Surfaces
Identifying Multiple Confi gurations of Complex Molecules on Metal Surfaces Qi Liu , Shixuan Du , * Yuyang Zhang , Nan Jiang , Dongxia Shi , and Hong-Jun Gao
1© 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim wileyonlinelibrary.com
E xperimental identifi cation of molecular confi gurations in diffusion processes of large complex molecules has been a demanding topic in the fi eld of molecular construction at solid surfaces. Such identifi cation is needed in order to control the self-assembly process and the properties and confi gurations of the resulting structures. This paper provides an overview of state-of-the-art techniques for identifi cation of molecular confi gurations in motion. First, a brief introduction to the conventional tools is presented, for example, low-energy electron diffraction and IR/Raman spectroscopy. Second, currently used techniques, scanning probe microscopy, and its application in molecular confi guration identifi cation are reviewed. In the last part, a methodology combining time-resolved tunneling spectroscopy and density functional theory calculation is reviewed in detail; this strategy has been successfully applied to two typical molecular systems, ( t -Bu) 4 -ZnPc and FePc (where Pc is phthalocyanine), with molecular rotation and laterial diffusion on the Au(111) surface.
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 1. 2
Molecular Confi guration Identifi cation 2. Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Scanning Probe Microscopy Techniques . . . 3. 4
Time-Resolved Tunneling Spectroscopy 4. Combined with Density Functional Theory Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Summary and Outlook . . . . . . . . . . . .. . . . . .5. 8
From the Contents
small 2012, DOI: 10.1002/smll.201101937
Q. Liu et al.reviews
DOI: 10.1002/smll.201101937
Dr. Q. Liu , Prof. S. X. Du , Dr. Y. Y. Zhang , Dr. N. Jiang , Prof. D. X. Shi , Prof. H.-J. Gao Institute of PhysicsChinese Academy of SciencesBeijing, 100190, P. R. China E-mail: [email protected]
Dr. Q. Liu State Key Laboratory of Superlattices and MicrostructuresInstitute of SemiconductorsChinese Academy of SciencesBeijing, 100083, P. R. China
1. Introduction
It has always been the dream of almost every physicist or
chemist to identify and record the movement of individual
atoms or molecules on substrate in experiments. However,
this is not easy to do because of several intractable problems
blocking the way. First, unlike the atoms in solids, the moving
atoms and molecules are changing positions all the time. So
the traditional crystal analysis methods such as X-ray dif-
fraction (XRD) are not applicable. Second, unlike gas mol-
ecules whose movement can be treated as ballistic trajectory
processes, the behavior of atoms and molecules on substrate
is highly dependent on interactions with each other and on
the circumstances. Additionally, due to the complex adsorp-
tion conditions, the atoms and molecules can have multiple
confi gurations, which make the precise analysis even more
diffi cult.
In the long history of science since atom theory was
accepted, people have been developing various different
methods and techniques to realize this dream. The Wilson
Chamber methods (1895) [ 1 ] were among the fi rst attempts
to track the moving atoms. Although this technique was lim-
ited for charged high-energy particles, the idea of using the
charge/electron as a probe pointed out a new way for identi-
fying and tracking atoms and molecules. Later, the low-energy
electron diffraction (LEED) [ 2–4 ] technique, whose inventors,
C. Davisson and L. H. Germer, won the Nobel Prize in 1937,
brought us a new tool for identifying the confi gurations of
atoms and molecules on surfaces. And in 1951, E. W. Müller
and K. Bahadur observed a single tungsten atom by using
fi eld ion microscopy (FIM). [ 5,6 ] The above two techniques are
very important not only for their wide applications, but also
for their capabilities of observing the dynamical process of
moving atoms [ 7–8 ] and surface molecular domain changes. [ 9,10 ]
However, their limitations are also evident: LEED shows
only the average information of the area under the electron
beam (several mm 2 ), while the strong electron fi eld in FIM
may cause deformation or even destruction on the sample
molecular structures.
