Unusual Regio- and Chemoselectivity in Oxidation of Pyrroles and Indoles Enabled by a Thianthrenium Salt Intermediate.

A dearomative oxidation of pyrroles to Δ3-pyrrol-2-ones is described, which employs a sulfoxide as oxidant, in conjunction with a carboxylic acid anhydride and a Brønsted acid additive. 3-substituted pyrroles undergo regioselective oxidation to give the product isomer in which oxygen has been introduced at the more hindered position. Regioselectivity is rationalized by a proposed mechanism that proceeds by initial thianthrenium introduction at the less-hindered pyrrole α-position, followed by distal attack of an oxygen nucleophile and subsequent elimination of thianthrene. The same reaction conditions are also able to effect a chemoselective oxidation of indoles to indolin-3-ones and additionally of indolin-3-ones to 2-hydroxyindolin-3-ones. Here again, the regio- and chemoselectivities are rationalized through the intermediacy of a thianthrenium salt.

The Influence of Chirality on the ß-Amino-Acid Naphthalenediimides/G-Quadruplex DNA Interaction.

G-quadruplexes (G4s) have been identified as a potential alternative chemotherapy target. A series of eight ß-amino acid derived naphthalenediimides (NDI) were screened against a series of oncogenic G4 sequences: c-KIT1, h-TELO, and TBA. Three sets of enantiomers were investigated to further our understanding of the effect of point chirality on G4 stabilisation. Enantioselective binding behaviour was observed with both c-KIT1 and h-TELO. Docking studies using GNINA and UV-vis titrations were employed to better understand this selective binding behaviour.

Mueller Matrix Polarimetry on Cyanine Dye J-Aggregates.

Cyanine dyes are known to form H- and J-aggregates in aqueous solutions. Here we show that the cyanine dye, S0271, assembles in water into vortex induced chiral J-aggregates. The chirality of the J-aggregates depends on the directionality of the vortex. This study utilised both conventional benchtop CD spectropolarimeters and Mueller matrix polarimetry. It was found that J-aggregates have real chirality alongside linear dichroism and linear and circular birefringence. We identify the factors that are key to the formation of metastable chiral J-aggregates and propose a mechanism for their assembly.

Triggering G-Quadruplex Conformation Switching with [7]Helicenes.

The dynamic interplay between two types of chiral structures; fully conjugated racemic hetero[7]helicenes and DNA strands prone to fold into G-quadruplex structures is described. Both the [7]helicenes and the G-quadruplex DNA structures exist in more than one conformation in solution. We show that the structures interact with and stabilise each other, mutually amplifying and stabilising certain conformations at increased temperatures. The [7]helicene ligands L1 and L2 stabilise the parallel conformation of k-ras significantly, whereas hybrid (K+ ) and antiparallel (Na+ ) h-telo G-quadruplexes are stabilised upon conformational switching into altered G-quadruplex conformations. Both L1 and L2 induce parallel G-quadruplexes from hybrid structures (K+ ) and L1 induces hybrid G-quadruplexes from antiparallel conformations (Na+ ). Enantioselective binding of one helicene enantiomer is observed for helicene ligand L2, and VTCD melting experiments are used to estimate the racemisation barrier of the helicene.

High-Yielding Synthesis of Chiral Donor-Acceptor Catenanes.

We report the synthesis of [2]catenanes (Hopf links) in water utilizing disulfides and aromatic donor-acceptor interactions. The electron-rich dialkoxynaphthalene (DN) building blocks interact with electron-deficient naphthalenediimide (NDI) moieties connected by a polyamine chain. We study the effect of the polyamine linkers on the behavior of the library. The polyamine's length and the number of nitrogen atoms in the chain affect the library distribution, leading in some cases to the assembly of catenanes in up to 93% yield.

Amino-Acid-Derived Naphthalenediimides as Versatile G-Quadruplex Binders.

