¹H NMR Investigation of Solvent Effects in Aromatic Stacking Interactions

One of the marquis challenges in modern Organic Chemistry concerns the design and synthesis of abiotic compounds that emulate the exquisite complex structures and/or functions of biological macromolecules. Oligomers possessing the propensity to adopt well-defined compact conformations, or foldamers, have been attained utilizing hydrogen bonding, torsional restriction, and solvophobic interactions. In this laboratory, aromatic electron donor−acceptor interactions have been exploited in the design of aedamersfoldamers that adopt a novel, pleated secondary structure in aqueous solution. Herein is reported detailed 1H NMR binding studies of aedamer monomers that were carried out in solvents and solvent mixtures covering a broad polarity range. Curve-fitting analysis of the binding data using a model that incorporated the formation of higher order and self-associated complexes yielded a linear free energy relationship between the free energy of complexation and the empirical solvent polarity parameter, ET(30). From these studies, the association of electron-rich and electron-deficient aedamer monomers was seen to be driven primarily by hydrophobic interactions in polar solvents. However, the magnitude of these interactions is modulated to a significant extent by the geometry of the donor−acceptor complex, which, in turn, is dictated by the electrostatic complementarity between the electron-deficient and electron-rich aromatic faces of the monomers

Reactions of Brominated Naphthalene Diimide with Bis(tributylstannyl)acetylene: A Simple Approach for Conjugated Polymers and Versatile Coupling Intermediates

A new synthetic approach to 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) containing materials and conjugates is described. A simple one-step Stille coupling procedure is used to create either novel alkyne-linked NDI polymers or a new stannylated diyne synthetic building block that provides a flexible approach to new NDI conjugates and polymers

Aromatic Oligomers that Form Hetero Duplexes in Aqueous Solution

The electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) and electron-rich 1,5-dialkoxynaphthalene (Dan) have been shown to complex strongly with each other in water due to the hydrophobic effect as modulated through the electrostatic complementarity of the stacked dimer. Previously, oligomers of alternating Ndi and Dan units, termed aedamers, were the first foldamers to employ intramolecular aromatic stacking to effect the formation of secondary structure of nonnatural chains in aqueous solution. Described here is the use of this aromatic−aromatic (or pi−pi) interaction, this time in an intermolecular format, to demonstrate the self-assembly of stable hetero duplexes from a set of molecular strands (1a−4a) and (1b−4b) incorporating Ndi and Dan units, respectively. A 1-to-1 binding stoichiometry was determined from NMR and isothermal titration calorimetry (ITC) investigations, and these experiments indicated that association is enthalpically favored with the tetra-Ndi (4a) and tetra-Dan (4b) strands forming hetero duplexes (4a:4b) with a stability constant of 350 000 M-1 at T = 318 K. Polyacrylamide gel electrophoresis (PAGE) also illustrated the strong interaction between 4a and 4b and support a 1-to-1 binding mode even when one component is in slight excess. Overall, this system is the first to utilize complementary aromatic units to drive discrete self-assembly in aqueous solution. This new approach for designing assemblies is encouraging for future development of duplex systems with highly programmable modes of binding in solution or on surfaces

Synthesis and Conformational Characterization of Tethered, Self-Complexing 1,5-Dialkoxynaphthalene/1,4,5,8-Naphthalenetetracarboxylic Diimide Systems

Chemists are beginning to explore the abiotic folding of synthetic chains, and the term “foldamers” has been used to characterize oligomers with a strong inclination to adopt specific, compact conformations. The characterization of folded structure in solution is one of the difficult challenges facing the foldamer field. Aedamers were the first foldamers to make use of aromatic−aromatic interactions in water to direct folding and were designed to have several spectroscopic handles with which to probe folding conformations in solution. Herein is reported the synthesis and spectroscopic characterization of eleven aedamer dimers, with linkers chosen to provide a spectrum of lengths and flexibilities. The dimers, composed of one electron rich (1,5-dialkoxynaphthalene) and one electron deficient (1,4,5,8-naphthalenetetracarboxylic diimide) aromatic group tethered by a linker, are the smallest aedamer folding unit. The powerful spectroscopic handles associated with the stacked aedamer groups were exploited in a comprehensive spectroscopic analysis of conformation that included UV−vis absorption spectroscopy, fluorescence measurements (including time-resolved studies), as well as detailed NMR studies. The spectra were interpreted in the context of molecular modeling/spectral prediction and structural models were developed for the different dimers in aqueous solution. In most instances, the observed data was best described by an ensemble of predicted structures as opposed to one or few conformers. Thus, in the case of these aedamer dimers, “folding” does not appear to imply a two-state model with a rigid, unique conformation. Rather, the reported analysis indicates the data can best be described by a more dynamic model in which a given molecule spends its time in different folded conformations that are related by having a characteristic face-to-face stacking arrangement of the aromatic units