Spectroscopy is an alternative developing direction of
identifying molecular confi guration and potential confi gu-
ration changes. IR/Raman spectroscopes can give valuable
information of molecular confi gurations according to the
vibrational modes of specifi c molecular functional groups. [ 11,12 ]
By using X-ray photoelectron spectroscopy (XPS),
K. Siegbahn (Nobel Prize winner in 1981) observed the sur-
face structure of cleaved NaCl in 1954. [ 13 ] And this technique
became popular soon because of its applications in identi-
fying element types and chemical states. These methods are
quite valuable because precise energy levels could be deter-
mined from the spectra. Besides, interactions among phonon,
photon and electrons could be well investigated by using
these techniques. However, as a common weakness of optical
spectroscopy, limited by the diffraction limit, it is still diffi cult
to identify the precise confi gurations and orientation of each
molecule and the dynamic processes.
A distant dream until very recent decades, the identifi -
cation and recording of the movement of individual atoms
or molecules on substrate now seems more achievable. The
2 www.small-journal.com © 2012 Wiley-VCH V
invention of scanning probe microscopy (SPM) techniques
(G. Binnig and H. Rohrer, Nobel Prize winner in 1986) [ 14 , –16 ]
has made a remarkably great advance towards our aim,
helping researchers to observe the nanoscale world with
atomic or even higher spatial resolution. Molecular identifi ca-
tion under very low temperature (liquid N 2 or liquid helium)
is no longer a problem. In this situation, the molecules are
“frozen” to the surface and not move around. As long as the
prepared tip is sharp enough, high spatial resolution images
of single molecule and molecular arrays can be acquired
easily in any laboratory equipped with low-temperature scan-
ning tunneling microscopy (LT-STM) [ 17 ] or low-temperature
atomic force microscopy (LT-AFM). [ 18,19 ]
However, the identifi cation of molecular confi gurations
in a dynamic process is not as easy as that in a static situ-
ation, especially for a large complex molecule, in which the
molecules’ positions and internal confi gurations will change
at any moment. Fortunately, based on the SPM technique,
some modern detection and analysis methods for molecular
confi guration identifi cation in dynamical process have been
invented and proved to be powerful tools for exploring sci-
entifi c phenomena and their underlying physics at the atomic
scale, such as time-resolved tunneling spectroscopy (TRTS) [ 20 ]
combined with density functional theory (DFT) [ 21,22 ] calcula-
tions, [ 23 ] action spectroscopy, [ 24 ] and so on.
This review will focus on the development of molecular
confi guration identifi cation techniques. In the fi rst section,
some conventional technique of molecular confi guration
identifi cation methods [ 2–4 , 11,12 ] is briefl y introduced. In the
second section, the key features of modern SPM technique
and both its advantages and disadvantages in molecular con-
fi guration identifi cation are discussed. And in the third sec-
tion, particular attention will be paid to the technique of
TRTS-DFT and its application on two kinds of large complex
molecules on substrate. Finally, a brief summary and outlook
will be given at the end of this review.
2. Molecular Confi guration Identifi cation Method
In order to identify the molecular confi gurations on substrate
in dynamic process, fi rst of all, the possible confi gurations
should be investigated by experimental methods or esti-
mated through theoretical calculations. At this stage, some
erlag GmbH & Co. KGaA, Weinheim small 2012, DOI: 10.1002/smll.201101937
Configurations of Complex Molecules on Metal Surfaces
Shixuan Du studied at Peking University
(B.S.), and received her Ph.D. in physical
chemistry from the Beijing Normal Uni-
versity in 2002. After that, she joined the
Nanoscale Physics and Devices Laboratory
of the Institute of Physics, Chinese Academy
of Sciences. She became a Professor of the
Institute of Physics in 2009. Her research
interests focus on the DFT calculations for
the structure, physical, and dynamic proper-
ties of molecules on metal surfaces. She
has published more than 50 journal papers
in journals, such as Phys. Rev. Lett. , J. Am.
