Rational modification of the hierarchy of intermolecular interactions in molecular crystal structures by using tunable halogen bonds

A family of 16 isomolecular salts (3-XpyH)(2)[MX'(4)] (3-XpyH=3-halopyridinium; M=Co, Zn; X=(F), Cl, Br, (I); X'=Cl, Br, I) each containing rigid organic cations and tetrahedral halometallate anions has been prepared and characterized by X-ray single crystal and/or powder diffraction. Their crystal structures reflect the competition and cooperation between non-covalent interactions: N-H center dot center dot center dot X'-M hydrogen bonds, C-X center dot center dot center dot X'-M halogen bonds and pi-pi stacking. The latter are essentially unchanged in strength across the series, but both halogen bonds and hydrogen bonds are modified in strength upon changing the halogens involved. Changing the organic halogen (X) from F to I strengthens the C-X center dot center dot center dot X'-M halogen bonds, whereas an analogous change of the inorganic halogen (X') weakens both halogen bonds and N-H center dot center dot center dot X'-M hydrogen bonds. By so tuning the strength of the putative halogen bonds from repulsive to weak to moderately strong attractive interactions, the hierarchy of the interactions has been modified rationally leading to systematic changes in crystal packing. Three classes of crystal structure are obtained. In type A (C-F center dot center dot center dot X'-M) halogen bonds are absent. The structure is directed by N-H center dot center dot center dot X'-M hydrogen bonds and pi-stacking interactions. In type B structures, involving small organic halogens (X) and large inorganic halogens (X'), long (weak) C-X center dot center dot center dot X'-M interactions are observed with type I halogen-halogen interaction geometries (C-X center dot center dot center dot X' approximate to X center dot center dot center dot X'-M approximate to 155 degrees), but hydrogen bonds still dominate. Thus, minor but quite significant perturbations from the type A structure arise. In type C, involving larger organic halogens (X) and smaller inorganic halogens (X'), stronger halogen bonds are formed with a type II halogen-halogen interaction geometry (C-X center dot center dot center dot X' approximate to 180 degrees; X center dot center dot center dot X'-M approximate to 110 degrees) that is electrostatically attractive. The halogen bonds play a major role alongside hydrogen bonds in directing the type C structures, which as a result are quite different from type A and B.

Binding studies of a protonated dioxatetraazamacrocycle with carboxylate substrates

The tetraprotonated form of the dioxatetraazamacrocycle, 6,19-dioxa-3,9,16,22-tetraaza[22.2.2.2(11,14)]-triaconta-1(26),11,13,24, 27,29-hexaene, (H4L1)(4+), was used as the receptor for binding studies with carboxylate anionic substrates of different shapes, sizes, and charges [succinate (suc(2-)), cyclo- hexanetricarboxylate (cta(3-)), phthalate (ph(2-)), isophthalate (iph(2-)), terephthalate (tph(2-)), and benezenetricarboxylate (btc(3-))]. Association constants were determined by potentiometry in aqueous solution at 298.2 K and 0.10 M KCl and by H-1 NMR titration in D2O. The strongest association was found for the btc3- anion at 5-7 pH region. From both techniques it was possible to establish the binding preference trend of the receptor for the different substrates, and the H-1 NMR spectroscopy gave important suggestions about the type of interactions between partners and the location of the substrates in the supramolecular entities formed. The effective binding constants at pH 6 follow the order: btc(3-)>iph(2-)>cta(3-) =ph(2-)>tph(2-)>suc(2-). All the studies suggest that the anionic substrates bind to the receptor via N-H center dot center dot center dot O = C hydrogen bonds and electrostatic interactions, and the aromatic substrates can also establish pi-pi stacking interactions. The crystal structures of (H4L1)(4+) and its supramolecular assemblies with ph(2-) and tph(2-) were determined by X-ray diffraction. The last two structures showed that the association process in solid state occurs via multiple N-H center dot center dot center dot O = C hydrogen bonds with the anionic substrate located outside the macrocyclic cavity of the receptor. Molecular dynamics simulations carried out for the association of (H4L1)(4+) with tph(2-) and btC(3-) in water solution established at atomic level the existence of all interactions suggested by the experimental studies, which act cooperatively in the binding process. Furthermore, the binding free energies were estimated and the values are in agreement with the experimental ones, indicating that the binding of these two anionic substrates occurs into the receptor cavity. However, the tph(2-) has also propensity to leave the macrocyclic cavity and its molecular recognition can also happen at the top of the receptor. (C) 2008 Elsevier Ltd. All rights reserved.

Anion-templated assembly of pseudorotaxanes: importance of anion template, strength of ion-pair thread association, and macrocycle ring size

A wide range of pseuclorotaxane assemblies containing positively charged pyridinium, pyridinium nicotinamide, imidazolium, benzimidazolium and guanidinium threading components, and macrocyclic isophthalamide polyether ligands have been prepared using a general anion templation procedure. In noncompetitive solvent media, coupling halide anion recognition by a macrocyclic ligand with ion-pairing between the halide anion and a strongly associated cation provides the driving force for interpenetration. Extensive solution H-1 NMR binding studies, thermodynamic investigations, and single-crystal X-ray structure determinations reveal that the nature of the halide anion template, strength of the ion-pairing between the anion template and the cationic threading component, and to a lesser extent favorable second sphere pi-pi aromatic stacking interactions between the positively charged threading component and macrocyclic ligand, together with macrocyclic ring size, affect the efficacy of pseudorotaxane formation.

Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation

The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide A beta 16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and Molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations, The Solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics Simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures Were used to simulate Circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally.(in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.

