Allosterically controlled threading of polymers through macrocyclic dimers.

As part of an ongoing study to construct a molecular Turing machine in which a polymer chain is encoded via allosteric information transfer between macrocyclic complexes, we describe the thermodynamic and kinetic characterization of a multicomponent self-assembled system based on a zinc porphyrin macrocyclic compound, a bidentate ligand (1,4-diazabicyclo[2.2.2]octane, DABCO), and a viologen-substituted polymer guest. Initial addition of DABCO to the porphyrin macrocycle in chloroform solution leads to the formation of a stable 2:1 (porphyrin:DABCO) dimeric complex, even under dilute conditions, by means of strong cooperative interactions involving hydrogen and metal-ligand bonds. Further titration of the porphyrin-DABCO mixtures with the polymer gives rise to a complex array of species in the solution. The system is analyzed in detail by a combination of spectroscopic measurements and computational modeling. Each association constant in the binding scheme and the fraction of each individual complex that is formed in solution are determined precisely using a mass-balance model. Kinetic studies revealed that the rates of the polymer threading and dethreading in and out of the dimeric system are remarkably slow, indicating that the polymer is locked inside the cavity of the stable 2:1 dimeric complex as a result of strong allosteric interactions.

Functional interlocked systems.

With the advent of supramolecular chemistry and later nanotechnology a great deal of research has been focused on new types of molecular structures, which are not held together by covalent bonds but by non-covalent mechanical interactions. Examples include the catenane, rotaxane, and knot interlocked structures. The design and synthesis of these architectures is an art by itself and as such is worth being reviewed. In this tutorial review we will focus, however, on the functional aspects of interlocked molecules and discuss how these can find applications, e.g. as artificial muscles, as molecular valves, as components of electronic devices, and as catalysts.

Designing processive catalytic systems. Threading polymers through a flexible macrocycle ring.

The translocation of polymers through pores is widely observed in nature and studying their mechanism may help understand the fundamental features of these processes. We describe here the mechanism of threading of a series of polymers through a flexible macrocyclic ring. Detailed kinetic studies show that the translocation speed is slower than the translocation speed through previously described more rigid macrocycles, most likely as a result of the wrapping of the macrocycle around the polymer chain. Temperature-dependent studies reveal that the threading rate increases on decreasing the temperature, resulting in a negative activation enthalpy of threading. The latter is related to the opening of the cavity of the macrocycle at lower temperatures, which facilitates binding. The translocation process along the polymer chain, on the other hand, is enthalpically unfavorable, which can be ascribed to the release of the tight binding of the macrocycle to the chain upon translocation. The combined kinetic and thermodynamic data are analyzed with our previously proposed consecutive-hopping model of threading. Our findings provide valuable insight into the translocation mechanism of macrocycles on polymers, which is of interest for the development of processive catalysts, i.e., catalysts that thread onto polymers and move along it while performing a catalytic action.

Conformational analysis of chiral supramolecular aggregates: modeling the subtle difference between hydrogen and deuterium.

A detailed analysis of the conformational states of self-assembled, stereoselectively deuterated benzene-1,3,5-tricarboxamides ((S,S,S)-D-BTAs) reveals four different conformers for the supramolecular polymers. The relative amount of the conformers depends on the solvent structure and the temperature. With the help of a model, the thermodynamic parameters that characterize the different conformational states were quantified as well as the amount of the species that occur at different stages of the polymerization process. The results show that small changes in the stability between different types of conformers formed by (S,S,S)-D-BTAs­in the order of a few J mol(­1)­arise from the combination of interactions between the solvent/supramolecular aggregate, temperature, and solvent structure. While the introduction of a deuterium label allows to sensitively probe the solvophobic effects in the supramolecular aggregation, a rationalization of the observed effects on a molecular level is not yet straightforward but is proposed to result from subtle effects in the vibrational enthalpy and entropy terms of the isotope effect.

Thioamides: versatile bonds to induce directional and cooperative hydrogen bonding in supramolecular polymers.

The amide bond is a versatile functional group and its directional hydrogen-bonding capabilities are widely applied in, for example, supramolecular chemistry. The potential of the thioamide bond, in contrast, is virtually unexplored as a structuring moiety in hydrogen-bonding-based self-assembling systems. We report herein the synthesis and characterisation of a new self-assembling motif comprising thioamides to induce directional hydrogen bonding. N,N',N''-Trialkylbenzene-1,3,5-tris(carbothioamide)s (thioBTAs) with either achiral or chiral side-chains have been readily obtained by treating their amide-based precursors with P2S5. The thioBTAs showed thermotropic liquid crystalline behaviour and a columnar mesophase was assigned. IR spectroscopy revealed that strong, three-fold, intermolecular hydrogen-bonding interactions stabilise the columnar structures. In apolar alkane solutions, thioBTAs self-assemble into one-dimensional, helical supramolecular polymers stabilised by three-fold hydrogen bonding. Concentration- and temperature-dependent self-assembly studies performed by using a combination of UV and CD spectroscopy demonstrated a cooperative supramolecular polymerisation mechanism and a strong amplification of supramolecular chirality. The high dipole moment of the thioamide bond in combination with the anisotropic shape of the resulting cylindrical aggregate gives rise to sufficiently strong depolarised light scattering to enable depolarised dynamic light scattering (DDLS) experiments in dilute alkane solution. The rotational and translational diffusion coefficients, D(trans) and D(rot), were obtained from the DDLS measurements, and the average length, L, and diameter, d, of the thioBTA aggregates were derived (L = 490 nm and d = 3.6 nm). These measured values are in good agreement with the value L(w) = 755 nm obtained from fitting the temperature-dependent CD data by using a recently developed equilibrium model. This experimental verification validates our common practice for determining the length of BTA-based supramolecular polymers from model fits to experimental CD data. The ability of thioamides to induce cooperative supramolecular polymerisation makes them effective and broadly applicable in supramolecular chemistry.

