PRL 99, 216102 (2007)

PHYSICAL REVIEW LETTERS

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What Orchestrates the Self-Assembly of Glycine Molecules on Cu(100)?
Ken Kanazawa, Atsushi Taninaka, Osamu Takeuchi, and Hidemi Shigekawa*
Institute of Applied Physics, CREST-JST, University of Tsukuba, Tsukuba 305-8573 Japan(Received 18 June 2007; published 20 November 2007)
The structures of two competing phases and their interrelationship in the self-organization of glycine
molecules on a Cu(100) surface were clarified. Despite their similar structural energies predicted using
first-principles calculation, completely different mechanisms were found to stabilize the two phases. Thebalance and coordination of the two mechanisms that induce a variety of self-assembled structures in thisattractive system were revealed. Furthermore, the importance of the microscopic arrangement of themolecules in designing the macroscopic electronic structures was directly demonstrated.
DOI: 10.1103/PhysRevLett.99.216102

PACS numbers: 81.16.Dn, 68.37.Ef

The formation of self-assembled structures is a result of
the balance of interactions among materials and environmental conditions, which produces a variety in the macroscopic functions of the system. Recent developments in theformation of nanostructures have been achieved by controlling the interactions depending, for example, on theelectronic and conformational structures, strains, andchemical reactions [1–3]. However, the balance of theseinteractions is, in general, extremely delicate and complex,
and furthermore, some interactions are hidden behind the
dynamics apparently observed. In a solution, for example,
the structure of the solvents plays an important role
through the solvophobic effects on the nanostructural formation of solute materials [4]. Even in the case of a more
solid environment such as adsorbate molecules on a substrate material, reconstruction of the substrate may be
induced to produce a stable superstructure [5], which
may be hidden behind the apparent molecular arrangement. Time-evolutional change is also included in theinteractions depending on the growth process [6]. Since
self-organization is governed by the interactions of thesefine variations, which determine the macroscopic functions, evaluation of the real dynamics is of great importance for further understanding, and subsequently the
manipulation of the mechanism.
Here, we demonstrate the intriguing two-step mechanism that governs the self-assembly of polarized moleculeswith chirality on a transition metal, glycine molecules on a
Cu(100) surface. The structures of two competing phases
and their interrelationship that induces a variety of selfassembled structures in this attractive system were revealed. Furthermore, the characteristic relationship between the microscopic molecular arrangements and themacroscopic electronic structure is discussed.
The glycine molecule is the simplest amino acid withcarboxyl and amino groups, which are both common for allamino acids, and is one of the fundamental components ofbiological molecules. Owing to the basic and practicalinterest in this material, adsorption of this molecule on aCu surface has been widely studied [3,7–9]. The observation of the anisotropic two-dimensional (2D) free0031-9007=07=99(21)=216102(4)electronlike electronic structure has made this system
more attractive [3]. Among all amino acids, glycine isthe only molecule that does not have chirality, but enantiomeric isomers appear on the Cu surface, through the dissociation of hydrogen, depending on the directional
relationship of the two groups in the adsorbed form as
schematically illustrated in Fig. 1(a) [7]. The adsorption
properties of this system have been expected to provide us
with the basis for understanding, and a method of applying,
the mechanism of the self-assembly of a polarized molecule with chirality.
Despite the extensive studies, however, there still remains controversy even in determining the ground stateof this system, namely, the c2  4 or p2  4 structure[Figs. 1(b) and 1(c)]. Recent theoretical calculation has
shown that the c2  4 and p2  4 structures have
similar structural energies [9]. In fact, from scanning tunneling microscopy (STM) observation at room temperature(RT) it was found, for example, that although molecules
were unstable at low densities, two structures with thec2  4 or p2  4 periodicity coexisted for high deposition concentrations [8]. In contrast, only the p2  4
pattern was observed using low energy electron diffraction(LEED) at RT, and formation of the p2  4 structure wasconfirmed using STM at 5 K, indicating the selective
growth of one phase [3,7]. These results suggest the existence of some complex mechanism behind the selfassembly of this system.

FIG. 1 (color online). (a) Two conformations of an adsorbed
glycine molecule, and molecular arrangements of (b) p2  4and (c) c2  4 structures.

