Large Macrocycles Research Articles

Synthesis of chiral cyclam analogues

Chiral non-racemic analogues of cyclam were prepared via reaction of (1R, 2R)-cyclohexane-1,2-diamine with appropriately substituted malonyl dichlorides. Larger macrocycles are formed as by-products in some cases. All new macrocycles were characterised by X-ray crystallography.

Deprotonation of Large Calixarenes – Cation Binding and Conformations

Single crystal X-ray studies of p-t-butylcalix[10]arene·2dmso·7H2O (1) and [NMe4][p-t-butylcalix[9]arene-H]·2dmso·H2O (2), provide new data on these large macrocycles and their conformations, that of 2 being the first where an encapsulated [NMe4]+ cation is present, while 1 contains the neutral ligand. Both were obtained as crystalline products of the reactions of the calixarenes with tetramethylammonium hydroxide after prolonged standing. The structure of [NEt4][calix[4]arene-H], in which the cation approaches inclusion in the shallow cone of the anion, is also defined and compared with various other alkylammonium derivatives of calixarenes as well as that of p-t-butylcalix[9]arene.

Conformations of large macrocycles and ring-in-ring complexes

A kinetically directed, stepwise approach towards molecular Borromean links enabled the isolation and structural characterization of synthetic intermediates along the way.

Molecularly Defined Nanostructures Based on a Novel AAA–DDD Triple Hydrogen‐Bonding Motif

AbstractA facile and flexible method for the synthesis of a new AAA–DDD triple hydrogen‐bonding motif is described. Polytopic supramolecular building blocks with precisely oriented AAA and DDD groups are thus accessible in few steps. These building blocks were used for the assembly of large macrocycles featuring four AAA–DDD interactions and a macrobicyclic complex with a total of six AAA–DDD interactions.

Molecularly Defined Nanostructures Based on a Novel AAA-DDD Triple Hydrogen-Bonding Motif.

A facile and flexible method for the synthesis of a new AAA-DDD triple hydrogen-bonding motif is described. Polytopic supramolecular building blocks with precisely oriented AAA and DDD groups are thus accessible in few steps. These building blocks were used for the assembly of large macrocycles featuring four AAA-DDD interactions and a macrobicyclic complex with a total of six AAA-DDD interactions.

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications.

Many natural products consist of large and flexible macrocycles that engage their targets via multiple contact points. This combination of contained flexibility and large contact area often allows natural products to bind at target surfaces rather than deep pockets, making them attractive scaffolds for inhibiting protein-protein interactions and other challenging therapeutic targets. The increasing ability to manipulate such compounds either biosynthetically or via semisynthetic modification means that these compounds can now be considered as starting points for medchem campaigns rather than solely as ends. Modern medchem benefits substantially from rational improvements made on the basis of molecular docking. As such, docking methods have been enhanced in recent years to deal with the complicated binding modalities and flexible scaffolds of macrocyclic natural products and natural product-like structures. Here, we comprehensively review methods for treating and docking these large macrocyclic scaffolds and discuss some of the resulting advances in medicinal chemistry.

Dynamic Formation of Noncovalent Calixsalen Aggregates.

A procedure for studying "dynamic structural behavior" of large chiral macrocycles is presented. Ion mobility MS, diffusion-ordered NMR spectroscopy (DOSY NMR), and optical rotation (OR) measurements, supported by calculations, are used together as effective complementary methods to study dynamic formation of noncovalent aggregates. It is shown that the monomer-dimer equilibrium is driven by π-π or CH-π interactions and controlled largely by the substitution pattern of the calixsalen skeleton.

