Figure 2. Schematic view of the basic
configuration for scanning tunneling microscopy.

Operating Principle
and Implications
Basic Setup and Modes
Like other types of scanning probe
microscopes, scanning tunnelingmicroscopes contain a sharp probe thatis scanned relative to a sample surface
using precisely controlled voltages
applied to piezoelectric elements while
the motion of the tip (or sample) normal
to the sample surface is controlled by a
feedback loop (see Figure 2). What
sets STM apart from other SPMs is theuse of the tunneling current between tip

and sample as error signal for that feedback loop. While this limits STM studies
to conductive substrates, the steep
exponential distance dependence ofthe tunneling current allows for spatial
resolution rarely achieved in other SPM
modes. Typical bias voltages vary frommillivolts for bare metal or graphite
surfaces to 1-2 volts for semiconductor
substrates and molecular adsorbates.
Tunneling currents are usually in thepico-ampere to nano-ampere range. As
no force measurement is taking place,the STM probe is not attached to acantilever. Instead, the probe is theatomically-sharp tip of a metal wire.
Typically, either mechanically formed
Pt/Ir-tips or electrochemically etched
Pt/Ir or W-tips are employed.
As with all SPMs, the probe (here theSTM tip) can be made to follow thesample topography in detail. In thatcase scan rates (in lines per time unit)
and feedback parameters employed
tend to be of the same order ofmagnitude as for AFM. However, in
STM the topography is defined by aconstant tunneling current (at the given
voltage bias), thus this mode ofoperation is referred to as constantcurrent mode.
Alternatively, the feedback parameters
can be reduced and the scan rates
increased drastically, so that the tip(or sample) moves at approximately

Figure 3. Imaging a surface in constant current mode. The surface
topography is defined by a constant tunneling current.

2

constant height (“constant heightmode”). Instead of the height, the error
signal (i.e., tunneling current) is being
recorded. The relatively flat samples
often interrogated in ambient STM
studies are conducive to this mode ofoperation, with the higher scan rates
helping to reduce the influence ofthermal and mechanical drift, which
can be important due to the small(often <100nm) scan sizes. However,
due to their more well-defined
tip-sample separation, STM topographs
acquired in constant current mode may
be preferable for comparisons withtheoretical predictions.
In analogy to other SPMs the imaging
capability of STM is complemented bya type of single-point spectroscopy(SPS), here also referred to as scanningtunneling spectroscopy (STS). In thismode, the current is recorded at agiven location of the sample as afunction of another parameter, typicallythe bias voltage or tip-sample separation.
Source of Image Contrast
In constant current mode the sample
topography displayed in an STM image
is defined by a constant tunnelingcurrent between tip and sample at thechosen bias voltage. The interpretationof such “topography” in terms of sample
properties is at first less straightforward
than in the case of AFM, where the

Figure 4. Imaging a surface in constant height mode. The error signal(i.e., tunneling current) is being recorded.

probe moves such as to press on thesample with constant force. As shownby Tersoff and Hamann, the tunnelingcurrent between a metallic tip and a
metallic surface is proportional to thesurface local density of states (LDOS)
at the Fermi level, EF, evaluated at
the location of the tip.5,6 While thissimple result is subject to certain
approximations, such as small bias,
low temperature, and a spherical tip
represented solely by an s-wave function,
the interpretation of STM images interms of the surface LDOS at (or near)
EF has met with overwhelming success.
The present application note is mainly
concerned with surfaces decorated withrelatively weakly interacting molecules.
In contrast to the assumptions underlying
Tersoff and Hamann’s theory, larger
bias voltages (typically on the orderof 1V) and higher temperatures (usually
approximately room temperature) are
employed for imaging such systems,
thus expanding somewhat the energy
range of surface states involved intunneling. In addition, when considering
the density of states of the overallsystem, the molecular orbitals
associated with the adsorbate must be
taken into account7,10,11 as illustrated in
Figure 5.
In constructing a diagram as shown
schematically in Figure 5, the energiesof the adsorbate states need to beplaced with respect to the energiesof the substrate surface states. Shownin Figure 5 are the frontier orbitals of
the molecular adsorbate, i.e., thehighest occupied molecular orbital,
HOMO, and the lowest unoccupied
molecular orbital, LUMO. As a first
approximation, the vacuum levels canbe “pinned” or “lined up”, as a freeelectron does not care where it camefrom. As indicated in Figure 5, theFermi level of the substrate and the
HOMO of a free molecule are referredto the vacuum level by the workfunction,
φ, and ionization potential, IP,

Figure 5. Energy diagram for an STM junction when applying a negative (a) or positive (b)sample bias. The position of molecular frontier orbitals (HOMO and LUMO) and Fermi levels of
substrate (ES) and tip (ET) are indicated. While molecular energy levels are broadened and shifteddue to electronic coupling (Γ) to substrate states (and other phenomena), their approximate position
can be estimated by pinning the vacuum level of the isolated molecule to that of the substrate.