Chem. Soc. , Adv. Mater. , and Nano Lett .
key points should be investigated in advance: 1) symmetry
of the molecule and the substrate, for example, C 4v or C 4h ;
2) interaction between molecules and between molecules and
the substrate, chemical bonds or weak van der Waals interac-
tions; 3) distribution of the molecules on substrate and the
coverage. The answers to these questions will help us to fi nd
out the possible confi gurations of molecules and give us clues
as to which method should be used to investigate the possible
confi gurations.
Among those techniques which could be used for molec-
ular confi guration analysis, especially for the ultrahigh vacuum
(UHV) conditions, LEED is worth noting for its in-situ fea-
ture and minimal damage to the sample. The physical picture
of LEED is well known as the Ewald sphere, and the pattern
on the screen provides a reciprocal section of the investigated
system. LEED diffraction patterns show us not only the self-
assembly domains of molecules on substrate, but also the lat-
tice parameters of the 2D structure. By using LEED, one can
observe the real-time molecular growth, and obtain the lattice
information of the assembled structures. For some molecules,
the temperature of the substrate will change their assembly
structures, and LEED can be used to monitor the process as it
happens, [ 10 ] as shown in Figure 1 . However, the LEED method
has its limitations. One essential problem is the result obtained
from LEED is the reciprocal section information, while gener-
ally the surface structure is not a perfectly fl at plane. Surface
defects, step edges, and multiple domains make the reconstruc-
Figure 1 . Temperature-driven structural evolutions of coronene molecules on Ag(110) substrate. [ 10 ] A) LEED patterns at different temperatures. B) STM images of the corresponding structures; both image size are 25 nm × 25 nm. C) A qualitative explanation of the evolution process. Reproduced with permission. Copyright 2009 American Chemical Society.
tion of the assembly structure in real space
from LEED very diffi cult. [ 25 ]
Another conventional molecular
confi guration analysis tool is IR/Raman
spectroscopy. IR spectroscopy works on
the adsorption of the light of specifi c
wavelengths due to harmonic vibration of
specifi c functional groups, while Raman
spectroscopy depends on the light shift of
inelastic scattering or Raman scattering,
which also results from specifi c vibration
modes of functional groups. [ 11,12 ] They are
widely used in identifying the components
of unknown specimens or as sensors for
the “fi ngerprint” feature of specifi c chemi-
cals [ 26 ] (see Figure 2 ). If the molecules are
in different confi gurations—that is, the
circumstance is different, or the molecules
have some kind of deformation—these
differences are refl ected as slight shifts in
the spectra, which can be used for confi gu-
ration analysis, especially in chemistry and
biochemistry [ 27,28 ] as shown in Figure 2 A,B.
IR/Raman spectroscopy also has in-situ
and nondestructive features. However, the
shift of an adsorption peak is usually very
small, and sometimes it is hard to fi nd an
intuitive model to explain the results, or
there are multiple alternative explana-
tions. This uncertainty makes results from
other methods necessary to complete the
explanation in certain conditions.
© 2012 Wiley-VCH Verlag Gmsmall 2012, DOI: 10.1002/smll.201101937
There is still one common diffi culty for the techniques
mentioned above—that is, most of them are not designed
for spatial-resolved observation, so the results only portray
a mixture of a large number of molecules under different
circumstances. As for the molecules in movement, the signal
only refl ects an average of all the molecules. In this situation,
even a cluster of molecules is hard to detect independently,
not to mention individual molecules. This problem was not
well solved until the invention of SPM. After this milestone,
the above methods have also been greatly enhanced accord-
ingly. New methods are emerging to replace their predeces-
sors, such as low-energy electron microscopy (LEEM), [ 30 ]
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Q. Liu et al.reviews
