Surface Structures Formed by a Copper(II) Complex of Alkyl-Derivatized Indigo

Assembled structures of dyes have great influence on their coloring function. For example, metal ions added in the dyeing process are known to prevent fading of color. Thus, we have investigated the influence of an addition of copper(II) ion on the surface structure of alkyl-derivatized indigo. Scanning tunneling microscope (STM) analysis revealed that the copper(II) complexes of indigo formed orderly lamellar structures on a HOPG substrate. These lamellar structures of the complexes are found to be more stable than those of alkyl-derivatized indigos alone. Furthermore, 2D chirality was observed.


Introduction
Dyes are colored substances capable of absorbing certain wavelengths of light intensively. Many of the dyes have a large π-conjugated system, and the color of dyes is highly influenced by the electronic state of the system. In consequence, assembled structural changes often induce the change in the electronic state of the π-conjugated system and result in color variations. Color changes via polymorphism, phase transition, etc. have been reported elsewhere [1][2][3]. Thus, an understanding of how molecular assembly of dyes is constructed is necessary for the design of a coloring function. Dyes often have a planar structure due to the large π-conjugated system, resulting in an affinity to the substrate onto which they adsorb. This is why the assembled structures formed by the dyes on substrates have been analyzed in detail [4][5][6]. A scanning tunneling microscope (STM) [7] is an instrument suitable for imaging the surface structures on a substrate, because STM is capable of resolving the surface structures at the atomic level, and the ordered molecular images of self-assembled structure of dyes can be observed [8][9][10][11][12].
Indigo dye is an organic dye exhibiting a distinct blue color, used for dyeing jeans blue. The indigo molecule has a planar structure due to the presence of a π-conjugated system and thus tends to assemble on a HOPG or metallic substrate. In our previous study, the surface structures of alkyl-derivatized indigo (CnIND, n = alkyl chains length) shown in Figure 1a were analyzed via STM, which revealed that CnIND formed characteristic monolayer structures on HOPG [13]. In this study, we synthesized [Cu(CnIND) 2 ], the copper(II) complex of CnIND, shown in Figure 1b and observed the surface structures formed by [Cu(CnIND) 2 ] using STM. This investigation was carried out to understand the influence of the addition of metal ions, which often stabilizes the adsorption of dyes on the substrate. This phenomenon is known as mordanting. Mordanting [14,15] is the process of adding metal ions (Cu, Fe, etc.) in a dyeing process, so as to prevent the color loss of a dyeing object. The role of metal ions is estimated as filling the possible space between dye molecules and to stabilize the adsorption of the dye molecules onto a dyeing object. By comparing the surface structures of CnIND and those of [Cu(CnIND) 2 ], the mechanism of stabilization via mordanting may be found. In addition, [Cu(CnIND) 2 ] exhibited a unique structure exhibiting 2D and 3D chirality, which is described later.
Materials 2016, 9,837 2 of 8 of dyes on the substrate. This phenomenon is known as mordanting. Mordanting [14,15] is the process of adding metal ions (Cu, Fe, etc.) in a dyeing process, so as to prevent the color loss of a dyeing object. The role of metal ions is estimated as filling the possible space between dye molecules and to stabilize the adsorption of the dye molecules onto a dyeing object. By comparing the surface structures of CnIND and those of [Cu(CnIND)2], the mechanism of stabilization via mordanting may be found. In addition, [Cu(CnIND)2] exhibited a unique structure exhibiting 2D and 3D chirality, which is described later.

STM Images of [Cu(C16IND)2] on HOPG
We successfully observed the structures of a self-assembled monolayer formed by [Cu(C16IND)2] on a HOPG surface using STM. The obtained STM image and structural model of the monolayer are shown in Figures 2a,b, respectively. [Cu(C16IND)2] molecules formed a lamellar structure, with complex moieties imaged as bright spots in the STM image, since π-conjugation is generally more conductive than aliphatic alkyl chains. Alkyl chains are assumed to align in the darker regions between the bright spots of an STM image and are interdigitated as shown in Figure 2b. Interdigitated alkyl chains are known to have large van der Waals interactions between alkyl chains and the HOPG substrate, seeming to play a great role in controlling the surface structures of [Cu(C16IND)2].