216102-1© 2007 The American Physical Society

PRL 99, 216102 (2007)

PHYSICAL REVIEW LETTERS

In response to the fundamental and intriguing requirement of clarifying the mechanism that governs the selfassembly of this basic and practically important material,
we performed a detailed analysis on the growth of thissystem using scanning tunneling microscopy or spectroscopy (STM/STS).
The sample preparation [3] and STM measurements
were performed under ultrahigh-vacuum conditions (basepressure <1  108 Pa). An electrochemically sharpened
tungsten tip (  0:3 mm) was used.
Figure 2 shows STM images obtained at 5 K for bare andglycine-deposited Cu(100) surfaces. For an increase in theconcentration of glycine molecules the domains consistingof the p2  4 arrangement grew, which appears to be

FIG. 2 (color online). STM images obtained at 5 K for the bare(a) and glycine-deposited Cu(100) surfaces ((b) 0.2, (c) 0.4, and(d) 0.6 ML). (e) A magnified STM image of the area indicated by
red circles in (b)–(d). (f) Magnifications of c2  4 and p2 
4 areas with molecular arrangements, (g) Structural models of
the molecular arrangements in (e).

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consistent with the recent STM/LEED results [3,7].
However, the details are more complicated.
Noteworthy points, observed for the fist time, are as
follows: first, the formation of h310i steps, which neverappear on the bare Cu(100) surface, was observed. Second,
there are domains that exhibit a triangular shape at the edgeof the p2  4 domains as indicated by red circles in
Figs. 2(b)–2(d). Figure 2(e) shows a magnified STM image of such an area. From the STM image together with thetheoretical result [9], the phase of the triangular shape isdetermined to be of the c2  4 homochiral structure[Figs. 1(c) and 2(f)], the existence of which has been an
object of long-term controversy [7,8]. The c2  4 domain always grows from a h310i step on the lower terrace.
A molecular row was observed on the upper side of the
h310i step edge where the c2  4 structure is on the lower
terrace. Third, all p2  4 domains are formed in thevicinity of the c2  4 triangular island and the edge ofthe step that differs from the h310i step. In contrast to thecase of the c2  4 structure formed at the h310i steps, nomolecular rows were observed on the upper of the stepedge. Fourth, there are boundaries in the p2  4 area as
indicated by the white arrows in Fig. 2(e), where molecularrows have the c2  4 arrangement. On the terrace, farfrom the h310i steps [for example, Fig. 2(c)], a completep2  4 arrangement without c2  4 boundaries isformed. In other words, a c2  4 arrangement is only
formed when it is in contact with the h310i step edge.
Figure 2(g) is an illustration of the structural models of
the molecular arrangements. The molecular arrangementof the c2  4 structure and its positional relationship withthe h310i step were determined by comparing the STM
image with theoretical calculations [Fig. 2(f)] [9]. This
structure can be supported as follows: as shown in
Fig. 1(a), amino and carboxyl groups in an adsorbed glycine molecule are positively and negatively charged, respectively. On a metal surface, the upper (lower) side of a
step is positively (negatively) polarized according to thewell-known Smoluchowski effect [10]. Therefore, glycine
molecules are adsorbed onto the surface with the positively
charged amino groups in contact with the lower edge of the
h310i step, which is negatively charged. Then the subsequent glycine molecules form the c2  4 structure as aresult of the attractive interaction between the oxygen (O)atoms in the molecules adsorbed ahead and the nitrogen(N) atoms in the subsequent molecules.
Why is the c2  4 domain always a triangular shape,even though the Cu(100) surface has a fourfold rotational
symmetry? Since the edge indicated by L in Figs. 2(e) and2(g) is always straight and no partially added molecules
were observed, the interaction between the edge and the
additional molecule, based on the attractive interaction
between N and O atoms, is not strong enough to stabilize
the structure. Positive and negative parts are arranged
alternately along the edge L, which may reduce the interaction of this edge with the additional molecules.

