Direct Imaging of the Induced‐Fit Effect in Molecular Self‐Assembly

Abstract

Molecular recognition is a crucial driving force for molecular self‐assembly. In many cases molecules arrange in the lowest energy configuration following a lock‐and‐key principle. When molecular flexibility comes into play, the induced‐fit effect may govern the self‐assembly. Here, the self‐assembly of dicyanovinyl‐hexathiophene (DCV6T) molecules, a prototype specie for highly efficient organic solar cells, on Au(111) by using low‐temperature scanning tunneling microscopy and atomic force microscopy is investigated. DCV6T molecules assemble on the surface forming either islands or chains. In the islands the molecules are straight—the lowest energy configuration in gas phase—and expose the dicyano moieties to form hydrogen bonds with neighbor molecules. In contrast, the structure of DCV6T molecules in the chain assemblies deviates significantly from their gas‐phase analogues. The seemingly energetically unfavorable bent geometry is enforced by hydrogen‐bonding intermolecular interactions. Density functional theory calculations of molecular dimers quantitatively demonstrate that the deformation of individual molecules optimizes the intermolecular bonding structure. The intermolecular bonding energy thus drives the chain structure formation, which is an expression of the induced‐fit effect.

Hydrogen bonded trimesic acid networks on Cu(111) reveal how basic chemical properties are imprinted in HR-AFM images

“…More importantly, our results demonstrate how key features in the HR-AFM image directly arise from the chemical properties and environment (large model) of the molecule, providing thus a qualitative access to those features via the HR-AFM images. Our new results are complementary to recent studies demonstrating the impact of the wider environment of the molecule on the image [36,37,38]. In particular, we show how the electron withdrawing character of the carboxylic groups plays a crucial role in the HR-AFM contrast.…”

Recent Advances in Molecular Mechanisms of the NKG2D Pathway in Hepatocellular Carcinoma

“…As a crucial activation receptor, NKG2D can specifically bind to DAP10 via the induced fit theory and further induce phosphorylation [54]. The meaning of induced fit theory is shown that when two molecules recognize and combine with each other, molecular flexibility plays a key role in the induced-fit effect to complete self-assembly [55]. DAP10, a kind of DNAX-associated protein 10, is related to the YxxM motif.…”

Metal–Organic Superlattices Induced by Long-Range Repulsive Interactions on a Metal Surface

“…The calculations were performed using the GAUSSIAN 09 program package with the B3LYP exchange−correlation functional and the 6-31G basis set. 26 As shown before, 37,46 the Au(111) substrate plays a negligible role in the bonding geometry and electronic states of the dicyanovinylenesubstituted oligothiophenes and their assemblies. The intact herringbone reconstruction is an indication of the weak influence of the Au(111) on the chains (see Figures S1 and S2 in the Supporting Information).…”