the knowledge about the mechanism of
switching behavior in single molecular devices, in the
current research, we present a detailed rst-principles
analysis of the IV characteristics of the BDT ring
sandwiched between two Au(1 1 1) electrodes. Our results
suggest that switching behavior is mainly attributed to the
changes of the coupling between the molecular orbitals in
the BDT and the incident states of the electrodes under
external bias.
We will use density functional non-equilibrium Greens
function (DFT-NEGF) method via the newly developed
method, SMEAGOL (spin and molecular electronics in an
atomically-generated orbital landscape) [23,24], to calculate the IV characteristics of BDT coupled to two
Au(1 1 1) surfaces via thiol bonds. With this method, it is
possible to make a full self-consistent description of a
nanostructure coupled to two electrodes with different
electro-chemical potentials. A virtue of the method is that
it employs the same level of approximation for the
electrodes and the nanostructure.
As mentioned above, previous calculation has used a
semiempirical description of the two-probe system [11].
Thus, the calculations presented in this paper are to
our knowledge with the rst calculation of the IV
characteristics of the switching behavior of BDT with a
full atomistic DFT-NEGF description of both the gold
electrodes and BDT molecular wire. Furthermore, we
calculate the transmission function under various external
voltage biases, which is not possible via the semiempirical
method, since it cannot take into account the modication
of the orbitals under various biases.
The organization of the paper is as follows. We start
with a brief description of the DFT-NEGF method
(Section 2), and in Section 3 we report our main results
for the transmission functions of the different structures
and discuss their implications, together with an analysis of
the molecular levels important for electron transmission. In
Section 4, the results are summarized.
2. Computational details
The calculations have been performed using a recently
developed rst-principles package SMEAGOL [23,24],
which is based on the combination of DFT (as implemented in the well-tested SIESTA method [25]) with the NEGF
technique [26,27]. SMEAGOL is capable of fully selfconsistently modeling the electrical properties of nanoscale devices that consist of an atomic scale system
coupling with two semi-innite electrodes. Such nano-scale
devices are referred to as two-probe systems and they are
divided into three parts for theoretical calculations: left and
right electrodes, and a central scattering region. The
scattering region actually includes a portion of the semiinnite electrodes. The simulation procedure of such twoprobe systems can be described briey as follows.

2607

Firstly, the electronic structure of two electrodes is

calculated only once by SMEAGOL to get a self-consistent
potential. This potential will be shifted rigidly relative to
each other by the external potential bias and provides
natural real-space boundary conditions for the Kohn
Sham (KS) effective potential of the central scattering
region. Then, from the Greens function of the central
scattering region, it can obtain the density matrix and
thereby the electron density. Once the electron density is
known, the DFT Hamiltonian matrix, which is used to
evaluate the Greens function, can be computed using the
above boundary conditions by means of standard methods.
h
i1
^L  S
^R ,
G^ lim E idS^  H^ Sr  S
(1)
d!0

^ L and S^ R are the

where H^ Sr is DFT Hamiltonian and S
self-energies, respectively, for the left and right lead. This
procedure is iterated until self-consistency is achieved.
Moreover, the current through the atomic-scale system can
be calculated from the corresponding Greens function and
self-energies using LandauerButtiker formula [28]:
Z
2e 1
IV
dEf l E  ml  f r E  mr TE; V ,
(2)
h 1
where ml and mr are the electrochemical potentials of the left
and right electrodes, respectively, i.e.,
mL  mR eV b

(3)

and fr and fl are the corresponding electron distribution of

the two electrodes. T(E, V) is the transmission coefcient at
energy E and bias voltage V, which is given by
TE; V TrIm Sl EG R EIm Sr EG A E,
R

(4)

where G (E) and G (E) are the retarded and advanced

Greens function of the central region. Based on the
eigenchannel decomposition of the conductance, this total
transmission T(E) can be decomposed into non-mixing
eigenchannels Tn(E) [29] as
X
TE
T n E.
(5)
n

