Domain Swapping in Abiotic Foldamers

Foldamer sequences that adopt tertiary helix-turn-helix folds mediated by helix-helix hydrogen bonding in organic solvents have been previously reported. In an attempt to create genuine abiotic quaternary structures, i.e. assemblies of tertiary structures, new sequences were prepared that possess additional hydrogen bond donors at positions that may promote an association between the tertiary folds. However, a solid state structure and extensive solution state investigations by Nuclear Magnetic Resonance (NMR) and Circular dichroism (CD) show that, instead of forming a quaternary structure, the tertiary folds assemble into stable swapped-domain dimer motifs. Domain swapping entails a complete reorganization of the arrays of hydrogen bonds and changes in relative helix orientation and handedness that can all be rationalized.

Polymorphism of Butyl Ester of Oleanolic Acid—The Dominance of Dispersive Interactions over Electrostatic

Oleanolic (OA) and glycyrrhetinic acids (GE), as well as their derivatives, show a variety of pharmacological properties. Their crystal structures provide valuable information related to the assembly modes of these biologically active compounds. In the known-to-date crystals of OA esters, their 11-oxo derivatives, and GE ester crystals, triterpenes associate, forming different types of ribbons and layers whose construction is based mainly on van der Waals forces and weak C-H···O interactions. New crystal structures of 11-oxo OA methyl ester and the polymorph of OA butyl ester reveal an alternative aggregation mode. Supramolecular architectures consist of helical chains which are stabilized by hydrogen bonds of O-H···O type. It was found that two polymorphic forms of butyl OA ester (layered and helical) are related monotropically. In a structure of metastable form, O-H···O hydrogen bonds occur, while the thermodynamically preferred phase is governed mainly by van der Waals interactions. The intermolecular interaction energies calculated using CrystalExplorer, PIXEL, and Psi4 programs showed that even in motifs formed through O-H···O hydrogen bonds, the dispersive forces have a significant impact.

Homochiral versus Heterochiral Dimeric Helical Foldamer Bundles: Chlorinated-Solvent-Dependent Self-Sorting

Aromatic oligoamide sequences programmed to fold into stable helical conformations were designed to display a linear array of hydrogen-bond donors and acceptors at their surface. Sequences were prepared by solid-phase synthesis. Solution ¹ H NMR spectroscopic studies and solid-state crystallographic structures demonstrated the formation of stable hydrogen-bond-mediated dimeric helix bundles that could be either heterochiral (with a P and an M helix) or homochiral (with two P or two M helices). Formation of the hetero- or homochiral dimers could be driven quantitatively using different chlorinated solvents-exemplifying a remarkable case of either social or narcissistic chiral self-sorting or upon imposing absolute handedness to the helices to forbid PM species.

Molecular torsion springs: alteration of helix curvature in frustrated tertiary folds

The first abiotic foldamer tertiary structures have been recently reported in the form of aromatic helix-turn-helix motifs based on oligo-quinolinecarboxamides held together by intramolecular hydrogen bonds. Tertiary folds were predicted by computational modelling of the hydrogen-bonding interfaces between helices and later verified by X-ray crystallography. However, the prognosis of how the conformational preference inherent to each helix influences the tertiary structure warranted further investigation. Several new helix-turn-helix sequences were synthesised in which some hydrogen bonds have been removed. Contrary to expectations, this change did not strongly destabilise the tertiary folds. On closer inspection, a new crystal structure revealed that helices adopt their natural curvature when some hydrogen bonds are missing and undergo some spring torsion upon forming the said hydrogen bonds, thus potentially giving rise to a conformational frustration. This phenomenon sheds light on the aggregation behaviour of the helices when they are not linked by a turn unit.

An abiotic, tetrameric, eight-helix bundle

Four helically folded aromatic oligoamide sequences containing either a chiral monomer based on 2-(2-aminophenoxy)-propionic acid, an N-terminal (1H)-camphanyl group, or both, were synthesized. Spectroscopic solution investigations using 1H NMR and...