Comparison between [Cu(C16IND)2] and C16IND
In the previous study, the self-assembled structures on HOPG of C16IND were analyzed via STM [13]. C16IND molecules formed a dimer via hydrogen bonds, and alkyl chains were interdigitated via van der Waals interactions. In addition, C16IND molecules formed a dislocation

STM Images of [Cu(C16IND) 2 ] on HOPG
We successfully observed the structures of a self-assembled monolayer formed by [Cu(C16IND) 2 ] on a HOPG surface using STM. The obtained STM image and structural model of the monolayer are shown in Figure 2a,b, respectively. [Cu(C16IND) 2 ] molecules formed a lamellar structure, with complex moieties imaged as bright spots in the STM image, since π-conjugation is generally more conductive than aliphatic alkyl chains. Alkyl chains are assumed to align in the darker regions between the bright spots of an STM image and are interdigitated as shown in Figure 2b. Interdigitated alkyl chains are known to have large van der Waals interactions between alkyl chains and the HOPG substrate, seeming to play a great role in controlling the surface structures of [Cu(C16IND) 2 ]. of dyes on the substrate. This phenomenon is known as mordanting. Mordanting [14,15] is the process of adding metal ions (Cu, Fe, etc.) in a dyeing process, so as to prevent the color loss of a dyeing object. The role of metal ions is estimated as filling the possible space between dye molecules and to stabilize the adsorption of the dye molecules onto a dyeing object. By comparing the surface structures of CnIND and those of [Cu(CnIND)2], the mechanism of stabilization via mordanting may be found. In addition, [Cu(CnIND)2] exhibited a unique structure exhibiting 2D and 3D chirality, which is described later.

STM Images of [Cu(C16IND)2] on HOPG
We successfully observed the structures of a self-assembled monolayer formed by [Cu(C16IND)2] on a HOPG surface using STM. The obtained STM image and structural model of the monolayer are shown in Figures 2a,b, respectively. [Cu(C16IND)2] molecules formed a lamellar structure, with complex moieties imaged as bright spots in the STM image, since π-conjugation is generally more conductive than aliphatic alkyl chains. Alkyl chains are assumed to align in the darker regions between the bright spots of an STM image and are interdigitated as shown in Figure 2b. Interdigitated alkyl chains are known to have large van der Waals interactions between alkyl chains and the HOPG substrate, seeming to play a great role in controlling the surface structures of [Cu(C16IND)2].

Comparison between [Cu(C16IND)2] and C16IND
In the previous study, the self-assembled structures on HOPG of C16IND were analyzed via STM [13]. C16IND molecules formed a dimer via hydrogen bonds, and alkyl chains were interdigitated via van der Waals interactions. In addition, C16IND molecules formed a dislocation

Comparison between [Cu(C16IND) 2 ] and C16IND
In the previous study, the self-assembled structures on HOPG of C16IND were analyzed via STM [13]. C16IND molecules formed a dimer via hydrogen bonds, and alkyl chains were interdigitated via van der Waals interactions. In addition, C16IND molecules formed a dislocation structure at every three molecules, as shown in Figure A1. This dislocation along the molecular lamella axis derives from the matching between the alkyl chains and the HOPG substrate lattice [16,17].
Compared with C16IND, the copper complex [Cu(C16IND) 2 ] formed an orderly structure, and the dislocation was not observed (Figure 3). The ordered structure of [Cu(C16IND) 2 ] indicates that adding copper ions to C16IND results in a stabilization of the adsorbed structures. The result may suggest the effect of mordanting, which is to add metal ions in a dyeing process.
Materials 2016, 9, 837 3 of 8 structure at every three molecules, as shown in Figure A1. This dislocation along the molecular lamella axis derives from the matching between the alkyl chains and the HOPG substrate lattice [16,17]. Compared with C16IND, the copper complex [Cu(C16IND)2] formed an orderly structure, and the dislocation was not observed (Figure 3). The ordered structure of [Cu(C16IND)2] indicates that adding copper ions to C16IND results in a stabilization of the adsorbed structures. The result may suggest the effect of mordanting, which is to add metal ions in a dyeing process.