In our DFT calculation, the local-density approximation

(LDA) to the exchange-correlation potential [30] is used.
Only valence electrons are considered in the calculation,
and the wave functions are expanded by localized
numerical (pseudo) atom orbitals (PAOs) [31]. The atomic
cores are described by norm-conserving pseudo potentials
[32]. We use a DZP basis set for the organic molecule and
s-only approximation with SZP basis set for the gold
atoms in the transport calculations. The k-grid sampling of
2  2  30 for the gold electrodes and a 2  2  1 k-grid
sampling for the two-probe system, together with the mesh
cutoff of 200 Ry for both of them, was implemented.
The structural model for our theoretical analysis is
illustrated in Fig. 1. In this two-probe system, BDT
molecule couples with two-atomic scale Au(1 1 1) electrodes which extend to reservoirs at 7N where the current is
collected. Three Au atomic layers have been chosen for the

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M.D. Ganji, F. Nourozi / Physica E 40 (2008) 26062613

Fig. 1. A schematic of a 1,4-benzene-dithiolate (BDT) molecular conformations: (a) ground-state (edge) conformation for BDT over the hollow-substrate
bonding site; (b) ground-state (face) conformation of BDT.

electrode cell in the z-direction. In the central scattering

region, the BDT molecule couples with three atomic
layers to the bottom side and with the scanning tunneling
microscope (STM) tip, which was represented by a
tetrahedron of Au atoms, to the top side. These
atomic layers in the central scattering region are large
enough [33] so that the perturbation effect from the
scattering region is screened and they are denoted as
surface atomic layers.
As we know, the distance between the molecule and
electrodes is an important parameter, but it is difcult to
precisely measure and control the present experiments
related to the molecular conductance, for example, the
separation between the tip and the surface in STM
experiments [34] and the moleculemetal separation in
the mechanically controllable break-junction (MCB) experiments, etc.
Since there is no direct experimental information
regarding the geometry of the BDT molecule and its
attachment to the leads, thus we place the molecule
between the electrodes assuming the AuS distance of
2.065 A [35].
In order to investigate the switching behavior of the
BDT, we consider two conformations (following Ref. [11])
for the BDT molecule attached to the Au electrodes. In the
rst conformation, the molecule orients itself so that the
Au-tip atom is approximately coplanar with the benzene
ring (Fig. 1(a)). This is referred as an edge conformation of
the wire since the Au-tip atom faces the edge of the benzene
ring. In the second conformation, on the other hand, the

Au-tip atom is over the at face of the benzene ring, as in

Fig. 1(b), this is referred as a face conformation.
According to the Emberlys total energy investigation
[11], the ground-state conformation of the molecular wire
can switch from edge to face as the STM tip moves laterally
away from the location where the molecule bonds to the
substrate.
3. Results and discussion
We now examine the implications of the conformational
switching and bi-stability described above for electrical
current through the molecular wire. In recent years, much
progress has been made in the developing theories of
electron transport through molecules [3644]. An important conclusion has been that the current at low bias is
carried by molecular orbitals. The overlap between the
orbitals and the states of the contacts is sensitive to the
orientation of the molecule relative to the contacts, which
implies a strong orientation-dependence of the molecular
wires conductance [11,40]. Such overlap effects have been
found in semi-empirical [36,41] and density-functional [38]
transport calculations.
Thus, it is reasonable to expect them to result in a
signicant change in conductance when an AuBDTAu
wire switches between an edge and a face conformation,
and our calculations show this to be the case. Since DFT
calculations have been successful in explaining the experimental currentvoltage characteristics of a variety molecular wires consisting of organic thiol molecules bonded to

ARTICLE IN PRESS
M.D. Ganji, F. Nourozi / Physica E 40 (2008) 26062613

gold electrodes [41,42,44], we adopted this approach here.