Figure 2 . IR/Raman spectroscopy. A) The IR spectra changes of proteins at temperatures from 290 to 13 K. The differences are from the 13 C label atom located at different positions in the protein. [ 28 ] Reproduced with permission. Copyright 2003, The Protein Society. B) Different single-wall carbon nanotubes (SWNT) presenting different vibration modes in Raman spectra. Data courtesy of Prof. R. Martel, University of Montreal. C) Tip-enhanced Raman spectroscopy diagram (TERS); for more details see the literature. [ 29 ]
tip-enhanced Raman spectroscopy (TERS), [ 29 , 31 ] and near-
fi eld scanning optical microscopy (NSOM). [ 32,33 ]
3. Scanning Probe Microscopy Techniques
Scanning probe microscopy is a family of diverse design for
measuring different physical properties, such as topographic,
electronic, optical, magnetic properties and so on, as shown in
Figure 3 . The common feature is that they all use a probe to
sense the desired properties. Based on the control para meter
or feed-back mechanism, they can be classifi ed into scanning
tunneling microscopy (STM), [ 34 ] scanning force microscopy
(SFM), scanning near-fi eld optical microscopy (SNOM) [ 35,36 ]
and others. Under each of these categories, there are more
specifi c types. Take STM for example, there are low-tem-
perature STM, [ 34 ] radiofrequency STM (RF-STM), [ 37 ] and
spin-polarization STM (SP-STM). [ 38 ] While within SFM,
there are atomic force microscopy (AFM), [ 16 , 39,40 ] magnetic
force microscopy (MFM), [ 41,42 ] electrostatic force microscopy
(EFM), [ 43 ] and so on. Here, we will not try to cover everything
about SPM, as there are already some decent reviews and
books. [ 15,16 , 34 , 38 , 43 ] We will focus on the common mechanism
of most SPM instruments, and discuss its application in the
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identifi cation of molecular confi gurations and their advan-
tages and disadvantages.
The four common components of SPM instruments are
a tip system, a movement system, a feedback system, and a
signal processing system. The tip system depends on the inter-
action type and should be optimized to utilize the interaction
between the tip and sample. For example, in STM, it should
be a sharp enough metal tip which has a fl at density of states
(DOS) near the Fermi level, [ 34 ] while an AFM tip should have
a long stiff cantilever and a high Q (or Q factor, a dimension-
less parameter which can be used to characterize the resona-
tor's bandwidth to its center frequency) value. [ 16 ] Another
common requirement is that the tip should not bring too
much interference to the sample. Though it seems contradic-
tory, a small perturbation is indeed needed to guarantee the
credibility of measured results. [ 49,50 ] The movement system
can be divided into the coarse movement system and the
scanner system. Most scanner systems use piezotechniques to
realize the subatomic scale fi ne movement. The feed-back sys-
tems generally use common proportional/integral/derivative
(PID) schema, [ 51,52 ] which keep a certain parameter smoothly
around a given set point value. As for the signal processing
system, there generally would be some analog to digital (A/D)
and digital to analog (D/A) conversions and visualizations.
erlag GmbH & Co. KGaA, Weinheim small 2012, DOI: 10.1002/smll.201101937
Configurations of Complex Molecules on Metal Surfaces
Figure 3 . The SPM families: A) Near-fi eld scanning optical microscopy (NSOM) schema. Reproduced with permission (http://www.nanonics.co.il/, last accessed Nov, 2009). Copyright 2009, Nanonics Imaging Ltd. B) General SPM model. [ 44 ] C) STM schema. Reproduced with permission (http://www.nanonics.co.il/, last accessed Nov, 2009). Copyright 2009, Nanonics Imaging Ltd. D) STM images at high resolution for Au(111) [ 45 ] (Copyright 1985, the American Physical Society), Si (111)-7 × 7 [ 46 ] (Copyright 2004, the American Physical Society), monolayer FePc/Au(111) [ 47 ] (Copyright 2007, the American Chemical Society), and single ( t -Bu)4ZnPc molecule on the second molecular layer, separately (Copyright 2011, Elsevier. [ 48 ] Copyright 2010 the American Physical Society [ 23 ] ). Pc represents phthalacyanine. All reproduced with permission.