2D Chirality of [Cu(C16IND)2]
"2D chirality" of the adsorbed molecules on the substrate has been intensively studied [18][19][20]. When a prochiral molecule adsorbs onto a substrate, the molecular inversion is restricted and the adsorbed molecules can be distinguished as enantiomers (λ and δ in Figure 4).
[Cu(C16IND)2] on the HOPG surface exhibits distinguishable 2D chirality, as shown in Figure 4. In the λ-structure shown in Figure 4a, molecular columns aligned counter-clockwise (CCW) versus the HOPG substrate lattice. The angle between them is approximately 10°. On the other hand, Figure 4b shows a δ-structure, and the molecules were aligned by the same angle but in a clockwise (CW) orientation versus the HOPG lattice.

2D Chirality of [Cu(C16IND) 2 ]
"2D chirality" of the adsorbed molecules on the substrate has been intensively studied [18][19][20]. When a prochiral molecule adsorbs onto a substrate, the molecular inversion is restricted and the adsorbed molecules can be distinguished as enantiomers (λ and δ in Figure 4).
[Cu(C16IND) 2 ] on the HOPG surface exhibits distinguishable 2D chirality, as shown in Figure 4. In the λ-structure shown in Figure 4a, molecular columns aligned counter-clockwise (CCW) versus the HOPG substrate lattice. The angle between them is approximately 10 • . On the other hand, Figure 4b shows a δ-structure, and the molecules were aligned by the same angle but in a clockwise (CW) orientation versus the HOPG lattice. structure at every three molecules, as shown in Figure A1. This dislocation along the molecular lamella axis derives from the matching between the alkyl chains and the HOPG substrate lattice [16,17]. Compared with C16IND, the copper complex [Cu(C16IND)2] formed an orderly structure, and the dislocation was not observed (Figure 3). The ordered structure of [Cu(C16IND)2] indicates that adding copper ions to C16IND results in a stabilization of the adsorbed structures. The result may suggest the effect of mordanting, which is to add metal ions in a dyeing process.

2D Chirality of [Cu(C16IND)2]
"2D chirality" of the adsorbed molecules on the substrate has been intensively studied [18][19][20]. When a prochiral molecule adsorbs onto a substrate, the molecular inversion is restricted and the adsorbed molecules can be distinguished as enantiomers (λ and δ in Figure 4).
[Cu(C16IND)2] on the HOPG surface exhibits distinguishable 2D chirality, as shown in Figure 4. In the λ-structure shown in Figure 4a, molecular columns aligned counter-clockwise (CCW) versus the HOPG substrate lattice. The angle between them is approximately 10°. On the other hand, Figure 4b shows a δ-structure, and the molecules were aligned by the same angle but in a clockwise (CW) orientation versus the HOPG lattice.

STM Images of [Cu(C18IND)2] and [Cu(C20IND)2] on HOPG
Alkyl chains lengths are known to influence the self-assembled structures of alkyl-derivatives [21][22][23][24][25][26]. Varying the chain lengths results in changing the intermolecular and molecule-substrate interactions, leading to a surface structural variation. Thus, we investigated surface structures   2 ]. These molecules formed a similar lamellar structure, and alkyl chains were interdigitated as shown in Figure 5a,b. The alkyl chains of [Cu(C18IND) 2 ] seem to be aligned along the HOPG substrate lattice, suggesting that the surface structure matches well with the HOPG lattice and becomes stable.