In Fig. 2, we show the calculated current of the molecular
wire in its ground-state conformation for two positions of
the STM tip along a linear trajectory over the molecule that
passes through the locations that the tip occupies in Fig. 1.
When the tip is furthest from the center where the
molecule bonds to the substrate the molecule in its ground
state is in the face conformation and has high current
intensity at a source-drain bias around 1.0 V. When the tip
moves towards the center, the molecules ground state
switches to the edge conguration, which is seen to be
much less conducting in the same range of bias. Thus,
whenever the molecule is made to ip from a face
conformation to an edge conformation, either by displacing the STM tip, the molecule is predicted to switch from
a highly conducting to a weakly conducting state, and vice

Fig. 2. Calculated current for ground-state BDT conformations at two

STM tip positions. At 1.0 V, the molecule is in the on state when the
molecule has the face conformation and off state when the molecule has
the edge conformation.

2609

versa. This large difference in conductance between the

edge and face conformations can be understood within
Landauer theory [21] by considering the transmission
probabilities, T, for electrons to scatter through the
molecular wire, taking account of orientational effects [40].
Fig. 3 shows the zero-bias transmission spectra of the
face conformation. It has a peak of weaker strength above
the Fermi energy, and a region of strong transmission
below, where electrons incident from one of the electrodes
can transmit across the molecule to the other electrode
signicantly.
The transmission peaks immediately below the Fermi
energy can be attributed to the highest-occupied molecular
orbitals (HOMO) of the BDT and those above to the
lowest-unoccupied molecular orbitals (LUMO). The Fermi
energy lies nearest the HOMO, so the onset of current is
due to electron transmission through the HOMO. Indeed
due to a strong overlap between the rst HOMO molecular
orbital and the atomic orbitals on the Au atoms.
There are two energy regions, [2.0, 0.1] and [2.0, 3.2],
where electrons incident from one of the electrodes can
transmit across the molecule to the other electrode
signicantly.
We refer, following Ref. [45], to these two energy regions
as signicant energy regions (SERs) because incident
electrons in these regions contribute most signicantly to
the transmission spectra. It is important to emphasize that
the SERs in the electrodes are determined by the
characteristics of both the molecule and the electrodes.
To understand why incident states in these low-energy
regions can transmit across the molecule signicantly, we
calculated the projection of the density of states (PDOS) of
the combined system onto all the BDT basis orbitals
(Fig. 4). The PDOS will give us information on how much
the basis orbitals in the molecule contribute to the
eigenstate of the whole open system and how strongly the

Fig. 3. Transmission function under zero bias as function of the injection energy of electron of the BDT molecule coupled to Au(1 1 1) electrodes (face
conformation). The dashed lines represent the eigenvalues of the isolated molecule. All energy is relative to the Fermi energy of the electrode.

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M.D. Ganji, F. Nourozi / Physica E 40 (2008) 26062613

Fig. 4. PDOS (arbitrary units) of the Sulfur atom of the BDT molecule attached to the STM tip gold, around the Fermi energy (face conformation). All
energy is relative to the Fermi energy of the electrode.

molecule couples with the electrodes at a certain energy E.

A strong coupling makes incident electrons at a certain
energy easily transmit across the molecule, and this will
give rise to a large transmission coefcient at this energy.
This is clearly shown by comparison of the transmission
spectra and PDOS spectra. As a consequence, a large
transmission coefcient indicates a strong coupling between the electrodes and the molecule, and the evolution of
transmission curves with external biases can help us
understand how the changes of the coupling between the
electrodes and molecule determines the IV characteristics
in the system.
We now analyze which orbitals on the BDT molecule are
involved in the transmission. The densities of states
projected only onto S atom attached to the Au atom are
considered, since it gives the main information for the
transport. The PDOS of the gold is just a mainly constant
value over the whole range.
Fig. 4 shows the PDOS of the sulfur atom of the BDT
molecule attached to the STM tip gold, in arbitrary units
around the Fermi energy. The main contribution to the
HOMO and LUMO levels comes from the px orbitals (the
z-axis is along the molecule, the y-axis is in the plane of
the molecule, and the x-axis is perpendicular to it). For the
isolated molecule, HOMO and HOMO-1 (mainly py)
are very close; however, when attached to gold, the
separation between the levels increases.
It can be seen from comparison of the transmission
coefcient and the PDOS curves that, there is a good
correspondence between the position and width of the
peaks in the transmission coefcient and those in
the PDOS for the Sulfur atom. The broad peaks in the
transmission indicate again strong coupling. At zero-bias
voltage, the HOMO is partly occupied, and therefore
pinned to the Fermi energy. Hence, due to the charge
transfer from the molecule to the gold, the molecule