Coaxial assembly of helical aromatic foldamers by metal coordination

Deprotonation of acid-terminated helical aromatic foldamers with a mineral base in chlorinated solvents led to their dimerization through the coordination of a metal cation (Li+, Na+, K+, Ag+, or Hg2+)...

Directing the Self-Assembly of Aromatic Foldamer Helices using Acridine Appendages and Metal Coordination

Folded molecules provide complex interaction interfaces amenable to sophisticated self-assembly motifs. Because of their high conformational stability, aromatic foldamers constitute suitable candidates for the rational elaboration of self-assembled architectures. Several multiturn helical aromatic oligoamides have been synthesized that possess arrays of acridine appendages pointing in one or two directions. The acridine units were shown to direct self-assembly in the solid state via aromatic stacking leading to recurrent helix-helix association patterns under the form of discrete dimers or extended arrays. In the presence of Pd(II), metal coordination of the acridine units overwhelms other forces and generates new metal-mediated multihelical self-assemblies, including macrocycles. These observations demonstrate simple access to different types of foldamer-containing architectures, ranging from discrete objects to 1D and, by extension, 2D and 3D arrays.

Photocatalytic Activity of Sulfanyl Porphyrazine/Titanium Dioxide Nanocomposites in Degradation of Organic Pollutants

Magnesium(II) sulfanyl porphyrazine with peripheral morpholinethoxy substituents was embedded on the surface of titanium(IV) dioxide nanoparticles. The obtained nanocomposites were characterized with the use of particle size and distribution (NTA analysis), electron microscopy (SEM), thermal analysis (TGA), FTIR-ATR spectroscopy, and X-ray powder diffraction (XRD). The measured particle size of the obtained material was 327.4 ± 15.5 nm. Analysis with XRD showed no visible changes in the crystallinity of the material after deposition of porphyrazine on the TiO₂ surface. However, SEM images revealed noticeable changes in the morphology of the obtained hybrid material: higher aggregation and less ordered structure of the aggregates. The TGA analysis revealed the lost 3.6% (0.4 mg) of the mass of obtained material in the range 250-550 °C. In the FTIR-ATR analysis, C-H stretching vibratins in the range of 3000-2800 cm^-1, originating from porphyrazine moieties, were detected. The photocatalytic applicability of the nanomaterial was assessed in photodegradation studies of methylene blue and bisphenol A as reference environmental pollutants. In addition, the photocatalytic degradation of carbamazepine with porphyrazine/TiO₂ hybrids as photocatalysts was studied, accompanied by an HPLC chromatography assessment of photodegradation. In total, 43% of the initial concentration was achieved in the case of bisphenol A, after 4 h of irradiation, whereas 57% was achieved in the case of carbamazepine. In each photodegradation reaction, the activity of the obtained photocatalytic nanomaterial was proved with almost linear degradation. The photodegradation reaction rate constants were calculated, and revealed 5.75 × 10^-5 s^-1 for bisphenol A and 5.66 × 10^-5 s^-1 for carbamazepine.

Insights into isostructural and non-isostructural crystals of esters of oleanolic acid and its 11-oxo derivatives

Synthesis and structural characterization of new esters of oleanolic acid and its 11-oxo derivatives are reported. Compounds crystallize in four isostructural groups, each containing one to four structures. Single-crystal X-ray analysis revealed that molecules belonging to non-isostructural groups self-associate according to two schemes that describe also supramolecular architectures in crystals of glycyrrhetinic acid derivatives. Structural motifs arise as a result of van der Waals forces. Parameters introduced for the analysis of one- and two-dimensional assemblies allow the comparison of motifs in isostructural and non-isostructural crystals, including polymorphs, and a qualitative assessment of differences in molecular self-assembly. One-, two- or three-dimensional similarity has been confirmed by XPac calculations.