SUZUKI-MIYAURA CROSS-COUPLING REACTION OF DICHLORO-HETEROAROMATICS: SYNTHESIS OF FUNCTIONALIZED DINUCLEOPHILIC FRAGMENTS

ABSTRACT The Suzuki-Miyaura cross-coupling reaction has successfully been applied for the synthesis of 4,4’- [6-(diethylamino)-1,3,5-triazine-2,4-diyl]diphenol ( 4a ), 4,4’-(pyrimidine-4,6-diyl)diphenol ( 4b ), 4,4’-(pyridine-2,6-diyl)diphenol ( 4c ). The reaction of 4,6-dichloro- N,N -diethyl-1,3,5-triazin-2-amine ( 1a ), 4,6-dichloropyrimidine ( 1b ) and 2,6-dichloropyridine ( 1c ) with p -methoxyphenylboronic acid ( 2 ) in the presence of palladium catalyst followed by demethylation reaction furnished the desired products in good to excellent yields. To test the reactivity of these nucleophiles, the compound 4a was further reacted with cyanuric chloride to get trimeric fragment ( 5a ). All the compounds were characterized by their physical, spectral ( 1 H and 13 C NMR and Mass) and microanalytical data. These dinucleophilic fragments ( 4a-4c ) having triazine, pyrimidine and pyridine rings, respectively, are excellent future candidates for the construction of large functional hetero-atom bridged macrocycles for diverse applications in host-guest chemistry, supramolecular catalysis, self-assembly and other related fields of supramolecular chemistry in addition to their potential in medicinal chemistry.

Macrocycle Conformational Sampling with MacroModel

Sampling low energy conformations of macrocycles is challenging due to the large size of many of these molecules and the constraints imposed by the macrocycle. We present a new conformational search method (implemented in MacroModel) that uses brief MD simulations followed by minimization and normal-mode search steps. The method was parametrized using a set of 100 macrocycles from the PDB and CSD. It was then tested on a publicly available data set for which there are published results using alternative methods; we found that when the same force field is used (in this case MMFFs in vacuum), our method tended to identify conformations with lower energies than what the other methods identified. The performance on a new set of 50 macrocycles from the PDB and CSD was also quite good; the mean and median RMSD values for just the ring atoms were 0.60 and 0.33 Å, respectively. However, the RMSD values for macrocycles with more than 30 ring-atoms were quite a bit larger compared to the smaller macrocycles. Possible origins for this and ideas for improving the performance on very large macrocycles are discussed.

ChemInform Abstract: Functionalizing Pillar[n]arenes

AbstractReview: 52 refs.

Enzyme-catalyzed macrocyclization of long unprotected peptides.

A glutathione S-transferase (GST) catalyzed macrocyclization reaction for peptides up to 40 amino acids in length is reported. GST catalyzes the selective SNAr reaction between an N-terminal glutathione (GSH, γ-Glu-Cys-Gly) tag and a C-terminal perfluoroaryl-modified cysteine on the same polypeptide chain. Cyclic peptides ranging from 9 to 24 residues were quantitatively produced within 2 h in aqueous pH = 8 buffer at room temperature. The reaction was highly selective for cyclization at the GSH tag, enabling the combination of GST-catalyzed ligation with native chemical ligation to generate a large 40-residue peptide macrocycle.

Functionalizing pillar[n]arenes.

Macrocyclic chemistry has relied on the dominance of some key cavitands, including cyclodextrins, calixarenes, cyclophanes, and cucurbiturils, to advance the field of host-guest science. Very few of the many other cavitands introduced by chemists during these past few decades have been developed to near the extent of these four key players. A relatively new family of macrocycles that are becoming increasingly dominant in the field of macrocyclic chemistry are the pillar[n]arenes composed of n hydroquinone rings connected in their 2- and 5-positions by methylene bridges. This substitution pattern creates a cylindrical or pillar-like structure that has identical upper and lower rims. The preparation of pillar[n]arenes is facile, with pillar[5]- through pillar[7]arene being readily accessible and the larger macrocycles (n = 8-14) being accessible in diminishing yields. The rigid pillar[n]arene cavities are highly π-electron-rich on account of the n activated aromatic faces pointing toward their centers, allowing the cavities to interact strongly with a range of π-electron-deficient guests including pyridiniums, alkylammoniums, and imidazoliums. The substitution pattern of pillar[n]arenes bestows chirality onto the macrocycle in the form of n chiral planes. The absolute configuration of the chiral planes in pillar[n]arenes can be either fixed or rapidly undergoing inversion. The future of pillar[n]arenes is going to be dependent on their ability to fulfill specific applications. Chemical modification of the parent pillar[n]arenes lets us create functionalized hosts with anticipated chemical or physical properties. The featured potential applications of pillar[n]arenes to date are far reaching and include novel hosts with relevance to nanotechnology, materials science, and medicine. Pillar[n]arenes have an overwhelming advantage over other hosts since the number of ways available to incorporate handles into their structures are diverse and easy to implement. In this Account, we describe the routes to chemically modified pillar[n]arenes by discussing the chemistry of their functionalization: monofunctionalization, difunctionalization, rim differentiation, perfunctionalization, and phenylene substitution. We assess the synthetic complications of employing these functionalization procedures and survey the potential applications and novel properties that arise with these functionalized pillar[n]arenes. We also highlight the challenges and the synthetic approaches that have yet to be fully explored for the selective chemical modification of these hosts. Finally, we examine a related class of macrocycles and consider their future applications. We trust that this Account will stimulate the development of new methods for functionalizing these novel hosts to realize pillar[n]arene-containing compounds capable of finding applications.

