www.nature.com/scientificreports

OPEN

Received: 26 June 2017
Accepted: 14 December 2017
Published: xx xx xxxx

Room temperature stable film
formation of π-conjugatedorganic molecules on 3d magnetic
substrate
Eiichi Inami1, Mikio Shimasaki2, Hideki Yorimitsu3 & Toyo Kazu Yamada1,4
An important step toward molecule-based electronics is to realize a robust and well-ordered molecular
network at room temperature. To this end, one key challenge is tuning the molecule–substrateelectronic interactions that influence not only the molecular selfassembly but also the stability of
the resulting structures. In this study, we investigate the film formation of π-conjugated metal-freephthalocyanine molecules on a 3d-bcc-Fe(001) whisker substrate at 300 K by using ultra-high-vacuum
scanning tunneling microscopy. On bare Fe(001), hybridization between the molecular π and theFe(001) d-states prevents the molecular assembly, resulting in the disordered patchy structures. The
second- and third-layer molecules form densely packed films, while the morphologies show clear
difference. The second-layer molecules partially form p(5 × 5)-ordered films with the rectangular edgesaligned along the [100] and [010] directions, while the edges of the third-layer films are rounded.
Remarkably, such film morphologies are stable even at 300 K. These findings suggest that themolecular self-assembly and the resulting morphologies in the second and third layers are affected by
the substrate bcc(001), despite that the Fe-d states hybridize only with the first-layer molecules. The
possible mechanism is discussed with the kinetic Monte Carlo simulation.
Organic molecules grown on crystalline substrates have received remarkable attention as an alternative to inorganic semiconductors because of their relatively low-cost synthesis and flexibility in tailoring their properties1,2.
Extensive investigation on molecules unveiled exciting novel properties that provide promising applications ina wide variety of areas as high-functional molecule-based devices3–11. One key challenge to achieve moleculardevices is the sophisticated regulation of the molecular assembly into well-ordered network (molecular film).
Furthermore, their practical applications require the stability of the molecular film against thermal fluctuationsat room temperature (RT).
Among several organic molecules, a family of phthalocyanines (Pc), which are typical π-conjugated molecules, are most extensively studied because of their fascinating properties, such as thermal and chemical
stabilities, strong optical response in the visible region, and a wide variety of derivatives depending on thecenter-coordinated metal atoms. These features support their use in electroluminescent devices12, photovoltaic
cells13, and field effect transistors14.
Pc single molecules and their film formations were successively investigated by using scanning tunnelingmicroscopy and spectroscopy (STM/STS). Numerous studies have been reported particularly on the Pc molecules grown on highly oriented pyrolytic graphite (HOPG)15–17, and on various noble metals (such as Au, Ag,
Cu, and Pt)18–21. As these substrate surfaces, which are characterized by s or p derived states, are chemically inert,
the molecules are mostly physisorbed on the substrates through van der Waals interactions. This allows the Pc tothermally diffuse along the surface, resulting in the formation of two-dimensional (2D) ordered films. However,1

Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan. 2Graduate
School of Advanced Integration Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
3
Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Oiwakecho, Sakyo-ku,
Kyoto, 606-8502, Japan. 4Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 2638522, Japan. Correspondence and requests for materials should be addressed to E.I. (email: e_inami@chiba-u.jp) or
T.K.Y. (email: toyoyamada@faculty.chiba-u.jp)
Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

1

www.nature.com/scientificreports/

Figure 1. H2Pc/Fe(001) in low-coverage regions. (a) STM topography image of Fe(001) with 0.1 ML coverageof H2Pc molecules (9 nm × 20 nm, Vs = −1.5 V, It = 300 pA). A, B, and C denote type A, type B, and type C
molecules, respectively (see text). (b–d) Magnified images of type A, (b), type B, (c), and type C, (d), molecules.
(e) Structural ball-stick models of type A (left), type B (middle), and type C (right) molecules. A green balllabeled X indicates unknown-atomic impurity. (f,g) STM topography images of Fe(001) surfaces (30 nm ×
40 nm) with (f) 0.1 ML (Vs = −1.0 V, It = 200 pA), (g) 0.8 ML (Vs = −0.6 V, It = 500 pA) coverage of H2Pc
molecules.

the realization of a robust molecular film at RT is not easy. A few studies reported that, at 300 K, the high-mobility
molecules on these substrates destabilize the film morphologies particularly at the edges15.
On the other hand, magnetic metals such as Fe, Co, Cr, and Mn have attracted increasing interest as the substrates of π-conjugated organic molecules. Magnetic metals are distinct from HOPG and noble metals in which
the surface states near the Fermi energy are dominated by the d state. Recently, STM studies22–24 reported thatthe interactions between the 3d magnets and the π-conjugated single molecules (hybridized π–d states) induce
giant magnetoresistance, which is a key feature for achieving spintronics devices, such as efficient data storage andcomputing devices. Significantly, the hybridized π–d states lead to strong chemisorption of the adsorbed single
molecules on the substrate. For this reason, the molecules are immobile even at RT25. This encourages us to utilize
the magnetic substrate for the fabrication of robust molecular films.
In this paper, using ultra-high-vacuum (UHV) STM, we have investigated the morphological characteristics of π-conjugated metal-free phthalocyanine (H2Pc) molecules on magnetic Fe(001) substrate from low
coverage to multilayer coverage regions at 300 K. Under monolayer coverages, H2Pc molecules on bare Fe(001)exhibited as disordered patchy structures. Above monolayer coverages, the second- and third-layer molecules
formed densely-packed films, which morphologies were found to be stable even at 300 K. The morphologies
also showed clear difference depending on the layer number. The second-layer films partially showed p(5 ×5)-ordered arrays with the rectangular edges aligned along the [100] and [010] directions, while the third-layer
films showed the rounded edges. These findings suggest that the film growth processes and the resulting morphologies in the second and third layers are affected by the substrate bcc(001) despite that the Fe-d stateshybridize only with the first-layer molecules. We discussed the layer-dependent molecules–substrate interactions, and then proposed possible film growth processes that was reasonably examined by a kinetic Monte
Carlo simulation.