The design and synthesis of water soluble, amino-acid-functionalised naphthalenediimides (NDIs) as potential ligands of native G-quadruplexes is reported. The NDIs were tested on a panel of oncogene promoters, on the human telomeric sequence h-telo, and on double-stranded DNA. Out of the ligands tested, NDI 3 (Nϵ -Boc-l-lysine NDI) exhibited a highly discriminating nature by only stabilising the oncogene promoter c-kit2, which is up-regulated up to 80 % in ovarian, gastrointestinal, and breast malignancies.

Molecular motion of donor-acceptor catenanes in water.

In this article, we use (1)H NMR spectroscopy to study the spontaneous molecular motion of donor-acceptor [2]catenanes in water. Our data supports the hypothesis that conformational motion dominantly occurs through a pirouetting mechanism, which involves less exposure of hydrophobic surfaces than in a rotation mechanism. Motion is controlled by the size of the catenane rings and the arrangement of the electron-deficient and electron-rich aromatic units.

Homochiral and meso figure eight knots and a Solomon link.

A homochiral naphthalenediimide-based building block forms in water a disulfide library of macrocycles containing topological isomers. We attempted to identify each of these isomers, and explored the mechanisms leading to their formation. The two most abundant species of the library were assigned as a topologically chiral Solomon link (60% of the library, as measured by high-performance liquid chromatography (HPLC)) and a topologically achiral figure eight knot (18% by HPLC), competing products with formally different geometries but remarkably similar 4-fold symmetries. In contrast, a racemic mixture of building blocks gives the near-quantitative formation of another new and more stable structure, assigned as a meso figure eight knot. Taken together, these results seem to uncover a correlation between the point chirality of the building block used and the topological chirality of the major structure formed. These and the earlier discovery of a trefoil knot also suggest that the number of rigid components in the building block may translate into corresponding knot symmetry and could set the basis of a new strategy for constructing complex topologies.

The thermodynamics of the self-assembly of covalently linked oligomeric naphthalenediimides into helical organic nanotubes.

The mechanism and thermodynamic functions of the self-assembly of a family of covalently linked oligomeric naphthalenediimides (NDIs) were investigated through variable-temperature NMR and CD studies. The NDIs were shown to self-assemble into helical supramolecular nanotubes via an isodesmic polymerisation mechanism, and regardless of the oligomer length a surprising entropy-enthalpy compensation was observed.

Chiroptical Second-Harmonic Tyndall Scattering from Silicon Nanohelices.

Chirality is omnipresent in the living world. As biomimetic nanotechnology and self-assembly advance, they too need chirality. Accordingly, there is a pressing need to develop general methods to characterize chiral building blocks at the nanoscale in liquids such as water─the medium of life. Here, we demonstrate the chiroptical second-harmonic Tyndall scattering effect. The effect was observed in Si nanohelices, an example of a high-refractive-index dielectric nanomaterial. For three wavelengths of illumination, we observe a clear difference in the second-harmonic scattered light that depends on the chirality of the nanohelices and the handedness of circularly polarized light. Importantly, we provide a theoretical analysis that explains the origin of the effect and its direction dependence, resulting from different specific contributions of "electric dipole-magnetic dipole" and "electric dipole-electric quadrupole" coupling tensors. Using numerical simulations, we narrow down the number of such terms to 8 in forward scattering and to a single one in right-angled scattering. For chiral scatterers such as high-refractive-index dielectric nanoparticles, our findings expand the Tyndall scattering regime to nonlinear optics. Moreover, our theory can be broadened and adapted to further classes where such scattering has already been observed or is yet to be observed.

A model system for the synthesis of complanadine alkaloids by "diverted Kondrat'eva" oxazole-olefin cycloaddition.

A synthetic approach to complanadine alkaloids is described which employs a Kondrat'eva reaction to construct the pyridine rings. The viability of this approach is demonstrated by its application to a model substrate accessed from unfunctionalized decalin. The key transformation affords the desired tetracyclic architecture with unprecedented incorporation of substituents on the pyridine ring, implicating the oxazole α-hydroxy group as an active participant in the cycloadduct fragmentation process.