The Influence of Hapten Size and Hydrophobicity on the Catalytic Activity of Elicited Polyclonal Antibodies

The Influence of Hapten Size and Hydrophobicity on the Catalytic Activity of Elicited Polyclonal Antibodie

The Influence of Hapten Size and Hydrophobicity on the Catalytic Activity of Elicited Polyclonal Antibodies

The Influence of Hapten Size and Hydrophobicity on the Catalytic Activity of Elicited Polyclonal Antibodie

Using Aromatic Donor Acceptor Interactions to Affect Macromolecular Assembly

Using Aromatic Donor Acceptor Interactions to Affect Macromolecular Assembl

Threading Polyintercalators with Extremely Slow Dissociation Rates and Extended DNA Binding Sites

The development of small molecules that bind DNA sequence specifically has the potential to modulate gene expression in a general way. One mode of DNA binding is intercalation, or the insertion of molecules between DNA base pairs. We have developed a modular polyintercalation system in which intercalating naphthalene diimide (NDI) units are connected by flexible linkers that alternate between the minor and major grooves of DNA when bound. We recently reported a threading tetraintercalator with a dissociation half-life of 16 days, the longest reported to date, from its preferred 14 bp binding site. Herein, three new tetraintercalator derivatives were synthesized with one, two, and three additional methylene units in the central major groove-binding linker. These molecules displayed dissociation half-lives of 57, 27, and 18 days, respectively, from the 14 bp site. The optimal major groove-binding linker was used in the design of an NDI hexaintercalator that was analyzed by gel-shift assays, DNase I footprinting, and UV–vis spectroscopy. The hexaintercalator bound its entire 22 bp binding site, the longest reported specific binding site for a synthetic, non-nucleic acid-based DNA binding molecule, but with a significantly faster dissociation rate compared to the tetraintercalators

Amyloid-like Behavior in Abiotic, Amphiphilic Foldamers

Previously, we reported an abiotic amphiphilic foldamer that, upon heating, undergoes an irreversible conformational change to a highly aggregated state (Nguyen, J.Q.; Iverson, B.L. J. Am. Chem. Soc. 1999, 121, 2639−2640.). Herein, we extend this work through the study of a series of structurally related amphiphilic foldamers and present a more refined model of their conformational switching behavior. Prior to heating, all foldamers of the series exhibited spectral characteristics consistent with folding in the pleated, stacked geometry characteristic of this class of foldamer. Following heating at 80 °C, three of the four molecules exhibited irreversible aggregation to produce hydrogels. The hydrogels were characterized by rheology measurements, and circular dichroism spectra revealed that hydrogel formation was dependent on highly ordered intermolecular assembly, conceptually analogous to protein amyloid formation. Hydrogel formation had the effect of amplifying the subtle structural differences between molecules, as the three amphiphilic foldamer constitutional isomers that formed hydrogels upon heating displayed significant differences in hydrogel properties. Taking a global view, our results indicate that amyloid-like behavior is not unique to proteins but may be a relatively general property of amphiphilic folding molecules in aqueous solution

A Pseudocatenane Structure Formed between DNA and A Cyclic Bisintercalator

Targeting double-stranded DNA with small molecules remains an active area of basic research. Herein is described a cyclic DNA bisintercalator that is based on two naphthalene diimide (NDI) intercalating units tethered by one linking element specific for binding in the minor groove and the other linking element specific for binding in the major groove. DNase I footprinting revealed a strong preference for binding the sequence 5′-GGTACC-3′. NMR structural studies of the complex with d(CGGTACCG)2 verified a pseudocatenane structure in which the NDI units reside four base pairs apart, with one linker segment located in the minor groove and the other in the major groove consistent with the linker designs. To the best of our knowledge, this is the first structurally well-characterized pseudocatenane complex between a sequence specific cyclic bisintercalator and intact DNA