Selective Effect of Guest Molecule Length and Hydrogen Bonding on the Supramolecular Host Structure

Half-Sandwich Ruthenium Complexes of Amide-Phosphine Based Ligands: H-Bonding Cavity Assisted Binding and Reduction of Nitro-substrates

We present synthesis and characterization of two half-sandwich Ru(II) complexes supported with amide-phosphine based ligands. These complexes presented a pyridine-2,6-dicarboxamide based pincer cavity, decorated with hydrogen bonds, that participated in the binding of nitro-substrates closer to the Ru(II) centers, which is further supported with binding and docking studies. These ruthenium complexes functioned as the noteworthy catalysts for the borohydride mediated reduction of assorted nitro-substrates. Mechanistic studies not only confirmed the intermediacy of [Ru-H] in the reduction but also asserted the involvement of several organic intermediates during the course of the catalysis. A similar Ru(II) complex that lacked pyridine-2,6-dicarboxamide based pincer cavity substantiated its unique role both in the substrate binding and the subsequent catalysis.

Molecular recognition of human islet amyloid polypeptide assembly by selective oligomerization of thioflavin T

Selective oligomerization is a common phenomenon existing widely in the formation of intricate biological structures in nature. The precise design of drug molecules with an oligomerization state that specifically recognizes its receptor, however, remains substantially challenging. Here, we used scanning tunneling microscopy (STM) to identify the oligomerization states of an amyloid probe thioflavin T (ThT) on hIAPP_8-37 assembly to be exclusively even numbers. We demonstrate that both adhesive interactions between ThT and the protein substrate and cohesive interactions among ThT molecules govern the oligomerization state of the bounded ThT. Specifically, the work of the cohesive interaction between two head/tail ThTs is determined to be 6.4 k _B T, around 50% larger than that of the cohesive interaction between two side-by-side ThTs (4.2 k _B T). Overall, our STM imaging and theoretical understanding at the single-molecule level provide valuable insights into the design of drug compounds using the selective oligomerization of molecular probes to recognize protein self-assembly.

Assemblies of porphyrin and phthalocyanine derivatives studied by STM

Porphyrins and phthalocyanines are currently a prevalent topic with great potential due to their abundant photonic/electronic properties. The study of porphyrin or phthalocyanine supramolecular architectures on solid surfaces is laying the foundation for the further development of molecular electronics or other structures in applications. Above all, the invention of scanning tunneling microscopy (STM) has opened a new path to explore these concepts on surfaces. Self-assemblies on solid surfaces can be probed with STM at submolecular resolutions to disclose the conformations and arrangements of molecules on an individual molecule basis. In this paper, the progress of STM research on porphyrin and phthalocyanine derivatives over past ten years is reviewed. We introduce the self-assembled structures of different porphyrins or phthalocyanines. Throughout the review, the structures, thermodynamics, and dynamics have been emphasized, which are essential current and future research themes.

The impact of grafted surface defects and their controlled removal on supramolecular self-assembly

We demonstrate the use of covalently modified graphite as a convenient and powerful test-bed for the versatile investigation and control of 2-D crystallization at the liquid solid interface. Grafted aryls act as surface defects and create barriers to supramolecular self-assembly. An easily tunable grafting density allows for varying the effect of such defects on supramolecular self-assembly. Finally, the defects can be locally removed, triggering monolayer reconstructions and allowing in situ investigations of thermodynamically unstable or metastable morphologies.

Synergistic Inhibitory Effect of Peptide-Organic Coassemblies on Amyloid Aggregation

Inhibition of amyloid aggregation is important for developing potential therapeutic strategies of amyloid-related diseases. Herein, we report that the inhibition effect of a pristine peptide motif (KLVFF) can be significantly improved by introducing a terminal regulatory moiety (terpyridine). The molecular-level observations by using scanning tunneling microscopy reveal stoichiometry-dependent polymorphism of the coassembly structures, which originates from the terminal interactions of peptide with organic modulator moieties and can be attributed to the secondary structures of peptides and conformations of the organic molecules. Furthermore, the polymorphism of the peptide-organic coassemblies is shown to be correlated to distinctively different inhibition effects on amyloid-β 42 (Aβ42) aggregations and cytotoxicity.

Solution concentration controlled self-assembling structure with host-guest recognition at the liquid-solid interface

In the present investigation, we reported the fabrication of a chicken-wire porous 2D network formed by triphenylene-2,6,10-tricarboxylic acid (H3TTCA) at the liquid-solid interface. When coronene (COR) molecules were added into the system, the H3TTCA honey-comb network was broken and the reconstructed structures of the H3TTCA/COR host-guest systems were subsequently formed. Scanning tunneling microscopic (STM) measurements and density function theory (DFT) calculations were utilized to reveal the structural variety in the co-assembly of H3TTCA/COR controlled by the solution concentration at 1-heptanoic acid/HOPG interface.

