Controllable Orientation of Ester-Group-Induced Intermolecular Halogen Bonding in a 2D Self-Assembly

Identifying Target Molecule and Trace Amount of the Byproduct by Two-Dimensional Self-Assembly with Different Solution Concentrations

Scanning tunneling microscopy (STM) is a powerful way to realize the recognition of self-assembled nanostructures on the atomic scale. In this article, dihexadecyl 6,9-bis((4-(hexadecyloxy)phenyl)ethynyl) phenanthro[9,10-c]thiophene-1,3-dicarboxylate (D-PT) and dihexadecyl 6-bromo-9-((4-(hexadecyloxy) phenyl)ethynyl)phenanthrol[9,10-c]thiophene-1,3-dicarboxylate (S-BrPT) with different substituents were chosen as the target system. D-PT with four side chains as the target molecule and S-BrPT with three side chains and a bromine substituent as the byproduct were mixed in a molar concentration ratio of 20:1. The effect of solution concentration on the molecular self-assembly of the mixture was investigated by STM at the hexadecane/HOPG interface. At high concentrations, only D-PT molecules formed a dimer pattern resulting from the intermolecular van der Waals force and self-adaption. Further diluting the solution, D-PT formed the coexisting dimer and linear structures, in which the linear pattern was formed via solvent coadsorption. At low concentrations, S-BrPT molecules forming N-shaped dimers appeared and filled the linear structure fabricated by D-PT molecules. With further decrease in the concentration, S-BrPT molecules formed N-shaped dimers covering almost half of the surface area, resulting from the C-Br···π and Br···H-C bonds. At very low concentrations, S-BrPT molecules formed N-shaped dimers to arrange the matrix architecture due to the coadsorption of more hexadecane molecules. Density functional theory (DFT) calculations demonstrated that the stronger intermolecular C-Br···π and Br···H-C bonds were significant factors in determining the formation of N-shaped dimers and the stability of this nanostructure. This work enriches the diversity of self-assembled motifs and provides a strategy to characterize different symmetric molecules with trace amounts in a mixed system by STM.

Halogen Bond Induced Structural and Photophysical Properties Modification in Organic-Inorganic Hybrid Manganese Halides

The role of halogen bonding in organic-inorganic hybrid (OIH) halides was seldom investigated despite its potential to enhance the stability of the compound. In this context, we have synthesized (2-methylbenzimidazolium)MnCl₃(H₂O)·H₂O (compound 1) crystallizing in a monoclinic space group P2₁/c with a 1D infinite chain of edge shared Mn octahedra. In contrast, the chloro-substituted derivative (5-chloro-2-methylbenzimidazolium)₂MnCl₄ (compound 2) exhibits 0D Mn tetrahedra with a triclinic P1̅ structure. This structural modification from 1D Mn octahedra to 0D Mn tetrahedra involves a unique type-II halogen bonding between organic chlorine (C-Cl) and inorganic chloride (Cl-Mn) ions. Compound 1 exhibits red emission, whereas compound 2 demonstrates dual-band emission, resulting from energy transfer from the organic amine to Mn centers. To rationalize this interesting modulation in structure and photophysical properties, the role of halogen bonding is explored in terms of quantitative electron density analysis and intermolecular interaction energies.

Halogen bonding controlled 2D self-assembled polymorphism of regioisomeric thienophenanthrene derivatives by coadsorption

5,10-BTD-C14 molecules display self-assembled polymorphism in different bromo-hydrocarbons with different solution concentrations at the liquid/solid interface.

Halogen Bonds Fabricate 2D Molecular Self-Assembled Nanostructures by Scanning Tunneling Microscopy

Halogen bonds are currently new noncovalent interactions due to their moderate strength and high directionality, which are widely investigated in crystal engineering. The study about supramolecular two-dimensional architectures on solid surfaces fabricated by halogen bonding has been performed recently. Scanning tunneling microscopy (STM) has the advantages of realizing in situ, real-time, and atomic-level characterization. Our group has carried out molecular self-assembly induced by halogen bonds at the liquid–solid interface for about ten years. In this review, we mainly describe the concept and history of halogen bonding and the progress in the self-assembly of halogen-based organic molecules at the liquid/graphite interface in our laboratory. Our focus is mainly on (1) the effect of position, number, and type of halogen substituent on the formation of nanostructures; (2) the competition and cooperation of the halogen bond and the hydrogen bond; (3) solution concentration and solvent effects on the molecular assembly; and (4) a deep understanding of the self-assembled mechanism by density functional theory (DFT) calculations.