respectively. However, a quantitative
treatment will have to take into accountshifts (and broadening) of energy levels
due to effects such as the electronic
coupling, Γ, between adsorbate andsubstrate states, the presence of any
solvent (typically lowering the energy ofions), and the electric field in the vicinityof the STM tip (typically ~107 V/cm).
At first it may seem that the adsorbate
does not contribute a significant numberof states to the overall system, especiallynot near the Fermi level. In the case of
Xe on Ni, not a single adsorbate statelies within several eV of the Fermi level.
Nevertheless, Xe atoms on Ni havebeen imaged successfully.12 The
presence of Xe has a significant
influence on the LDOS near the Fermi
level as evaluated at the position of
the STM tip. Simply due to its spatial
location even this most insulating

adsorbate can serve as “antenna” (i.e.,
at least a better antenna than vacuum)for the transport of electrons across thetunneling junction. Thus, STM imagesof insulating adsorbates can provide
a topographic map of the topmost
adsorbate atoms.13
When the surface adsorbate exhibits
electronic states near the Fermi level(i.e., for a moderate HOMO-LUMOgap), then individual molecular orbitals
may dominate in the mediation of theelectron transmission. For negative
sample bias, electrons from filledsurface states tunnel to the tip. As
illustrated in Figure 5a, mediation of thisprocess is dominated by the HOMO ofthe adsorbate, if the HOMO is situatednear the Fermi level. Conversely,
electrons tunnel into empty surface
states for positive sample bias. As
illustrated in Figure 5b, the LUMO may

3

play a dominant role in this case if it islocated near the Fermi level. Thus, withappropriately chosen bias voltages
STM images can reveal the shape ofindividual molecular orbitals.
The energy diagram shown in Figure 5
not only applies for adsorbate species
in an STM tunneling junction. Essentiallythe same diagram is used in theanalysis of single-molecule device
studies performed with break junctions
and electromigration junctions. The
only difference is the assumption ofsignificant electronic coupling to bothelectrodes in those cases. Therefore, theschematic diagram shown in Figure 5
not only explains why essentiallyinsulating adsorbate molecules can beimaged with STM but also illustrates
how STM and STS provide information
relevant to molecular device properties.
STM and STS data for appropriately
chosen systems can intrinsically provide
information about the mediation of
charge transport by individual molecularstates of single molecules.
In the above treatment the adsorbed
molecule is being considered solely as
an object with an electronic structurethat plays a role in mediating theelectron tunneling by changing theoverall LDOS of the decorated surface.
In general, molecules exhibit additional
degrees of freedom (vibrations,rotations, translations). The associateddynamics need to be considered forthe interpretation of STM and STS data
for several reasons. First, large-scale
nuclear motion entails a corresponding
spatial redistribution of electron
density that can affect the tunnelingprobability.7,14 Second, vibrationaland rotational degrees of freedom areassociated with spectral fine structure.
In experiments performed at or nearroom temperature (the focus of thisapplication note), thermal broadening
reduces the energy resolution oftunneling spectra sufficiently to prevent
detection of such fine structure.

4

However, this is not the case in UHV
STM experiments performed a few
degrees above absolute zero where
vibrational structure has been observed
due to its influence on both, the elastic
and inelastic tunneling probability.15

Application Examples
2-D Self-Assembly: Chemisorbed
and Physisorbed Systems
The study of two-dimensional selfassembly on surfaces and at interfaces
is motivated by many practicalapplications ranging from lubricationand catalysis to the role envisioned for
self-assembly in future nanoscaleengineering. Several types of selfassembling systems have received
considerable interest, including thiols
chemisorbed on Au(111)9 and alkane
derivatives physisorbed on the basal
plane of graphite.7 The chemisorptionof thiols on gold is an irreversible

process driven by the formation of thestrong Au-S bond. Intermolecularinteractions and the structure of theAu(111) surface also play a role during
the self-assembly. Dense monolayers areformed, where only the thiol headgroupis in contact with the gold surface. In
the case of alkane thiols, acommensurate (√3 x √3)R30° overlayer
structure is formed with additional
superstructures depending on chain
length and functionalization.
Figure 6 shows an example of anambient high-resolution STM image
where the ordered structure of a thiollayer can be seen clearly.16 The
monolayer was prepared by exposing
a gold substrate to an ethanol solution.
Both molecular species of interest wereincorporated in the monolayer and canbe distinguished in the STM image.
Thus, model systems for nanosciencecan be embedded in a sea of simple
alkane thiols and studied by STM.

Figure 6. Low-current STM topographic images of mixed self-assembled monolayers on Au(111)formed from a solution of 11-mercaptoundecanoic acid and decanethiol (1:9) at 65°C with abias voltage of 1.02 V and a set point current of 1.10 pA. Reprinted in part with permission from
Lingyan Li, Shengfu Chen, and Shaoyi Jiang, Langmuir 2003, 19 (8), 3266 -3271. © (2003)
American Chemical Society.

Alkane thiols are subject to oxidation in
air and high-resolution STM studies areoften performed in UHV, even when the
preparation takes place by immersing
the substrate in a solution. The present
application note is mainly concernedwith physisorbed monolayers selfassembled on the basal plane ofgraphite, which are frequently generated
and probed in ambient conditions at
the liquid/solid interface. In contrast to
thiols on gold, physisorbed monolayers
on graphite are not based on theirreversible formation of a chemicalbond between a surface atom and a
specific adsorbate functional group.
Numerous types of organic molecules
permit the formation of weakly-adsorbed
monolayers on graphite that exist in
equilibrium with a supernatant solution.
Often, either long alkyl chains orfunctional groups (or both) are present
with both the associated intermolecularand molecule-substrate interactions
providing key driving forces for the
self-assembly process. The following
sections of this application note will
provide several examples for STM
work on such self-assembled systems,
including molecules that were customtailored to exhibit both, the desired
self-assembly and the molecular device
properties of interest.