Although the SPM technique still has some shortcom-
ings, for example, limited scanning speed, diffi culty in simul-
taneous multiple scanning, high probe dependency, it has
become a standard tool for many researchers. With the help
of subatomic-resolution piezoscanners, SPM makes the iden-
tifi cation of individual molecular confi gurations no longer a
dream. Figure 3 D shows some STM images at high resolu-
tion. [ 46 ] However, in the above cases, most measurements are
performed either under low temperature, in which case the
molecules are “frozen” to the surfaces, or at a high coverage,
in which the molecules are “fi xed” inside a close-packed
neighborhood. [ 48 , 53–56 ] Movement of mole cules makes tradi-
Figure 4 . STM images of ( t -Bu) 4 ZnPc (A) and FePc (B) molecules on a Au(111) surface acquired at LHe (blue frame) and LN 2 temperatures. The single-molecule rotors at different positions on Au(111) are shown as elbow, fcc (face-centered cubic), hcp (hexagonally close-packed), and across the ridge in (A). The coverages are 0.1, 0.3, and 0.6 ML for top, middle, and bottom panels in B, respectively. ML represents a monolayer. More information on these systems can be found in references [ 57 ] and [ 58 ] .
tional STM observation useless. Consid-
ering Figure 4 we can see the comparison
between STM images acquired under
liquid-helium (LHe) temperature and
those acquired under liquid-nitrogen
(LN 2 ) temperature; the molecules begin to
travel around at higher temperature (LN 2 )
while they are stationary at lower temper-
ature (LHe). [ 57 ]
In a dynamic molecular system, investi-
gating confi gurations is a challenge. There are
two main diffi culties. The fi rst is that the mol-
ecules have diffusion behavior, which could
be termed a “nonlocal” problem, and this
could be seen in previous images. The second
is that, even if a molecule stays inside a lim-
ited region, it can have several alternative
confi gurations, which is called the “unstable”
problem. For example, they can “rotate” [ 59,60 ]
or “travel in line.” [ 60,61 ] Under lower temper-
atures, we may observe their behavior “slide
by slide” by manipulation with an STM
tip. [ 62 ] However, when the temperature rises,
© 2012 Wiley-VCH Verlag Gmsmall 2012, DOI: 10.1002/smll.201101937
the images soon become a mess and no individual molecules can
be seen. In a general dynamical system, both the “nonlocal” and
“unstable” problems exist, which makes systemic analysis even
more diffi cult.
There have been some pioneering work attempting to
resolve these problems as shown in Figure 5 . For the “non-
local” problem, a natural idea would be tracking. However,
considering the tracking target is only a single atom or mol-
ecule, this is quite hard. In 1996, B. S. Swartzentruber demon-
strated the “dither” technique for tracking a moving atom. [ 63 ]
And E. Hill et al. tracked a hydrogen atom hopping along the
dimer row of a Si(001) surface at around 600 K in 1999. [ 64 ] In
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Q. Liu et al.
6
reviews
Figure 5 . Typical techniques for investigating the diffusion process and their applications. A) The “tracking” methods of atoms and molecules on the surface, including the Si dimer on Si(001) [ 63 ] (Copyright 1996, the American Physical Society) and a H atom hopping along a Si(001) dimer row [ 64 ] (Copyright 1999, the American Physical Society) and long-time tracking of H atom on Cu(001). [ 68 ] (Copyright 2000, the American Physical Society). B) The “snapshot” methods, including the fast STM recording of In atoms move along Cu(001) [ 66 ] (Copyright 2004, Elsevier B. V.), the tip-induced chemical reaction [ 62 ] (Copyright 2000, the American Physical Society) and molecular conformation change under UV light [ 67 ] (Copyright 2008, the American Chemical Society). All images reproduced with permission from the indicated references.
the same year, L. J. Lauhon and W. Ho showed their impressive
work of tracking a single hydrogen atom moving on a Cu(001)
surface at 74 K for 69 s. [ 65 ] These works are very exciting and
enlightening. However, the tracking method itself still has some
inevitable disadvantages. First, due to the low speed of STM tip
movement and the necessary feed-back time, tracking must be
performed under low diffusion speed conditions; second, there
should not be too many atom/molecules in the investigated
area, otherwise the tracking target may get lost when another
molecule comes into view. At the same time, another method
tries to solve this problem in a different way: snapshot. Just like
recording a movie, R. van Gastel et al. used high-speed STM,
which can achieve 0.64 s per frame, and showed the process of
indium atoms moving along the step edge of Cu(001) in 2004. [ 66 ]
And P. S. Weiss showed the molecular confi guration changes
under ultraviolet light by using a series of STM images. [ 67 ] This
snapshot technique is also a good way to observe the molecular
confi guration changes in a dynamical process, but this method
still cannot overcome the weakness of slow speed, which arises
from the physical limitation of piezotechniques, because even
with high-speed STM it is hard to record the molecules dif-
fusing at milliseconds or microseconds.
