Swit
hing me
hanism of photo
hromi
 diarylethene derivatives
mole
ular jun
tions
Jing Huang,
Qunxiang Li,
Hao Ren,
Haibin Su,
Q.W.Shi,
and Jinlong Yang
Hefei National Laboratory for Physi
al S
ien
es at Mi
ros
ale,
University of S
ien
e and Te
hnology of China,
Hefei, Anhui 230026, People's Republi
 of China
Division of Materials S
ien
e, Nanyang Te
hnologi
al University,
50 Nanyang Avenue, 639798, Singapore
(Dated: November 4, 2018)
Abstra
t
The ele
troni
 transport properties and swit
hing me
hanism of single photo
hromi
 diarylethene
derivatives sandwi
hed between two gold surfa
es with 
losed and open 
on�gurations are inves-
tigated by a fully self-
onsistent nonequilibrium Green's fun
tion method 
ombined with density
fun
tional theory. The 
al
ulated transmission spe
tra of two 
on�gurations are strikingly distin
-
tive. The open form la
ks any signi�
ant transmission peak within a wide energy window, while the

losed stru
ture has two signi�
ant transmission peaks on the both sides of the Fermi level. The
ele
troni
 transport properties of the mole
ular jun
tion with 
losed stru
ture under a small bias
voltage are mainly determined by the tail of the transmission peak 
ontributed unusually by the
perturbed lowest perturbed uno

upied mole
ular orbital. The 
al
ulated on-o� ratio of 
urrents
between the 
losed and open 
on�gurations is about two orders of magnitude, whi
h reprodu
es
the essential features of the experimental measured results. Moreover, we �nd that the swit
hing
behavior within a wide bias voltage window is extremely robust to both substituting F or S for H
or O and varying end an
horing atoms from S to Se and Te.
PACS numbers: 73.63.-b, 85.65.+h, 82.37.Vb
http://arxiv.org/abs/0704.0176v1
I. INTRODUCTION
A 
riti
al mission of the mole
ular ele
troni
s is to develop innovative devi
es at single
mole
ular s
ale. The representative mole
ular wires, re
ti�ers, swit
hes, and transistors
have been intensively studied in the past years.
Obviously, a single mole
ular swit
h holds
great promise sin
e the swit
h is a 
ru
ial element of any modern design of memory and
logi
 appli
ations. Now various s
hemes have been proposed to realize mole
ular swit
hing
pro
ess in
luding relative motion of mole
ule internal stru
ture,
3,4,5,6,7

hange of mole
ule

harge states,
and bond �u
tuation between the mole
ule and their ele
tri
al 
onta
ts.
Re
ently, an alternative routine has been suggested to design swit
hes based on single stably
existing mole
ule whi
h 
an reversibly transform between two 
ondu
tive states in response
to external triggers.
11,12,13,14
Among various triggers, light is a very attra
tive external stim-
ulus be
ause of the ease of addressability, fast response times, and 
ompatibility with a wide
range of 
ondensed phases.
The swit
hing properties through the so-
alled photo
hromi
 mole
ules have been 
ar-
ried out by several experimental and theoreti
al groups.
15,16,17,18,19,20,21,22
In parti
ular, the
dithienyl
y
lopentene (DTC) derivatives (as the 
entral swit
hing unit) hold great promise
as arti�
ial photoele
troni
 swit
hing mole
ules be
ause of their reversible photo-indu
ed
transformations that modulate ele
tri
al 
ondu
tivity and their ex
eptional thermal sta-
bility and fatigue resistan
e.
15,16,17,18,19
Using the me
hani
ally 
ontrollable break-jun
tion
te
hnique, Dulić et al.16 designed mole
ular swit
hes based on DTC mole
ules (1,2-bis[5′-
-a
etylsulfanylthien-2
- yl)-2
-methylthien-3
-yl℄ 
y
lopentene) with two thiophene link-
ers, however, whi
h operates only one-way, i.e. from 
ondu
ting to the insulating state under
visible light with λ=546 nm with resistan
e 
hange at 2-3 orders of magnitude. Interestingly,
He et al.
found that the transition 
an be opti
al two-way for DTC mole
ules where H
atoms in 
y
lopentene are substituted by six F atoms (�uorined-DTC). The single-mole
ule
resistan
e in the open form is about 130 times larger than that of in the 
losed stru
ture
measured by using s
anning tunneling mi
ros
opy with a gold tip. In a parallel study, Kat-
sonis et al.
used aromati
 (meta-phenyl) linkers and observed that the light-
ontrolled
swit
hing of single DTC mole
ules 
onne
ted to gold nanoparti
les was reversible. Very
re
ently, to improve the poor stability of su
h kind of 
onjugated mole
ules with thiols on
both ends, Tanigu
hi et al.
developed an inter
onne
t method in solution for diarylethene
photo
hromi
 mole
ular swit
hes that 
an ameliorate ele
trode-mole
ule binding, mole
u-
lar orientation, and devi
e fun
tions. In their experiment, one light-
ontrolled swit
hing
mole
ule 
onsists of a 
entral �uorined-DTC mole
ule, diaryls on two sides and two thiol
groups at both ends. The 
orresponding 
losed and open forms are shown Figure 1(a).
Consequently, the 
urrent through the mole
ular jun
tion with 
losed stru
ture is about 20
times larger than that of the open form measured by STM.
To gain better understanding of these experimental observations, several theoreti
al work
have been 
arried out.
20,21,22
Li et al.
performed quantum mole
ular dynami
s and density
fun
tional theory (DFT) 
al
ulations on the ele
troni
 stru
tures and transport properties
through several photo
hromi
 mole
ules with several di�erent spa
ers sandwi
hed between
gold 
onta
ts. They 
hose dithienylethene (DTE) derivatives to model the experimental
measured mole
ules and predi
ted an about 30 times 
ondu
tion enhan
ement when 
on-
verting the open form into a 
losed one by opti
al te
hnique. Subsequently, two resear
h
groups independently investigated the swit
hing properties of DTC mole
ular jun
tions,
and found that the transmission peak originates from the highest o

upied mole
ular orbital
(HOMO) of the 
losed form lying near the ele
trode Fermi level.
21,22
In their 
al
ulations,
the ele
trodes are simulated with 
luster models and the e�e
ts on the transport properties

oming from six H hydrogen atoms substituted by F atom are not 
onsidered. Till now, to
our best knowledge, there is no theoreti
al study about the swit
hing me
hanism through
exa
tly the same measured mole
ules (�uorined-DTC with two diaryls on two sides, named
diarylethene in Tanigu
hi et al.'s experiment). In this paper, we employ the non-equilibrium
green's fun
tion te
hnique (NEGF) 
ombined with DFT method to address ele
troni
 trans-
port and swit
hing behavior of diarylethene based mole
ular jun
tion. Moreover, we examine
the robustness of this type of swit
hing devi
e against various 
hemi
al substitution (where
six F atoms in the peripheral of 
y
lopentene and S atoms in thienyl are substituted by H
and O atoms, respe
tively) and alternations of an
horing atoms.
II. COMPUTATIONAL MODEL AND METHOD
The 
omputational model system is s
hemati
ally illustrated in Fig. 1(b). The mole
ules
with open and 
losed 
on�gurations are sandwi
hed between two gold ele
trodes through
S-Au bonds. The Au (111) surfa
e is represented by a (4×4) 
ell with periodi
 boundary 
on-
ditions. Sin
e the hollow site 
on�guration is energeti
ally preferable by 0.2 and 0.6 eV than
the bridge and atop sites, respe
tively,
the diarylethene mole
ule 
onne
ts to sulfur atoms
whi
h are lo
ated at hollow sites of two Au (111) surfa
es. Both ele
trodes are repeated by
three layers (A, B, and C). The whole system is arranged as (BCA)-(BC-mole
ule-CBA)-
(CBA), whi
h 
an be divided into three regions in
luding the left lead (BCA), the s
attering
region, and the right lead (CBA). The s
attering regions in
lude a diarylethene mole
ule,
two surfa
e layers of the left (BC), and three surfa
e layers of the right lead (CBA), where
all the s
reening e�e
ts are in
luded into the 
onta
t region, within whi
h the 
harge-density
matrix is solved self-
onsistently with the NEGF method.
The ele
troni
 transport properties are studied by the NEGF 
ombined with DFT 
al-