Results and Discussion

H2Pc/Fe(001) in low coverage regions (0.1–0.8 ML). Figure 1(a) and (f) show the STM images of H2Pc
single molecules on Fe(001) at a coverage of 0.1 ML. One can identify the isolated single molecules with characteristic four-lobed shapes. Each lobe corresponds to one H2Pc arm, thereby confirming that the molecularplane is oriented parallel to the substrate surface. Our previous study25 revealed that the H2Pc single molecules
are adsorbed onto the Fe(001) substrate with three in-plane orientations, namely type A, type B, and type C[Fig. 2(e)]. The type A molecule, which exhibits the most energetically stable geometry, is adsorbed parallel tothe [100] direction. The type B molecule, which exhibits the second most stable geometry, is adsorbed with arotation of approximately 23 ± 2 deg. out of the [100] direction. The type C molecule, which is rarely observed
Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

2

www.nature.com/scientificreports/

Figure 2. H2Pc/Fe(001) in high coverage regions. (a) STM topography image (48 nm × 38 nm, Vs = −0.8 V,
It = 100 pA) of Fe(001) surfaces with 1.5 ML coverage of H2Pc molecules. (b) Molecular resolution STM imageof second H2Pc layer (30 nm × 40 nm, Vs = −2.0 V, It = 500 pA). The lateral thermal drift of the image wascompensated (see the Method section). Inset image shows 2D fast Fourier transform (2D-FFT) of therectangular area in (b). (c) Sketch of the proposed molecular arrangements in first and second layers. The
adsorption configuration of the second-layer molecule was assumed to type B. (d) STM topography image(53 nm × 42 nm, Vs = −1.5 V, It = 50 pA) of Fe(001) surfaces with 2.4 ML coverage of H2Pc molecules.

and expected to include some impurities at the core, is adsorbed with a rotation of approximately 45 ± 2 deg. outof the [100] direction. In the present experiment, these adsorption geometries were confirmed in the STM images[Fig. 1(b)–(d)].
We increased the coverage of H2Pc molecules up to 0.8 ML [Fig. 1(g)]. Although most of the Fe(001) surface
was covered with molecules, they did not form domains but still remained isolated, thereby resulting in disordered patchy structures. This result reveals that the molecules absorbed on the Fe(001) surface are immobile, andthey cannot aggregate with each other. The reason for this activity is discussed in detail later. It was also foundthat the molecules did not form second layers. Therefore, under monolayer coverages, the molecules prefer to beadsorbed on the Fe(001) substrate, that is, adsorptions onto the pre-existing molecules are unfavorable.

H2Pc/Fe(001) in high coverage regions (>1 ML). Above monolayer coverages, H2Pc molecules started
forming multilayers. Figure 2(a) shows the STM image of approximately 1.5 ML H2Pc molecules on Fe(001) substrate. Interestingly, the second-layer molecules (labeled “2nd”) were revealed to form films with densely packed
structures, while the substrate (first-layer molecules) remained as disordered patchy structures. It is also noteworthy that the edges of the films align along the [100] and [010] directions, which are crystallographically equivalentorientations of the Fe(001) surface. The molecular resolution image of the second layer is shown in Fig. 2(b). The
molecules were found to form partially-ordered arrays. From the fast Fourier transform (FFT) analysis of therectangular region in Fig. 2(b) [inset in Fig. 2(b)], the intermolecular distance in the ordered domain was evaluated to be 1.43 ± 0.02 nm; thus, the molecules form p(5 × 5) superstructure with respect to the Fe(001) surface.
Under the assumptions that the adsorption geometries (adsorption site and the in-plane rotational angle) of thefilm constituent molecules are the same with those in the first layer, the molecular arrangements in the first andsecond layers were deduced as sketched by Fig. 2(c). In Fig. 2(c), the hollow sites of Fe(001) are partially occupiedby the first-layer molecules (colored light blue) with two typical configurations (type A and type B), above which
the second-layer molecules (colored dark blue) are adsorbed with type B configuration at the sites corresponding
Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

3

www.nature.com/scientificreports/

Figure 3. Thermal stability of H2Pc on Fe(001). (a,b) Continuous STM topography images of H2Pc molecules
on Fe(001) surface (16 nm × 20 nm, Vs = −1.0 V, It = 200 pA). (c,d) Continuous STM topography images
including first, second, and third H2Pc layers on Fe(001) surface (64 nm × 77 nm, Vs = −2.0 V, It = 500 pA).
Labeled numbers, 1st, 2nd, and 3rd, indicate first, second, and third H2Pc layers, respectively.