Although STM brings a bright prospect for molecular con-
fi guration identifi cation, to perform STM measurement for
confi guration identifi cation in a dynamical system, some novel
methods are still needed to overcome the technical barriers.
4. Time-Resolved Tunneling Spectroscopy Combined with Density Functional Theory Calculation
Considering the speed limitation of the piezotechnique,
the only way which can be used to overcome the low speed
of the STM seems to be avoiding the usage of piezotech-
nique to follow the molecule's movement. In fact, this is an
www.small-journal.com © 2012 Wiley-VCH V
indeed good idea. B. C. Stipe and W. Ho [ 69 ] used a tip hov-
ering over a rotating C 2 H 2 molecule on Cu(001) and moni-
tored the tunneling current changing as shown in Figure 6 A.
This method of time-resolved tunneling spectroscopy [ 20 , 70 ]
could well avoid the mechanical problem because the elec-
tronic signal sampling time could be much shorter. By moni-
toring the switching frequency of “high” and “low” states
with changing temperature, they successfully obtained the
rotation barrier. [ 65 , 68 ] This technique and their analysis
model were soon used in other research, including a report
involving Co atoms and CoCu 2 on Cu(111) by J. A. Stro-
scio and R. J. Celotta, [ 71,72 ] Ge dimers on Ge(001) by A. von
Houselt et al. [ 73 ] and A. Saedi et al., [ 74 ] Ag atoms on Si(111)-
7 × 7 by K. D. Wang et al., [ 75,76 ] as shown in Figure 6 . It is worth
noting that the TRTS can be used for both molecular diffusion
observation and molecular confi guration switching. The differ-
ence between the two is not distinct; however, in the switching
cases, the function of the applied bias voltages plays a more
important role, and it is generally larger than those in the
observation cases. For example, there are dehydrogenation, [ 77 ]
supramolecules switching, [ 78 ] and action spectroscopy. [ 24 ]
While most of these published works are about single
atoms or small molecules, they cover very few different
states (two for most cases) in the dynamical processes. In this
situation, the observations are relatively easy to analyze, since
the specifi c current and corresponding confi guration can be
seen at a glance. However, there are generally more distinct
states in the dynamical processes of a molecular system. [ 23 , 74 ]
In fact, even in the published work, this phenomenon has
been shown in the results to some extent. [ 65 , 71 , 79 ] In a system
consisting of complex molecules, it would be quite confusing
to decide which current belongs to the specifi c confi guration.
This is a big problem for the direct application of TRTS in a
system consisting of large complex molecules.
Fortunately, we have another powerful tool to solve this
problem: density functional theory calculations. The possible
erlag GmbH & Co. KGaA, Weinheim small 2012, DOI: 10.1002/smll.201101937
Configurations of Complex Molecules on Metal Surfaces
Figure 6 . The TRTS methods application for molecular dynamic observation in STM measurements. A) C 2 H 2 on Cu(001). Adapted with permission. Copyright 1998, the American Association for the Advancement of Science; [ 59 ] Copyright 1999, the American Chemical Society; [ 65 ] Copyright 1998 & 2000, the American Physical Society. [ 68,69 ] B) Co/CoCu 2 on Cu(111). [ 71,72 ] Reproduced with permission. Copyright 2004 & 2006, the American Association for the Advancement of Science. C,D) Ge dimer on Ge(001). [ 73,74 ] Reproduced with permission. Copyright 2006, the American Physical Society; Copyright 2009, the American Chemical Society. E) Ag on Si(111)-7 × 7. [ 76 ] Reproduced with permission. Copyright 2008, the American Physical Society.
