Self-Organization of L-Serine on Cu(001)

Fabrication of well-ordered organic molecule layers on metal surfaces influences development of applications in organic device, separation column, polarizer, asymmetric catalysis and biomaterials. So far two-dimensional and long-range ordered overlayer structures with chirality of adsorbed amino acids on metal surfaces have been studied in using low energy electron diffraction (LEED) and scanning tunneling microscope (STM) [1–11]. In most cases of amino acids on Cu(001) surface, the amino acids adsorb on substrate through the two oxygen atoms of carboxylate group and the nitrogen atom of amino group at a near atop site in its anionic form. Recently, we have studied self-organized structure of alanine and L-serine on Cu(001) surface at 310 K using LEED and STM [10– 12]. In the case of D-alanine (NH2–CH(CH3)–COOH) on the substrate, a stable c(2×4) structure was formed and dominantly aligned along the [310] or [1̄30] directions which were equivalent on Cu(001) surface of four-rotation symmetry as shown in Figs. 1(b) and 1(c) [10, 11]. In the c(2×4) structure, the D-alanine is bound on the substrate pointing methyl group away from the surface and the adjacent adsorbates probably interact between amino group and carboxylate group by hydrogen bonds. In the case of L-alanine adsorption, domain of mirror symmetry to one of D-alanine with c(2×4) periodicity is formed, which is dominantly aligns along the [130] or [3̄10] directions as shown in Fig. 1(a). On the other hand, in adsorption of L-serine (NH2–CH(CH2OH)–COOH) with hydroxy group instead of a hydrogen atom in methyl group of alanine, a few different ordered overlayer structures were observed [12]. The first structure just after L-serine deposition formed as thick line domains with width of


I. INTRODUCTION
Fabrication of well-ordered organic molecule layers on metal surfaces influences development of applications in organic device, separation column, polarizer, asymmetric catalysis and biomaterials.So far two-dimensional and long-range ordered overlayer structures with chirality of adsorbed amino acids on metal surfaces have been studied in using low energy electron diffraction (LEED) and scanning tunneling microscope (STM) [1][2][3][4][5][6][7][8][9][10][11].In most cases of amino acids on Cu(001) surface, the amino acids adsorb on substrate through the two oxygen atoms of carboxylate group and the nitrogen atom of amino group at a near atop site in its anionic form.Recently, we have studied self-organized structure of alanine and L-serine on Cu(001) surface at 310 K using LEED and STM [10][11][12].In the case of D-alanine (NH 2 -CH(CH 3 )-COOH) on the substrate, a stable c(2×4) structure was formed and dominantly aligned along the [310] or [ 130] directions which were equivalent on Cu(001) surface of four-rotation symmetry as shown in Figs.1(b) and 1(c) [10,11].In the c(2×4) structure, the D-alanine is bound on the substrate pointing methyl group away from the surface and the adjacent adsorbates probably interact between amino group and carboxylate group by hydrogen bonds.In the case of L-alanine adsorption, domain of mirror symmetry to one of D-alanine with c(2×4) periodicity is formed, which is dominantly aligns along the [130] or [ 310] directions as shown in Fig. 1(a).On the other hand, in adsorption of L-serine (NH 2 -CH(CH 2 OH)-COOH) with hydroxy group instead of a hydrogen atom in methyl group of alanine, a few different ordered overlayer structures were observed [12].The first structure just after L-serine deposition formed as thick line domains with width of about 9 to 11 nm in 2 −1 2 4 (or 4 −2 1 2 ) periodicities, and the domain dominantly grows along the [ 130] (or [310]) directions similar to D-alanine on Cu(001) [11].
The structure model has been proposed, using both results of the observation and some assumptions, that the * Corresponding author: iwai@cc.utsunomiya-u.ac.jp x and y are any integer) streak pattern are observed as double diffraction and these periodic structures are relation of mirror symmetry.We had not been able to discuss about detailed structure of the thin line due to no high resolution STM image for the domain in the previous report [12].In this article, we will propose the second structure model of L-serine on Cu(001) using an STM image which a protrusion is discriminated as an adsorbate.

