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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

http://doi.wiley.com/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 ]

3www.small-journal.combH & Co. KGaA, Weinheim


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


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.



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,


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


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



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


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



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

8 www.small-journal.com © 2012 Wiley-VCH Verlag GmbH & Co. KGaA

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


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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