ulations, whi
h are implemented in ATK pa
kage.
This methodology has been adopted
to explain various experimental results su

essfully.
26,27
In our 
al
ulations, Ceperley-Alder
lo
al-density approximation is used.
Core ele
trons are modeled with Troullier-Matrins
nonlo
al pseudopotential, and valen
e ele
trons are expanded in a SIESTA lo
alized basis
29,30
A energy 
uto� of 150 Ry for the grid integration is set to present the a

urate 
harge
density. The optimized ele
trode-ele
trode distan
e is 39.5 Å for the 
losed 
on�guration
whi
h is 0.7 Å longer than that of the open one. All atomi
 positions are relaxed and the

orresponding gold-sulfur distan
e is 2.5 Å, whi
h is 
lose to the typi
al theoreti
al values.
In addition, we �nd that the geometri
 
hanges of two diarylethene mole
ule sandwi
hed
between two Au(111) surfa
es are negligible 
omparing to the 
orresponding free mole
ules.
III. RESULTS AND DISCUSSION
A. Ele
troni
 stru
tures of free diarylethene mole
ules with 
losed and open stru
-
tures
Atomi
 positions of two free diarylethene mole
ules with 
losed and open stru
tures are
optimized by Gaussion03 pa
kage at general gradient approximation level.
In the ground
ele
troni
 states, both optimized 
on�gurations are featured by out-of-plane distortions. The

entral dihedral angle is 60 degrees for the open form, while only about 8 degrees for the

losed one. This distortion leads the distan
e between 
arbon and 
arbon bond (the bond

an be broken by photon) 
lose to 4.0 Å in the open 
ase 
ompared to 1.5 Å for the 
losed

on�guration. These important geometri
 parameters are 
onsistent with the previous DFT
predi
tions for bisbenzothienylethene mole
ules.
Experimental studies have demonstrated
that the mole
ule 
an transform reversibly between the 
losed and open forms by shining
ultraviolet and visible lights, respe
tively.
Drawing from the 
hemi
al intuition, one would expe
t that the ele
troni
 stru
tures
have distin
tive 
hara
teristi
s due to the signi�
ant geometri
 di�eren
e between 
losed
and open stru
tures. For example, it is 
lear that both single and double bonds appearing
in the 
entral swit
hing unit get almost swapped within the 
losed and open 
on�gurations
as shown in Fig. 1(a). The number of double bonds is 9 in the open form in 
ontrast to 8 in
the 
losed one. Thus, the energy of HOMO in the open form is expe
ted to be lower than
that in the 
losed one.
In deed, the energies of the HOMO and lowest uno

upied mole
ular
orbital (LUMO) of the 
losed form are -4.6 and -3.3 eV, respe
tively, whereas the HOMO
and LUMO energies of the open one are -4.9 and -2.7 eV. The frontier orbital lo
alizes
primarily on ea
h 
onjugated unit of the mole
ule or on the 
entral swit
hing unit for the
diarylethene mole
ule with open 
on�guration. The mole
ule in the 
losed form belongs to a

onjugated system, whose HOMO and LOMO orbitals are essentially delo
alizated π orbitals
extending over the entire mole
ule. More interesting, when six F atoms in the peripheral of

y
lopentene are substituted by H atoms, we �nd that the HOMO and LUMO energies of
this modi�ed mole
ule shift dramati
ally to -4.2 and -2.5 eV for the 
losed form, and to -4.7
and -1.6 eV for the open one respe
tively. These remarkable di�eren
es of the geometries
and ele
troni
 stru
tures are expe
ted to a�e
t signi�
antly transport properties.
B. Transport properties of diarylethene mole
ular jun
tions
The 
urrents through the mole
ular jun
tion with 
losed and open 
on�gurations in the
bias voltage range [-1.0, 1.0V℄ are 
al
ulated by the Landauer-Bütiker formalism.
It should
be pointed out that at ea
h bias voltage, the 
urrent is determined self-
onsistently under
the nonequilibrium 
ondition. The 
al
ulated I-V 
urves are presented in Figure 2. The
triangles linking with bla
k solid lines are for the diarylethene mole
ular jun
tion, while
the 
ir
les linking with short red dotted lines stand for the jun
tion where six F atoms
in the peripheral of 
y
lopentene are substituted by H atoms. The �lled (empty) symbols

orrespond to the 
losed (open) stru
tures. Our 
al
ulations 
apture the key features of the
experimental results.
The 
urrent through the 
losed form is remarkably higher than that
of the open one. When the diarylethene mole
ule in the jun
tion 
hanges from a 
losed

on�guration to the open one, the mole
ular wire is predi
ted to swit
h from the on (low
resistan
e) state to the o� (high resistan
e) state. The 
urrent enhan
ement is quanti�ed by
the on-o� ratio of 
urrent de�ned as R(V ) = Iclosed(V )/Iopen(V ). For example, the 
urrent
of the 
losed form at 1.0 V is about 4.5 µA, whi
h is about 500 times larger than that of
the open 
ase. Su
h a large on-o� ratio in this given range of bias voltage 
an be readily
measured and is desirable for the real appli
ation. Note that the predi
ted on-o� ratio at
1.0 V is larger by about one order of magnitude 
ompared to experiment.
We think one
possible reason for this dis
repan
y is the limitation of the 
omputational method. It is
well known that the 
al
ulated value of the 
urrent through mole
ular jun
tion using NEGF

ombined with DFT is larger about 1-2 orders of magnitude than that of these experimental
measured result.
26,31
Other two possible reasons are environment e�e
t and geometry dif-
feren
e. Firstly, solvent e�e
t is not 
onsidered in presented 
al
ulations. Se
ondly, in our

omputational model, diarylethene mole
ules are dire
tly bound to gold ele
trodes through
Au-S bonds in va
uum. In the experimental setup, the 
entral swit
hing mole
ules bind to
the long orientation 
ontrol mole
ules (polyrotaxane), whi
h 
onne
t to the interfa
e 
ontrol
mole
ules (4-iodobenzenethiol) an
hored with gold nanoele
trodes in solution (the distan
e
between two ele
trodes is about 30 nm).
Note that the slight geometri
 distortion due to
the mole
ule-ele
trode intera
tion 
an result in a slight asymmetry in the 
al
ulated I-V

urves at small bias voltage range as shown in the inset below right of Fig. 2 in small s
ale
for 
larity.
To understand the dramati
 di�eren
e in 
ondu
tivities of the 
losed and open 
on�gu-
rations, we 
ompute the energy dependen
e of total zero-bias voltage transmission spe
tra
shown in Figure 3, where the Fermi level (EF ) is set to be zero for 
larity. Generally
speaking, the 
ondu
tan
e of the mole
ular jun
tion is determined by the number of the
eigen
hannel, the properties of the perturbed frontier orbitals of the mole
ule due to the
presen
e of the gold ele
trodes and the alignment of the metal Fermi level within the per-
turbed HOMO-LUMO gap.
Applying an e�e
tive s
heme named mole
ular proje
ted self-

