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Geometry Symmetry of Conjugated Cores along C–Br Bond Effect on the 2D Self-Assembly by Intermolecular H···Br and Br···Br Bonds Jinxing Li, Juntian Wu, Siwei Chen, Xinrui Miao, Fabien Silly, and Wenli Deng J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b02730 • Publication Date (Web): 19 Jun 2018 Downloaded from http://pubs.acs.org on June 19, 2018

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The Journal of Physical Chemistry

Geometry Symmetry of Conjugated Cores along C–Br Bond Effect on the 2D Self-Assembly by Intermolecular H···Br and Br···Br Bonds Jinxing Li,† Juntian Wu,† Siwei Chen,‡ Xinrui Miao,*,†,§ Fabien Silly,§ and Wenli Deng*,† †

College of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, People’s Republic of China.

‡

College of Materials Science and Engineering, Central South University, Changsha, 410083, People’s Republic of China.

§

TITANS, SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay, Gif sur Yvette, F-91191, France

Corresponding author：：Xinrui Miao ([email protected]) Wenli Deng ([email protected])

Abstract Supramolecular self-assemblies of bromine substituted benzene and naphthalene derivatives (Br-BC16 and BrNC16) are investigated using scanning tunneling microscopy at the liquid-solid interface. These two molecules arrange in different linear patterns stabilized by intermolecular H···Br and Br···Br bonds. Due to the different geometry symmetry of conjugated cores along the C–Br bond, the side chains and conjugated cores of Br-BC16 pack with the same direction; however, the side chains of Br-NC16 stretch into different directions along the graphite lattices and the conjugated cores of Br-NC16 in each dimer adopt the reverse orientation. Electrostatic potential (ESP) maps and density functional theory (DFT) calculations show that a pair of intermolecular H···Br bonds between the hydrogen atoms with the positive charge and the bromine atoms with the negative charge in each dimer dominate the structural formation. In addition, a Br···Br bond in each dimer for Br-BC16 and a Br···Br bond between the neighboring dimers for Br-NC16 are formed to stabilize the nanostructures. The results provide insights into the understanding of molecular self-assembly at the liquid-solid interface through the hydrogen bond or the halogen bond for bromine substituted molecules. 1 ACS Paragon Plus Environment

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1. Introduction Supramolecular self-assembly based on non-covalent interactions has been widely employed as an efficient strategy for controllable fabricating surface nanopatterns.1-6 Two cooperating types of interactions that control and stabilize the assembled process on surfaces: molecule-molecule noncovalent interactions and moleculesubstrate van der Waals interactions. Hydrogen bond (HB)7-13 and halogen bond (XB)14-19 are two kinds of key intermolecular interactions due to their strength, directionality, and high selectivity, although the former has been more extensively studied. For the halogen atom (X), there is a positive charge (σ-hole) along the C-X bond and a negative ring-like charge distribution along the vector perpendicular to the C-X bond.20 The halogens could form XB with other atoms with rich electron, such as nitrogen, oxygen, and sulfur.15, 21, 22 Type-II XB could be formed between the positive region and the negative region for the halogen atoms. It also could form HB with hydrogen atom. These two kinds of interactions involve the competition and cooperation in the molecular self-assembly.14, 23-25 The competition mechanism between the formation of HB and XB in molecular self-assembly still remains obscure and predicting structures involving both XB and HB is still challenging. The formation of HB or XB is associated with several factors: 1) Molecular geometry. At the liquid/solid interface, the molecules incline to pack with the closest density. Thus the steric constraint will affect the intermolecular interactions. 2) Relative position of electron-rich atom and hydrogen atom in the conjugated core. Due to the directionality of the HB and XB, the position of the substituted groups is an important factor to determine the bond formation. 3) Halogen atom. For example, the XB strength of iodine is larger than that of bromine, however, the HB strength is on the contrary. Our previous investigations have displayed that the cooperative of HB and XB was the driving force in the monolayer for the bromine-substituted derivatives, in which the molecules had the ester or carboxyl groups.25-27 However, for the iodine-substituted derivative, in most cases the XB control the 2D molecular self-assembly.27 Furthermore, for the molecules only have the halogen substituted group, the HB is the key dominated force to form the 2D monolayer.28, 29 In order to explore the halogen atom and the geometry symmetry of conjugated cores along C–Br bond effect on the 2D self-assembly, we choose the 1-bromo-4-(hexadecyloxy)benzene (BrBC16) and 2-bromo-6-(hexadecyloxy)naphthalene (Br-NC16) as the target molecules as show in Figure 1a. From the electrostatic potential (ESP) maps (Figure 1b), it can be found that the charge distribution of conjugated core along the C-Br bond for Br-BC16 is symmetrical and that of Br-NC16 is asymmetrical, which might induce the different molecular packing fashion. STM images and DFT calculations show that the BrBC16 molecules form dimers by intermolecular H···Br and Br··· Br bonds. The side chains and the benzene rings arrange in a line with the same stretch direction. For Br-NC16, the conjugated cores in each dimer pack in a reverse orientation by intermolecular H···Br bonds resulting from the unsymmetrical geometry and distribution of the surface charge along the C-Br bond for the conjugated core. The side chains in neighboring 2 ACS Paragon Plus Environment

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lamellae arrange in different directions along two of the graphite lattices. The results provide insights into the understanding of intermolecular interactions for bromine substituted molecules on the 2D self-assembly.