Conversion of aldoximes into nitriles and amides under mild conditions.

A series of Pd(en)X2 salts were used as catalysts for the conversion of aldoximes into nitriles and amides. Highlights of this protocol include the use of inexpensive polar solvents, including water, and moderate reaction temperatures. A high degree of selectivity in the reaction outcome was observed when using aliphatic vs. aromatic/conjugated aldoximes.

Aliphatic C-H activation with aluminium trichloride-acetyl chloride: expanding the scope of the Baddeley reaction for the functionalisation of saturated hydrocarbons.

The functionalisation of decalin by means of an "aliphatic Friedel-Crafts" reaction was reported over fifty years ago by Baddeley et al. This protocol is of current relevance in the context of C-H activation and here we demonstrate its applicability to a range of other saturated hydrocarbons. Structural elucidation of the products is described and a mechanistic rationale for their formation is presented. The "aliphatic Friedel-Crafts" procedure allows for production of novel oxygenated building blocks from abundant hydrocarbons and as such can be considered to add significant synthetic value in a single step.

Structural parameters governing the dynamic combinatorial synthesis of catenanes in water.

We report the first dynamic combinatorial synthesis in water of an all-acceptor [2]catenane and of different types of donor-acceptor [2] and [3]catenanes. Linking two electron-deficient motifs within one building block using a series of homologous alkyl chains provides efficient and selective access to a variety of catenanes and offers an unprecedented opportunity to explore the parameters that govern their synthesis in water. In this series, catenane assembly is controlled by a fine balance between kinetics and thermodynamics and subtle variations in the building block structure, such as the linker length and building block chirality. A remarkable and unexpected odd-even effect with respect to the number of atoms in the alkyl linker is reported.

Thermodynamics of supramolecular naphthalenediimide nanotube formation: the influence of solvents, side chains, and guest templates.

Amino-acid functionalized naphthalenediimides self-assemble into hydrogen-bonded supramolecular helical nanotubes via a noncooperative, isodesmic process; the self-assembly of ordered helical systems is usually realized through a cooperative process. This unexpected behavior was rationalized as a manifestation of entropy-enthalpy compensation. Fundamental insights into the thermodynamics governing this self-assembly were obtained through the fitting of the isodesmic model to (1)H NMR spectrometry and circular dichroism spectroscopy measurements. Furthermore, we have extended the application of this mathematical model, for the first time, to quantitatively estimate the effect of guests, solvents, and side chains on the stability of the supramolecular nanotube; most significantly, we demonstrate that C(60) acts as a template to stabilize the nanotube assembly and thereby substantially increase the degree of polymerization.

Supramolecular naphthalenediimide nanotubes.

Amino acid functionalized naphthalenediimides (NDIs) when dissolved in chloroform form a dynamic combinatorial library (DCL) in which the NDI building blocks are connected through reversible hydrogen bonds forming a versatile new supramolecular assembly in solution with intriguing host-guest properties. In chlorinated solvents the NDIs form supramolecular nanotubes which complex C(60), ion-pairs, and extended aromatic molecules. In the presence of C(70) a new hexameric receptor is formed at the expense of the nanotube; the equilibrium nanotube - hexameric receptor can be influenced by acid-base reactions. Achiral NDIs are incorporated in nanotubes formed by either dichiral or monochiral NDIs experiencing the "sergeants-and-soldiers" effect.

Synthesis of bis-indole carboxamides as G-quadruplex stabilizing and inducing ligands.