becomes slightly positively charged. Consequently, for the

face conformation, there is a strong overlap between the
rst HOMO molecular orbital and the atomic orbitals on
the Au-tip atom. This results in the strong transmission due
to the rst HOMO below the Fermi energy in Fig. 3 and in
the strong current peak seen for the face conformation in
Fig. 2.
Regarding the edge conformation, the molecular orbitals
are oriented differently and their overlap with the orbitals
on the Au-tip atom is weaker. As shown in Fig. 5, the
Fermi energy lies, also, nearest to the HOMO, but in
contrast to the face conformation, the transmission spectra
is very weak due to the weak overlap between the rst
HOMO molecular orbital and the atomic orbitals on the
gold-tip atom. This results in the weak transmission due to
the rst HOMO below the Fermi energy in Fig. 5 and in
the weak current peak seen for the edge conformation in
Fig. 2.
Thus, we arrive at the prediction that a molecule as
simple as BDT can be made to switch through its
interaction with a suitable STM tip. The on state
corresponds to the molecule oriented in such a way that
its ring faces the tip, whereas in the off state the edge of the
ring faces the tip. The switching can be induced by passing
the tip over the molecule (the transition between Fig. 1(a)
and (b)).
The current intensity should be low at the center
of the STM image of the molecule where the edge
conformation is stable and high when the tip moves away
from the center of the image and the face conformation
becomes stable.
We will show, for the face conformation, that the
increases in the current can be understood by studying
the changes of coupling between the molecular orbitals in
the BDT and incident states in the electrodes under various
external biases.

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M.D. Ganji, F. Nourozi / Physica E 40 (2008) 26062613

2611

Fig. 5. Transmission function under zero bias as function of the injection energy of electron of the BDT molecule coupled to the Au(1 1 1) electrodes (edge
conformation). All energy is relative to the Fermi energy of the electrode.

Fig. 6. Transmission coefcient T as function of bias voltage V of the injection energy of electron of the BDT molecule coupled to the Au(1 1 1) electrodes
(face conformation). All energy is relative to the Fermi energy of the electrode.

As mentioned above, a large transmission coefcient

indicates a strong coupling between the electrodes and the
molecule, and the evolution of transmission curves with
external biases can help us understand how the changes of
the coupling between the electrodes and molecule determines the IV characteristics in the system. Therefore, the
voltage dependence of the transmission function will be
studied next.
Now we divide the whole energy region into two kinds of
regions according to whether T(E, Vb) 0 or not in them
[45]. In the regions where T(E, Vb) is not zero, the incident
electrons can transmit across the molecule, and we call
them transmission regions. In the other regions where
T(E, Vb) is zero, the incident electrons cannot transmit
across the molecule, and we call them transmission
intervals. Since the current in the system isR calculated by
the LandauerButtiker formula, I 2e=h TE; V b dE,

thus it is transmission spectra dependent. We will now

show the changes of the transmission function under
various biases (Fig. 6).
It can be seen that the transmission interval near the
Fermi energy under zero bias is broadened by increasing
the voltage biases. It can be explained by the relative shift
of the energy regions of the left and right electrodes.
Now let us see why the current was increased by
increasing the voltage biases. As mentioned
R 1above the
current, I, is obtained from IV 2e=h 1 dEf l E
ml  f r E  mr TE; V , where ml and mr are the electrochemical potentials of the left/right electrodes. The region
between ml and mr is called the bias window or integral
window [45], as shown in Fig. 6 with strong peaks at the
Fermi energy. Thus, the current is determined by T(E, Vb)
in the bias window and is further only determined by the
transmission regions in the bias window because T(E, Vb) is