Figure 1. (a) Chemical structures of Br-BC16 and Br-NC16. (b) Calculated electrostatic potential (ESP) maps of Br-BC16 and Br-NC16 under vacuum shown by red (negative) and blue (positive) regions; the map color scales from −5 to 5 kcal/mol. The hexadecyloxy chain was replaced by the ethyl group. 2. Experimental section Br-BC16 and Br-NC16 were home synthesized according to the reported procedure. 1-Octanoic acid solvent used in this work was purchased from TCI and used without further purification. Highly ordered pyrolytic graphite (HOPG, grade ZYB, Bruker, USA) as the substrate was freshly cleaved to obtain a flat surface. All the STM experiments were performed at ambient conditions using a Multimode Nanoscope IIIA (Bruker) with positive sample bias. STM tips were mechanically cut from Pt/Ir wire (80%/20%, diameter 0.25 mm). All the STM images were obtained in the constant current mode. Most images obtained at the liquid/solid interface were recorded within 3 h after dropping a droplet of solution. Two kinds of molecules were dissolved separately in 1-octanoic acid (concentration: 10-4 ~ 10-6 M) and the samples were prepared by depositing a droplet (about 1 µL) of solution onto HOPG surfaces. After a while, the samples were studied by STM with the tips immersed into the droplet directly. Different tips and samples were used to check the result reproducibility. Tunneling parameters are given in the corresponding figure captions. Material studio 7.0 was used to build molecular models for the assembled structures. The models were constructed based on the intermolecular distances, angles, and analysis of the STM results. DFT calculations were performed using the Gaussian 09 software package. The electrostatic maps and full-geometry optimization of dimer for Br-BC16 and Br-NC16 were conducted using the hybrid M06-2X method and the split-valence polarized 6-31+g(d) basis set. The M06-2X functional is known to be more accurate for systems involving noncovalent interactions, and hence was chosen for the description of halogen-bonded complexes.30,31 The 631+g(d) basis set was found to provide the lowest total energy and to be more suitable for modeling hydrogen bonded species.32 Basis set superposition errors (BSSE) inherent in the computation of molecular interactions were also corrected via counterpoise technique. The electrostatic potential maps were carried out using the 3 ACS Paragon Plus Environment


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Multiwfn program and visualized with VMD program. 3. Results and discussion

c

Figure 2. (a) Large-scale and (b) high-resolution STM images of a monolayer formed by Br-BC16 at the 1octanoic acid/graphite interface (Iset = 410 pA, Vbis = 600 mV). (c) Molecular model for the linear pattern. Inset shows the intermolecular interactions. The red lines show the H···Br bonds and the green black line shows the Br···Br bond. Figure 2a shows an STM image of the well-ordered 2D self-assembly of Br-BC16 at the 1-octanoic acid/graphite interface. The molecules are packed in a linear fashion. Molecular domain can be 200 nm2 large. A high-resolution STM image of the molecular arrangement is presented in Figure 2b. Molecular alkyl chains appear dark in the STM images, whereas the molecular heads appear bright owing to the high electron density 4 ACS Paragon Plus Environment

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of the benzene ring. The STM images reveal that molecules adopt a head-to-head arrangement and are forming parallel lines, Figure 2a. Two Br-BC16 molecules form a dimer as the red circle indicated in Figure 2b,c. The dimers arrange into a line in a dislocation mode and consist of the linear pattern. A corresponding molecular model of the molecular arrangement is presented in Figure 2c. The measured unit cell parameters are a = 1.0 ± 0.1 nm, b = 2.70 ± 0.05 nm, and γ = 86 ± 2º. Each unit cell contains two Br-BC16 molecules, and the calculated area density is 1.35 nm2 per molecule. All the side chains in each lamella stretch into the same direction along one of the HOPG lattices and interdigitate with the side chains in neighboring lamellae. The model of the molecular assembly reveals that the organic adlayer is stabilized by the H···Br and Br···Br bonds in each dimer and H···Br bonds between molecular heads in neighboring dimers as the inset indicated in Figure 2c and the van der Waals force between neighboring alkyl chains.