Driving Forces for Self-Assemblyon Graphite
Among the first STM studies of selfassembly from solution were those of
the monolayers formed by alkanes andtheir derivatives on graphite.7,13,17 As
can be seen in Figures 7-14, closepacked lamellar structures are formed
where the lamellae are composed ofparallel alkyl chains each assuming an
extended, all-trans conformation. In
contrast to the dense self-assembled
monolayers formed by alkane thiols ongold substrates,9 the backbone axis ofeach molecule is oriented parallel to theplane defined by the substrate surface,a.

b.

Figure 7. (a) Constant height STM image (20nm 3 20nm, sample bias –1.235V, 166pA
tunneling current) of triacontane (C30H62) in phenyloctane physisorbed on graphite. One
molecular length is represented by a black bar. The molecules are oriented with a 90° angle
between the molecular axis and the direction of the lamellae. (b) Constant current STM image(20nm x 20nm, sample bias –1.4V, 80pA tunneling current) of triacontanol (CH3(CH2)29OH)
in phenyloctane physisorbed on graphite. One molecular length is indicated by a black bar.
The molecules are oriented with a 60° angle between the molecular axis and the direction of
the lamellae as indicated on the image. Reprinted in part with permission from Donna M. Cyr,
Bhawani Venkataraman, and George W. Flynn, J. Phys. Chem. 1996, 100(32), 13747-59.
Copyright (1996) American Chemical Society.

thus bringing the entire alkyl chain into
contact with the graphite substrate.
Dispersion interactions with both, thesubstrate and neighboring molecules
play an important role in the formationof this structure. In the case of alkanes aright angle is formed by the backbone
and lamella axes (see Figure 7a), while
the introduction of terminal functionalgroups can lead to different lamellabackbone angles (see Figure 7b).7
Alkane functionalization affects such
structural parameters as the lamellabackbone angle as functional groupinteractions can exhibit a pronounced
angular dependence (in addition tosteric requirements) compared to themore isotropic alkane-alkane andalkane-graphite dispersion forces.

5

The presence of functional groups has
effects on the self-assembly that are
more subtle than changing the lamellabackbone angle. Note that some ofthese STM images (e.g., see Figures 8
and 9) clearly reveal the position ofindividual hydrogen atoms associatedwith the methylene groups of the carbon
backbone. The orientation of individual
methylene groups and thus of the wholecarbon skeleton with respect to thesurface plane can be determined.
As shown in Figure 8, alkanes can
exhibit different spot patterns, even insuccessively acquired STM images.
Apparently, the plane formed by the
all-trans carbon backbone can assume
a variety of angles with respect tothe substrate surface plane.13,17 The
distribution of angles is influenced
by temperature and the presenceof solvent.18,19
In contrast, a well-defined backbone
plane rotation angle is found foralkanoic acids. Figure 9 clearly reveals
the zig-zag spot pattern characteristicof the topmost hydrogen atoms whenthe molecular backbone plane isparallel to the surface plane. Alkanoic
acids form hydrogen-bonded dimers.
The bulky, hydrogen-bonded acidheadgroups force the backbone into
the “flat” orientation.
Even more subtle effects follow. The
lateral spacing (within lamellae) of
alkanes and their derivatives can be
expected to depend on the rotation
angle around the backbone axis. In
bulk alkane crystals, nearest neighbordistances of 4.2Å and 4.8Å are foundperpendicular and parallel, respectively,
to the planes formed by the carbon
skeletons. Ambient STM images suggestthat nonfunctionalized alkanes undersolution form a commensurate structurewith a lateral spacing of 4.26Å,17
while a wider, noncommensurate
structure is formed by alkanoic acids.

6

Figure 8. Constant current STM image (sample bias –168mV, 300pA tunneling current) of
hexatriacontane at the interface between a dodecane solution and the basal plane of graphite.
Panels (a) and (b) show raw data acquired in two successive scans. Panels (c) and (d) show
filtered versions of the STM images in (a) and (b), respectively. Used with permission from Weigen
Liang, Myung-Hwan Whangbo, Aleksander Wawkuschewski, Hans-Joachim Cantow, and Sergei
N. Magonov, Adv. Mater. 1993, 5, 817. Copyright 1993 VCH Verlagsgesellschaft mbH,
D-69469 Weinheim.

Figure 9. Constant current STM images (-1.4V sample bias, 300 pA tunneling current) and acorresponding model of (R)-2-bromohexadecanoic acid in phenyloctane physisorbed on graphite.
Numbers and letters in the image refer to individual hydrogen atoms and functional groups while
the dashed line emphasizes the 45° angle between lamella and molecular backbone. Reproducedwith permission from www.columbia.edu/cu/chemistry/groups/flynn/r2bromo.html.

Self-Assembly and Expressionof Chirality

Figure 10. Constant current STM images (12nm X 12nm, sample bias –1.4V, 300pA tunnelingcurrent) are shown of (a) 12-bromododecanoic acid and (b) 11-bromoundecanoic acid ongraphite under phenyloctane solution. Black bars indicate a molecular length. Capital letters S,
D, and T point to strips of single, double, and triple-twin structures, respectively. Capital letters R
and L point respectively to the positions where the lower twin in a double or triple twin shifts rightor left relative to the twin lying above it. The small numbers 1-11 in (a) point to the positions ofindividual hydrogen and bromine atoms and Br refers to the bromine substituent. (c) and (d) show
molecular models for the images displayed in (a) and (b), respectively. Numbers 1 and 2 in (c)refer to rows, where the molecules shift right or left relative to the row above. Reprinted withpermission from Hongbin Fang, Leanna C. Giancarlo, and George W. Flynn, J. Phys. Chem. B
1998, 102(38), 7421-4 (1998). Copyright (1998) American Chemical Society.