The Effect of 3D Chirality of [Cu(C20IND)2] to 2D Self-Assembly
[Cu(C20IND)2] also exhibited a different surface structure (namely type 2 structure shown in Figure 6a) from that described in Figure 5b [28]. Figure 6b shows the calculated structure, and it revealed that [Cu(IND)2] adopts the twisted square planar geometry due to the steric repulsion between coordinated indigo moieties in a complex. Owing to the twisted structure, 3D chirality of [Cu(IND)2] appears as shown in Figure 6c. As a result, Λ-structure and Δ-structure can be distinguished. Compared with the type 1 structure of [Cu(C20IND)2] shown in Figure 5b, the type 2 structure shown in Figure 6a has a longer b-axis. Since the b-axis is taken along the orientation of alkyl chains, the difference in the b-axis length suggests a variation in the assembled structure of alkyl chains. When the twisted complex adsorbs onto the HOPG substrate, a space between the complex and the substrate appears due to the non-planarity. Thus, the end group of alkyl chains can enter into the space depending on the situation. In the type 1 structure, the short length of the b-axis indicates that

The Effect of 3D Chirality of [Cu(C20IND) 2 ] to 2D Self-Assembly
[Cu(C20IND) 2 ] also exhibited a different surface structure (namely type 2 structure shown in Figure 6a) from that described in Figure 5b [28]. Figure 6b shows the calculated structure, and it revealed that [Cu(IND) 2 ] adopts the twisted square planar geometry due to the steric repulsion between coordinated indigo moieties in a complex. Owing to the twisted structure, 3D chirality of [Cu(IND) 2 ] appears as shown in Figure 6c. As a result, Λ-structure and ∆-structure can be distinguished.

The Effect of 3D Chirality of [Cu(C20IND)2] to 2D Self-Assembly
[Cu(C20IND)2] also exhibited a different surface structure (namely type 2 structure shown in Figure 6a) from that described in Figure 5b [28]. Figure 6b shows the calculated structure, and it revealed that [Cu(IND)2] adopts the twisted square planar geometry due to the steric repulsion between coordinated indigo moieties in a complex. Owing to the twisted structure, 3D chirality of [Cu(IND)2] appears as shown in Figure 6c. As a result, Λ-structure and Δ-structure can be distinguished. Compared with the type 1 structure of [Cu(C20IND)2] shown in Figure 5b, the type 2 structure shown in Figure 6a has a longer b-axis. Since the b-axis is taken along the orientation of alkyl chains, the difference in the b-axis length suggests a variation in the assembled structure of alkyl chains. When the twisted complex adsorbs onto the HOPG substrate, a space between the complex and the substrate appears due to the non-planarity. Thus, the end group of alkyl chains can enter into the space depending on the situation. In the type 1 structure, the short length of the b-axis indicates that Compared with the type 1 structure of [Cu(C20IND) 2 ] shown in Figure 5b, the type 2 structure shown in Figure 6a has a longer b-axis. Since the b-axis is taken along the orientation of alkyl chains, the difference in the b-axis length suggests a variation in the assembled structure of alkyl chains. When the twisted complex adsorbs onto the HOPG substrate, a space between the complex and the substrate appears due to the non-planarity. Thus, the end group of alkyl chains can enter into the space depending on the situation. In the type 1 structure, the short length of the b-axis indicates that the end group of alkyl chains is inserted into the space. On the other hand, this insertion is blocked by the phenyl groups of the indigo in the type 2 structure. Hence, the steric structure of [Cu(C20IND) 2 ] molecules in the type 1 structure is different from that in the type 2 structure. In other words, the 3D chirality of [Cu(C20IND) 2 ] induced a structural difference.