120º

c

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Figure 3. (a) Large-scale and (b) high-resolution STM images of a monolayer formed by Br-NC16 at the 1octanoic acid/graphite interface (Iset = 450 pA, Vbis = 620 mV). (c) Proposed molecular model of the linear structure. Inset shows the intermolecular interactions. The red lines show the H···Br bonds and the green line shows the Br···Br bond. Figure 3a shows an STM image of the self-assembly of the Br-NC16 at the1-octanoic acid/graphite interface. This molecule has two benzene rings in its conjugated core, whereas the Br-NC16 molecule has only one. More detailed information about the linear monolayer of the Br-NC16 molecules is shown in the highresolution STM image (Figure 3b), in which the bright lamellae appear as ordered bright robs that are determined as the conjugated naphthalene cores. The side chains of the Br-NC16 molecules in neighboring lamellae interdigitate each other to form the darker stripe owing to their low tunneling efficiency.33, 34 As for the Br-NC16, the molecules adopt a head-to-head arrangement. However molecular alkyl chains adopt two different orientation on the surface, whereas only one orientation was observed for Br-BC16. The angle between the alkyl chains of neighboring molecules is 120°, which corresponds to the angle between the equivalent crystalline directions of the graphite surface. The molecular packing model is proposed in Figure 3c. The conjugated cores in each trough arrange in a head-to-head fashion to form dimers with the reverse symmetry in order to minimize the polarity of the monolayer. The unit cell is superimposed on the STM image (Figure 3b) and the molecular model (Figure 3c), with the parameters of a = 1.05 ± 0.02 nm, b = 6.0 ± 0.1 nm, and γ = 82 ± 1º. Each unit cell contains four Br-NC16 molecules, and the calculated area density is 1.56 nm2 per molecule. According to the molecular packing, except for the interchain van der Waals forces, the H···Br and Br···Br bonds between neighboring molecular head in each lamella as the inset shown in Figure 3c are the dominate factor to stabilize the pattern.

a

b

Figure 4. Proposed molecular models of Br-BC16 and Br-NC16 displaying the molecular arrangement and 6 ACS Paragon Plus Environment

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intermolecular interactions. The brown arrows show the geometry symmetry of the cores along the C-Br bonds. The red dotted lines indicate the H···Br bonds and the black dotted lines show the Br··· Br bonds. Both Br-BC16 and Br-NC16 molecules form one kind of adlayer at the liquid/solid interface, respectively. Although in some cases, the solution concentration and solvent could affect the resulting morphology of the monolayers,35-37 no solution concentration and solvent effects were observed in the systems. The geometry symmetry of conjugated core for Br-BC16 is better than that for Br-NC16, so the dipole moment of Br-BC16 (3.01 Debye) is smaller than that of Br-NC16 (3.23 Debye). Except for the van der Waals forces between the side chains, the intermolecular interactions mainly derive from the noncovalent bonds relative to the bromine. As shown in Figure 1b, the σ-hole of bromine for these two molecules has almost the same large, indicating that the ability to form intermolecular H···Br or Br···Br bonds is the same. It is noted that the geometry structure of conjugated core for Br-BC16 is symmetrical along the C-Br bond and that of Br-NC16 is asymmetrical, as the brown arrows indicate. Thus, the arrangement of the conjugated cores for these molecules is different. In the 2D self-assembled patterns, the conjugated cores of Br-BC16 in each dimer (indicated by color circles) are symmetrical and those of Br-NC16 are reverse symmetrical. Accordingly, the side chains of Br-BC16 are packed towards one direction and those of Br-NC16 stretch into different directions. From the molecular models (Figure 4), we can find that the intermolecular H···Br bonds are the mainly driving forces to determine the formation of dimers, because the positive charges in the conjugated cores are mainly located on the hydrogen atoms and the negative charge distributes on the ring of bromine atom perpendicular to the C-Br bond. Thus, it is a more possibility to form a pair of intermolecular H···Br bonds instead of the type-II Br···Br halogen bond. In addition, based on the molecular packing, we propose that the type-I Br···Br interactions exist in the dimers for Br-BC16 and between the dimers for Br-NC16. The relative Lewis acid-Lewis base complementarity plays a crucial role in the competitive formation of supramolecular halogen and hydrogen bonding motifs. Although bromine is a strong XB donor, the STM results indicate that the HB is more favorable due to the higher Lewis acidity of the C-H proton. To further investigate the self-assembly mechanism of the architectures of Br-BC16 and Br-NC16, DFT calculations were performed based on the STM results (Figure 5). Because the dominated factor to determine the molecular packing nanopatterns is the interactions between the conjugated cores, these two molecules are simplified with two carbon atoms in the side chains. The DFT calculations (Figure 5a,b) show that the binding energy of Br-BC16 dimer is –4.59 kcal/mol and that of Br-NC16 dimer is –4.37 kcal/mol, indicating the H···Br bonds are relative strong hydrogen bonds.38 The binding energy is associated with the bond length and bond angle. Because the negative charge of bromine locates on the vectors perpendicular to the C-Br bond, the bond energy is the strongest when the angle of C-Br-H is 90º.28,39 The angle of C-Br-H for Br-BC16 is 105º and that of Br-NC16 is 94º. The H···Br bond angle for Br-BC16 is 2.80 Å and that for Br-NC16 is 2.82 Å. Therefore, 7 ACS Paragon Plus Environment