Benzene-1,3,5-tricarboxamide: a versatile ordering moiety for supramolecular chemistry.

After their first synthesis in 1915 by Curtius, benzene-1,3,5-tricarboxamides (BTAs) have become increasingly important in a wide range of scientific disciplines. Their simple structure and wide accessibility in combination with a detailed understanding of their supramolecular self-assembly behaviour allow full utilization of this versatile, supramolecular building block in applications ranging from nanotechnology to polymer processing and biomedical applications. While the opportunities in the former cases are connected to the self-assembly of BTAs into one-dimensional, nanometer-sized rod like structures stabilised by threefold H-bonding, their multivalent nature drives applications in the biomedical field. This review summarises the different types of BTAs that appeared in the recent literature and the applications they have been evaluated in. Currently, the first commercial applications of BTAs are emerging. The adaptable nature of this multipurpose building block promises a bright future.

Consequences of cooperativity in racemizing supramolecular systems.

Saluting the sergeant: Phg-BTA (see scheme) cooperatively self-assembles into helical aggregates and shows unprecedented racemization behavior in the presence of base. In thermodynamically controlled conditions, the addition of a small amount of chiral auxiliary to this mixture results in a deracemization reaction and a final enantiomeric excess of 32 %. A theoretical model is presented to understand in detail the results obtained.

Towards racemizable chiral organogelators.

A chiral organogelator has been synthesized that can be racemized and self-assembled in apolar solvents whilst at higher concentrations organogels are formed. Field emission scanning and transmission electron microscopy revealed the formation of bundle fibrils that are able to gelate the solvent. ¹H NMR studies showed hydrogen-bond interactions between the peptide head groups of neighbouring organogelator molecules. The enantiomerically pure organogelator can be racemized by the base DBU (1,8-diazabicyclo[5.4.0]undec-7-ene) as was evident from chiral high-performance liquid chromatography analysis.

A stereoselectively deuterated supramolecular motif to probe the role of solvent during self-assembly processes.

Small changes in the alkane solvent structure in combination with temperature effects lead to four different conformations of stereoselectively deuterated benzene-1,3,5-tricarboxamides in the aggregated state, affecting the expression of the supramolecular chirality and highlighting the role of the solvent structure in self-assembly processes.

The effect of isotopic substitution on the chirality of a self-assembled helix.

N,N',N″-trialkylbenzene-1,3,5-tricarboxamides (BTAs) self-assemble by means of strong, threefold α-helix-type intermolecular hydrogen bonding into well-defined, helical, one-dimensional columnar aggregates. When a stereogenic centre is introduced into the alkyl side chains of these BTAs, strong Cotton effects are observed in dilute apolar solutions, indicating the preference for one helical conformation over the other. Here, we report the creation of a helical sense preference in self-assembled BTAs by introducing deuterium/hydrogen isotope chirality into the alkyl side chains. We determine the relative stabilities of the left- and right-handed helical conformations of these deuterated supramolecular polymers by performing a conformational analysis. Our findings show that the results of deuterium/hydrogen substitution in BTA-based supramolecular polymers and helical polyisocyanates are very similar, although the formation mechanisms differ. The selectively deuterated BTAs discussed here represent the first example of supramolecular chirality resulting from isotope substitution.

Synthesis of bromo-conduritol-B and bromo-conduritol-C as glycosidase inhibitors.

For the synthesis of bromo-conduritol-B skeleton, bromo-1,4-benzoquinone was subjected to bromination followed by the reduction of the carbonyl groups with NaBH(4). Substitution of bromides bonded to sp(3)-hybridized carbon atoms with AgOAc gave the bromo-conduritol-B tetraacetate in high yield. For the construction of bromo-conduritol-C skeleton, 2,2-dimethyl-3a,7a-dihydro-1,3-benzodioxole was used as the starting material. Photooxygenation of the diene unit gave an unsaturated bicyclic endoperoxide. Bromine was incorporated into the molecule by the addition of bromine to the double bond. Opening of the peroxide linkage followed by HBr elimination and reduction of the carbonyl group provided the conduritol-C structure in good yield. Bromo-conduritol-B exhibited strong enzyme-specific inhibition against alpha-glycosidase.