Figure 11. Constant current STM images (~12nm X 12nm, sample bias –1.3V, 800pA
tunneling current) are shown of (a,b) behenic acid and (c) nonadecanoic acid on graphite underphenyloctane solution. Unit cells are indicated by parallelograms (a,b) and a rectangle (c).
Reprinted with permission from Masahiro Hibino, Akinori Sumi, Hiroshi Tsuchiya, and Ichiro Hatta,
J. Phys. Chem. B 1998, 102(23), 4544-7. Copyright (1998) American Chemical Society.

The geometric requirement of closepacked monolayer structures allows
such seemingly negligible changes as
the addition of a single methylenegroup to a long alkyl chain to alter
the self-assembly significantly. Panelsa and b of Figure 10 display STM
images of 12-bromododecanoic acidand 11-bromoundecanoic acid,respectively.20 Although only differing by
one methylene group, the monolayer
structures resulting for these two species
are obviously very different. An
additional geometric subtlety is
associated with the transition from three
to two dimensions. The bromoalkanoic
acids under consideration are notchiral, i.e., they can be superimposedon their mirror images (assuming freerotation of the terminal bromomethylenegroup). However, the introduction of theliquid-solid interface removes symmetry
elements and prevents free molecularrotation about the carbon backbone
axis. As a consequence, two adsorbed
states can be distinguished that are
mirror images of each other. Alkanoic
acids become prochiral uponadsorption on the basal plane ofgraphite. Close inspection of Figure 10
reveals that in the case of
11-bromoundecanoic acid,immobilization at the interface leads
to the formation of chiral (orenantiomorphous) domains, i.e.,
domains distinct from their mirror image,where all molecules within a domain
are of identical “chirality”. In contrast,
geometric packing requirements leadto the formation of achiral domains for
12-bromoundecanoic acid, where
adsorbed molecules of both “chiralities”
are present within each domain.20
The same effect is known for alkanoic
acids without the terminal bromine
substituents. In that case, enantiomorphous domains are observed for aneven number of carbon atoms (including

7

Figure 12. (a) Chemical structure of 5-[10-(2-methylbutoxy)decyloxy]isophthalic acid (ISA). (b) Constant heightt STM image(11.7nm X 11.7nm) of an (S)-ISA/heptanol monolayer on graphite
under heptanol solution. Note the angle between the heptanol
and ISA backbones. This domain will be referred to as “positive”.
(c) Proposed molecular model for the self-assembled monolayer
giving rise to the STM image displayed in (b). (d) Constant height
STM image (11.5nm X 11.5nm) of an (R)-ISA/heptanol monolayer
on graphite under heptanol solution. Note the angle between theheptanol and ISA backbones. This domain will be referred to as“negative”. (e) Proposed molecular model for the self-assembled
monolayer giving rise to the STM image displayed in (c).
(f) Proposed model emphasizing the molecular arrangement in a
“positive” domain. (g) Proposed model emphasizing the moleculararrangement in a “negative” domain. Reproduced with permission
from Steven de Feyter, Petrus C. M. Grim, Markus Rücker, Peter
Vanoppen, Christian Meiners, Michel Sieffert, Suresh Valiyaveettil,
Klaus Müllen, and Frans C. De Schryver, Angew Chem Int Ed
1998, 37(9), 1223-6. Copyright 1998 Wiley-VCH Verlag
GmbH, D-69469 Weinheim.

the acid group).21 An example of this isshown in Figure 11. Panels (a) and (b)show the two opposite enantiomorphous domains formed by behenic acid
(C21H43COOH, i.e., with an evennumber of carbon atoms). The mirror
image relationship between the two
types of domains is emphasized by theunit cells shown as (non-rectangular)
parallelograms. As can be seen inpanel (c), nonadecanoic acid (with an
odd number of carbon atoms) forms a
packing structure with a rectangular unit
cell that is identical to its mirror image.
The expression of chirality has also
been examined for self-assembled
monolayers composed of several distinct
molecular building blocks. When mixing

8chiral with achiral species, the chirality
can be not only transferred to the twodimensional array but also from thechiral to the achiral component. An
example of this is shown in Figure 12,
where the chiral 5-[10-(2-methylbutoxy)decyloxy]isophthalic acid (ISA) is selfassembled at the heptanol/graphite
interface.22 Enantiomorphous domains
are formed composed of alternating
ISA-heptanol lamellae stabilized byhydrogen bonding. The domains arechirally pure not only with respect to
ISA but also with respect to the senseof rotation of the HOC bond angle ofthe coadsorbed heptanol molecules
and the angle between the ISA andheptanol molecular backbone axes.
The multi-component self-assembly has

extended the enantiomorphouscharacter to heptanol.22 Heptanol has
become prochiral.
The opposite effect has also been
observed. An achiral solute can form
enantiomorphous domains that direct
the self-assembly of a chiral cosolute.
In that case the template created by
the achiral species can afford theresolution of racemic mixtures by
separately depositing each enantiomer
into chirally pure domains. Exactly thisoutcome can be seen in Figure 13,
where a self-assembled domain ofhexadecanoic acid at the phenyloctanegraphite interface is shown, decorated
with the chiral (S)-2-bromohexadecanoic
acid also present in the solution.