to the hollow sites of Fe(001). For p(5 × 5) structure, the type A configuration (see Supplementary Figure 2) is
considered to be energetically unfavorable due to the repulsive H-H interactions between benzene groups ofneighboring molecules. We emphasize that, even under the dense-packed ordered second-layer, the first layer
should not be packed but still forms disordered patchy structure. That is, the some of the second-layer molecules
should not be “perfectly” but “partially” supported by the first layer. This is undetectable by STM, but reasonable
based on the fact that the chemisorbed first-layer molecules do not diffuse and immobilize even by the STM
manipulation25. At a coverage of 2.4 ML [Fig. 2(d)], the molecules in the third layer also formed densely packed
structures (labeled “3rd”) as well as the growth of the second layers. However, in comparison with the second layer,
the edges of the third layers were found to be rounded.
The thermal stability of the H2Pc single molecules and the films on Fe(001) were investigated by consecutive
STM imaging. Figure 3(a) and (b) show the consecutive STM images focused on the H2Pc single molecules on
the Fe(001) surface. To check the stability, first, a particular area including single molecules was imaged. Then,the same area was imaged again after 15 min. Since the image area shifts with time due to the lateral thermal
drift, the overlap regions of the two images were extracted to investigate the morphological variation at exactly
the same area (the detailed procedure is described in Supplementary Method 1). It is clear that no changes in theadsorption sites and the geometries were observed during the repeated scans. This result indicates that the H2Pc
single molecules on Fe(001) are thermally stable at RT, as reported by the previous study25. In similar manner, theconsecutive STM images of the H2Pc films are also obtained as shown by Fig. 3(c) and (d), where Fig. 3(d) was
obtained 17 min after the STM image in Fig. 3(c) was obtained (see Supplementary Method 1). We can observethat the edge features in Fig. 3(c) are maintained by repeated imaging, as indicated by dashed lines in Fig. 3(d).
Therefore, the H2Pc molecules form densely packed and thermally stable films in the second and the third layers
even at RT.
To obtain further insight into the formations of the second and third molecular films, the distributions of the
pixel heights were analyzed from the STM images. In Fig. 4(a) and (b), we picked up two typical STM topography
images; Fig. 4(a) includes the Fe(001) substrate and the first layer of the H2Pc single molecules, while Fig. 4(b)includes the Fe(001) substrate, the second layer, and the third layer. The apparent height distributions of the corresponding images are shown in Fig. 4(c). The remarkable peaks labeled h0, h1, h2, and h3 are attributed to theFe(001) substrate, the first, second, and third layers of H2Pc, respectively. By fitting with the Gaussian functions,the peak positions and the widths (hi ± σi for i = 0, 1, 2, 3) were determined. Then, the peak-to-peak intervals(Hii−1 = h i − h i −1), which correspond to the interlayer distances between the n-th and the (n − 1)-th layers (0-thlayer corresponds to the Fe(001) substrate), were evaluated. The results are shown in an inset of Fig. 4(c). Hii−1
increased monotonically with i (H01 = 0.13 ± 0.03 nm, H12 = 0.16 ± 0.06 nm, and H23 = 0.23 ± 0.05 nm),thereby indicating that the distance between the adsorbed molecules and their contacting substrate increases withlayer number.
Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

4

www.nature.com/scientificreports/

Figure 4. Topographic height distributions of H2Pc on Fe(001). (a,b) STM topography images of Fe(001)surfaces with (a) 0.1 ML (4.2 nm × 4.2 nm,–1.5 V, 300 pA), (b) 2.4 ML (28 nm × 28 nm, −1.5 V, 50 pA) coverageof H2Pc molecules. Labeled numbers, 0th, 1st, 2nd, and 3rd, indicate Fe(001) substrate, first, second, and third
H2Pc layers, respectively. (c) Height histograms taken from (a) and (b), where height = 0 is defined as the
topographic height of the Fe(001) substrate. Inset shows estimated layer distances (see text).

Layer-dependent molecule–substrate interaction. We remark that the molecule–substrate distanceis determined by the bonding strength. The theoretical calculation in our previous study25 demonstrated that thestrong interaction between the π-conjugated H2Pc single molecule and the 3d-Fe state originates from thehybridized π–d bond. Owing to this strong interaction, the molecules are chemisorbed at the hollow sites of theFe(001) surface with large adsorption energy (–4.2 eV) and the small molecular height from the substrate(0.15 nm). The feature is in good agreement with the present case, that is, the H2Pc single molecule stably exists
on Fe(001) substrate with a small molecular height (H01 = 0.13 ± 0.03 nm). Our previous calculation also
demonstrated that the molecular height becomes larger (0.2 nm) on Ag(001) where the molecules are physisorbed on the substrate with small adsorption energy (−1.5 eV). This physisorbed state allows the molecules todiffuse along the surface. In the present study, the second- and third-layer H2Pc molecules form well-packed
films, which indicates that, at RT, the H2Pc single molecules thermally diffuse and stabilize by aggregations inindividual layers. Therefore, the increase in interlayer distance [inset of Fig. 4(c)] is attributed to the weakened
molecule–substrate interactions.
Based on the result, we discuss the layer-dependent molecule–substrate interactions as illustrated schematically in Fig. 5(a)–(c). As previously mentioned, the chemical interaction of the first-layer molecule with the substrate attributes to the hybridized molecular π and Fe(001) d-states [Fig. 5(a)]. We suggest that this π–d state of
the first-layer molecule (π1st state) interacts with the π state of the second-layer molecules, as sketched in Fig. 5(b).
Due to the energy split of the hybridized π–d states25, π state of the second-layer molecule is energetically lessresonant with π1st state. Thus, the π–π1st hybridization and the corresponding chemical bond should be weakened
relative to those of the π–d states. By similar idea, the π–π1st state of the second layer molecule (π2nd state) should
further interact with the π state of the third layer molecules [Fig. 5(c)]. Although such π–π2nd (=π3rd) hybridization should be further weakened due to the energy split of the hybridized π–π1st state, the interaction should be
different from pure van-der Waals type. This is because that, at RT, molecules physisorbed on substrate through
π–π interactions do not from robust film15, while, in our experiment, the third-layer films were found to be stable[Fig. 3(c) and (d)]. The robust but rounded edge-shaped films indicate that some additional contributions otherthan van-der Waals interactions stabilized the films. Therefore, small but finite hybridization should be performedfor π–π2nd states, and thus the third-layer molecules are considered to be in “almost-physisorbed” state [Fig. 5(c)].
It should be noted that the weakened hybridization enables the molecular diffusions in second and thirdlayers, it still plays a significant role in the robust film formations at RT. Since such hybridization is triggeredby the π–d state, the d-state of the magnetic metal is essentially important to stabilize the π-conjugated molecular films, and this is the crucial difference with the other noble metals. From a more common perspective,
the role of d-state was further demonstrated by investigating stability of the other π-conjugated molecular film
on a nonmagnetic metal substrate. As a system, metal-free tetraphenylporphine (H2TPP) on a Au(111) substrate (see Supplementary Method 2–3) was applied. It was found that the H2TPP molecules organized stable andScientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