onsistent Hamiltonian (MPSH) method,
the orbital energies and eigenstates (referred as
perturbed MOs) of the MPSH are obtained and plotted in Fig. 3. The energy positions of
these perturbed MOs relative to the EF are denoted in Figs. 3(a) and 3(b) with red short
verti
al lines, whi
h mat
h ni
ely with the transmission peaks. The spatial distributions of
the perturbed-HOMOs and -LUMOs are presented in Fig. 3 lo
ating on the right and left
sides of the EF , respe
tively. Both 
al
ulated 
ondu
tan
es are very small at zero bias. It
is 4.2×10
G0 (G0=2e
/h) for the 
losed 
on�guration at the EF , and only 5.4×10
for the open one whi
h is about 800 times smaller than the former one. The diarylethene
mole
ule with a 
losed stru
ture has two broad and strong transmission peaks lo
ating at
-0.8 and 0.5 eV, respe
tively. For the open form, note that the la
k of any signi�
ant peaks
in between -1.5 and 1.7 eV 
learly elu
idates its lower 
ondu
tivity.
More importantly, the transmission spe
tra display extraordinarily dis
repant 
hara
ter-
isti
s. It is 
lear that for the diarylethene mole
ular jun
tion with 
losed stru
ture, the
signi�
ant transmission peaks lo
ating below and above the EF (about -0.8 and 0.5 eV)
are mainly 
ontributed by the perturbed-HOMO and -LUMO, respe
tively. Notably, the
perturbed HOMOs and LUMOs of the 
losed 
on�guration in Fig. 3(a) are delo
alized π-

onjugated orbitals, whi
h provide good 
hannels for ele
tron tunneling through the mole
u-
lar jun
tion and lead to two signi�
ant transmission peaks. Very interestingly, the transport
properties are predominated by the tail of the perturbed LUMO 
ontributed transmission
peak at small bias voltage (for example, less than 1.0 V), sin
e the transmission 
oming from
the perturbed LUMO is just 0.5 eV away from EF , whi
h is 0.3 eV 
loser than that of the
perturbed HOMO. Note that this �nding is di�erent from the mi
ros
opi
 pi
tures of other
existing mole
ular jun
tions based on photo
hromi
 DTE and DTC swit
hing mole
ules,
21,22
azobenzene,
and quintuple bond [PhCrCrPh℄ mole
ules,
whose transport properties are
prevailed by the transmission peak 
ontributed by the perturbed HOMO.
Yet 
ontradi
torily, the spatial pro�les shown in Fig.3 (b) of the perturbed LUMO
strongly lo
alizes at the 
entral swit
hing unit with open 
on�guration. This leads to no
appre
iable transmission peaks in the wide bias window (i.e. from -1.5 to 1.7 eV). The sig-
ni�
ant transmission peak at -1.7 eV originates from the perturbed HOMO and HOMO-1
(both are π orbitals) for the open stru
ture, however, it is lo
ated too far away from the EF .
Here, 
omparing to the 
losed 
ase, we note that the position of the perturbed HOMO for
the open 
on�guration is buried deeply below the EF , whi
h is 
onsistent with the previous
theoreti
al results of DTC mole
ules.
21,22
These theoreti
al �ndings ensure us to 
on
lude
that the sharp 
ontrast of the alignment of the perturbed orbital energies with respe
t to
the ele
trode Fermi level and the shape of these perturbed frontier mole
ular orbitals are
the essential 
auses for the striking 
ontrast in transport properties through diarylethene
mole
ular jun
tions with 
losed and open 
on�gurations.
It should be pointed out that the number of transmission paths 
an not a

ount for
the dramati
 di�eren
e in 
ondu
tivities of the 
losed and open 
on�gurations sin
e the
eigen
hannel analysis indi
ates that there is a single eigen
hannel for both 
ases within a
wide window (i.e. [-1.5, 1.5 eV℄). A

ording to the features mentioned above of the 
al
ulated
zero-bias transmission spe
tra (Fig. 3), One 
an spe
ulate that this type of mole
ular
swit
h 
an operate robustly in a pretty wide range of bias voltages with fairly large on -o�
ratio. Additional 
urrents through the diarylethene mole
ular jun
tions with two di�erent

on�gurations at -2.0, -1.5, 1.5 and 2.0 V are also 
al
ulated. The on-o� ratios of 
urrent are
predi
ted to be about two orders of magnitude. This suggests that the bias voltage window
of this kind of mole
ular swit
h (in Tanigu
hi et al.'s experiments
) with reasonably large
on-o� ratio is surprisingly wider than that of other photo-sensitive mole
ules.
13,21
Experimentalist found that diarylethene mole
ular swit
h is reversible when the mole
ules
are sandwi
hed through aromati
 linkers.
18,23
Theoreti
al 
al
ulations argued that whether
it 
an be swit
hed reversibly or not depending on the mole
ule-ele
trode hybridization.
The weak intera
tion between mole
ule and ele
trode is required to fa
ilitate the desired
reversible transition. A

ording to these �ndings, the reversible transition between the open
and 
losed 
on�gurations in this diarylethtene derivatives based mole
ular jun
tion is highly
possible, sin
e the mole
ules are sandwi
hed with phenyl linkers and the mole
ule-ele
trode
hybridization is weak.
C. Substituting e�e
t on diarylethene mole
ule
Previous theoreti
al 
al
ulations fo
us on the end linking groups,
no attempts so far
have been made to examine the side substituting e�e
t on transport properties through the
diarylethene derivations. It is important to investigate the 
ondu
tan
e of the mole
ular
jun
tion, where six F atoms in the peripheral of 
y
lopentene are substituted by H atoms.
The 
al
ulated transmission spe
tra for the H-substituted mole
ular jun
tion with the 
losed
and open forms at zero bias voltage are shown by bla
k solid lines in Figures. 4(a) and
4(b), and two 
orresponding I-V 
urves are presented in Fig. 2 with �lled and empty

ir
les (linked by red dotted lines), respe
tively. The 
urrent through the H-substituted
mole
ular jun
tion with 
losed 
on�guration is about half of that of the 
y
lopentene with
six F atoms in the peripheral. The reasons are summarized in the following three points.
(1) The repla
ement of H with F on the swit
hing unit results in the variation of band
gaps. The energy gap of the H-substituted diarylethene mole
ule is about 1.7 eV, while the
gap of diarylethene (F) mole
ule is about 1.3 eV. (2) The alignment of the Fermi level is
di�erent for two systems. For the jun
tion with the H-substituted mole
ule, the peak 
oming
from the perturbed HOMO lo
ates at -0.7 eV, whi
h is 
loser to the Fermi level than the
perturbed LUMO transmission peak (at 1.0 eV). This result is 
onsistent with these previous
theoreti
al studies on other DTC and DTE derivations.
21,22
However, the Fermi level lies

lose to the transmission 
ontributed by the perturbed LUMO for the diarylethene (F)
mole
ular jun
tion, as shown in Fig. 3. (3) The transport properties under small bias voltage
are mainly determined by the tail of the transmission peak 
oming from the perturbed LUMO
for the 
losed diarylethene (F) mole
ular jun
tion. However, the 
ondu
tivity of the 
losed
H-substituted one is 
ontrolled the tail of transmission peak 
ontributed by the perturbed
HOMO. Nonetheless, the light-
ontrolled swit
hing feature is undoubtedly retained.
Experimental and theoreti
al results revealed that the visible adsorption spe
tra 
hanged
when two S atoms of the swit
hing unit were substituted by O atoms.
Thus, the trans-
mission spe
tra of the mole
ular jun
tion shown in Fig.1 (b) where two S atoms in 
entral
swit
hing unit are repla
ed by O atoms are also 
al
ulated here, as shown in Fig. 4 with
red dotted lines. Clearly, the swit
hing behavior does not depend sensitively on the O-
substituent. However, it should be pointed out that the positions of signi�
ant transmission
peaks obviously shift when 
ompared to Fig. 3. Parti
ularly, the transmission peaks 
oming
from the perturbed HOMO and LUMO lo
ates at -0.7 and 0.8 eV, respe
tively. Again, the
tail of perturbed HOMO transmission peak 
ontributes largely to the low bias ele
troni