ARTICLE IN PRESS
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M.D. Ganji, F. Nourozi / Physica E 40 (2008) 26062613

zero in the transmission interval and has no contribution to

the current.
It can be seen from Fig. 6 that with the external bias
increasing from 0.0 to 0.5 V, the new transmission region
broadens rapidly since the electrons in the higher energy
regions of the left electrode can transmit across the
molecule to the lower energy regions of the right electrode
in an increasingly wider energy region. This procedure has
been observed at higher voltage biases, e.g. at 1.5 V, where
by increasing the voltage bias, the transmission region
broadens more and more.
As a result, the broadened-transmission coefcient
spectrum indicates a strong coupling between the molecular orbitals in the BDT and the incident states from the
electrodes, thus the current increases with increase in the
bias voltage.
On the other hand, since the HOMO is pinned at the
Fermi energy, for small voltages, the energy levels of the
molecule move down with the voltage, since the HOMO
gets occupied more (the extra charge on the HOMO causes
the energy to move down, the resulting extra charge is a
balance between the applied potential and the shift of the
level). Since the level is broad it can be occupied with a
fractional charge, therefore it moves down continuously
with the bias.
At a bias of about 1.5 V, however, the HOMO-1 starts to
get into the bias window (delimited with blue vertical lines).
Decharging of the HOMO-1 pushes the level down, so that
the states now follow the lower end of the bias window (the
levels are pushed down because since the HOMO is almost
fully lled, a decharging of the HOMO causes the molecule
to get closer to charge neutrality, so that the electrostatic
energy, and with it the energy levels goes down). The
HOMO is by now fully charged so it does not affect the
motion of the levels with the bias. Anyway, the net result is
that the levels move down all the time, and the result of this
movement is given by the fact that the molecule tries to be
charge neutral.

predicted to switch from a highly conducting to a weakly

conducting state.
There is one relevant theoretical study to support this
point of view. Emberly and Kirczenow [11] used the semiempirical approximation method and chose Au clusters as
the electrodes to calculate the conductance of the
AuBDTAu system. They observed that the switching
behavior appears at 1.5 V. This difference might be due to
the different modeling of the electrodes and the different
couplings between the molecule and the electrodes or
because of the various implemented computational methods. However, this may present a challenge for experimentalists.
The PDOS and the transmission coefcients (T(E)) of
the two-probe system at zero bias are analyzed, and it
suggests that the variation of the coupling between the
molecule and the electrodes with external bias leads to
switching behavior.
The investigation of the transmission coefcients of the
system at various external voltage biases showed that, the
broadening of the transmission coefcient spectrum with
increasing of the external voltage bias indicates a strong
coupling between the molecular orbitals in the BDT and
the incident states from the electrodes, thus the current
increases with increase in the bias voltage.
The switching mechanism that we have introduced here
relies on the coupling between the molecule and contacts
and thus should be broadly applicable.
We hope that the ideas put forward here will facilitate
bridging the gap between theory and molecular-switching
experiments.

4. Conclusions

References

In conclusion, we demonstrate theoretically by DFTNEGF method that a much smaller and simpler twoterminal molecular wire can exhibit switching, and we
present a realistic theory of its behavior. We consider a 1,
4-benzene-dithiolate molecular wire with one sulfur end
group bonded to an Au(1 1 1) substrate and the other to
a monatomic Au STM tip as depicted in Fig. 1. We
investigated two conformations of the BDT molecule
linked to the Au(1 1 1) electrodes (edge and face conformations (Fig. 1(a) and (b), respectively)).
We found that the face conformation of the molecular
wire showed highly conducting, on condition, at the rst
current peak near 1.0 V while the edge conformation are
weakly conducting, off condition, there (Fig. 2). Thus,
whenever the molecule is made to ip from a face
conformation to an edge conformation, the molecule is

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Azad University of Ghaemshahr.

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