(a)

(b)

(c)

Figure 13. (a) A constant current STM image (13nm X 13nm, sample bias –1.5V, 300pA tunneling current) of a domain of hexadecanoic acidinterspersed with (S)-2-bromohexadecanoic acid is shown where a solid black bar depicts hexadecanoic acid and a blue bar depicts
2-bromohexadecanoic acid. An enlarged portion of (a) is presented in (b) where the bromine atom lies above and to the right or below and to theleft of the carboxyl group as highlighted by the superimposed thin black lines. The orientation of the bromine, carboxyl, and alkyl chain on the chiralcarbon is used to identify the 2-bromohexadecanoic acid molecules in this domain as the S chiral conformers of the molecule. A top view of a modelof hexadecanoic acid interspersed by (S)-2-bromohexadecanoic acid on the graphite surface is shown in (c). The thin black line superimposed on abromine/carboxylic combination shows the same pattern depicted in the STM image (b). An arrow demonstrating the counterclockwise direction of
the brominecarboxyl group-alkyl group orientation identifies the brominated molecules as the S conformer. Reprinted with permission from Dalia G.
Yablon, Leanna C. Giancarlo, and George W. Flynn, J. Phys. Chem. B 2000, 104(32), 7627-35. Copyright (2000) American Chemical Society.

(a)

(b)

Domains of opposite chirality were
found not to contain any coadsorbed(S)-2-bromohexadecanoic acid.23
Note that in the absence of the achiralcosolute, 2-bromohexadecanoic acidforms a monolayer structure
characterized by a different lamellabackbone angle (see Figure 14).8 The
formation of bromine dimers suggeststhat intermolecular interactions between
bromine substituents play a role indriving this self-assembly.8,24 Again,chiral micro-separation results, asinter-molecular interactions drive
the formation of chirally pure,enantio-morphous domains, composedof a single type of chirally pure,hydrogen-bonded acid dimers.

(c)

(d)

Figure 14. (a) STM topograph of one of the domains formed by the assembly of (R)/(S)-2-bromohexadecanoic acid on graphite. The “bright” topographic protrusions are assigned as the positionsof the α-Br atoms, while the adjacent “dark” topographic depressions correspond to the hydrogenbonding COOH groups. An alternating pattern of “bright”-“dark”-“bright” runs through the image
from lower left to upper right, as denoted by the black arrow. This domain has been assigned as
containing R-enantiomers exclusively. Two parallelograms denote a hydrogen-bonded molecularpair lying flat on the surface. The angle‚ formed by the molecular axis, OC, and the direction of
the hydrogen-bond, OD, has been measured as 53±5°. (b) A second domain of 2-bromohexadecanoic acid molecules found at the phenyloctane-graphite interface. The alternating “bright”-“dark”“bright” pattern now extends from lower right to upper left in the topographic image. This domain
is the mirror image of that shown in (a) and is comprised only of the S-enantiomer. Both (a) and (b)are 12nm X 12nm images (-1.4V sample bias, 300 pA tunneling current). (c) A molecular model of(R)-2-bromohexadecanoic acid organized on a graphite lattice based on the image shown in (a).
The black bars denote a chiral pair of R-R molecules bonded through their carboxylic acid groups.
The yellow circles represent Br, the red balls oxygen, the green areas carbon, and the whitespheres hydrogen atoms. The alternating pattern seen in the STM image is also reproduced here.
Further, as indicated by the parallelograms, the dimerized acid molecules occupy four rows of thegraphite surface. (d) Molecular model representing the STM image of (b). Here, only S-enantiomers
are depicted, and the black bars denote an S-S chiral pair. Again, the alternating Br-COOH-Br
pattern is shown. Reprinted with permission from Leanna C. Giancarlo and George W. Flynn,
Acc. Chem. Res. 2000, 33(7), 491-501. Copyright (2000) American Chemical Society.

9Self-Assembly and Manipulation
Self-assembly on graphite has beenprobed for a wide variety of molecularspecies, some of which include
functional groups that permit further,post-assembly manipulation. As
an example, an STM image andcorresponding model are shown in
Figures 15a and 15b for an isophthalicacid derivative (ISA) self-assembled at
the undecanol/graphite interface.25,26
An ordered, lamellar structure isobserved, with alternating rows ofclose-packed ISA and solvent(undecanol) molecules, stabilized bydispersion interactions (involving alkyl
chains and the graphite substrate),electrostatic forces (involving the polarcarboxylic acid groups and thesemi-metallic graphite substrate),and hydrogen bonds (between the
carboxylic acid and alcohol groups).
The isophthalic acid derivative underconsideration belongs to the class of_ C-C=_ C-R’)
diacetylene compounds (R-C=
where polymerization is known to occurin (three-dimensional) solid crystals
upon exposure to ultraviolet radiation.
High-resolution STM studies of ISA
monolayers with submolecular resolution
can address the question whether the
UV-induced polymerization reaction also
occurs in two dimensions. The STM
images and proposed model shown in
Figures 15a and 15b suggest that thismight indeed be the case. As in threedimensional crystals, the diacetylene_ C-C=_ C-) moieties of neighboring(-C=
molecules are seen to occupy adjacentpositions, presumably mimicking thetransition state of the topochemical
polymerization reaction. This is not thecase for any additional ISA molecules
present in the supernatant solution. Thus,
it can be expected that UV irradiation
will lead to selective polymerization of
the interfacial layer only.
The results of UV illumination are shownin Figures 15c and 15d. The clear
changes in STM image contrast suggest