ondu
tan
e.
D. E�e
t of varing end an
horing atoms
In general, the transport properties of mole
ular jun
tions depend nontrivially on the end
linking atoms.
36,37
Now we turn to explore the e�e
t of alternating end an
horing atoms.
The 
al
ulated transmission spe
tra at zero bias voltage are shown in Figure 5. The bla
k
solid and red dotted lines stand for end Se- and Te-an
hored 
ases, respe
tively. It is 
lear
that the main 
hara
teristi
s of the transmission spe
tra are maintained and the 
losed
stru
ture is undoubtedly more 
ondu
tive. For the end Se-an
hored 
ase, the energies of
perturbed MO are quite 
lose to the data presented in Fig. 3 of the end S-an
hored one.
Interestingly, 
learly observable 
hanges have been shown for the end Te-an
hored 
ase. The
transmission peaks originating from the perturbed HOMO and LUMO for the mole
ular
jun
tion 
onne
ting to gold ele
trodes through Te atoms lo
ates at -1.0 (-0.8 for S-an
hored
one) and 0.3 eV (0.5 for S-an
hored one), respe
tively. The very interesting �nding of this
study is that the swit
hing behavior of diarylethene derivatives based mole
ular jun
tions
is robust to vary end an
horing atoms from S to Se and Te.
To examine the sensitivity of results shown in Fig. 3 to small 
hange of the ele
trode-
ele
trode distan
e, we 
ompute the zero-bias transmission spe
tra of diarylethene swit
hes
with the 
losed and open stru
tures as elongating and shortening ele
trode-ele
trode separa-
tion up to 0.3 Å. We �nd that the transmission spe
tra experien
e little 
hange, and trans-
port properties of this kind of diarylethene mole
ular jun
tion is not dete
tably sensitive
to the ele
trode-ele
trode distan
e. It indi
ates that this kind of light-
ontrolled swit
hing
based on diarylethene derivatives is stable as a mole
ular swit
hing devi
e. Note that the
transport behavior is des
ribed by the ele
tron elasti
 s
attering theory in our 
al
ulations.
The e�e
t arising from the ele
troni
 vibration and the a

ompanying heat dissipation on
the 
al
ulated on-o� ratio 
an be negle
ted be
ause of the remarkable di�eren
e of the I-V

urves.
IV. CONCLUSION
In summary, we investigate the transport properties of the diarylethene with 
losed and
open stru
tures using the NEGF 
ombined the DFT method. The zero-bias transmission
fun
tion of two di�erent forms is strikingly distin
tive. The open form la
ks any signi�-

ant transmission peak within a wide energy window, while the 
losed stru
ture has two
signi�
ant transmission peaks on the both sides of the Fermi level. The ele
troni
 trans-
port properties of the mole
ular jun
tion with 
losed stru
ture under a small bias voltage
are mainly determined by the tail of the transmission peak 
ontributed unusually by the
perturbed lowest perturbed uno

upied mole
ular orbital. The 
al
ulated on-o� ratio of 
ur-
rents between the 
losed and open 
on�gurations is about two orders of magnitude, whi
h
reprodu
es the essential features of the experimental measured results. Moreover, although
the alignments of the perturbed mole
ular orbitals's energies with respe
t to the ele
trode's
Fermi level are not exa
tly the same, we �nd that the swit
hing behavior within a wide bias
voltage window is extremely robust to both substituting F or S for H or O and varying end
an
horing atoms from S to Se and Te.
ACKNOWLEDGMENTS
This work was partially supported by the National Natural S
ien
e Foundation of China
under Grants 10674121, 10574119, 50121202, and 20533030, by National Key Basi
 Resear
h
Program under Grant No. 2006CB922004, by the USTC-HP HPC proje
t, and by the
SCCAS and Shanghai Super
omputer Center.Work at NTU is supported in part by A*STAR
SERC grant (No. 0521170032).
Corresponding author. E-mail: liqun�ust
.edu.
n
Corresponding author. E-mail: jlyang�ust
.edu.
n
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al
ulations for the diarylethene mole
ule adsorbing on the hollow,
bridge, and atop sites. The 
al
ulated results show that the mole
ule prefers to the hollow site.
Its adsorption energy is lower about 0.2 and 0.6 eV than that of the bridge and atop adsorption

on�guration, respe
tively.
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(DZP) basis set for other atoms are adopted. Test 
al
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are obtained by using DZP basis set for all atoms.
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al
ulations are 
ondu
ted by using Gassian03 pa
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h, M. J. Fris
h, G. W. Tru
ks, H. B. S
hlegel, G. E. S
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Mali
k, A. D. Rabu
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Figure 1: (Color online) (a) The diarylethene derivative in 
losed and open 
on�gurations. (b) A
s
hemati
 of the swit
hing jun
tion. Diarylethene mole
ules are sandwi
hed between two Au (111)
surfa
es, and two S an
horing atoms are lo
ated at the hollow site. The verti
al blue line denotes
the interfa
e between the s
attering region and the left or right gold ele
trode.
Figure 2: (Color online) The 
al
ulated 
urrent-voltage 
hara
teristi
s of the diarylethene and its
derivative mole
ular jun
tions with two di�erent 
on�gurations. The triangles linking with bla
k
solid lines are for the diarylethene mole
ular jun
tion, while the 
ir
les linking with short red dotted
lines stand for the jun
tion where six F atoms in the peripheral of 
y
lopentene are substituted by
H atoms. The �lled (empty) symbols 
orrespond to the 
losed (open) stru
tures. The inset below
right is the I-V 
urve for the open stru
tures (with F and H atoms in the peripheral, respe
tively)
in small s
ale for 
larity.
Figure 3: (Color online) The zero-bias voltage transmission spe
tra versus the energy E-EF of
diarylethene mole
ular jun
tions with the 
losed (a) and open (b) 
on�gurations. Here, EF is the
Fermi level of ele
trodes. The red short verti
al lines stand for the positions of MPSH mole
ular
energy levels. The spatial distributions of the perturbed HOMOs and LUMOs are inserted in the
�gure, and pla
ed at the right and left sides of the EF , respe
tively.
Figure 4: (Color online) The 
al
ulated transmission spe
tra versus the energy E-EF at zero-bias
voltage for diarylethene mole
ular jun
tions with 
losed (a) and open (b) forms, respe
tively. One

ase is that six F atoms in the peripheral of 
entral 
y
lopentene are substituted by H atoms (with
bla
k solid lines); the other is that two S atoms are repla
ed by O atoms (with red dotted lines).
The red short verti
al lines stand for the positions of MPSH mole
ular energy levels.
Figure 5: (Color online) The 
al
ulated transmission spe
tra for diarylethene mole
ular jun
tions
with 
losed (a) and open (b) stru
tures. The bla
k solid and red dotted lines stand for the end
an
horing Se and Te atoms, respe
tively. Here, the red short verti
al lines stand for the positions
of MPSH mole
ular energy levels.
Fig.1 of Huang et al.
Fig.2 of Huang et al.
Fig.3 of Huang et al.
Fig.4 of Huang et al.
Fig.5 of Huang et al.
	INTRODUCTION
	COMPUTATIONAL MODEL AND METHOD
	RESULTS AND DISCUSSION
	Electronic structures of free diarylethene molecules with closed and open structures
	Transport properties of diarylethene molecular junctions
	Substituting effect on diarylethene molecule
	Effect of varing end anchoring atoms 
	CONCLUSION
	ACKNOWLEDGMENTS
	References

  The electronic transport properties and switching mechanism of single
photochromic diarylethene derivatives sandwiched between two gold surfaces with
closed and open configurations are investigated by a fully self-consistent
nonequilibrium Green's function method combined with density functional theory.
The calculated transmission spectra of two configurations are strikingly
distinctive. The open form lacks any significant transmission peak within a
wide energy window, while the closed structure has two significant transmission
peaks on the both sides of the Fermi level. The electronic transport properties
of the molecular junction with closed structure under a small bias voltage are
mainly determined by the tail of the transmission peak contributed unusually by
the perturbed lowest perturbed unoccupied molecular orbital. The calculated
on-off ratio of currents between the closed and open configurations is about
two orders of magnitude, which reproduces the essential features of the
experimental measured results. Moreover, we find that the switching behavior
within a wide bias voltage window is extremely robust to both substituting F or
S for H or O and varying end anchoring atoms from S to Se and Te.