II. EXPERIMENTAL
The experiments were performed in an UHV chamber with a VT-STM system of Oxford Instruments.Preparation of Cu(001) clean surface and L-serine deposition to the substrate were carried out by typical method and exposure from a handmade doser at 310 K in the UHV chamber as described in detail in ref. [12], respectively.The STM images were measured using a tungsten tip.

III. RESULTS AND DISCUSSIONS
A LEED pattern and a typically STM image of adsorbed L-serine on Cu(001) surface just after deposition of 0.9 L at 310 K are shown in Fig.As the height difference is almost the same as that of the case of D-alanine adsorption on Cu(001) [11], it is considered that the elevated place around this domain is Cu surface.We have discussed that a lot of elliptic-like protrusions revealed in the thick line domain correspond to L-serine dimers and the dimers are assembled in the 2 −1 2 4 periodicity along the [ 130] direction [12].Furthermore, structure model of the thick line has been proposed that L-serine molecule in domain adsorbs on the same relative position of amino group to carboxylate group with D-alanine on Cu(001) pointing hydroxymethyl group toward substrate.
On the other hand, the 2 1 x y (or −1 2 x y ) streak patterns make existence of very narrow width domains x y streak patterns reflects the thin line domains.The width can be allotted into two (or three) serine molecules based on an assumption that each serine is bound by two oxygen atoms of carboxylate group and nitrogen atom of amino group on the copper substrate similar other amino acids adsorption on Cu(001).In Fig. 3, some twin protrusions aligned to the [130] or [ 310] directions as "fastener" are observed in the thin line domain and the size of each protrusion corresponds to one adsorbate.That is, it is considered that the thin line domain consists of two L-serine rows with periodicity of √ 5 times to unit vector of Cu(001) only along the [130] or [ 310] directions.As the thin line domains are dominantly aligned to the [130] or [ 310] directions, it is expected that the adjacent adsorbates interact to the [130] or [ 310] directions due to hydrogen bonds.It has been reported that almost amino acids on Cu(001) have formed two-dimensional periodic structure by the hydrogen bonds between adjacent adsorbates along not only dominant direction but another direction [1][2][3][4][5][6][7][8][9][10][11].However, in the serine on Cu(001) system, one-dimensional structure as thin line domain is formed as shown in Fig. 3.If the two serine rows in the thin line domain are located in configuration as shown in Figs. 4 (a) or (b), the domain will be observed as width of more than two serine rows, and this is contradictory to experimental results.If configuration of the serine rows is relation of rotational symmetry as shown in Fig. 5, no adsorbate is attracted by outside of the domain.We propose the model of Fig. 5  As the height difference is almost the same as that of the case of D-alanine adsorption on Cu(001) [11], it is considered that the elevated place around this domain is Cu surface.However, as the Cu surface is too noisy, the migrating serines have been probably studded on the surface.
are formed in the domain along to the [ 310] direction.Moreover, between the rows are jointed by another hydrogen bonds between amino group and carboxylate group (N-H••O 2 ) and between hydroxyl groups (O 3 -H••O 3 ).It is seem that the hydrogen bonds N-H••O 2 are formed doubly between two adsorbates, which are observed also in thick line domain and in octameric cluster of serine [12].It is speculated that the hydrogen bond between hydroxyl groups (O 3 -H••O 3 ) also is able to exist between the serine rows and the coupling of the serine rows is firmer than structure of thick line domain.The thick line domains completely changed to the thin line domains after 2 hours in deposition of less than 0.7 L as reported in ref. [12].The O 3 -H••O 3 hydrogen bond should influence greatly to this transition probably, and it is considered that the thick line domain is stable kinetically, but the thin line domain is more stable thermodynamically than the thick line owing to the O 3 -H••O 3 hydrogen bond especially.Although the thick line domains have completely changed to the thin line domains less than 0.7 L, the domain structures at 0.9 L (Fig. 2(b)) have remained even after 3 hours.It is considered that sufficient and available vacant area is required in order for thick line domain to restructure to thin line domain completely.According to Fig. 2(b) and Fig. 3, it is seem that thin line domain generates from edge of thick line domain.Although detail of the mechanism is unknown, it is guessed that transition between the domains begins from pulling down edge of thick line domain, secondly serine migrates on the surface, and then the thin line domain is assembled by itself.However, the vacant area at 0.9 L is small, almost of serine cannot probably leave the site in thick line domain.The area of Cu surface in Fig. 3 is very noisy is probably because the migrating serines have been studded on the Cu surface.
Finally, according to study of glycine on Cu(001) by DFT, it is reported that the brightest protrusions of STM image are located just above the highest hydrogen atom bonded to a carbon atom and the parts are observed as bright protrusions in the domain in the STM image [14].In Fig. 5, the highest parts in the structure are each methylene group indicated by circles and it is considered that methylene groups in serine is observed as protrusion in the domain of thin line in the STM image.Although the transition between the domains begins from pulling down edge of thick line domain, besides sufficient and available vacant area are required to be exchanged completely.