5

www.nature.com/scientificreports/

Figure 5. Layer-dependent H2Pc-substrate interactions. (a–c) Schematic illustration, representing dominantmolecule–substrate interaction in first layer, (a), second layer, (b), and third layer, (c). (d–f) Schematic
illustrations, representing diffusion of H2Pc single molecule in first layer, (d), second layer, (e), and thirdlayer, (f).

2D-ordered monomolecular films at 78 K, while the morphologies at RT become unstable (see Supplementary
Figure 7 and Supplementary Note 2). It was revealed that such unstable film is due to the thermal diffusion of thephysisorbed H2TPP molecules (see Supplementary Note 1), which attach/detach from the film edges with time.
Therefore, π-conjugated molecular films cannot exist stably on nonmagnetic metals at RT, thereby further supporting the importance of the d-state in robust film formation.

Layer-dependent film formation processes. Based on the layer-dependent molecule–substrate interaction, here we discuss the H2Pc film formation processes. On the bare Fe(001) substrate, the π–d chemisorbed
bonds fix the adsorbed single molecules in particular in-plane configurations (type A and type B). This prevents
molecular diffusion and aggregation even at RT [Fig. 5(d)], thereby leading to the disordered patchy structures,as shown in Fig. 1(g). On the first layer, the weakened chemical interaction allows for the molecular diffusion
along the surface. However, due to the hybridized π–π1st states, the stable adsorption sites and the in-plane configurations of the molecules are considered to be still restricted by the Fe(001) substrate. As the molecular diffusion occurs by sequential hopping between the neighboring stable sites that are related to the Fe(001) surface, thesecond-layer molecule is considered to diffuse along the [100] and [010] directions [Fig. 5(e)]. We suggest thatsuch restricted diffusion channel and/or the adsorbed configurations result in the aggregation and stabilization of
the second-layer molecules along the [100] or [010] directions, forming rectangular shaped well-packed films[Fig. 2(a)]. One may argue that since the first layer forms disordered patchy structure, some of the second-layer
molecules partially supported on the first layer should directly interact with the Fe(001) d-states through thevacant regions, which pins the molecules at the sites. Nevertheless, even in this case, the molecular diffusion
should be allowed since such π–d interactions between separated molecule and Fe(001) substrate [H02~0.29 nm(see Fig. 4)] are considerably weakened from those of the first–layer molecules25. On the other hand, since thethird–layer molecules are almost physisorbed on the second layer, they are considered to be in the several in-plane
adsorbed configurations and allowed to diffuse two-dimensionally [Fig. 5(f)]. These features also result in thewell-packed films but relatively rounded edges [Fig. 2(d)].
Kinetic Monte Carlo simulation.

To examine that the film growth processes we proposed in Fig. 5(d–f)
actually result in the layer-dependent film morphologies, we performed kinetic Monte Carlo simulations andcompared the resultant morphologies with the observed STM images. Figure 6(a) shows the scheme of oursimulation, where depositions, diffusions, and aggregations of H2Pc molecules are included as elementary
processes. The Fe(001) substrate was modeled as a 2D array of sites located along a 150 × 150 square lattice,which corresponds to a surface area of 43 nm × 43 nm (one lattice spacing corresponds to the bcc-Fe(001)lattice constant of 0.286 nm). Periodic boundary conditions were applied to the four edges of the 2D-grid to
avoid discontinuity. For simplicity, this in-plane coordinate system (the 150 × 150 square lattice sites and theperiodic boundary conditions) was also applied to the substrate surfaces of the second- and the third-layer
molecules. H2Pc single molecules with a size of approximately 1.0 nm × 1.0 nm were modeled as 3 × 3 grids
Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

6

www.nature.com/scientificreports/

Figure 6. The method of the kinetic Monte Carlo simulation. (a) Schematic illustration representing
deposition, diffusion and aggregation processes of H2Pc molecules on Fe(001) substrate. (b) Sketches of 9 × 9grids square lattice including single adsorbed molecules (indicated by red rectangular area). Pi(i = 0, 1, 2, …, 8)
represent the hopping probabilities, and Si(i = 1, 2, 3, …, 8) represent the candidate sites where occupations ofmolecules freeze the target molecule.

1st layer H2Pc

D

W0

Wi = 1, 2, 3, 4

Wi = 5, 6, 7, 8

0.1

arb. const.