The design and synthesis of a series of bis-indole carboxamides with varying amine containing side chains as G-quadruplex DNA stabilising small molecules are reported. Their interactions with quadruplexes have been evaluated by means of Förster resonance energy transfer (FRET) melting analysis, UV/Vis spectroscopy, circular dichroism spectroscopy and molecular modelling studies. FRET analysis indicates that these ligands exhibit significant selectivity for quadruplex over duplex DNA, and the position of the carboxamide side chains is of paramount importance in G-quadruplex stabilisation. UV/Vis titration studies reveal that bis-indole ligands bind tightly to quadruplexes and show a three- to fivefold preference for c-kit2 over h-telo quadruplex DNA. CD studies revealed that bis-indole carboxamide with a central pyridine ring induces the formation of a single, antiparallel, conformation of the h-telo quadruplex in the presence and absence of added salt. The chirality of h-telo quadruplex was transferred to the achiral ligand (induced CD) and the formation of a preferred atropisomer was observed.

Molecular recognition and self-assembly special feature: Dynamic combinatorial synthesis of a catenane based on donor-acceptor interactions in water.

A new type of neutral donor-acceptor [2]-catenane, containing both complementary units in the same ring was synthesized from a dynamic combinatorial library in water. The yield of the water soluble [2]-catenane is enhanced by increasing either building-block concentrations or ionic strength, or by the addition of an electron-rich template. NMR spectroscopy demonstrates that the template is intercalated between the 2 electron-deficient naphthalenediimide units of the catenane.

Borazatruxenes as precursors for hybrid C-BN 2D molecular networks.

Synthesizing atomically thin, crystalline two-dimensional (2D) molecular materials which combine carbon with other elements is an emerging field requiring both custom-designed molecular precursors and their ability to organize into networks (hydrogen-bonded or covalent). Hybrid carbon-boron nitride (C-BN) networks face the additional challenge of needing hydrolytically-stable BN-containing molecular precursors. Here, we show that borazatruxenes (truxene-like molecules with a borazine core) and their halogenated derivatives are highly stable precursors suitable for on-surface assembly. Using scanning tunneling microscopy (STM) and density functional theory (DFT) simulations we demonstrate hierarchical H-bonded assembly based on chiral homodimers of tribromo-borazatruxenes (3Br-borazatruxenes) as building blocks for both 1D chains and 2D networks. A low-symmetry, H-bonded chiral 2D lattice forms on Au(111) from the C3-symmetric 3Br-borazatruxenes, leading to large enantiomorphic domains that are molecularly homochiral. Such homochiral segregation is a necessary condition if chiral C-BN covalent networks are to be obtained via subsequent on-surface reactions. We show via DFT that up to two Na atoms can be trapped within the small pores of this dense lattice, while further Na atoms can adsorb on preferred network sites; this leads to hybrid Na-molecular network electronic bands with anisotropic dispersion and significant (up to hundreds of meV) bandwidths, as well as significant doping, that can engender anisotropic transport through the network. Finally, electronic structure comparisons (combining both experiment and computation) between borazatruxene, its tri-brominated derivative and truxene show that the borazine core controls the band gap increase, while also inducing C-B pz-pz electron delocalization that facilitates a continuous electron path across the molecule. Furthermore, as shown by DFT, the borazine core drives inter-layer B-N polar interactions that promote adsorption of BN containing molecules in a staggered configuration, a mechanism to be exploited in layer-by-layer supra-molecular assembly of novel hybrid C-BN materials.

Exploring the formation pathways of donor-acceptor catenanes in aqueous dynamic combinatorial libraries.

The discovery through dynamic combinatorial chemistry (DCC) of a new generation of donor-acceptor [2]catenanes highlights the power of DCC to access unprecedented structures. While conventional thinking has limited the scope of donor-acceptor catenanes to strictly alternating stacks of donor (D) and acceptor (A) aromatic units, DCC is demonstrated in this paper to give access to unusual DAAD, DADD, and ADAA stacks. Each of these catenanes has specific structural requirements, allowing control of their formation. On the basis of these results, and on the observation that the catenanes represent kinetic bottlenecks in the reaction pathway, we propose a mechanism that explains and predicts the structures formed. Furthermore, the spontaneous assembly of catenanes in aqueous dynamic systems gives a fundamental insight into the role played by hydrophobic effect and donor-acceptor interactions when building such complex architectures.