Solvent-induced variable conformation of bis(terpyridine) derivatives during supramolecular self-assembly at liquid/HOPG interfaces

Variable supramolecular structures of bis-(2,2′:6′,2′′-terpyridine)-4′-oxyhexadecane (BT-O-C16) at various liquid–HOPG interfaces were observed by scanning tunneling microscopy (STM).

Temperature-induced structural phase transitions in a two-dimensional self-assembled network

Two-dimensional (2D) supramolecular self-assembly at liquid-solid interfaces is a thermodynamically complex process producing a variety of structures. The formation of multiple network morphologies from the same molecular building blocks is a common occurrence. We use scanning tunnelling microscopy (STM) to investigate a structural phase transition between a densely packed and a porous phase of an alkylated dehydrobenzo[12]annulene (DBA) derivative physisorbed at a solvent-graphite interface. The influence of temperature and concentration are studied and the results combined using a thermodynamic model to measure enthalpy and entropy changes associated with the transition. These experimental results are compared to corresponding values obtained from simulations and theoretical calculations. This comparison highlights the importance of considering the solvent when modeling porous self-assembled networks. The results also demonstrate the power of using structural phase transitions to study the thermodynamics of these systems and will have implications for the development of predictive models for 2D self-assembly.

Role of hydrogen bonding on the self-organization of phenyleneethynylenes on surfaces

A series of carboxylic acid substituted phenyleneethynylenes, having a rigid backbone of 2.7 ± 0.1 nm, were synthesized by following the Heck-Cassar-Sonagashira-Hagihara cross-coupling reaction. Hydrogen bonding, through the formation of cyclic dimers of carboxylic acid, is more preferred over catemeric structures in all the molecular systems under investigation. The formation of extended two-dimensional patterns on highly oriented pyrolitic graphite (HOPG) surface is dictated by the position as well as number of the carboxylic acid groups on the phenyleneethynylenes. Highly ordered extended arrangements, in the linear and stepwise fashion, were observed when the carboxylic acid groups are attached in the para and meta positions of phenyleneethynylenes. The vital role of the number of carboxylic acid on the organization of molecules is evident in the case of tetracarboxylic acid derivative wherein a Kagome-type structure was observed. Further, the coassembly of two types of phenyleneethynylenes was achieved on HOPG surface through acid base interaction.

Coadsorption-Induced Reconstruction of Supramolecular Assembly Characteristics

A host supramolecular structure consisting of bis-(2,2':6',2"-terpyridine)-4'-oxyhexadecane (BT-O-C16) is shown to respond to coadsorbed molecules in dramatic ways, as observed by scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite (HOPG) surface under ambient conditions. Interestingly, the lattice parameter of the triphenylene-filled complex differs significantly from that of the coronene-filled one, although the triphenylene and coronene molecules are nearly the same size. The STM study and density functional theory calculations reveal that intermolecular hydrogen-bond interactions play an essential role in forming the assembly structures. The different electronic properties of coronene and triphenylene molecules are responsible for the difference in lattice parameters and consequently for the difference in filling behaviors in the coronene/BT-O-C16 and triphenylene/BT-O-C16 binary systems.

Molecular Architecture of Oligothiophene on a Highly Oriented Pyrolytic Graphite Surface by Employing Hydrogen Bondings

To achieve a controllable and predictable molecular architecture on a two-dimensional (2D) surface, a series of oligothiophenes with carboxylic groups and alkane chains were synthesized. The alkane chains and carboxylic groups, which can form hydrogen bonding, were intentionally designed in different positions of the oligothiophenes. The resulted molecular architectures by using the so-prepared oligothiophenes on a highly oriented pyrolytic graphite (HOPG) surface were investigated by scanning tunneling microscopy (STM) and density functional theory (DFT). It is found that the hydrogen bonding plays an essential role in the formation of the ordered assemblies. A controlled 2D molecular assembly could be fabricated by using hydrogen bondings.

Adsorption and Dynamics of Long-Range Interacting Fullerenes in a Flexible, Two-Dimensional, Nanoporous Porphyrin Network

Herein, a detailed investigation of the adsorption and dynamics of C60 and C70 fullerenes hosted in a self-assembled, two-dimensional, nanoporous porphyrin network on a solid Ag surface is presented. Time-resolved scanning tunneling microscopy (STM) studies of these supramolecular systems at the molecular scale reveal distinct host-guest interactions giving rise to a pronounced dissimilar mobility of the two fullerenes within the porphyrin network. Furthermore, long-range coverage-dependent interactions between the all-carbon guests, which clearly affect their mobility and are likely mediated by a complex mechanism involving the Ag substrate and the flexible porphyrin host network, are observed. At increased fullerene coverage, this unprecedented interplay results in the formation of large fullerene chains and islands. By applying a lattice gas model with nearest-neighbor interactions and by evaluating the fullerene-pair distribution functions, the respective coverage-dependent guest-guest interaction energies are estimated.