stable molecular confi gurations and their adsorption ener-
gies can be calculated by using DFT fi rst. Then we can apply
frequency-counting statistics to the time-resolved tunneling
current data to get the occupation probability of each current
value, from which the stable molecular states can be fi gured
out with corresponding currents. Thanks to the Boltzmann
statistics, we can then connect the occupation probability
with the energy by the following simple equation:
Ei − E j = − kB T ln ( Pi
Pj)
(1)
E i and E j are energies of the states i and j , respectively; P j and
Figure 7 . ( t -Bu) 4 ZnPc molecular rotor on Au(111), which is described in additional detail in reference [ 58 ] . A) Rotation mechanism of a ( t -Bu) 4 ZnPc single-molecule rotor on Au(111). B) The STM images agree well with the DFT calculations and explain the structures observed in experiments. Image size is 3 nm × 3 nm.
P j are the occupation time sums for states
i and j , respectively; and k B and T are the
Boltzmann constant the temperature,
respectively. By the calculated energy dif-
ferences between states, we can correspond-
ingly determine which states occurred in
the experiment and their confi gurations in
space. However, for a system consisting of
large complex molecules, as we mentioned
before, there are two problems, “unstable”
and “nonlocal.” The method described above
solved the “unstable” one. What about the
“nonlocal” problem? The answer may be
“mapping.” As long as the molecules are
all treated the same, the confi gurations of
molecule at position A and B only depends
on the substrate. Thus the TRTS grid-by-grid
mapping will give us the molecular confi gu-
ration distributions all over the interesting
area. After combining such observations
© 2012 Wiley-VCH Verlag Gmsmall 2012, DOI: 10.1002/smll.201101937
with the DFT calculation results, the surface adsorption energy
contour can be obtained by this technique, which provides pre-
cise experimental results for surface diffusion research.
In order to demonstrate the above methods, we will
consider two systems consisting of large complex molecules
as examples. The fi rst is the single-molecule rotation in
the ( t -Bu) 4 -ZnPc/Au(111) system. STM experiments have
shown that single ( t -Bu) 4 -ZnPc molecules rotate at 80 K
without lateral diffusion, but the remain fully stationary at
5 K (Figure 4 A). So the typical “unstable” feature is clearly
present. Under 80 K, the pattern of the two concentric rings
in the STM image is due to the fast confi guration change,
and its schema is shown in Figure 7 . [ 58 ] The STM tip was
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Q. Liu et al.reviews
Figure 8 . The application of TRTS-DFT on ( t -Bu) 4 ZnPc (A) and FePc (B) molecules on Au(111). [ 23 ] The spots indicated by white and blue arrows in (A) and (B) show the tip positions of the TRTS measurements, and the corresponding molecular confi gurations are given by DFT calculations. Reproduced with permission. Copyright 2010 American Physical Society.
located over the rotating molecule for recording the current–
time, I–t , data. TRTS data could be obtained and several
distinct current values could be recognized in the telegraph-
like signals as shown in Figure 8 A,c. After the frequency
counting statistics, several peaks indicate the probabilities
of each current, which corresponds to the occupation ratio
of each occurring confi guration; thus the adsorption ener-
gies can be estimated by the ratios. For example, current
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Figure 9 . The application of the TRTS-DFT-mapping method on the FePc/Au(111) system at LN 2 temperature, which is described in additional detail in reference [ 23 ]. The result of the TRTS-DFT-mapping shows the adsorption energy difference of molecules on the surface and provides valuable information for the surface diffusion process, as shown in the 3D image (D).
II in Figure 8 A,d possesses the highest
occupation probability, while current IV
has the smallest occupation probability.
Therefore, we can conclude that the cor-
responding confi guration II is the most
stable molecular confi guration and thus
possesses the lowest adsorption energy
on the surface during rotation. Follow the
Equation 1 , the energy differences can
also be calculated. Combining this with
DFT calculations, the specifi c molecular
confi guration in rotation can be identifi ed
accordingly.