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PHYSICAL REVIEW LETTERS

Since the upper side of a step is positively polarized, themolecular arrangement of the c2  4 structure on theupper side of the step is supposed to have an orientation
similar to that on the lower terrace. On the upper h310i stepedge, the growth of the c2  4 structure was slow, indicating the weaker interaction in this direction. No negatively charged O atoms on its island edge and the formationof an intramolecular hydrogen bond (N-H-O) [11] may
cause a weaker molecular interaction resulting in the observed slow growth in this direction.
Considering the molecular arrangement of the c2  4
structure with the fact that the p2  4 domain exists only
on one side of the c2  4 island, that is in the vicinity ofthe edge along the 110
direction [Fig. 2(e)], the molecularorientation in the p2  4 domain was determined as
illustrated in Fig. 2(g). In both structures, molecules arewell ordered along the 110
direction to form a molecularrow. As was pointed out, there are boundaries formed by
the c2  4 structure in the p2  4 area as indicated by
the white arrows in Fig. 2(e) [red dashed-dotted line in
Fig. 2(g)]. Since a phase defect is induced by the substitution of a molecular row of one chirality with a molecularrow of the other chirality [appearance of SS or RR ordering
instead of the alternate SR ordering as in Fig. 2(f)], themolecular interaction in each row is stronger than thatbetween the rows. In fact, tenfold-different anisotropy inthe effective masses was observed for the 2D electronic
structure formed in the p2  4 structure [3], indicating alarger overlap of electronic states in the molecules along
the [110] direction, which results in a stronger interaction.
Which is the ground state of this system? One important
point is that the step edge forming the c2  4 structural
domain boundaries is a short h310i step. Thus, the relationship between the c2  4 structure and the h310i step,that is the formation of the h310i step through molecularadsorption, is considered to play an essential role in the
self-organization of this system.
To investigate the h310i step formation process and its
stability in relation to the c2  4 structure, we performed
a continuous observation of one location at RT. Figures 3(a) and 3(c)–3(e) show a sequence of STM images
obtained every 512 sec. Figure 3(b) is a magnification of
the area indicated by the arrow T in Fig. 3(a). A remarkable
point is that straight h310i steps are formed and, as shownin the lowest wide terrace, molecules are adsorbed along
the straight h310i steps, and stable triangular c2  4
islands exist at the short step area even at RT; althoughsome steps exhibit fluctuations. A c2  4 phase with
h310i steps was observed on the narrow terrace, where
the width is close to the size of the c2  4 triangle(10 –15 molecular edge size at RT). The c2  4 structuralarea along the straight h310i steps is darker (lower) than theterrace far from the steps, indicating that the wide terracearea is not a bare Cu surface, but many molecules diffuse
on the surface as pointed out in a previous paper [8].
Despite this, no p2  4 island formation was observed.

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FIG. 3 (color online). (a), (c) –(e) show a sequence of STM
images obtained every 512 sec; (b) shows a magnification of thearea indicated by the arrow T in (a). The inset in (b) is a highcontrast image of the triangular structure.

These results suggest that the c2  4 structure is morestable. When the temperature is lowered, the surface is
expected to be covered by the c2  4 phase. However, inthe terrace far from the h310i steps [see Fig. 2(c)], acomplete p2  4 arrangement without c2  4 boundaries is formed. A c2  4 arrangement is not formed
without the molecular rows being in contact with theh310i step edge. Therefore, although a c2  4 triangularisland is necessary as a nucleus to stabilize the p2  4
island, the p2  4 arrangement appears to be more stable
than the c2  4 arrangement at low temperatures.
The results obtained at 5 K and RT indicate the existenceof the two different mechanisms that govern the observed
self-assembly of glycine molecules. When glycine molecules are deposited onto a Cu(100) surface at RT, h310i
steps, which are never observed on the bare surface, areformed by the adsorption of the molecules, and c2  4
structure islands grow from the steps until a triangularshape with the edge corresponding to the stable length
depending on the temperature is achieved.
Despite the strong interaction at the h310i steps, which
stabilizes the c2  4 phase, as the temperature is lowered, p2  4 islands grow from the edge of the c2  4triangle along the 110
direction [blue dashed-dotted line
in Fig. 2(g)]. When the sample temperature is maintainedat RT for a long enough time to form a narrow terrace
sandwiched by the h310i steps, the c2  4 phase is stabilized there; however, the c2  4 phase does not cover
the entire surface. This change indicates that the moleculesin the p2  4 arrangement have a stronger interaction
with the substrate at lower temperatures. Recent STM
work has revealed the formation of a 2D electronic structure for the p2  4 structure [3]. Does this make thep2  4 structure more stable than c2  4? To investigate the temperature dependence of the electronic structure, we performed STS at RT and 5 K on an area that216102-3

