Controlling the Two-Dimensional Self-Assembly of Functionalized Porphyrins via Adenine–Thymine Quartet Formation

Abstract

The development of supramolecular synthons capable of driving hierarchical two-dimensional self-assembly is an important step towards the growth of complex and functional molecular surfaces. In this work the formation of nucleobase quartets consisting of adenine and thymine groups was used to control the 2D self-assembly of porphyrins. Tetra-(phenylthymine) zinc porphyrin (Zn-tetra-TP) and tetra-(phenyladenine) porphyrin (tetra-AP) were synthesised and scanning tunneling microscopy (STM) experiments performed to visualize their self-assembly at the liquid-solid interface between an organic solvent and a graphite surface. Mono-component solutions of both Zn-tetra-TP and tetra-AP form stable 2D structures with either thyminethymine or adenine-adenine hydrogen bonding. Structural models based on STM data were validated using molecular mechanics (MM) simulations. In contrast, bi-component mixtures showed the formation of a structure with p4 symmetry consisting of alternating Zn-tetra-TP and tetra-AP molecules in a chessboard type pattern. The relative positions of the porphyrin components were identified from STM images via contrast changes associated with the zinc atom present in Zn-tetra-TP. MM simulations suggest that hydrogen bonding interactions within these structures are based on the formation of adenine-thymine (ATAT) quartets with Watson-Crick base pairing between adenine and thymine groups.

Functional Systems Derived from Nucleobase Self‐assembly

“…The possibility of forming highly ordered porous network without metal coordination was hinted early by the structural elucidation of an ethylene‐spaced G : C dinucleoside in solution, a G/C base hybrid (pyrido[4,3‐ d ]pyrimidine ring skeleton) in the crystal, and of a modified G and C nucleobases pairs on the Au(111) surface . Following these studies, recent STM imaging of structurally rigid G : C or A : U dinucleobase molecules and an equimolar mixture of porphyrins with tetra‐A/T groups revealed the formation of continuous 2D pores on the highly ordered pyrolytic graphite (HOPG) surface. These structures feature classic Watson−Crick base pairing, and the incorporation of phenylene‐ethynylene and porphyrin moieties, common elements in organic electronics, suggests functional materials can be derived using this strategy.…”

“…The initial attempts to create porous frameworks using (semi)rigid molecules with multiple nucleobase analogous to Champness’ and González‐Rodríguez's “crystal tectons” were proven, however, quite challenging. Weber and co‐workers prepared a series of linear or tetrahedral molecules featuring 2 or 4 nucleobases .…”

Tailoring molecular island shapes: influence of microscopic interaction on mesostructure

“…For example, structures ranging from perfectly ordered two-dimensional layers [27], unidirectional rows [28,29], porous networks [30,31] to complex structures have been presented as a function of the specific molecular design [27,32,33]. Even richer structures have been demonstrated in multicomponent systems, i.e., upon co-deposition of two types of molecules [34][35][36][37][38][39].…”

Synthesis of Porphyrins Di‐ and Tetra‐Functionalized with Nucleobases

“…Nature has provided nucleobases (NBs) that are known for their complementary base pairing properties in DNA and RNA as stable, reliable, and predictable hydrogen bonding patterns, indeed thymine ( T ) (in DNA) or uracil ( U ) (in RNA) is complementary to adenine ( A ) whereas cytosine ( C ) is complementary to guanine ( G ) (in DNA and RNA) (Figure 1). [6] Therefore, several examples of nucleobase‐functionalized porphyrin were reported in the past decade [7–12] …”

“…NB‐Porphyrins were synthesized following different strategies, such as Sonogashira cross‐coupling reaction [10,13a] or by reacting aldehydes bearing the corresponding nucleobases with pyrrole [11,12] or dipyrromethanes [8,9] . Other synthetic approaches were also used to introduce NBs to the porphyrin scaffold.…”