Single-crystal-to-single-crystal phase transition of 18β-glycyrrhetinic acid isopropyl ester

Due to the destruction of the integrity of the parent crystal, single-crystal-to-single-crystal phase transition in organic compounds is still a relatively rare phenomenon. The phase transition in glycyrrhetinic acid isopropyl ester is triggered by temperature change. The increasing volume of the isopropyl substituent as a result of increasing temperature forces a remodelling of the structural motifs. These changes cause a single-crystal-to-single-crystal phase transition. The low-temperature form is isostructural with glycyrrhetinic acid methanol solvate, while the high-temperature phase is isostructural with the ethyl ester of this acid.

Loading Linear Arrays of CuII Inside Aromatic Amide Helices

The very stable helices of 8-amino-2-quinolinecarboxylic acid oligoamides are shown to uptake CuII ions in their cavity through deprotonation of their amide functions with minimal alteration of their shape, unlike most metallo-organic structures which generally differ from their organic precursors. The outcome is the formation of intramolecular linear arrays of a defined number of CuII centers (up to sixteen in this study) at a 3 Å distance, forming a molecular mimic of a metal wire completely surrounded by an organic sheath. The helices pack in the solid state so that the arrays of CuII extend intermolecularly. Conductive-AFM and cyclic voltammetry suggest that electrons are transported throughout the metal-loaded helices in contrast with hole transport observed for analogous foldamers devoid of metal ions.

Oligo-Quinolylene-Vinylene Foldamers

Quinoline based aromatic amide foldamers are known to adopt stable folded conformations. We have developed a synthetic approach to produce similar oligomers where all amide bonds, or part of them, have been replaced by an isosteric vinylene group. The results of solution and solid state structural studies show that oligomers exclusively containing vinylene linkages are not well folded, and adopt predominantly flat conformations. In contrast, a vinylene segment flanked by helical oligoamides also folds in a helix, albeit with a slightly lower curvature. The presence of vinylene functions also result in an extension of π-conjugation across the oligomer that may change charge transport properties. Altogether, these results pave the way to foldamers in which both structural control and specific electronic properties may be engineered.

Aromatic Foldamer Helices as α-Helix Extended Surface Mimetics

Helically folded aromatic oligoamide foldamers have a size and geometrical parameters very distinct from those of α-helices and are not obvious candidates for α-helix mimicry. Nevertheless, they offer multiple sites for attaching side chains. It was found that some arrays of side chains at the surface of an aromatic helix make it possible to mimic extended α-helical surfaces. Synthetic methods were developed to produce quinoline monomers suitably functionalized for solid phase synthesis. A dodecamer was prepared. Its crystal structure validated the initial design and showed helix bundling involving the α-helix-like interface. These results open up new uses of aromatic helices to recognize protein surfaces and to program helix bundling in water.

Parallel Homochiral and Anti-Parallel Heterochiral Hydrogen-Bonding Interfaces in Multi-Helical Abiotic Foldamers

A hydrogen-bonding interface between helical aromatic oligoamide foldamers has been designed to promote the folding of a helix-turn-helix motif with a head-to-tail arrangement of two helices of opposite handedness. This design complements an earlier helix-turn-helix motif with a head-to-head arrangement of two helices of identical handedness interface. The two motifs were shown to have comparable stability and were combined in a unimolecular tetra-helix fold constituting the largest abiotic tertiary structure to date.