0

0

Td

ε

σ

Nm

2nd layer H2Pc

0.15

0

30

0

3

−30

3

2

3rd layer H2Pc

0.2

0

50

50

3

−30

3

3

Table 1. Optimized parameters used in the Monte Carlo simulation. D is the desorption probability, Wi = 0, 1, 2, ..., 8
the hopping weight, Td the trapping weight, ε the potential depth of the Lennard-Jones potential, σ the distance atwhich the Lennard-Jones potential becomes zero, Nm the number of molecules required to freeze the target molecule(see text).

[red blocks in Fig. 6(a)], and deposited randomly with constant flux (50 molecules per one calculation loop)
onto the substrate. Desorption of the deposited molecules from the substrate to vacuum was allowed witha probability D. Note that D value determines the total molecular coverage, but not the film morphologies(see Supplementary Figure 8). Therefore, the values were roughly set to reproduce the observed STM images,
D = 0.1 for the first-layer molecules, D = 0.15 for the second-layer molecules, and D = 0.2 for the third-layer
molecules (see Table 1), while we just considered that the D value increases with the layer number due to theweakened molecule–substrate interaction.
Molecular diffusion was set to be induced by sequential hopping of the molecules between the neighboringsites. To determine the hopping direction, we defined the hopping weight Wi and the corresponding hopping
probability Pi as:
8

Pi = Wi / ∑ Wj (i = 0, 1, 2, ... , 8),
j =0

(1)

where P0 corresponds to the probability that a molecule does not hop, Pi (i = 1, 2, 3, 4) the probabilities that amolecule hops along the [100] and [010] directions, and Pi (i = 5, 6, 7, 8) the probabilities that a molecule hops
along the diagonal directions, that is, the [110] and [1 1 0] directions. The summary of Pi is shown in Fig. 6(b). The
diffusion activation barrier, which was conventionally considered to determine Pi26,27, was not considered.
Alternatively, Pi was initialized and modified by fixing Wi under the following assumptions.
Layer-dependent effect. Based on the discussion in Fig. 5(d–f), the hopping directions were restricted dependingon the layer number. Hopping of the molecules on the Fe(001) surface was prohibited. The molecules in the second layer were allowed to hop along the [100] and [010] directions. The molecules in the third layer were allowed
to hop two-dimensionally. Analytically, Wi for the first, second, and third layers were fixed as
Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

7

www.nature.com/scientificreports/

 arbitrary constant (arb. const.) (i = 0)
1st layer: Wi = (i = 1, 2, 3, ... , 8),

0

(2)


(i = 0, 5, 6, 7, 8)
0
2nd layer: Wi = const. (i = 1, 2, 3, 4),


(3)

0
(i = 0)
3rd layer: Wi = 

const
.
(i = 1, 2, 3, ..., 8).



(4)

We can deduce that the Wi (i = 1, 2, 3, 4) for the second layer is smaller than Wi (i = 1, 2, 3, …, 8) for the thirdlayer, since the molecules on higher layer are more mobile. However, more precise assignments of Wi require
further information on the diffusion barrier which has not been obtained in the present experiments. Therefore,
we tentatively assigned Wi (i = 1, 2, 3, 4) = 30 for the second-layer molecules and Wi (i = 1, 2, 3, …, 8) = 50 for
the third-layer molecules (see Table 1), while we confirmed that simulations with different Wi values do not substantially change the results (see Supplementary Figure 9).
Intermolecular interaction. When more than two molecules are located within the same layer, Wi fixed previously was modified by the in-plane intermolecular interactions. Physically, this is equivalent to that the diffusion
barrier is determined by the superposition between potential due to the molecule–substrate interaction and that
due to the in-plane intermolecular interactions. For the interaction, the Lennard-Jones potential was applied. The
potential was not treated quantitatively because we used the potential in order to determine the hopping weight
qualitatively. Here, we assume that the N molecules, labeled Mn (n = 1, 2, 3, …, N), are located at the positions rn
in the same layer. The force Fm(rm) acting on the target molecule Mm can be written as∂Umn(rmn) rmn,∂rmn rmnn ≠mFm(rm) = −∑

(5)

with
Umn(rmn) = 4ε[(σ /rmn)12 − (σ /rmn)6 ].

(6)where rmn = rn − rm, rmn ≡ |rmn|, Umn is the pairwise Lennard-Jones potential between Mm and Mn, ε the potential
depth, and σ the distance at which the intermolecular potential is zero. According to the direction and the magnitude of Fm, Wi of Mm was modified as follows. For the second-layer molecules, the hopping weights modified by
the intermolecular interactions W′i (i = 1, 2, 3, 4) were written asW1 + Fm ⋅ e1 (Fm ⋅ e1 > 0)W1′ = (Fm ⋅ e1 < 0)

W1

(7)


(Fm ⋅ e1 > 0)
W2
W2′ = 


W
F
e
+
|
⋅
|
m
1 (Fm ⋅ e1 < 0)

 2

(8)

W3 + |Fm ⋅ e 2| (Fm ⋅ e 2 > 0)W3′ = (Fm ⋅ e 2 < 0)

W3

(9)

W4
(Fm ⋅ e 2 > 0)W4′ = 


F
e
W
+
|
⋅
|
m
2 (Fm ⋅ e 2 < 0).