10

Figure 15. The isophthalic acid derivative under consideration (ISA) is shown in the top panel.
(a) Constant height STM image (sample bias –1.2V, 1.0nA tunneling current) of a mixed
ISA/undecanol monolayer formed at the undecanol/graphite interface before UV illumination.
Yellow symbols highlight a pair of ISA molecules. (b) Proposed molecular model for the array ofmolecules included in the white box overlaid on the STM image shown in (a). (c) Constant height
STM image (sample bias –0.5V, 1.0nA tunneling current) of ISA after UV illumination. (d) Proposed
molecular model for the polymerized monolayer giving rise to the STM image shown in (c).
Reprinted with permission from Steven de Feyter, Andre Gesquiere, Mohamed M. Abdel-Mottaleb,Petrus C. M. Grim, and Frans C. de Schryver, Acc. Chem. Res. 2000, 33(8), 520-31. Copyright(2000) American Chemical Society.

that the intermolecular polymerization
reaction has taken place as
anticipated.25,26 Each individual lamellathat used to consist of separate
molecular entities has been transformed
into a single conjugated polydiacety_ C-CR’=)n moiety with newlene (=RC-C=
mechanical and electronic properties.
Due to their conjugated double andtriple bonds, these molecularly thin“tapes” might serve as model systems
for molecular wires.

In general, post-assembly manipulationof interfacial monolayers can be
induced through a variety of means.
Aside from electromagnetic radiation,
electrochemical control can be used
to initiate chemical reactions. The
application of brief voltage pulses
through the STM tip can provide ameans for highly localized nanoscale
manipulation. As shown by Okawa
et al.,27,28 this strategy can be usedsuccessfully with dry monolayers ofFigure 16. (a) Constant current STM image (sample bias –1.0V,
70pA tunneling current) of a 10,12-pentacosadiynoic acid monolayer
at the air/graphite interface. (b) High-resolution STM image (sample
bias +0.5V, 1.0nA tunneling current) emphasizing the packing
structure. As indicated by the black arrows, the molecular axis isaligned with high symmetry axes of the underlying graphite substrate.
(c) Proposed molecular model for the monolayer giving rise to the STM
images displayed in (a) and (b). Black parallelograms shown in (b)and (c) depict a unit cell of the monolayer structure. Reprinted withpermission from Y. Okawa and M. Aono, J. Chem. Phys. (2001),
115(5), 2317-22 (2001). Copyright (2001) by the American
Institute of Physics.

diacetylene derivatives self-assembled
on graphite substrates. Figure 16 shows
an STM image of a monolayer formedby 10,12-pentacosadiynoic acid (PCA)
at the air/graphite interface.27,28
As in the previous example, thediacetylene derivative is found to forma monolayer structure that may be
conducive to the topochemical
polymerization reaction. Again, the_ C-) moieties of_ C-C=
diacetylene (-C=neighboring molecules occupy adjacentFigure 17. (a) Constant current STM image (sample bias –1.0V,
70pA tunneling current) of the original monomolecular layer of
10,12-pentacosadiynoic acid at the air/graphite interface. (b) Constantcurrent STM image of the same area as in (a) but with application of abias voltage pulse during imaging while the STM tip passed the location
indicated by the white arrow. The image was acquired from the bottom
to the top. The contrast of a single molecular row has changed
drastically (c) Constant current STM image acquired immediately after
the image shown in (b). The bright feature is seen to extend in both
directions from the location where the voltage pulse was applied. (d),(e) Diagrams illustrating the initiation of chain polymerization with the
STM tip. Reprinted with permission from Y. Okawa and M. Aono,
J. Chem. Phys. (2001), 115(5), 2317-22 (2001). Copyright (2001) by
the American Institute of Physics.

positions with the required mutualorientation. The result of applying abrief voltage pulse through the STM
tip is illustrated in Figure 17. A single
row (~3nm wide) of individual PCA
molecules has been transformed into
a conjugated polydiacetylene, thus
demonstrating the targeted creation ofa molecular wire from self-assembled
precursors. One could envision theutilization of such a process for thetargeted interconnection ofco-assembled molecular devices, model
systems for which will be discussed in
the next sections.
STM is seen to be a powerful tool not
only for local probing but also for local
nanoscale manipulation. Molecular
self-assembly is often cited as an
essential ingredient for future nanoscaleengineering. These studies demonstratea path for augmenting the power ofself-assembly through targeted postassembly manipulation.
11

Ring Systems and Electronic Structure
STM studies of self-assembly ongraphite have not been limited to
substituted alkanes. A wide rangeof molecular species has beeninterrogated, often containing a coreof interest surrounded by alkyl tails
and/or functional groups to facilitate
self-assembly on graphite. Suchinvestigations include an abundanceof organic molecules with planar,
extended, conjugated π-systems andmoderate HOMO-LUMO gaps. In
particular, numerous STM studies
performed in UHV29-32 as well as underambient conditions33,34 have focused on
monolayers composed of porphyrins
and phthalocyanines. Due to theirinteresting and easily tunable opticaland electronic properties members of
this versatile class of compounds areoften considered candidates for model
systems of molecular devices.
Figure 18 shows a high-resolution STM
image of 21,23-Dihydro-5,10,15,20tetrakis[4-(tetradecyloxy)phenyl]
porphyrin (TTPP) at the air/graphite
interface.34 Clearly, an ordered monolayer structure is observed, presumably
stabilized by the interdigitization of the
14-carbon long alkyl chains attachedto each porphyrin. Consistent with thishypothesis, shorter chain analogs
were found to produce less orderedmonolayer structures.
The STM image shown in Figure 18 isclearly dominated by bright features.
Their size and four-fold symmetry
suggest that they arise from porphyrincores that lie flat on the graphite
substrate. The porphyrin cores are seen
to be consistently brighter than the alkyl
chains at their periphery as expectedfrom the fact that the extended
π-electron system of the porphyrin coresgives rise to occupied and unoccupied
states that are much closer to the Fermi
level than any electronic states withappreciable density on the alkyl
chains.7,11 UHV STM studies of

12

Figure 18. Constant current STM
image (15nm X 15nm, sample bias
0.752V, 1.032nA tunneling current)of 21,23-Dihydro-5,10,15,20-tetrakis[4-(tetradecyloxy)phenyl]
porphyrin on graphite. The porphyrincores appear as bright features offour-fold symmetry. Hongna Wang,
Chen Wang, Qingdao Zeng,
Shandong Xu, Shuxia Yin, Bo Xu,
and Chunli Bai, Surf. Interface Anal.
2001; 32: 267. Copyright 2001
John Wiley and Sons Limited.
Reprinted with permission.