Conformation modification of terthiophene during the on-surface synthesis of pure polythiophene

On-surface coupling under ultra-high vacuum is employed as a versatile approach to synthesize pure polythiophene from a 5,5''-dibromo-2,2':5',2''-terthiophene (DBTT) precursor and the corresponding temperature-dependent stepwise reaction mechanism is systematically studied by scanning tunneling microscopy (STM). After thermal deposition of the precursor onto a Au(111) surface that is kept at room temperature, a triangle-like pattern and a linear self-assembled pattern are formed with different molecular coverages through BrBrS halogen bonds and BrBr type-I contact bonds, respectively. In the self-assembled nanostructures, the thiophene units adopt trans-conformation. Mild annealing promotes the structural transition of both nanostructures into ordered zigzag organometallic linear chains with all-cis configured thiophene units connected through coordination bonds to the Au adatoms. Such conformational variety is easily recognized by STM, particularly in the case of DBTT-CH3 with the extra -CH3 signals. The covalently coupled products from the DBTT precursor are obtained by further annealing the organometallic intermediate at higher temperatures, which leads to the removal of Au atoms and the formation of ordered polymer chains and disordered polythiophene networks. Further characterization suggests that the reaction mechanism is associated with Ullmann-type coupling to form the ordered chains as well as Ullmann-type and dehydrogenative C-C coupling to fabricate cross-linked polymer networks. Compared with the on-surface synthesis process of DBTT on the Cu(111) surface, it can be confirmed that the Au adatoms are vital to synthesize polythiophene. These findings provide important insight into the reaction mechanism of on-surface synthesized pure polythiophene and on-surface coupling can potentially be applied to synthesize other functional conjugated polymers.

Construction of 2D extended cocrystals on the Au(111) surface via IOaldehyde halogen bonds

2D extended organic cocrystals were constructed using 1,4-diiodotetrafluorobenzene and aromatic aldehydes via IOaldehyde halogen bonds on an Au(111) surface. The competition and synergy of halogen bonds and hydrogen bonds in 2D co-crystallization were revealed by scanning tunneling microscopy.

Elucidating the intramolecular contrast in the STM images of 2,4,6-tris(4',4'',4'''-trimethylphenyl)-1,3,5-triazine molecules recorded at room-temperature and at the liquid-solid interface

Star-shaped 2,4,6-tris(4',4'',4'''-trimethylphenyl)-1,3,5-triazine molecules self-assemble at the solid-liquid interface into a compact hexagonal nanoarchitecture on graphite. High resolution scanning tunneling microscopy (STM) images of the molecules reveal intramolecular features. Comparison of the experimental data with calculated molecular charge density contours shows that the molecular features in the STM images correspond to molecular LUMO+2.

Ordering self-assembly structures via intermolecular BrS interactions

Recent research studies have shown that the halogenated benzo[1,2-b:4,5-b']dithiophene (DTBDT) unit as a polymer donor exhibits high charge carrier mobility due to the well-ordered molecular packing and high crystallinity, which is meaningful for achieving highly efficient organic solar cells (OSCs). However, it is difficult to acquire the accurate packing information of polymer materials. Herein, we investigated the self-assembled behaviors of two DTBDT derivatives, 4,8-bis(4-octadecylthiophen-2-yl)benzo[1,2-b:4,5-b']dithiophene (H-DTBDT) and 4,8-bis(5-bromo-4-octadecylthiophen-2-yl)benzo[1,2-b:4,5-b']dithiophene (Br-DTBDT), to elucidate the effect of introducing a bromine atom on molecular packing structures by STM at the 1-phenyloctane/HOPG interface. It is observed that the H-DTBDT molecules exhibit a random arrangement along each lamella, while the Br-DTBDT molecules self-assemble into a highly ordered lamellar structure. Density functional theory (DFT) analysis combined with the topological properties of the electron density at the bond critical points revealed that the existence of weak intermolecular interactions of BrS facilitates the regular packing motif of Br-DTBDT molecules. The results helped us to understand that the BrS bond generally acted as the auxiliary force and can play the primary role in the construction of supramolecular nanostructures.

Cooperation and competition of hydrogen and halogen bonds in 2D self-assembled nanostructures based on bromine substituted coumarins

Three coumarin derivatives (Co16, 6-Br-Co16 and 6,8-Br-Co16) with ester, ether, and carbonyl groups and different numbers of bromine substituents on the coumarin cores were synthesized.

Self-assembled flower structures formed by C3-symmetric aromatic carboxylic acids with meta-carboxyl groups

H₆BTE self-assembled into flower-like structures with two types of cavities at the HA/HOPG interface, and the guest molecule COR was only trapped in the A-type cavities at low and high concentrations of COR.