Synthesis and crystal structures of p-tert-butylcalix[4]arene 1,3-distal acylhydrazones and macrocyclic nickel complex

A series of the calix[4]arene 1,3-distal diacylhydrazones were successfully prepared by the condensation of calix[4]arene propylene and butylene bridged vanillines with 2-hydroxybenzohydrazide or pyridinecarbohydrazides. The coordination chemistry of these calixarene diacylhydrazone with transition metal salts was studied. X-ray single crystal diffraction of nickel complex shows that a very large metallic macrocycle with 2:2 stoichiometric is formed by two calixarene acylhydrazone domains act as bidentated planar chelators to coordinate to two nickel ion in a approximately square-planar geometry.

Molecular Docking Investigation of the Binding Interactions of Macrocyclic Inhibitors with HCV NS3 Protease and its Mutants (R155K, D168A and A156V)

Hepatitis C Virus (HCV) non-structural protein 3 (NS3) protease drug resistance poses serious challenges on the design of an effective treatment. Substrate Envelope Hypothesis, "the substrates of HCV NS3/4A protease have a consensus volume inside the active site called substrate envelope" is used to design potent and specific drugs to overcome this problem. Using molecular docking, we studied the binding interaction of the different inhibitors and protein and evaluated the effect of three different mutations (R155K, D168A and A156V) on the binding of inhibitors. P2-P4 macrocycles of 5A/5B and modified 5A/5B hexapeptide sequences have the best scores against the wild-type protein -204.506 and -206.823kcal/mole, respectively. Also, charged P2-P4 macrocycles of 3/4A and 4A/4B hexapeptide sequences have low scores with the wild-type protein -200.467 and -203.186kcal/mole, respectively. R155K mutation greatly affects the conformation of the compounds inside the active site. It inverts its orientations, and this is because the large and free side chain of K155 which restricts the conformation of the large P2-P4 macrocycle. The conformation of charged P2-P4 macrocycle of 3/4A hexapeptide sequence in wild-type, A156V and D168A proteins is nearly equal; while that of charged P2-P4 macrocycle of 4A/4B hexapeptide sequence is different. Nevertheless, these compounds have a slight increase of Van der Waals volume compared to that of substrates, they are potent against mutations and have good scores. Therefore, the suggested drugs can be used as an effective treatment solving HCV NS3/4A protease drug resistance problem.

Asararenes—A Family of Large Aromatic Macrocycles

We announce the establishment of a new family of macrocycles--the asararenes, which are based on para-methylene linked "asarol methyl ether" (1,2,4,5-tetramethoxybenzene) units. Macrocycles with 6-12 aromatic units have been synthesized and isolated in a single step from asarol methyl ether and paraformaldehyde. Even larger rings, with up to 15 asarol methyl ether units, have been observed by high-resolution mass spectrometry. Single-crystal X-ray structures of asar[6]-, asar[7]-, asar[8]-, asar[9]-, asar[10]- and asar[11]arene highlight the diverse structural features of this family of macrocycles. While the cavities of the asar[6-8]arene macrocycles are mostly filled with methoxyl groups, the asar[9]- and asar[10]arene rings contain accessible cavities and self-assemble into infinite channels filled with solvent molecules in the solid state. These solid-state structures highlight the potential of this family of macrocycles for a wide range of potential applications.

Synthesis of borasiloxane-based macrocycles by multicomponent condensation reactions in solution or in a ball mill

Large macrocycles containing imine and borasiloxane links are obtained in polycondensation reactions of 4-formylbenzeneboronic acid, t-Bu(2)Si(OH)(2), and diamines. The multicomponent reactions can be performed in solution or--advantageously--by mechanochemical syntheses in a ball mill.