Figure 19. Constant current STM image(27nm X 27nm, negative sample bias, 40pA
tunneling current) of the 70° angled herringbone
phase formed by bis(4-dibutylamino-2-hydroxyphenyl)squaraine adsorbed at the interface
between a phenyloctane solution and the basal
plane of graphite. Elongated bright features are
assigned to the chromophores of individual
molecules. Each feature appears slightly bisected,
indicating enhanced tunneling over the phenyl rings
as compared with the central squaraines unit.
Reprinted with permission from M. E. Stawasz,
D. L. Sampson, and B. A. Parkinson, Langmuir
2000, 16(5), 2326-42. Copyright (2000)
American Chemical Society.

porphyrins and phthalocyanines haveadditionally uncovered characteristic
differences in submolecular image
contrast depending on bias voltage
polarity and metal atom substitution.32,35,36
STM studies of planar ring-systems havebeen extended to include molecules
consisting of several linked cyclic
subunits. Figure 19 shows an STM
image of a monolayer formed bybis(4-dibutylamino-2-hydroxyphenyl)
squaraine.37 While the image contrast
does not reveal the exact configurationof the butyl chains, alkyl dispersion
interactions presumably play a rolein monolayer stabilization, as dointeractions between the polar coregroups. Depending on alkyl chain
length a variety of self-assembled
monolayer structures are observed.
As with the porphyrins discussed above,
the bright contrast of the aromatic cores
dominating the STM image displayedin Figure 19 may be attributed toelectronic structure, rather than purely

geometric effects. Electronic states near
the Fermi level are likely to be localized
at the aromatic ring system, rather
than the insulating alkyl chains. Close
inspection of Figure 19 reveals theelongated bright spots to be consistently
bisected by a slight depression near
their center. A simple consideration ofelectronic structure may explain thisobserved contrast within the aromaticcore. In the symmetrically substituted
squaraines under consideration, thephenyl groups are known to serve aselectron donors while the central
squaraine functions as electron
acceptor. The donor-acceptor-donor
structure of this compound leads to(aggregation-dependent) charge transfer
behavior manifest in optical absorption
bands. Giving up electrons most easily,
the donor units must be where thehighest occupied molecular orbital islocalized. At negative sample bias, the
HOMO (if sufficiently close to the Fermi
level) may be expected to dominate
electron tunneling. Indeed, the STM

image displayed in Figure 19 was
acquired at negative sample polarity
and the phenyl (donor) units appear as
the brightest features.

Toward Molecular Electronics
Recently, STM studies have included
large molecules specifically tailoredboth to facilitate self-assembly and forprobing electron transport at thenanoscale in model systems formolecular electronics. Following earlysuggestions by Aviram and Ratner,38
molecular analogs for current rectifiers(diodes) and transistors are being
investigated where electron donor (D)and acceptors (A) units are linked
covalently. STM constitutes an ideal
tool for such studies, as the tunneling
junction at the center of the STM
technique intrinsically probes chargetransport at the nanoscale. As illustrated
in Figure 5 (see Section “Source of
Image Contrast”), STM studies ofmolecules adsorbed on surfaces
intrinsically address the mediation of
charge transport by molecular states
and their coupling to one of theelectrodes (i.e., the conducting substrate
supporting the molecule). Essentially thesame diagram as shown in Figure 5
also applies for molecular conductancejunctions (e.g., break or electromigration junctions). However, STM
provides the added advantage of(lateral) scanning, thus combining thespectroscopic mode with an imaging
mode. In molecular conductancejunctions, the presence of a molecule
has to be inferred from the spectroscopic data alone. The same is true formolecular orientation and bonding to
the electrodes. In contrast, STM images
can complement STS data acquired witha scanning tunneling microscope toascertain the presence of the species ofinterest and determine its orientation andconformation. In addition, STS data canbe acquired with the STM tip positioned
over different parts of a given molecule,effectively mapping out the spatial
variation of the conductance contributions
associated with molecular orbitals.
Miura et al. have investigated a large,
symmetric D-A-D system where oligop-phenylene vinylene (OPV) donor units
are attached to a perylenediimide (PDI)
acceptor moiety (see Figure 20a).39 The
STM images displayed in Figures 20b,
20c, and 20e reveal the formation ofordered monolayer domains at theliquid-solid interface. Dispersion

interactions between the alkyl chainsattached to the D-A-D triad may play arole in stabilizing the self-assembled
structure as suggested by the interdigitated dodecyloxy chains in the molecularmodel displayed in Figure 20d. The
large molecular size and orderedmonolayer structure observed in STM
images permits the identification ofdonor and acceptor subunits (within
individual molecules) so that theirrelative image contrast can be

