Determine the Role of Alkyl Chains and Hydrogen Bonds in the Assembling Process of Fused Thiophene Indacene Derivatives by Scanning Tunneling Microscopy and Theoretical Calculation

The surface patterns of fused thiophene indacene (FTI) derivatives with different alkyl chains are investigated with scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The FTI with ethyl chains (FTI 2) arranges into linear and fishbone structures. Both of them are defective, and FTI 2 is easily disturbed during experiments. FTI 6, the molecule carrying hexyl chains, is fixed on the surface much better than FTI 2, and defects in its assembly are reduced greatly. However, the essential characteristics of FTI 6 assembly are similar to those of the FTI 2 linear one. For the compound with dodecyl chains, FTI 12 organizes into the lamellar structure showing critical alterations from that of FTI 6 or FTI 2. The DFT-optimized models disclose that hydrogen bonds exist in all the rows of three studied molecules although the stacking of the respective compound is different. STM and DFT results indicate that hydrogen bonds are responsible for the formation of FTI 2 assembly, whereas...