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PHYSICAL REVIEW LETTERS

FIG. 4 (color online). (a) Spectra obtained at 5 K. (b) LBH
spectra obtained at 5 K (set point: 1 M, 0.1 nA, 0.1 V). Data
were obtained by measuring the I-Z curve as the STM tip was
retracted 0.3 nm from the set point; (c), (d) show topographic and
dI=dV images of a glycine-deposited surface (200 nm 
200 nm, 0:11 V, 1.2 nA), and (e) shows magnified topographicand dI=dV images, where c2  4 triangular (indicated bywhite arrow) and neighboring p2  4 structures coexist(0:13 V, 0.2 nA).

includes a bare Cu substrate, and c2  4 and p2  4
structures. Since molecules are unstable at RT, we prepareda sample with a high deposition concentration to stabilize
the structures for the measurement at RT.
Figure 4(a) shows the spectra obtained at 5 K [12]. A
sharp edge of the local density of states near 100 mV,
which corresponds to the anisotropic 2D electronic structure formed in the p2  4 structure [3], does not appear
for the c2  4 structure. Figures 4(c) and 4(d) show STM
and dI=dV images (lock-in modulation: 8 mV, 2.74 kHz)of a glycine-deposited surface, and Fig. 4(e) shows magnified images where the c2  4 triangular and p2  4
phases coexist. As expected, the standing wave that appears in the p2  4 structure is not observed in the c2 
4 structure. As shown in the inset of Fig. 4(a), the sharpedge disappears at RT, and the spectrum for the p2  4
structure becomes similar to that of the c2  4.
These results suggest that the electronic state observed
for the p2  4 structure at 5 K is a result of the interaction between the molecular layer and the Cu(100) substrate[3]. To confirm this point, we performed local barrierheight (LBH) measurement by STM for the bare Cu substrate and c2  4 and p2  4 structures at 5 K; Fig. 4(b)shows the result. Although there is an effect of the 2D
electronic structure for the region of bias voltage larger
than 0.1 V, the value of LBH obtained for the p2  4
structure is the smallest over the entire voltage range,
suggesting a larger charge transfer from the molecularlayer to the Cu substrate in the p2  4 structure. This isdue to the coupling of the electronic states between theweek ending
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molecular layer and the Cu substrate. This interaction muststabilize the p2  4 structure, making the p2  4 phase
the ground state of this system. In fact, as observed in thechange in the STS spectra shown in Fig. 4(a), the interaction breaks off and the stronger interaction through theformation of the h310i step is dominant at RT, resulting in
the apparent high stability of the c2  4 arrangement.
Despite the similar structural energies predicted using firstprinciples calculation, microscopic molecular arrangementof glycine molecules on a Cu surface produces characteristic variations in the associated interactions and macroscopic electronic structures.
In conclusion, the structures of two competing phases,c2  4 and p2  4, and their interrelationship thatgoverns the observed variety in the self-organization ofglycine molecules on a Cu(100) surface, which had been along-term controversy, were clarified for the first time. Thec2  4 phase was produced by the formation of h310i
steps, which has not been observed on the bare Cu(100)surface, through the adsorption of glycine molecules.
Direct observations of the formation and fluctuation of
the h310i step at RT indicate a strong interaction between
glycine molecules for the c2  4 phase and the h310i
step. The hidden role of the c2  4 structure as a nucleus
for the growth of the p2  4 structure was also revealed.
Finally, we characterized the difference in the electronic
structures between the two arrangements, which is theorigin of the mechanism that stabilizes the p2  4 structure as the ground state of the system. These results are
direct evidence of the important role of local moleculararrangement in the design of the macroscopic electronic
structure.
We thank Ms. Rie Yamashita, in our group at Universityof Tsukuba, for her help in preparing this Letter.

*http://dora.ims.tsukuba.ac.jp/[1] J. V. Barth, G. Costantini, and K. Kern, Nature (London)
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[4] S. Yasuda, I. Suzuki, K. Shinohara, and H. Shigekawa,Phys. Rev. Lett. 96, 228303 (2006).
[5] A. Kuhnle et al., Phys. Rev. Lett. 93, 086101 (2004).
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[12] We adopted dI=dV in Fig. 4(a) instead of dI=dV=I=V
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voltage and to reduce the influence of the rapid increase in
I on the spectra. C. Wagner, R. Franke, and T. Fritz, Phys.
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