Same building block, but diverse surface-confined self-assemblies: solvent and concentration effects-induced structural diversity towards chirality and achirality

Fabricating complex nano-networks on solid substrates is a research area that has attracted much attention in the field of molecular self-assembly. By designing a fluorenone derivative of 2-heptyloxy-7-pentadecyloxy-9-fluorenone (HPF), we obtained a surface-confined system that presented diverse nanostructures. The assembled networks for HPF were highly dependent on the solvent and concentration. At the liquid/solid interface, chiral tetramer-S, hexamer-S, and tetramer-linear structures as well as achiral irregular-linear and random structures were recorded. On the dry surface, we observed chiral octamer-S and achiral alternate configurations. During the self-assembly process, the short and long alkyl chains of HPF showed selective identification, which contributed to the formation of S-like or anti-S-like tetramers, hexamers and octamers, resulting in chiral structures. The nanopatterns were stabilized under the driving forces of dipolar interactions, hydrogen bonds and van der Waals interactions. Moreover, we performed forcefield calculations in order to further understand the underlying mechanisms from the viewpoints of their force strengths and binding energies. In general, the present work provides a significant impetus to induce polymorphous structures, and we believe that it will promote the study of chirality and achirality in the field of molecular self-assembly.

Chiral polymorphism in the self-assemblies of achiral molecules induced by multiple hydrogen bonds

Driven by multiple hydrogen bonds, chiral and achiral polymorphs are successfully fabricated at a liquid–solid interface.

Halogen bonding versus hydrogen bonding induced 2D self-assembled nanostructures at the liquid-solid interface revealed by STM

We design a bifunctional molecule (5-bromo-2-hexadecyloxy-benzoic acid, 5-BHBA) with a bromine atom and a carboxyl group and its two-dimensional self-assembly is experimentally and theoretically investigated by using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The supramolecular self-organization of 5-BHBA in two different solvents (1-octanoic acid and n-hexadecane) at the liquid-solid interface at different solution concentrations is obviously different due to the cooperative and competitive intermolecular halogen and hydrogen bonds. Three kinds of nanoarchitectures composed of dimers, trimers and tetramers are formed at the 1-octanoic acid/graphite interface based on -COOHHOOC-, triangular C[double bond, length as m-dash]OBrH-C, -BrO(H), BrBr, and OH interactions. Furthermore, by using n-hexadecane as the solvent, two kinds of self-assembled linear patterns can be observed due to the coadsorption, in which the dimers are formed by intermolecular -COOHHOOC- hydrogen bonds. The molecule-solvent and solvent-solvent van der Waals force and intermolecular hydrogen bonds dominate the formation of coadsorbed patterns. We propose that the cooperative and competitive halogen and hydrogen bonds are related to the polarity of the solvent and the type of molecule-solvent interaction. The intermolecular binding energy of different dimers and their stability are supported by theoretical calculations. The result provides a new and innovative insight to induce the 2D self-assembled nanostructures by halogen and hydrogen bonds at the liquid-solid interface.

Self-Assembly and External Modulation of a Flexible Porphyrin Derivative on Highly Oriented Pyrolytic Graphite

With the aid of scanning tunneling microscopy, we have examined the two-dimensional hydrogen-bonded networks of carboxyl-functionalized porphyrin derivative H₂TCPp molecules at the heptanoic acid/HOPG interface. Moreover, we have successfully modulated the self-assembly structure of H₂TCPp by introducing 1,2-di(4-pyridyl)ethylene molecules into the assembled system. By performing density functional theory calculations, we also revealed the formation mechanisms of the different assemblies and the modulation process. Comparing the self-assembly structures at the liquid/solid interface with those in bulk crystals, we have obtained deep insight into the differences in H₂TCPp assemblies between 2D and 3D networks. Furthermore, this research is expected to deepen our understanding of on-surface phenomena and to provide a feasible process toward 2D assembly regulation.

Cooperation and competition between halogen bonding and van der Waals forces in supramolecular engineering at the aliphatic hydrocarbon/graphite interface: position and number of bromine group effects

Herein, the photophysical properties of two π-conjugated thienophenanthrene derivatives (6,9- and 5,10-DBTD) are reported. Their self-assembled monolayers in aliphatic hydrocarbon solvents under different concentrations were investigated by scanning tunneling microscopy on a graphite surface. The STM results revealed that the self-assembled structures of the two geometrical isomers exhibited absolutely different behaviors. At the aliphatic solvent/graphite interface, 6,9-DBTD produced almost a single stable coassembled linear structure, except for that with n-tridecane as the solvent. However, the self-assembly of 5,10-DBTD showed structural diversity, and it presented a gradient variety through increasing the chain length of the aliphatic solvents as well as the solution concentration. All ordered self-assembled adlayers critically depend on not only the interchain van der Waals (vdW) interactions, but also on multiple intermolecular interactions, including BrO[double bond, length as m-dash]C and BrS hetero-halogen bonds, homo-BrBr interactions, and HBr and HO hydrogen bonds. We proposed that the cooperation and competition of the intermolecular interactions involving a Br atom and interchain vdW forces induce this structural variety. Density functional theory calculations support to unravel the different elementary structural units based on halogen bonds and hydrogen bonds and were useful tools to dissect and explain the formation mechanism.

Role of halogen⋯halogen interactions in the 2D crystallization of n-semiconductors at the liquid–solid interface

The impact of X⋯X interactions on the 2D crystallization of perylene-based n-semiconductors at the liquid–solid interface was investigated.