Swit
hing me
hanism of photo
hromi
 diarylethene derivatives
mole
ular jun
tions
Jing Huang,
Qunxiang Li,
Hao Ren,
Haibin Su,
Q.W.Shi,
and Jinlong Yang
Hefei National Laboratory for Physi
al S
ien
es at Mi
ros
ale,
University of S
ien
e and Te
hnology of China,
Hefei, Anhui 230026, People's Republi
 of China
Division of Materials S
ien
e, Nanyang Te
hnologi
al University,
50 Nanyang Avenue, 639798, Singapore
(Dated: November 4, 2018)
Abstra
t
The ele
troni
 transport properties and swit
hing me
hanism of single photo
hromi
 diarylethene
derivatives sandwi
hed between two gold surfa
es with 
losed and open 
on�gurations are inves-
tigated by a fully self-
onsistent nonequilibrium Green's fun
tion method 
ombined with density
fun
tional theory. The 
al
ulated transmission spe
tra of two 
on�gurations are strikingly distin
-
tive. The open form la
ks any signi�
ant transmission peak within a wide energy window, while the

losed stru
ture has two signi�
ant transmission peaks on the both sides of the Fermi level. The
ele
troni
 transport properties of the mole
ular jun
tion with 
losed stru
ture under a small bias
voltage are mainly determined by the tail of the transmission peak 
ontributed unusually by the
perturbed lowest perturbed uno

upied mole
ular orbital. The 
al
ulated on-o� ratio of 
urrents
between the 
losed and open 
on�gurations is about two orders of magnitude, whi
h reprodu
es
the essential features of the experimental measured results. Moreover, we �nd that the swit
hing
behavior within a wide bias voltage window is extremely robust to both substituting F or S for H
or O and varying end an
horing atoms from S to Se and Te.
PACS numbers: 73.63.-b, 85.65.+h, 82.37.Vb
http://arxiv.org/abs/0704.0176v1
I. INTRODUCTION
A 
riti
al mission of the mole
ular ele
troni
s is to develop innovative devi
es at single
mole
ular s
ale. The representative mole
ular wires, re
ti�ers, swit
hes, and transistors
have been intensively studied in the past years.
Obviously, a single mole
ular swit
h holds
great promise sin
e the swit
h is a 
ru
ial element of any modern design of memory and
logi
 appli
ations. Now various s
hemes have been proposed to realize mole
ular swit
hing
pro
ess in
luding relative motion of mole
ule internal stru
ture,
3,4,5,6,7

hange of mole
ule

harge states,
and bond �u
tuation between the mole
ule and their ele
tri
al 
onta
ts.
Re
ently, an alternative routine has been suggested to design swit
hes based on single stably
existing mole
ule whi
h 
an reversibly transform between two 
ondu
tive states in response
to external triggers.
11,12,13,14
Among various triggers, light is a very attra
tive external stim-
ulus be
ause of the ease of addressability, fast response times, and 
ompatibility with a wide
range of 
ondensed phases.
The swit
hing properties through the so-
alled photo
hromi
 mole
ules have been 
ar-
ried out by several experimental and theoreti
al groups.
15,16,17,18,19,20,21,22
In parti
ular, the
dithienyl
y
lopentene (DTC) derivatives (as the 
entral swit
hing unit) hold great promise
as arti�
ial photoele
troni
 swit
hing mole
ules be
ause of their reversible photo-indu
ed
transformations that modulate ele
tri
al 
ondu
tivity and their ex
eptional thermal sta-
bility and fatigue resistan
e.
15,16,17,18,19
Using the me
hani
ally 
ontrollable break-jun
tion
te
hnique, Dulić et al.16 designed mole
ular swit
hes based on DTC mole
ules (1,2-bis[5′-
-a
etylsulfanylthien-2
- yl)-2
-methylthien-3
-yl℄ 
y
lopentene) with two thiophene link-
ers, however, whi
h operates only one-way, i.e. from 
ondu
ting to the insulating state under
visible light with λ=546 nm with resistan
e 
hange at 2-3 orders of magnitude. Interestingly,
He et al.
found that the transition 
an be opti
al two-way for DTC mole
ules where H
atoms in 
y
lopentene are substituted by six F atoms (�uorined-DTC). The single-mole
ule
resistan
e in the open form is about 130 times larger than that of in the 
losed stru
ture
measured by using s
anning tunneling mi
ros
opy with a gold tip. In a parallel study, Kat-
sonis et al.
used aromati
 (meta-phenyl) linkers and observed that the light-
ontrolled
swit
hing of single DTC mole
ules 
onne
ted to gold nanoparti
les was reversible. Very
re
ently, to improve the poor stability of su
h kind of 
onjugated mole
ules with thiols on
both ends, Tanigu
hi et al.
developed an inter
onne
t method in solution for diarylethene
photo
hromi
 mole
ular swit
hes that 
an ameliorate ele
trode-mole
ule binding, mole
u-
lar orientation, and devi
e fun
tions. In their experiment, one light-
ontrolled swit
hing
mole
ule 
onsists of a 
entral �uorined-DTC mole
ule, diaryls on two sides and two thiol
groups at both ends. The 
orresponding 
losed and open forms are shown Figure 1(a).
Consequently, the 
urrent through the mole
ular jun
tion with 
losed stru
ture is about 20
times larger than that of the open form measured by STM.
To gain better understanding of these experimental observations, several theoreti
al work
have been 
arried out.
20,21,22
Li et al.
performed quantum mole
ular dynami
s and density
fun
tional theory (DFT) 
al
ulations on the ele
troni
 stru
tures and transport properties
through several photo
hromi
 mole
ules with several di�erent spa
ers sandwi
hed between
gold 
onta
ts. They 
hose dithienylethene (DTE) derivatives to model the experimental
measured mole
ules and predi
ted an about 30 times 
ondu
tion enhan
ement when 
on-
verting the open form into a 
losed one by opti
al te
hnique. Subsequently, two resear
h
groups independently investigated the swit
hing properties of DTC mole
ular jun
tions,
and found that the transmission peak originates from the highest o

upied mole
ular orbital
(HOMO) of the 
losed form lying near the ele
trode Fermi level.
21,22
In their 
al
ulations,
the ele
trodes are simulated with 
luster models and the e�e
ts on the transport properties