Figure 20. (a) Chemical structure of the D-A-D triad. (b) Constant height STM image(70.2nm X 70.2nm, sample bias –0.96V, 150pA tunneling current) of a D-A-D monolayer at theinterface between a 1-phenyloctane solution and the basal plane of graphite. Arrows indicate
mirror-image type packing. (c) High-resolution STM image (15.5nm X 15.5nm, sample bias
–0.70V, 400pA tunneling current) with overlaid parallelogram indicating a monolayer unit cell.
(d) Proposed molecular model reflecting the ordering in (c). (e) Bias-dependent imaging of the
D-A-D triad (10.1nm X 10.1nm, 400pA tunneling current, sample bias indicated below each
image). In order top-to-bottom, the arrows on the left refer to alkyl chains, donor units, acceptor
units, and donor units. Reprinted with permission from Atsushi Miura, Zhijian Chen, Hiroshi Uji-i,
Steven de Feyter, Magdalena Zdanowska, Pascal Jonkheijm, Albertus P. H. J. Schenning, E. W.
Meijer, Frank Würthner, and Frans C. de Schryver, J. Am. Chem. Soc., 2003, 125(49),14968-9. Copyright (2003) American Chemical Society.

13

examined as a function of bias voltage.
Bias dependent imaging reveals brighter
contrast (i.e., higher tunneling current)
for the donor moieties at negative
sample bias, while the acceptor
moieties are brighter at positive sample
bias (see Figure 20e).
A simple physical picture has been
proposed relating the observed bias
dependent charge transmission to theelectronic structure of the D-A-D system.39
Absorption spectra indicate that thedonor and acceptor moieties areelectronically decoupled or weakly
coupled, allowing frontier orbitals of the
D-A-D triad to be assigned as belonging
to individual subunits. As the electron
donor units give up electrons most easily(by definition), the donor HOMO
constitutes the highest filled state of theoverall molecule and has a dominant
influence on the surface LDOS justbelow the Fermi level. Thus, the OPV
donor moieties support a higher
tunneling current at negative sample
bias, where filled surface states arebeing probed. Conversely, the LUMO
of the PDI acceptor moiety dominates
the density of empty surface states justabove the Fermi level, making the PDI
unit more transmissive at positive sample
bias. Thus, the bias dependent chargetransmission through this moleculardevice analog can be understood interms of resonantly enhanced electron
tunneling dominated by individual
electronic states associated withmolecular subunits.39
Recent STM studies of model systems
for molecular devices also include a
prototypical single-molecule chemicalfield-effect transistor where nanometersized charge transfer complexes control
current rectification through a covalentlylinked ring system.40 At the center ofthese investigations is an electron-richhexa-peri-hexabenzocoronene (HBC)
core, surrounded by six electron-poor
anthraquinone (AQ) subunits.40 As in theprevious example, individual molecular

14

subunits can be identified in highresolution STM images and the bias
polarity dependent tunneling probability
can be understood in terms ofresonantly enhanced electron tunneling.
Upon adding the electron-rich 9,10dimethoxyanthracene (DMA) to thesolution, DMA-AQ charge-transfer (CT)complexes are formed. New selfassembled domains that incorporate
CT complexes are found to coexist withremaining domains free of DMA. As alocal, high-resolution probe, STM allows
the separate interrogation of individual
molecules in these coexisting selfassembled structures. Current-voltage
curves obtained atop the HBC coresare found to be asymmetric (rectifying)
with the degree of asymmetry controlled
by the presence (or absence) of the
DMA-AQ-CT complex. The interfacial
dipole associated with formation of the
CT complex causes a relative shift
between the adsorbate’s electronic
states and the Fermi level of thesubstrate.40 Thus, STM has been used toprobe the charge transmission through asingle molecule and its control by achemically-induced electric field effect.
The STM studies discussed in thissection have combined self-assembly ongraphite with detailed single-molecule
conductance measurements by using
specifically tailored molecules
synthesized prior to deposition on thegraphite substrate. Other examples
discussed in this application note
include the post-assembly modificationof self-assembled monolayers (e.g.,
topochemical polymerization ofdiacetylene derivatives)25,27,28 ongraphite. Furthermore, self-assembled
monolayers of substituted alkanes ongraphite have been used as templates
for organizing nanoparticles.41 Based on
combinations of these ingredients one
could envision powerful recipes for thetargeted creation and interrogation ofcomplex model systems for moleculardevices with STM playing a central role.

Summary and Conclusions
What sets STM apart from other SPMs
is the use of the tunneling current
between tip and sample as error signal
for the SPM feedback loop. While thisfeature limits STM studies to sufficiently
conductive samples, the steep
exponential distance dependence ofthe tunneling current allows for a spatial
resolution rarely achieved in other SPM
modes. At the same time, the ability
to perform STM work in air, undersolutions, and within electrochemicalcells has made the interrogation ofself-assembly practical. Veeco SPMs
have played a prominent role in thisendeavor with numerous STM studies
addressing the structure and dynamics
of self-assembled monolayers inexquisite detail.
Aside from the controlled bottom-up(self) assembly at interfaces, important
ingredients envisioned for futurenanoscale engineering include singlemolecule devices. The understanding
and control of charge transport in model
systems for such molecular devices
constitutes an important focal point of
current efforts in nanoscience. Due to its
ability to interrogate the mediation of
charge transport by individual molecularstates, STM is uniquely positioned as animportant tool in this area. Applications
discussed in the present note include
recent STM studies that have been
designed to interrogate charge transport
in molecular devices while building on
previous work to self-assemble thespecies of interest into ordered arrays.
Future studies can be envisioned
where the power of this approach isaugmented further through combination
with post-assembly modification andco-assembly of multiple nanoscale
components, thus allowing STM toplay an even more important rolein nanoscience.

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15