The second example is a molecular
liquid in the FePc/Au(111) system, which
shows a typical “nonlocal” feature. Unlike
( t -Bu) 4 -ZnPc, FePc shows a quite different
behavior at 80 K with small coverage. The
molecules begin to diffuse all over the
surface and cannot be distinguished in
the STM images. This can be attributed
to its fl at structure and low diffusion bar-
rier. TRTS and frequency counting reveal
that there are four typical confi gurations,
and their energy difference can be calcu-
lated directly from the curve following
Equation 1 as shown in the table in Figure 9 F. As we know,
the Au(111) surface has herringbone reconstructions, and we
can apply TRTS at different regions of the surface to get the
energy differences at each position. In this experiment, 32 × 32
grids were measured and the adsorption energy difference sur-
face was drawn in 3D from the measured data (Figure 9 A,D).
The blue region in Figure 9 B means the small energy differ-
ence between the most energy-preferred confi guration and
the second energy-preferred confi guration,
while the red region means high energy dif-
ference. A lower energy difference implies
that the molecule could change to another
confi guration more easily and frequently;
thus the STM image, is more “noisy,” and
vice versa. This can be confi rmed well by
STM images. All the processes of this
method are shown in Figure 9 .
We have considered the TRTS-DFT
method and its application in two large
complex molecules, and we have shown
that the identifi cation of molecular con-
fi guration in a dynamical process can be
realized by using such a method. It has
long been a challenging task for research
into diffusing molecular systems, and this
method provides a new route for further
research.
5. Summary and Outlook
With the aid of STM, more and more
novel techniques have been invented to
, Weinheim small 2012, DOI: 10.1002/smll.201101937
Configurations of Complex Molecules on Metal Surfaces
enrich the tools for dynamical system observation: tracking,
snapshot, TRTS, time-bin counting, frequency counting,
DFT-assisted identifi cation, grid-by-grid mapping and so on.
Nowadays it is easier than ever before to analyze a dynam-
ical molecular system thoroughly: the molecular confi gura-
tions, their corresponding total energies, adsorption energy,
switching frequency, energy barriers, and so on. With these
new techniques, we investigated the surface diffusion path,
surface catalytic processes under high temperature, and the
molecular interaction change with respect to coverage, tem-
perature, and bias. Taking the surface diffusion path as an
example, the traditional treatment of such problem would
use the kinetic Monte Carlo (KMC) [ 80,81 ] calculation or the
nudged elastic band (NEB) [ 82–84 ] calculation to fi nd the min-
imum energy diffusion path. Such analysis generally would
be very computationally demanding and limited to small sys-
tems. Now we can use the TRTS method with DFT to directly
detect the intermediate molecular confi gurations during
diffusion and confi rm the calculation results. This would be
very helpful in both the application of catalysis research
and the construction of a more effective diffusion calcula-
tion theory for complex molecular systems. It is anticipated
that the dynamical molecular system research will be an area
full of new discoveries and exciting progress, and that new
techniques and methods will emerge to fulfi ll the demanding
needs of experiments and theoretical calculations. Finally, we
would like to express that there are plenty of opportunities
in the understanding and control of dynamical molecular sys-
tems at solid surfaces.
Acknowledgements
We thank Prof. H. Fuchs, Prof. L. F. Chi, Prof. W. A. Hofer, and Prof. S. T. Pantelides for helpful discussions and suggestions. We would also like to thank L. Gao, X. Lin, Z. H. Cheng, Z. T. Deng, H. G. Zhang, J. H. Mao, and Y. L. Wang for experimental assist-ance and discussions. This work is supported by the Collaborative Research Centre TRR61, the National Natural Science Foundation of China (Grant No. 10834011), the National Basic Research Pro-gram “973” projects of China (Grant No. 2011CB921702 and 2011CB808401), and the Shanghai Supercomputing Center.
This Review is a contribution from the Transregional Collabo-rative Research Center (TRR 61), Multilevel Molecular Assemblies: Structure, Dynamics, and Function.
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