Specific Interactions between Rifamycin Antibiotics and Water Influencing Ability To Overcome Natural Cell Barriers and the Range of Antibacterial Potency

Rifamycins are a group of macrocyclic antibiotics mainly used for the treatment of various bacterial infections including tuberculosis. Spectroscopic studies of rifamycins evidence the formation of temperature- and solvent-dependent equilibria between A-, B-, and C-type conformers in solutions. The B- and C-type conformers of rifamycin antibiotics are exclusively formed in the presence of water molecules. A- and B-type conformers exhibit a hydrophilic and "open" ansa-bridge nature whereas the C-type conformer is more lipophilic due to the presence of a "closed" ansa-bridge structure. The involvement of the lactam moiety of the ansa-bridge in intramolecular H-bonds within rifapentine and rifampicin implicates the formation of a more hydrophilic A-type conformer. In contrast to rifampicin and rifapentine, for rifabutin and rifaximin, the "free" lactam group enhances conformational flexibility of the ansa-bridge, thereby enabling interconversion between A- and C-type conformers. In turn, an equilibrium between A- and C-type conformers for rifamycins improves their adaptation to the changing nature of bacteria cell membranes, especially those of Gram-negative strains and/or to efflux pump systems.

Interplay of secondary and tertiary folding in abiotic foldamers

The first true abiotic tertiary folded structures, i.e. at the exclusion of any aliphatic amino acid, have recently been introduced under the form of aromatic oligoamide helix-turn-helix foldamers stabilized by hydrogen bonds in organic solvents. We present an investigation of the interplay of secondary and tertiary folding and of some cooperative effects in these systems. A solid phase synthesis approach to the preparation of these sequences was developed to facilitate systematic variation. Flexible pyridine-based units were introduced in various proportions in replacement of more rigid quinoline-based units. Conformational behaviour was assessed in solution by NMR, in the solid state by X-ray crystallography, and computationally through molecular dynamics simulations. Altogether, our results demonstrate that tertiary folding stabilizes otherwise flexible secondary structures, and that the disruption of tertiary folds upon adding polar solvents follows different mechanisms depending on whether secondary structures are inherently stable or not. These findings constitute a solid basis on which to further increase the size and complexity of abiotic folded structures and to eventually orchestrate folding dynamics and responsiveness.

Directional Threading and Sliding of a Dissymmetrical Foldamer Helix on Dissymmetrical Axles

We have investigated the self-assembly of a dissymmetrical aromatic oligoamide helix on linear amido-carbamate rods. A dissymmetric sequence bearing two differentiated ends is able to wrap around dissymmetric dumbbell guest molecules. Structural and thermodynamic investigations allowed us to decipher the mode of binding of the helix that can bind specifically to the amide and carbamate groups of the rod. In parallel kinetic studies of threading and sliding of the helix along linear axles were also monitored by ¹ H NMR. Results show that threading of a dissymmetrical host can be kinetically biased by the nature of the guest terminus allowing a preferential sense of sliding of the helix. The study presented below further demonstrates the valuable potential of foldaxanes to combine designed molecular recognition patterns with fine control of self-assembly kinetics to conceive complex supramolecular events.

Carbohydrate binding through first- and second-sphere coordination within aromatic oligoamide metallofoldamers

Aromatic oligoamide capsules that fold upon metal binding recognize carbohydrate guests in solution as evidenced by CD and NMR titrations. Crystallographic data reveal that, besides their structural role, metal ions also contribute to guest recognition through either first- or second-sphere coordination.

Alkali and alkaline earth metal ion binding by a foldamer capsule: selective recognition of magnesium hydrate

Alkali and alkaline earth metal ion binding by an aromatic oligoamide foldamer was shown to induce its folding into a helical capsule. CD and NMR titrations revealed tight and selective binding of Mg²⁺. Crystallographic studies demonstrated that, depending on the metal, binding may involve the first or second coordination spheres of the metal hydrates.