oming from six H hydrogen atoms substituted by F atom are not 
onsidered. Till now, to
our best knowledge, there is no theoreti
al study about the swit
hing me
hanism through
exa
tly the same measured mole
ules (�uorined-DTC with two diaryls on two sides, named
diarylethene in Tanigu
hi et al.'s experiment). In this paper, we employ the non-equilibrium
green's fun
tion te
hnique (NEGF) 
ombined with DFT method to address ele
troni
 trans-
port and swit
hing behavior of diarylethene based mole
ular jun
tion. Moreover, we examine
the robustness of this type of swit
hing devi
e against various 
hemi
al substitution (where
six F atoms in the peripheral of 
y
lopentene and S atoms in thienyl are substituted by H
and O atoms, respe
tively) and alternations of an
horing atoms.
II. COMPUTATIONAL MODEL AND METHOD
The 
omputational model system is s
hemati
ally illustrated in Fig. 1(b). The mole
ules
with open and 
losed 
on�gurations are sandwi
hed between two gold ele
trodes through
S-Au bonds. The Au (111) surfa
e is represented by a (4×4) 
ell with periodi
 boundary 
on-
ditions. Sin
e the hollow site 
on�guration is energeti
ally preferable by 0.2 and 0.6 eV than
the bridge and atop sites, respe
tively,
the diarylethene mole
ule 
onne
ts to sulfur atoms
whi
h are lo
ated at hollow sites of two Au (111) surfa
es. Both ele
trodes are repeated by
three layers (A, B, and C). The whole system is arranged as (BCA)-(BC-mole
ule-CBA)-
(CBA), whi
h 
an be divided into three regions in
luding the left lead (BCA), the s
attering
region, and the right lead (CBA). The s
attering regions in
lude a diarylethene mole
ule,
two surfa
e layers of the left (BC), and three surfa
e layers of the right lead (CBA), where
all the s
reening e�e
ts are in
luded into the 
onta
t region, within whi
h the 
harge-density
matrix is solved self-
onsistently with the NEGF method.
The ele
troni
 transport properties are studied by the NEGF 
ombined with DFT 
al-

ulations, whi
h are implemented in ATK pa
kage.
This methodology has been adopted
to explain various experimental results su

essfully.
26,27
In our 
al
ulations, Ceperley-Alder
lo
al-density approximation is used.
Core ele
trons are modeled with Troullier-Matrins
nonlo
al pseudopotential, and valen
e ele
trons are expanded in a SIESTA lo
alized basis
29,30
A energy 
uto� of 150 Ry for the grid integration is set to present the a

urate 
harge
density. The optimized ele
trode-ele
trode distan
e is 39.5 Å for the 
losed 
on�guration
whi
h is 0.7 Å longer than that of the open one. All atomi
 positions are relaxed and the

orresponding gold-sulfur distan
e is 2.5 Å, whi
h is 
lose to the typi
al theoreti
al values.
In addition, we �nd that the geometri
 
hanges of two diarylethene mole
ule sandwi
hed
between two Au(111) surfa
es are negligible 
omparing to the 
orresponding free mole
ules.
III. RESULTS AND DISCUSSION
A. Ele
troni
 stru
tures of free diarylethene mole
ules with 
losed and open stru
-
tures
Atomi
 positions of two free diarylethene mole
ules with 
losed and open stru
tures are
optimized by Gaussion03 pa
kage at general gradient approximation level.
In the ground
ele
troni
 states, both optimized 
on�gurations are featured by out-of-plane distortions. The

entral dihedral angle is 60 degrees for the open form, while only about 8 degrees for the

losed one. This distortion leads the distan
e between 
arbon and 
arbon bond (the bond

an be broken by photon) 
lose to 4.0 Å in the open 
ase 
ompared to 1.5 Å for the 
losed

on�guration. These important geometri
 parameters are 
onsistent with the previous DFT
predi
tions for bisbenzothienylethene mole
ules.
Experimental studies have demonstrated
that the mole
ule 
an transform reversibly between the 
losed and open forms by shining
ultraviolet and visible lights, respe
tively.
Drawing from the 
hemi
al intuition, one would expe
t that the ele
troni
 stru
tures
have distin
tive 
hara
teristi
s due to the signi�
ant geometri
 di�eren
e between 
losed
and open stru
tures. For example, it is 
lear that both single and double bonds appearing
in the 
entral swit
hing unit get almost swapped within the 
losed and open 
on�gurations
as shown in Fig. 1(a). The number of double bonds is 9 in the open form in 
ontrast to 8 in
the 
losed one. Thus, the energy of HOMO in the open form is expe
ted to be lower than
that in the 
losed one.
In deed, the energies of the HOMO and lowest uno

upied mole
ular
orbital (LUMO) of the 
losed form are -4.6 and -3.3 eV, respe
tively, whereas the HOMO
and LUMO energies of the open one are -4.9 and -2.7 eV. The frontier orbital lo
alizes
primarily on ea
h 
onjugated unit of the mole
ule or on the 
entral swit
hing unit for the
diarylethene mole
ule with open 
on�guration. The mole
ule in the 
losed form belongs to a

onjugated system, whose HOMO and LOMO orbitals are essentially delo
alizated π orbitals
extending over the entire mole
ule. More interesting, when six F atoms in the peripheral of

y
lopentene are substituted by H atoms, we �nd that the HOMO and LUMO energies of
this modi�ed mole
ule shift dramati
ally to -4.2 and -2.5 eV for the 
losed form, and to -4.7
and -1.6 eV for the open one respe
tively. These remarkable di�eren
es of the geometries
and ele
troni
 stru
tures are expe
ted to a�e
t signi�
antly transport properties.
B. Transport properties of diarylethene mole
ular jun
tions
The 
urrents through the mole
ular jun
tion with 
losed and open 
on�gurations in the
bias voltage range [-1.0, 1.0V℄ are 
al
ulated by the Landauer-Bütiker formalism.
It should
be pointed out that at ea
h bias voltage, the 
urrent is determined self-
onsistently under
the nonequilibrium 
ondition. The 
al
ulated I-V 
urves are presented in Figure 2. The
triangles linking with bla
k solid lines are for the diarylethene mole
ular jun
tion, while
the 
ir
les linking with short red dotted lines stand for the jun
tion where six F atoms
in the peripheral of 
y
lopentene are substituted by H atoms. The �lled (empty) symbols

orrespond to the 
losed (open) stru
tures. Our 
al
ulations 
apture the key features of the
experimental results.
The 
urrent through the 
losed form is remarkably higher than that
of the open one. When the diarylethene mole
ule in the jun
tion 
hanges from a 
losed

on�guration to the open one, the mole
ular wire is predi
ted to swit
h from the on (low
resistan
e) state to the o� (high resistan
e) state. The 
urrent enhan
ement is quanti�ed by
the on-o� ratio of 
urrent de�ned as R(V ) = Iclosed(V )/Iopen(V ). For example, the 
urrent
of the 
losed form at 1.0 V is about 4.5 µA, whi
h is about 500 times larger than that of
the open 
ase. Su
h a large on-o� ratio in this given range of bias voltage 
an be readily
measured and is desirable for the real appli
ation. Note that the predi
ted on-o� ratio at
1.0 V is larger by about one order of magnitude 
ompared to experiment.
We think one
possible reason for this dis
repan
y is the limitation of the 
omputational method. It is
well known that the 
al
ulated value of the 
urrent through mole
ular jun
tion using NEGF

ombined with DFT is larger about 1-2 orders of magnitude than that of these experimental
measured result.
26,31
Other two possible reasons are environment e�e
t and geometry dif-
feren
e. Firstly, solvent e�e
t is not 
onsidered in presented 
al
ulations. Se
ondly, in our

omputational model, diarylethene mole
ules are dire
tly bound to gold ele
trodes through
Au-S bonds in va
uum. In the experimental setup, the 
entral swit
hing mole
ules bind to
the long orientation 
ontrol mole
ules (polyrotaxane), whi
h 
onne
t to the interfa
e 
ontrol
mole
ules (4-iodobenzenethiol) an
hored with gold nanoele
trodes in solution (the distan
e
between two ele
trodes is about 30 nm).
Note that the slight geometri
 distortion due to
the mole
ule-ele
trode intera
tion 
an result in a slight asymmetry in the 
al
ulated I-V