 4

(10)

where e1 and e2 are the unit vectors along the [100] and [010] directions, respectively. For the third-layer molecules, W′i (i = 1, 2, 3, 4) were written by Eqs (7)–(10). Additionally, W′i (i = 5, 6, 7, 8) were written as
W5 + |Fm ⋅ e 3| (Fm ⋅ e 3 > 0)W5′ = (Fm ⋅ e 3 < 0)

W5

(11)


(Fm ⋅ e 3 > 0)
W6W6′ = 
W6 + |Fm ⋅ e 3| (Fm ⋅ e 3 < 0)(12)W7 + |Fm ⋅ e4| (Fm ⋅ e4 > 0)W7′ = (Fm ⋅ e4 < 0)

W7

(13)

Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

8

www.nature.com/scientificreports/

W8(Fm ⋅ e4 > 0)W8′ = 


W
+
|
F
⋅
e
|
m
4 (Fm ⋅ e4 < 0).

 8

(14)

where e3 and e4 are the unit vectors along the [110] and [1 1 0] directions, respectively.
Trapping effect at the molecular vacancies. We considered the effect of vacant regions, which are formed primarily as sparse areas in the first layer. The second-layer molecule located at the molecular vacancy interacts with theFe(001) d-state rather than the π1st state. Although this π–d interaction is weaker than that of the first-layer molecule owing to H02 > H01 [see Fig. 4(c)], it can be considered stronger than the π–π1st interactions. Therefore, themolecule located at the molecular vacancy is more likely to stay at the site, thereby reducing the hopping probability. To include this effect in our simulation, a finite value Td (=3 in the present case, see Table 1) was added to
W0, that is, P0 becomes relatively increased while Pi (i = 1, 2, 3, …, 8) become relatively reduced. Note that thistrapping effect should be considered only when the vacancy size is smaller than the single molecular size (3 × 3
grids). Otherwise (the vacancy size is larger than 3 × 3 grids), the molecule in the second layer moves to the firstlayer though the vacancy. This process is highlighted as Process A in Fig. 6(a).
Aggregation effect. We imposed an additional effect to stabilize the molecular hopping so that the molecules
located adjacent to each other were set to become immobile. This aggregation effect was applied to the secondand third-layer molecules with different conditions, where two parameters were considered. One is the numberof adjacent molecules Nm required to freeze the target molecule. Another is the candidates of the adjacent sites
where occupations of molecules freeze the target molecule, which are labeled as Si (i = 1, 2, 3, …, 8) in Fig. 6(b).
As the diffusion and the in-plane adsorbed configurations of the second-layer molecules were restricted by the
π–π1st interactions, the molecules were considered to be aggregated in particular directions, that is, the [100] and[010] directions. Therefore, the hopping of the second-layer molecule was set to be prohibited when not less than
two molecules (Nm = 2, see Table 1) are located at either Si (i = 1, 2, 3, 4) sites. In the third layer, in contrast,
π–π2nd interactions allow the molecules to be physisorbed with several in-plane rotational angles and 2D diffusion with relatively higher mobility than the second-layer molecules. Correspondingly, their aggregation was also
considered to be promoted two-dimensionally with larger Nm compared to the second-layer molecules. Therefore,
the hopping of the third-layer molecule was set to be prohibited when not less than three molecules (Nm = 3, see
Table 1) were located at either Si (i = 1, 2, 3, …, 8) sites.
After predetermined steps of calculations (including adsorptions, diffusions, and aggregations of all deposited
molecules), the additional molecules were set to be re-deposited, and the calculation was performed in the samemanner. This loop calculation was repeated until the total number of deposited molecules increases up to thepredetermined coverages. The number of steps of the final calculation loop was set to be sufficiently large so that
all the adsorbed molecules can stabilize sufficiently.
Resultant molecular morphologies. Figure 7(a)–(d) shows the surface morphologies obtained by the simulations. The optimized parameters used in the simulations are summarized in Table 1. At a coverage of 0.1 ML[Fig. 7(a)], almost all molecules were isolated. With increasing coverage up to 0.8 ML [Fig. 7(b)], the surface
was covered with the dispersed molecules. These results of the submonolayer coverages are in good agreementwith the observed STM images [Fig. 1(f) and (g)]. Above monolayer coverages [Fig. 7(c) and (d)], the surface
was covered with second and third H2Pc layers. They together formed densely packed structures, while the edge
features were clearly different; the edges of the second layer aligned along the [100] and [010] directions, while
those in the third layer were rounded. These features excellently reproduce the characteristic film morphologies[Fig. 2(a) and (d)].
In our film growth model, the second-layer molecules were assumed to diffuse along the [100] and [010]
directions. However, one cannot completely exclude that the molecules diffuse also along diagonal direction
with a small but finite probabilities since the present experiments could not quantitatively determine thestrength of the π–π1st interactions. To test this case, we performed additional simulations where Wi = 5, 6, 7, 8 of
the second-layer molecules were set to be small values (from 1 to 5). It should be note that such simulations
also resulted in the rectangular shaped second-layer films (see Supplementary Figure 10). Thus, the characteristic film morphologies results not only from the simplistic assumptions. On the other hand, our simulation
was simplified on the assumption that the molecules in second and third layers are adsorbed at 150 × 150
square lattice sites. This assumption slightly deviates from the STM image [Fig. 2(b)] where some molecules
are relaxed to be adsorbed at the intermediate sites. Such relaxation disorders the molecular arrangement,
while it will further promote the film compactness. Nevertheless, our simulation, at least, qualitatively well
explains that the layer-dependent molecule–substrate interaction results in the characteristic film morphologies. The further experimental/theoretical studies on the diffusion barrier, adsorbed sites and configurationsof film constituent molecules will enable the quantitative simulation that can more fully reproduce the film
morphologies.