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these two dimers has the similar binding energy. The binding energy for Br-BC16 is slightly larger than that for Br-NC16, which is ascribed to the formation of Br···Br bond. These results also confirm that the formation of the different packing fashion derives from the symmetry of the conjugated cores along the C–Br bonds. The importance of H···Br and Br···Br interactions in these adlayers are further explored by the calculated electrostatic potential maps for the dimers (Figure 5c,d). From these maps, the interactions between H and Br atoms can be seen, arising from the small positive region on Br that interacts with the negative charge on H. The Br···Br in the Br-BC16 dimer can be observed due to the rearrangement of the charges, however, no such interaction is possible in the Br-NC16 dimer due to unfavorable geometric constraints. The positive charge of H in Br-NC16 dimer can also be seen as the black ring indicated. This is consistent with previous work of Davey et al.40 The Br···Br bonds are formed between the dimers of Br-NC16. Overall, these different H···Br and Br···Br interactions are another dominated factors that allow the Br-BC16 and Br-NC16 molecules to adopt different linear structures.

a

b

∆E = –4.59 kal/mol c

∆E = –4.37 kal/mol d

Figure 5. DFT optimized geometries of a free standing dimers of (a) Br-BC16 and (b) Br-NC16. Dash lines showing possible intermolecular H···Br and Br···Br bonds. (c,d) ESP maps of Br-BC16 and Br-NC16 dimers under vacuum shown by red (negative) and blue (positive) regions; the map color scales from −5 to 5 kcal/mol. The hexadecyloxy chain was replaced by the ethyl group. 4. Conclusions 8 ACS Paragon Plus Environment

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In conclusion, from the combination of STM imaging and DFT calculations, we have demonstrated that the geometry symmetry of conjugated cores along C–Br bond effect on the 2D self-assembly. For Br-BC16, the molecules form dimers by intermolecular H···Br and Br··· Br bonds and arrange in a line with the same stretch direction of the side chains. For Br-NC16, the conjugated cores in each dimer pack in a reverse orientation by intermolecular H···Br bonds resulting from the unsymmetrical distribution of the surface charge along the C-Br bond, in which the side chain in neighboring lamellae arrange in different directions. The Br··· Br bond is formed between the neighboring Br-NC16 dimers. These findings would make a step forward towards understanding the importance of molecular geometry on the self-assembled nanostructures and the formation of the intermolecular hydrogen or halogen bond. AUTHOR INFORMATION Corresponding Author *E-mail: [email protected], [email protected] Notes The authors declare no competing financial interest. Acknowledgements Financial supports from the National Natural Science Foundation of China (51373055and 21573077) and the Fundamental Research Funds for the Central Universities (SCUT) are gratefully acknowledged. X. Miao acknowledges receipt of the China Scholarship Council (CSC, 201706155092). References 1. Wu, S.; Xu, S.; Geng, Y.; Liu, Z.; Nie, H.; Shu, L.; Deng, K.; Zeng, Q.; Wang, C., Scanning Tunneling Microscopy Study on Self-Assembly Behavior of Hexylaniline Derivatives Spaced with Diynes. J. Phys. Chem. C 2016, 120, 12618–12625. 2. Ecija, D.; Vijayaraghavan, S.; Auwärter, W.; Joshi, S.; Seufert, K.; Aurisicchio, C.; Bonifazi, D.; Barth, J. V., Two-Dimensional Short-Range Disordered Crystalline Networks from Flexible Molecular Modules. ACS Nano 2012, 6, 4258–4265. 3. Otero, R.; Gallego, J. M.; de Parga, A. L. V.; Martín, N.; Miranda, R., Molecular Self-Assembly at Solid Surfaces. Adv. Mater. 2011, 23, 5148–5176. 4. Jester, S.-S.; Sigmund, E.; Röck, L. M.; Höger, S., Hierarchical Self-Assembly of Polycyclic Heteroaromatic Stars into Snowflake Patterns. Angew. Chem. Int. Ed. 2012, 51, 8555–8559. 5. Chen, T.; Yang, W.-H.; Wang, D.; Wan, L.-J., Globally Homochiral Assembly of Two-Dimensional Molecular Networks Triggered by Co-Absorbers. Nat. Commun. 2013, 4, 1389. 9 ACS Paragon Plus Environment


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Br and Br - American Chemical Society

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