urves at small bias voltage range as shown in the inset below right of Fig. 2 in small s
ale
for 
larity.
To understand the dramati
 di�eren
e in 
ondu
tivities of the 
losed and open 
on�gu-
rations, we 
ompute the energy dependen
e of total zero-bias voltage transmission spe
tra
shown in Figure 3, where the Fermi level (EF ) is set to be zero for 
larity. Generally
speaking, the 
ondu
tan
e of the mole
ular jun
tion is determined by the number of the
eigen
hannel, the properties of the perturbed frontier orbitals of the mole
ule due to the
presen
e of the gold ele
trodes and the alignment of the metal Fermi level within the per-
turbed HOMO-LUMO gap.
Applying an e�e
tive s
heme named mole
ular proje
ted self-

onsistent Hamiltonian (MPSH) method,
the orbital energies and eigenstates (referred as
perturbed MOs) of the MPSH are obtained and plotted in Fig. 3. The energy positions of
these perturbed MOs relative to the EF are denoted in Figs. 3(a) and 3(b) with red short
verti
al lines, whi
h mat
h ni
ely with the transmission peaks. The spatial distributions of
the perturbed-HOMOs and -LUMOs are presented in Fig. 3 lo
ating on the right and left
sides of the EF , respe
tively. Both 
al
ulated 
ondu
tan
es are very small at zero bias. It
is 4.2×10
G0 (G0=2e
/h) for the 
losed 
on�guration at the EF , and only 5.4×10
for the open one whi
h is about 800 times smaller than the former one. The diarylethene
mole
ule with a 
losed stru
ture has two broad and strong transmission peaks lo
ating at
-0.8 and 0.5 eV, respe
tively. For the open form, note that the la
k of any signi�
ant peaks
in between -1.5 and 1.7 eV 
learly elu
idates its lower 
ondu
tivity.
More importantly, the transmission spe
tra display extraordinarily dis
repant 
hara
ter-
isti
s. It is 
lear that for the diarylethene mole
ular jun
tion with 
losed stru
ture, the
signi�
ant transmission peaks lo
ating below and above the EF (about -0.8 and 0.5 eV)
are mainly 
ontributed by the perturbed-HOMO and -LUMO, respe
tively. Notably, the
perturbed HOMOs and LUMOs of the 
losed 
on�guration in Fig. 3(a) are delo
alized π-

onjugated orbitals, whi
h provide good 
hannels for ele
tron tunneling through the mole
u-
lar jun
tion and lead to two signi�
ant transmission peaks. Very interestingly, the transport
properties are predominated by the tail of the perturbed LUMO 
ontributed transmission
peak at small bias voltage (for example, less than 1.0 V), sin
e the transmission 
oming from
the perturbed LUMO is just 0.5 eV away from EF , whi
h is 0.3 eV 
loser than that of the
perturbed HOMO. Note that this �nding is di�erent from the mi
ros
opi
 pi
tures of other
existing mole
ular jun
tions based on photo
hromi
 DTE and DTC swit
hing mole
ules,
21,22
azobenzene,
and quintuple bond [PhCrCrPh℄ mole
ules,
whose transport properties are
prevailed by the transmission peak 
ontributed by the perturbed HOMO.
Yet 
ontradi
torily, the spatial pro�les shown in Fig.3 (b) of the perturbed LUMO
strongly lo
alizes at the 
entral swit
hing unit with open 
on�guration. This leads to no
appre
iable transmission peaks in the wide bias window (i.e. from -1.5 to 1.7 eV). The sig-
ni�
ant transmission peak at -1.7 eV originates from the perturbed HOMO and HOMO-1
(both are π orbitals) for the open stru
ture, however, it is lo
ated too far away from the EF .
Here, 
omparing to the 
losed 
ase, we note that the position of the perturbed HOMO for
the open 
on�guration is buried deeply below the EF , whi
h is 
onsistent with the previous
theoreti
al results of DTC mole
ules.
21,22
These theoreti
al �ndings ensure us to 
on
lude
that the sharp 
ontrast of the alignment of the perturbed orbital energies with respe
t to
the ele
trode Fermi level and the shape of these perturbed frontier mole
ular orbitals are
the essential 
auses for the striking 
ontrast in transport properties through diarylethene
mole
ular jun
tions with 
losed and open 
on�gurations.
It should be pointed out that the number of transmission paths 
an not a

ount for
the dramati
 di�eren
e in 
ondu
tivities of the 
losed and open 
on�gurations sin
e the
eigen
hannel analysis indi
ates that there is a single eigen
hannel for both 
ases within a
wide window (i.e. [-1.5, 1.5 eV℄). A

ording to the features mentioned above of the 
al
ulated
zero-bias transmission spe
tra (Fig. 3), One 
an spe
ulate that this type of mole
ular
swit
h 
an operate robustly in a pretty wide range of bias voltages with fairly large on -o�
ratio. Additional 
urrents through the diarylethene mole
ular jun
tions with two di�erent

on�gurations at -2.0, -1.5, 1.5 and 2.0 V are also 
al
ulated. The on-o� ratios of 
urrent are
predi
ted to be about two orders of magnitude. This suggests that the bias voltage window
of this kind of mole
ular swit
h (in Tanigu
hi et al.'s experiments
) with reasonably large
on-o� ratio is surprisingly wider than that of other photo-sensitive mole
ules.
13,21
Experimentalist found that diarylethene mole
ular swit
h is reversible when the mole
ules
are sandwi
hed through aromati
 linkers.
18,23
Theoreti
al 
al
ulations argued that whether
it 
an be swit
hed reversibly or not depending on the mole
ule-ele
trode hybridization.
The weak intera
tion between mole
ule and ele
trode is required to fa
ilitate the desired
reversible transition. A

ording to these �ndings, the reversible transition between the open
and 
losed 
on�gurations in this diarylethtene derivatives based mole
ular jun
tion is highly
possible, sin
e the mole
ules are sandwi
hed with phenyl linkers and the mole
ule-ele
trode
hybridization is weak.
C. Substituting e�e
t on diarylethene mole
ule
Previous theoreti
al 
al
ulations fo
us on the end linking groups,
no attempts so far
have been made to examine the side substituting e�e
t on transport properties through the
diarylethene derivations. It is important to investigate the 
ondu
tan
e of the mole
ular
jun
tion, where six F atoms in the peripheral of 
y
lopentene are substituted by H atoms.
The 
al
ulated transmission spe
tra for the H-substituted mole
ular jun
tion with the 
losed
and open forms at zero bias voltage are shown by bla
k solid lines in Figures. 4(a) and
4(b), and two 
orresponding I-V 
urves are presented in Fig. 2 with �lled and empty

ir
les (linked by red dotted lines), respe
tively. The 
urrent through the H-substituted
mole
ular jun
tion with 
losed 
on�guration is about half of that of the 
y
lopentene with
six F atoms in the peripheral. The reasons are summarized in the following three points.
(1) The repla
ement of H with F on the swit
hing unit results in the variation of band
gaps. The energy gap of the H-substituted diarylethene mole
ule is about 1.7 eV, while the
gap of diarylethene (F) mole
ule is about 1.3 eV. (2) The alignment of the Fermi level is
di�erent for two systems. For the jun
tion with the H-substituted mole
ule, the peak 
oming
from the perturbed HOMO lo
ates at -0.7 eV, whi
h is 
loser to the Fermi level than the
perturbed LUMO transmission peak (at 1.0 eV). This result is 
onsistent with these previous
theoreti
al studies on other DTC and DTE derivations.
21,22
However, the Fermi level lies