Conclusion

We investigated the formation of π-conjugated H2Pc molecular films on a 3d -bcc-Fe(001) whisker surface at
300 K. On bare Fe(001), strong π–d chemisorbed bonds prevent molecular diffusion and aggregation, leading
to disordered patchy structures, while densely packed films were formed in the second and third layers. The
morphologies of such densely packed films were revealed to be stable even at 300 K. We also found that thesecond and third layer films show a clear difference in their morphologies. Partially p(5 × 5) ordered films with
Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

9

www.nature.com/scientificreports/

Figure 7. The result of the kinetic Monte Carlo simulation. H2Pc distributions on Fe(001) substrate simulatedby the kinetic Monte Carlo method at different coverages, (a) 0.1 ML, (b) 0.8 ML, (c) 1.5 ML, (d) 2.4 ML.

the rectangular edges were formed in the second layer, while the film edges in the third layer were rounded. Fromthese finding, we suggested that the film growth processes and the resulting morphologies are still affected by thesubstrate bcc(001), and concluded that d-states of the magnetic Fe substrate play a crucial role in the robust film
formation. Also, we discussed the layer-dependent molecule–substrate interaction and proposed the film growthmodel that was reasonably examined by the kinetic Monte Carlo simulation. The present results demonstrate thatthe monomolecular layers can be potentially utilized to precisely control the molecule–substrate interaction,
which is a key for sophisticated molecular integration toward highly-functional devices.

Methods

UHV-STM system. The experiments were performed in a home-built UHV-STM system (base pressure<8 × 10−9 Pa). The system comprises a load-lock chamber, a sample preparation chamber, a molecular chamber,and a STM observation chamber. They are interconnected for performing substrate cleaning, molecular deposition, and STM observation without exposing the sample to the atmosphere.
Sample preparation. An Fe whisker prepared by chemical vapor deposition method28–30 was introduced
into the preparation chamber. The whisker was then cleaned and flattened by Ar+-ion sputtering (+0.8 kV,
30 min), with annealing the substrate at 870 K. The annealing was stopped 5 min after stopping the sputtering,which produced a clean and atomically flat Fe(001) surface25. Commercial H2Pc powder (Alfa Aesar, purigy 95%) was purified by sublimation at 653 K and recrystallization at 473 K under a pressure of 10−3 Pa (yield 30 %).
The obtained high-purity H2Pc powder was then located into a crucible, which was fixed in the molecular chamber, and it was first degassed at a temperature of 550 K for 5 min. During degasification, the valve between themolecular chamber and the sample preparation chamber was closed. After degassing, the H2Pc molecules were
deposited on the Fe(001) substrate by opening the valve with the crucible held at 550 K. During deposition, theFe(001) substrate was held at RT. Moreover, annealing was not performed after deposition. The deposition rate
was controlled at a value of approximately 0.11 monolayer (ML)/min.
STM measurements. The STM measurements were performed in the constant current mode using electrochemically etched W-tips (φ = 0.3 mm, purity 99.99 %) that were carefully cleaned by annealing in the load-lockchamber prior to utilization31. Bias voltage (Vs) was applied to the sample with respect to the tip being heldat the virtual ground potential. Tunneling current was detected from the tip. All STM images was obtained at
300 K. Lateral (in-plane) thermal drift in our STM system is around 0.02 nm/s. Only one drift-induced distortion image (see Supplementary Figure 1) was analytically corrected [Fig. 2(b)] by applying an inverse distortiontransformation32.

Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

10

www.nature.com/scientificreports/

References

1. Joachim, C., Gimzewski, J. K. & Aviram, A. Electronics using hybrid-molecular and mono-molecular devices. Nature 408, 541–548(2000).
2. Nitzan, A. & Ratner, M. A. Electron transport in molecular wire junctions. Science 300, 1384–1389 (2003).
3. Barth, J. V., Costantini, G. & Kern, K. Engineering atomic and molecular nanostructures at surfaces. Nature 437, 671–679 (2005).
4. Blum, A. S. et al. Molecularly inherent voltage-controlled conductance switching. Nature Materials 4, 167–172 (2005).
5. Schull, G., Frederiksen, T., Arnau, A., Sanchez-Portal, D. & Berndt, R. Atomic-scale engineering of electrodes for single-moleculecontacts. Nature Nanotechnology 6, 23–27 (2011).
6. Zhou, H. T. et al. Direct imaging of intrinsic molecular orbitals using two-dimensional, epitaxially-grown, nanostructured graphene
for study of single molecule and interactions. Applied Physics Letters 99, 153101 (2011).
7. Zang, Y. et al. Integrated molecular, interfacial, and device engineering towards high-performance non-fullerene based organic solar
cells. Advanced Materials 26, 5708–5714 (2014).
8. Zhou, Y.-H., Zeng, J., Tang, L.-M., Chen, K.-Q. & Hu, W. Giant magnetoresistance effect and spin filters in phthalocyanine-based
molecular devices. Organic Electronics 14, 2940–2947 (2013).
9. Jahn, B. O., Ottosson, H., Galperin, M. & Fransson, J. Organic single molecular structures for light induced spin-pump devices. ACS
Nano 7, 1064–1071 (2013).
10. Mahato, P., Monguzzi, A., Yanai, N., Yamada, T. & Kimizuka, N. Fast and long-range triplet exciton diffusion in metal-organic
frameworks for photon upconversion at ultralow excitation power. Nature Materials 14, 924–930 (2015).
11. Kaji, H. et al. Purely organic electroluminescent material realizing 100% conversion from electricity to light. Nature Communications
6, 8476 (2015).
12. Van Slyke, S. A., Chen, C. & Tang, C. W. Organic electroluminescent devices with improved stability. Applied Physics Letters 69,
2160–2162 (1996).
13. Tang, C. W. Two-layer organic photovoltaic cell. Applied Physics Letters 48, 183–185 (1986).
14. Kraus, M. et al. High-mobility copper-phthalocyanine field-effect transistors with tetratetracontane passivation layer and organic
metal contacts. Journal of Applied Physics 107, 094503 (2010).
15. Naitoh, Y., Matsumoto, T., Sugiura, K., Sakata, Y. & Kawai, T. Self-assembled stripe structure of zinc–phthalocyanine on graphite
surfaces. Surface Science 487, L534–L540 (2001).
16. Nilson, K. et al. Scanning tunneling microscopy study of metal-free phthalocyanine monolayer structures on graphite. Journal ofChemical Physics 127, 114702 (2007).
17. Xie, W., Xu, J., An, J. & Xue, K. Correlation between molecular packing and surface potential at vanadyl phthalocyanine/HOPG
interface. Journal of Physical Chemistry C 114, 19044–19047 (2010).
18. Tsukahara, N. et al. Adsorption-induced switching of magnetic anisotropy in a single iron (II) phthalocyanine molecule on anoxidized Cu(110) surface. Physical Review Letters 102, 167203 (2009).
19. Chizhov, I., Scoles, G. & Kahn, A. The influence of steps on the orientation of copper phthalocyanine monolayers on Au(111).
Langmuir 16, 4358–4361 (2000).
20. Scarfato, A. et al. Scanning tunneling microscope study of iron(II) phthalocyanine growth on metals and insulating surfaces. Surface
Science 602, 677–683 (2008).
21. Komeda, T., Isshiki, H. & Liu, J. Metal-free phthalocyanine (H2Pc) molecule adsorbed on the Au(111) surface: formation of a wide
domain along a single lattice direction. Science and Technology of Advanced Materials 11, 054602 (2010).
22. Schmaus, S. et al. Giant magnetoresistance through a single molecule. Nature Nanotechnology 6, 185–189 (2011).
23. Kawahara, S. L. et al. Large magnetoresistance through a single molecule due to a spin-split hybridized orbital. Nano Letters 12,4558–4563 (2012).
24. Bagrets, A. et al. Single molecule magnetoresistance with combined antiferromagnetic and ferromagnetic electrodes. Nano Lett. 12,
5131–5136 (2012).
25. Yamada, T. K., Yamagishi, Y., Nakashima, S., Kitaoka, Y. & Nakamura, K. Role of π-d hybridization in 300-K organic-magnetic
interface: metal-free phthalocyanine single molecules on bcc Fe(001)-whisker. Physical Review B 94, 195437 (2016).
26. Bruschi, P., Cagnoni, P. & Nannini, A. Temperature-dependent Monte Carlo simulations of thin metal film growth and percolation.
Physical Review B 55, 7955–7963 (1997).
27. Elsholz, F., Meixner, M. & Scholl, E. Kinetic Monte Carlo simulation of self-organized pattern formation in thin film deposition.
Nucl. Instrum. Meth. B 202, 249–254 (2003).
28. Stroscio, J. A., Pierce, D. T., Davies, A., Celotta, R. J. & Weinert, M. Tunneling spectroscopy of bcc (001) surface states. PhysicalReview Letters 75, 2960–2963 (1995).
29. Unguris, J., Celotta, R. J. & Pierce, D. T. Determination of the exchange coupling strengths for Fe/Au/Fe. Physical Review Letters 79,
2734–2737 (1997).
30. Bischoff, M. M. J., Yamada, T. K., Fang, C. M., de Groot, R. A. & van Kempen, H. Local electronic structure of Fe(001) surfaces
studied by scanning tunneling spectroscopy. Physical Review B 68, 045422 (2003).
31. Yamada, T. K., Abe, T., Nazriq, N. M. K. & Irisawa, T. Electron-bombarded 〈110〉-oriented tungsten tips for stable tunneling electron
emission. Rev. Sci. Instrum 87, 033703 (2016).
32. Rahe, P., Bechstein, R. & Kühnle, A. Vertical and lateral drift corrections of scanning probe microscopy images. J. Vac. Sci. Technol.
B 28, C4E31–C4E38 (2010).

Acknowledgements

The authors are grateful to Mr. Yuhei Yamagishi for his supports of the H2Pc film preparation. This work was
supported by JSPS KAKENHI Grant Number (16K17521, 16K05887, 25110011, 17H05353, JP25107002) as well
as JST ACT-C Grant Number JPMJCR12ZE, Japan. One of the authors (EI) also acknowledges financial support
from the Murata Science Foundation.

Author Contributions

E.I. and T.K.Y. conceived and designed the experiments. E.I., M.S., and T.K.Y. performed the experiments. E.I.,
M.S., and T.K.Y. analyzed the data. E.I. and T.K.Y. designed the calculations. E.I. performed the calculations. H.Y.
provided the molecules. M.S. purified the molecules. E.I. and T.K.Y. co-wrote the paper. All authors discussed theresults and commented on the manuscript.

Additional Information

Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-017-18605-2.
Competing Interests: The authors declare that they have no competing interests.

Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

11

www.nature.com/scientificreports/
Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps andinstitutional affiliations.
Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in thisarticle are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to thematerial. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the
copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
© The Author(s) 2017

Scientific REPOrTS | (2018) 8:353 | DOI:10.1038/s41598-017-18605-2

12