Structural polymorphism in self-assembled networks of a triphenylene based macrocycle

Understanding and controlling the structural polymorphism in self-assembled networks of functional molecules merit special attention. In this contribution, we describe the concentration controlled structural evolution in self-assembled monolayers of a large triangular discotic macrocycle at the liquid-solid interface. Scanning tunneling microscopy (STM) reveals that the adlayers formed by an alkoxy substituted cyclo-tris(7,9-triphenylenylene) macrocycle exhibit concentration dependent 2D phase behavior at the 1,2,4-trichlorobenzene/HOPG interface. The self-assembled network evolves from high-density linear packing which is formed at relatively high concentrations to a low-density porous pattern at lower concentrations. A trimeric hexagonal phase exists at intermediate concentrations examined. The transformation of the trimeric hexagonal phase to the linear phase could be monitored by recording time-dependent STM images. The self-assembly behavior is affected significantly by the choice of the organic solvent where an amorphous network is formed along with high-density linear packing at the 1-phenyloctane/HOPG interface. The results presented here provide detailed insight into the polymorphism phenomenon exhibited by an organic semiconductor and furnish general guidelines to control the morphology of thin films of such technologically important materials.

Bending Rigid Molecular Rods: Formation of Oligoproline Macrocycles

Bent but not broken: cyclic oligoprolines are accessed in a reaction that effectively bends rigid oligoproline peptides (see scheme; TBDMS=tert-butyldimethylsilyl). The stitching is accomplished during macrocyclization enabled by aziridine aldehydes and isocyanides. Molecular modeling studies suggest that electrostatic attraction between the termini of the linear peptide is pivotal for macrocyclization. The macrocycles were studied by circular dichroism with a polyproline II structure being observed in larger macrocycles.

A novel 2D organic–inorganic hybrid based on [P2W18O62]6− polyoxoanion and Cu–bbi coordination polymers

Abstract A novel 2D compound based on Wells–Dawson polyoxometalates, [Cu3(bbi)6(P2W18O62)] (bbi = 1,1′-(1,4-butanediyl)bis(imidazole)) (1) has been hydrothermally synthesized and characterized by elemental analyse, IR, TG, PXRD and single crystal X-ray diffraction. In compound 1, each Cu2+ ion is connected with four adjacent Cu2+ ions by bbi ligands along four different directions and each bbi ligand is two-coordinated by two Cu2+ ions, which results in an unusual 2D interlink lock-liked layer. Interestingly, two kinds of macrocycles exist in the structure, in which six smaller 33-membered rings are placed end to end to form the larger ones (66-membered macrocycles). The [P2W18O62]6− polyoxoanions as bidentate ‘guest’ is incorporated into the larger macrocycles. These 2D layers are further packed into 3D framework through strong supramolecular interactions. Additionally, electrochemical and electrocatalysis behavior of 1-CPE have been studied in detail.

Synthesis and X-ray Structures of Novel Macrocycles and Macrobicycles Containing N,N-Di(pyrrolylmethyl)-N-methylamine Moiety: Preliminary Anion Binding Study

The [2 + 2] Schiff base condensation reactions between the newly synthesized dialdehyde, N,N-di(α-formylpyrrolyl-α-methyl)-N-methylamine), and ethylenediamine or p-phenylenediamine dihydrochloride readily afforded the 30- and 34-membered large size macrocycles in very high yields. Subsequent reduction reactions of these macrocycles with NaBH(4) gave the corresponding saturated macrocyclic hexaamines in good yields. The analogous reaction of the new dialdehyde with a triamine molecule afforded the [3 + 2] Schiff base macrobicycle in high yield, which was then reduced by reaction with NaBH(4) to give the saturated macrobicycle. All these compounds were characterized by spectroscopic methods. The anion binding properties of the saturated macrocycles having the ethylene and the phenylene linkers in CDCl(3) were studied by NMR titration methods. Although they have similar pyrrolic and amine NH groups their binding properties are different and interesting, owing to the conformational flexibility or rigidness rendered by the ethylene or phenylene groups, respectively. The macrocycle having the ethylene linkers binds anions in a 1:1 fashion, while the other receptor having the phenylene linkers prefers to bind anions in a sequential 1:2 fashion and has a multiple equilibria between a 1:1 and a 1:2 complexes, as shown by their binding constants, curve fittings by EQNMR, and Job plots. The X-ray structures of the 1:2 methanol, the aqua and the benzoate anion complexes of the macrocycles show two cavities in which the guests are bound, correlating with the high affinity found for the formation of stable 1:2 complexes in solution. The X-ray structure showed that the macrobicycle Schiff base adopts an eclipsed paddle-wheel shaped conformation and exhibits an out-out configuration at the bridgehead nitrogen atoms.