FIG. 1 :
FIG. 1: STM images and a LEED pattern for alanine adsorption on Cu(001) at 310 K. (a) STM image for L-alanine (tip bias +0.1 V, current 0.1 nA), (b) STM image for D-alanine (tip bias +0.1 V, current 0.05 nA), (c) LEED pattern for both alanine (Ep = 50 eV).Darker areas in (a) and (b) STM images indicate each alanine domain.The alanine domains are obviously observed as double domains in both STM images and it is reflected in the LEED pattern (c).
and y are any integer) streak (Fig.2(a)) and the STM image reveals several domains of thick line of about 10 nm width and many domains of very thin line of about 10 Å width on terraces as discussed also in ref.[12] (Fig.2(b)).These are chiral overlayer structures.The domains of thick and thin line are aligned along the [ 130] (or [310]) and the [130] (or [ 310]) directions, respectively.A magnified STM image of around a thick line domain on the surface is shown in Fig. 3.A domain encircled by dark circle in the Fig. 3 is a thick line aligned to the [ 130] direction and another domains with narrower width around the dark circle are thin lines aligned to the [130] and [ 310] directions.A graph over the STM image in Fig. 3 corresponds to line profile of between A-B on the thick line domain.

FIG. 2 :
FIG. 2: (a) A LEED pattern (Ep = 34 eV) and (b) an STM image (tip bias +0.2 V, current 0.7 nA) of L-serine adsorption on Cu(001) exposed to 0.9 L at 310 K. (a) The LEED pattern is observed as double diffraction of (2 −1, 2 4) and (2 1, x y) (where x and y are integer) streak patterns.(b) Several domains of thick line about 10 nm width and many domains of thin line about 10 Å width are revealed on the surface.expect, and the periodicity has √ 5 times to unit vector of Cu(001) only along the [130] or [ 310] directions.According to an STM image as shown in Fig. 3, width of the domain is all about 10±1 Å.As coherent length of an electron beam in LEED is typically ∼10 nm, it is considered that 2 1 x y streak patterns reflects the thin line

FIG. 3 :
FIG. 3: A higher resolution STM image around a domain of thick line.Tip bias +0.05 V, current 0.7 nA.A circled area is domain of thick line aligned to the [ 130] direction, and several thin line domains around the thick line domain are observed as fastener along to the [130] and [ 310].A graph over the STM image corresponds to line profile of between A-B on the thick line domain.As the height difference is almost the same as that of the case of D-alanine adsorption on Cu(001)[11], it is considered that the elevated place around this domain is Cu surface.However, as the Cu surface is too noisy, the migrating serines have been probably studded on the surface.

FIG. 4 :
FIG. 4: Schematic view in which every L-serine in the domain of thin line adsorbs by same conformation on the Cu(001).(a) Adsorption pointing hydroxymethyl group away from surface.(b) Adsorption pointing hydroxymethyl group toward surface.In both model, it is possible to grow to large two-dimensional overlayer and the width is not fixed into about 10 Å.

5 FIG. 5 :
FIG. 5: A proposed schematic view for thin line domain in L-serine on the Cu(001).Adsorbed L-serine points hydroxymethyl group away from surface and connects along the [ 310] direction by hydrogen bond N-H••O 1 .It is seem that hydrogen bonds N-H••O 2 and O 3 -H••O 3 are formed between the serine rows.