Metal-Coordination-Assisted Folding and Guest Binding in Helical Aromatic Oligoamide Molecular Capsules

The development of foldamer-based receptors is driven by the design of monomers with specific properties. Herein, we introduce a pyridazine-pyridine-pyridazine diacid monomer and its incorporation into helical aromatic oligoamide foldamer containers. This monomer codes for a wide helix diameter and can sequester metal ions on the inner wall of the helix cavity. Crystallographic studies and NMR titrations show that part of the metal coordination sphere remains available and may then promote the binding of a guest within the cavity. In addition to metal coordination, binding of the guest is assisted by cooperative interactions with the helix host, thereby resulting in significant enhancements depending on the foldamer sequence, and in slow guest capture and release on the NMR time scale. In the absence of metal ions, the pyridazine-pyridine-pyridazine monomer promotes an extended conformation of the foldamer that results in aggregation, including the formation of an intertwined duplex.

Synthesis and singlet oxygen generation of pyrazinoporphyrazines containing dendrimeric aryl substituents

Singlet oxygen generation yields and aggregation tendencies were studied for porphyrazines bearing dendrimeric substituents.

Self-assembly modes of glycyrrhetinic acid esters in view of the crystal packing of related triterpene molecules

The crystal structures of three ester derivatives of glycyrrhetinic acid (GE) are reported. X-ray crystallography revealed that despite differences in the size of the ester substituents (ethyl, isopropyl and 2-morpholinoethyl) the scheme of molecular self-assembly is similar in all three cases but differs significantly from that observed in other known GE esters. According to our analysis, the two basic patterns of self-assembly of GE esters observed in their unsolvated crystals correspond to two distinct orientations of the ester groups relative to the triterpene backbone. Moreover, comparison of the self-assembly modes of GE esters in their unsolvated forms with the supramolecular organization of GE and carbenoxolone in their solvated crystals revealed that ester substituents replace solvent molecules hydrogen bonded to the COOH group at the triterpene skeleton, resulting in similar packing arrangements of these compounds.

Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic

Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975). Acta Cryst. B 31, 1454-1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol -OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-acetyloxy-6,9,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-[(E)-N-(4-methylpiperazin-4-ium-1-yl)formimidoyl]-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienimino)naphtho[2,1-b]furan-5-olate pentahydrate, C(43)H(58)N(4)O(12)·5H(2)O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O-H···O and N-H···N hydrogen bonds. Four of the symmetry-independent water molecules are arranged via hydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interact via O-H···O hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.

Intramolecular proton transfer impact on antibacterial properties of ansamycin antibiotic rifampicin and its new amino analogues

Intramolecular proton transfer in rifampicin (1) and its analogues 2-9 with the formation of zwitterions has been indicated by multinuclear NMR and crystallographic studies. Biological tests of 1-9 in combination with the analysis of ligand-protein interactions have revealed the relationship between the protonation site and extremely high antibacterial activity.

A third polymorph of N,N'-bis-(pyridin-2-yl)benzene-1,4-diamine

A third polymorph of the title compound, C(16)H(14)N(4), has been obtained. The mol-ecule adopts a non-planar conformation with an E configuration at the two partially double exo C N bonds of the 2-pyridyl-amine units. Like in the triclinic form [Bensemann et al. (2002 ▶). New J. Chem.26, 448-456], the recognition process between 2-pyridyl-amine units takes place through formation of a cyclic R(2) (2)(8) hydrogen-bond motif, leading to the creation of tapes parallel to [001].

N,N'-Bis(pyridin-2-yl)benzene-1,4-diamine-naphthalene (2/1)

The asymmetric unit of the title compound, C₁₀H₈·2C₁₆H₁₄N₄, consists of one mol­ecule of N,N′-bis­(pyridin-2-yl)benzene-1,4-diamine (PDAB) and one half of the centrosymmetric naphthalene mol­ecule. The PDAB mol­ecule adopts a non-planar conformation with an E configuration at the two partially double exo C N bonds of the 2-pyridyl­amine units. In the crystal, N—H⋯N hydrogen bonds between the PDAB mol­ecules generate a cyclic R₂²(8) motif, leading to the formation of PDAB tapes extending along [100]. The tapes are arranged into (010) layers and the naphthalene mol­ecules are enclosed in cavities formed between the PDAB layers.