lose to the transmission 
ontributed by the perturbed LUMO for the diarylethene (F)
mole
ular jun
tion, as shown in Fig. 3. (3) The transport properties under small bias voltage
are mainly determined by the tail of the transmission peak 
oming from the perturbed LUMO
for the 
losed diarylethene (F) mole
ular jun
tion. However, the 
ondu
tivity of the 
losed
H-substituted one is 
ontrolled the tail of transmission peak 
ontributed by the perturbed
HOMO. Nonetheless, the light-
ontrolled swit
hing feature is undoubtedly retained.
Experimental and theoreti
al results revealed that the visible adsorption spe
tra 
hanged
when two S atoms of the swit
hing unit were substituted by O atoms.
Thus, the trans-
mission spe
tra of the mole
ular jun
tion shown in Fig.1 (b) where two S atoms in 
entral
swit
hing unit are repla
ed by O atoms are also 
al
ulated here, as shown in Fig. 4 with
red dotted lines. Clearly, the swit
hing behavior does not depend sensitively on the O-
substituent. However, it should be pointed out that the positions of signi�
ant transmission
peaks obviously shift when 
ompared to Fig. 3. Parti
ularly, the transmission peaks 
oming
from the perturbed HOMO and LUMO lo
ates at -0.7 and 0.8 eV, respe
tively. Again, the
tail of perturbed HOMO transmission peak 
ontributes largely to the low bias ele
troni

ondu
tan
e.
D. E�e
t of varing end an
horing atoms
In general, the transport properties of mole
ular jun
tions depend nontrivially on the end
linking atoms.
36,37
Now we turn to explore the e�e
t of alternating end an
horing atoms.
The 
al
ulated transmission spe
tra at zero bias voltage are shown in Figure 5. The bla
k
solid and red dotted lines stand for end Se- and Te-an
hored 
ases, respe
tively. It is 
lear
that the main 
hara
teristi
s of the transmission spe
tra are maintained and the 
losed
stru
ture is undoubtedly more 
ondu
tive. For the end Se-an
hored 
ase, the energies of
perturbed MO are quite 
lose to the data presented in Fig. 3 of the end S-an
hored one.
Interestingly, 
learly observable 
hanges have been shown for the end Te-an
hored 
ase. The
transmission peaks originating from the perturbed HOMO and LUMO for the mole
ular
jun
tion 
onne
ting to gold ele
trodes through Te atoms lo
ates at -1.0 (-0.8 for S-an
hored
one) and 0.3 eV (0.5 for S-an
hored one), respe
tively. The very interesting �nding of this
study is that the swit
hing behavior of diarylethene derivatives based mole
ular jun
tions
is robust to vary end an
horing atoms from S to Se and Te.
To examine the sensitivity of results shown in Fig. 3 to small 
hange of the ele
trode-
ele
trode distan
e, we 
ompute the zero-bias transmission spe
tra of diarylethene swit
hes
with the 
losed and open stru
tures as elongating and shortening ele
trode-ele
trode separa-
tion up to 0.3 Å. We �nd that the transmission spe
tra experien
e little 
hange, and trans-
port properties of this kind of diarylethene mole
ular jun
tion is not dete
tably sensitive
to the ele
trode-ele
trode distan
e. It indi
ates that this kind of light-
ontrolled swit
hing
based on diarylethene derivatives is stable as a mole
ular swit
hing devi
e. Note that the
transport behavior is des
ribed by the ele
tron elasti
 s
attering theory in our 
al
ulations.
The e�e
t arising from the ele
troni
 vibration and the a

ompanying heat dissipation on
the 
al
ulated on-o� ratio 
an be negle
ted be
ause of the remarkable di�eren
e of the I-V

urves.
IV. CONCLUSION
In summary, we investigate the transport properties of the diarylethene with 
losed and
open stru
tures using the NEGF 
ombined the DFT method. The zero-bias transmission
fun
tion of two di�erent forms is strikingly distin
tive. The open form la
ks any signi�-

ant transmission peak within a wide energy window, while the 
losed stru
ture has two
signi�
ant transmission peaks on the both sides of the Fermi level. The ele
troni
 trans-
port properties of the mole
ular jun
tion with 
losed stru
ture under a small bias voltage
are mainly determined by the tail of the transmission peak 
ontributed unusually by the
perturbed lowest perturbed uno

upied mole
ular orbital. The 
al
ulated on-o� ratio of 
ur-
rents between the 
losed and open 
on�gurations is about two orders of magnitude, whi
h
reprodu
es the essential features of the experimental measured results. Moreover, although
the alignments of the perturbed mole
ular orbitals's energies with respe
t to the ele
trode's
Fermi level are not exa
tly the same, we �nd that the swit
hing behavior within a wide bias
voltage window is extremely robust to both substituting F or S for H or O and varying end
an
horing atoms from S to Se and Te.
ACKNOWLEDGMENTS
This work was partially supported by the National Natural S
ien
e Foundation of China
under Grants 10674121, 10574119, 50121202, and 20533030, by National Key Basi
 Resear
h
Program under Grant No. 2006CB922004, by the USTC-HP HPC proje
t, and by the
SCCAS and Shanghai Super
omputer Center.Work at NTU is supported in part by A*STAR
SERC grant (No. 0521170032).
Corresponding author. E-mail: liqun�ust
.edu.
n
Corresponding author. E-mail: jlyang�ust
.edu.
n
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Figure 1: (Color online) (a) The diarylethene derivative in 
losed and open 
on�gurations. (b) A
s
hemati
 of the swit
hing jun
tion. Diarylethene mole
ules are sandwi
hed between two Au (111)
surfa
es, and two S an
horing atoms are lo
ated at the hollow site. The verti
al blue line denotes
the interfa
e between the s
attering region and the left or right gold ele
trode.
Figure 2: (Color online) The 
al
ulated 
urrent-voltage 
hara
teristi
s of the diarylethene and its
derivative mole
ular jun
tions with two di�erent 
on�gurations. The triangles linking with bla
k
solid lines are for the diarylethene mole
ular jun
tion, while the 
ir
les linking with short red dotted
lines stand for the jun
tion where six F atoms in the peripheral of 
y
lopentene are substituted by
H atoms. The �lled (empty) symbols 
orrespond to the 
losed (open) stru
tures. The inset below
right is the I-V 
urve for the open stru
tures (with F and H atoms in the peripheral, respe
tively)
in small s
ale for 
larity.
Figure 3: (Color online) The zero-bias voltage transmission spe
tra versus the energy E-EF of
diarylethene mole
ular jun
tions with the 
losed (a) and open (b) 
on�gurations. Here, EF is the
Fermi level of ele
trodes. The red short verti
al lines stand for the positions of MPSH mole
ular
energy levels. The spatial distributions of the perturbed HOMOs and LUMOs are inserted in the
�gure, and pla
ed at the right and left sides of the EF , respe
tively.
Figure 4: (Color online) The 
al
ulated transmission spe
tra versus the energy E-EF at zero-bias
voltage for diarylethene mole
ular jun
tions with 
losed (a) and open (b) forms, respe
tively. One

ase is that six F atoms in the peripheral of 
entral 
y
lopentene are substituted by H atoms (with
bla
k solid lines); the other is that two S atoms are repla
ed by O atoms (with red dotted lines).
The red short verti
al lines stand for the positions of MPSH mole
ular energy levels.
Figure 5: (Color online) The 
al
ulated transmission spe
tra for diarylethene mole
ular jun
tions
with 
losed (a) and open (b) stru
tures. The bla
k solid and red dotted lines stand for the end
an
horing Se and Te atoms, respe
tively. Here, the red short verti
al lines stand for the positions
of MPSH mole
ular energy levels.
Fig.1 of Huang et al.
Fig.2 of Huang et al.
Fig.3 of Huang et al.
Fig.4 of Huang et al.
Fig.5 of Huang et al.
	INTRODUCTION
	COMPUTATIONAL MODEL AND METHOD
	RESULTS AND DISCUSSION
	Electronic structures of free diarylethene molecules with closed and open structures
	Transport properties of diarylethene molecular junctions
	Substituting effect on diarylethene molecule
	Effect of varing end anchoring atoms 
	CONCLUSION
	ACKNOWLEDGMENTS
	References