Materials and Identification
All chemicals including indigo were purchased from Tokyo Chemical Industry, Aldrich or Kanto Chemicals, and used without further purification. Elemental analyses were performed on a Perkin-Elmer 2400II CHN analyzer. IR spectra were measured on a JASCO FT/IR-4200 spectrophotometer using KBr pellets. UV-vis absorption spectra were measured on a JASCO V-750 spectrophotometer using chloroform as a solvent. The concentration of the sample for UV-vis absorption spectra was 1.0 × 10 −5 mol·L −1 .

Synthesis of the Copper(II) Complex of Hexadecyl-Indigo ([Cu(C16IND) 2 ])
N-hexadecyl-indigo (C16IND) was synthesized by the scheme in a previous study [13]. A total of 3.0 mmol (1.5 g) of C16IND in 40 mL of N,N-dimethylformamide was added to a 200 mL recovery flask equipped with a magnetic stirring bar. After the addition of 1.5 mmol (0.27 g) of copper(II) acetate, the mixture was stirred and refluxed for 8 h. After the reflux, a blue suspension was obtained. The suspension was cooled to room temperature, and then filtrated under suction to remove the solvent.   [29] (Nanotec, Madrid, Spain), using the HOPG substrate images recorded for calibration. Structural models fitting in the STM images were made by the Materials Studio 7.0 software (Accelrys Inc., San Diego, CA, USA).

Conclusions
We investigated the two-dimensional self-assembled structures formed by copper(II) complexes of alkyl-derivatized indigo ([Cu(CnIND) 2 ]). STM images revealed that the assembled structures of the complexes were more stable than those of alkyl-derivatized indigos alone, suggesting the effect of mordanting. [Cu(CnIND) 2 ] formed orderly lamellar structures on a HOPG substrate, and their alkyl chains were interdigitated. In the STM study of [Cu(C16IND) 2 ], 2D chirality was observed; λ-structure and δ-structure were distinguished by molecular orientation. In the STM study of [Cu(C20IND) 2 ], two types of structures with different lengths of b-axis were observed. The difference between these structures was found to derive from the 3D chirality of [Cu(C20IND) 2 ]. In summary, [Cu(CnIND) 2 ] formed orderly surface structures involving 2D chirality, and these surface structures were altered by 3D chirality.
Author Contributions: Akinori Honda, Keisuke Noda, Yoshinori Tamaki and Kazuo Miyamura conceived and designed the experiments; Akinori Honda and Keisuke Noda performed the experiments; Akinori Honda and Keisuke Noda analyzed the data; Akinori Honda wrote the paper.

Conflicts of Interest:
The authors declare no conflict of interest.

Abbreviations
The following abbreviations are used in this manuscript:

Appendix A
In the previous study, a dislocated structure of C16IND was observed as shown in Figure A1.

Conclusions
We investigated the two-dimensional self-assembled structures formed by copper(II) complexes of alkyl-derivatized indigo ([Cu(CnIND)2]). STM images revealed that the assembled structures of the complexes were more stable than those of alkyl-derivatized indigos alone, suggesting the effect of mordanting. [Cu(CnIND)2] formed orderly lamellar structures on a HOPG substrate, and their alkyl chains were interdigitated. In the STM study of [Cu(C16IND)2], 2D chirality was observed; λ-structure and δ-structure were distinguished by molecular orientation. In the STM study of [Cu(C20IND)2], two types of structures with different lengths of b-axis were observed. The difference between these structures was found to derive from the 3D chirality of [Cu(C20IND)2]. In summary, [Cu(CnIND)2] formed orderly surface structures involving 2D chirality, and these surface structures were altered by 3D chirality.
Author Contributions: Akinori Honda, Keisuke Noda, Yoshinori Tamaki and Kazuo Miyamura conceived and designed the experiments; Akinori Honda and Keisuke Noda performed the experiments; Akinori Honda and Keisuke Noda analyzed the data; Akinori Honda wrote the paper.

Conflicts of Interest:
The authors declare no conflict of interest.

Abbreviations
The following abbreviations are used in this manuscript:

Appendix A
In the previous study, a dislocated structure of C16IND was observed as shown in Figure A1.