Hydrogelation of self-assembling RGD-based peptides

The self-assembly of tripeptides based on the RGD cell adhesion motif is investigated. Two tripeptides containing the Fmoc [N-(fluorenyl)-9-methoxycarbonyl] aromatic unit were synthesized, Fmoc-RGD and a control peptide containing a scrambled sequence, Fmoc-GRD. The Fmoc is used to control selfassembly via aromatic stacking interactions. The self-assembly and hydrogelation properties of the two Fmoc-tripeptides are compared. Both form well defined amyloid fibrils (as shown by cryo-TEM and SAXS) with b-sheet features in their circular dichroism and FTIR spectra. Both peptides form selfsupporting hydrogels, the dynamic shear modulus of which was measured. Preliminary cell culture experiments reveal that Fmoc-RGD can be used as a support for bovine fibroblasts, but not Fmoc- GRD, consistent with the incorporation of the cell adhesion motif in the former peptide.

Influence of end-capping on the self-assembly of model amyloid peptide fragments

The influence of charge and aromatic stacking interactions on the self-assembly of a series of four model amyloid peptides has been examined. The four model peptides are based on the KLVFF motif from the amyloid Beta peptide, ABeta(16-20) extended at the N terminus with two Beta-alanine residues. We have studied NH2-BetaABetaAKLVFF-COOH (FF), NH2-BetaABetaAKLVFCOOH (F), CH3CONH-BetaABetaAKLVFF-CONH2 (CapF), and CH3CONH-BetaABetaAKLVFFCONH2 (CapFF). The former two are uncapped (net charge plus 2) and differ by one hydrophobic phenylalanine residue; the latter two are the analogous capped peptides (net charge plus 1). The self-assembly characteristics of these peptides are remarkably different and strongly dependent on concentration. NMR shows a shift from carboxylate to carboxylic acid forms upon increasing concentration. Saturation transfer measurements of solvent molecules indicate selective involvement of phenylalanine residues in driving the self-assembly process of CapFF due presumably to the effect of aromatic stacking interactions. FTIR spectroscopy reveals beta-sheet features for the two peptides containing two phenylalanine residues but not the single phenylalanine residue, pointing again to the driving force for self-assembly. Circular dichroism (CD) in dilute solution reveals the polyproline II conformation, except for F which is disordered. We discuss the relationship of this observation to the significant pH shift observed for this peptide when compared the calculated value. Atomic force microscopy and cryogenic-TEM reveals the formation of twisted fibrils for CapFF, as previously also observed for FF. The influence of salt on the self-assembly of the model beta-sheet forming capped peptide CapFF was investigated by FTIR. Cryo-TEM reveals that the extent of twisting decreases with increased salt concentration, leading to the formation of flat ribbon structures. These results highlight the important role of aggregation-induced pKa shifts in the self-assembly of model beta-sheet peptides.

Direct observation of time-resolved polymorphic states in the self-assembly of end-capped heptapeptides

Amyloid fibrils resulting from uncontrolled peptide aggregation are associated with several neurodegenerative diseases. Their polymorphism depends on a number of factors including pH, ionic strength, electrostatic interactions, hydrophobic interactions, hydrogen bonding, aromatic stacking interactions, and chirality. Understanding the mechanism of amyloid fibril formation can improve strategies towards the prevention of fibrillation processes and enable a wide range of potential applications in nanotemplating and nanotechnology.

Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif

Self-assembly in aqueous solution has been investigated for two Fmoc [Fmoc ¼ N-(fluorenyl)-9-methoxycarbonyl] tetrapeptides comprising the RGDS cell adhesion motif from fibronectin or the scrambled sequence GRDS. The hydrophobic Fmoc unit confers amphiphilicity on the molecules, and introduces aromatic stacking interactions. Circular dichroism and FTIR spectroscopy show that the self-assembly of both peptides at low concentration is dominated by interactions among Fmoc units, although Fmoc-GRDS shows b-sheet features, at lower concentration than Fmoc-RGDS. Fibre X-ray diffraction indicates b-sheet formation by both peptides at sufficiently high concentration. Strong alignment effects are revealed by linear dichroism experiments for Fmoc-GRDS. Cryo-TEM and smallangle X-ray scattering (SAXS) reveal that both samples form fibrils with a diameter of approximately 10 nm. Both Fmoc-tetrapeptides form self-supporting hydrogels at sufficiently high concentration. Dynamic shear rheometry enabled measurements of the moduli for the Fmoc-GRDS hydrogel, however syneresis was observed for the Fmoc-RGDS hydrogel which was significantly less stable to shear. Molecular dynamics computer simulations were carried out considering parallel and antiparallel b-sheet configurations of systems containing 7 and 21 molecules of Fmoc-RGDS or Fmoc-GRDS, the results being analyzed in terms of both intermolecular structural parameters and energy contributions.

Spectroscopic signatures of an Fmoc–tetrapeptide, Fmoc and fluorene

The hydrophobic Fmoc [N-(fluorenyl)-9-methoxycarbonyl] unit is often conjugated to peptides to confer amphiphilicity on the molecules, and to introduce the potential for aromatic stacking interactions. In this paper we report spectroscopic data for fluorene, Fmoc and Fmoc conjugated to a small peptide (GRDS in this case) to enable interpretation of spectroscopic data collected on complex structures that can be created with Fmoc–peptide molecules. We report absorbance data (ultra violet and infrared), circular dichroism, linear dichroism (both film and Couette flow orientation) and Raman spectra. Orientations of the Fmoc chromophores in the linear dichroism studies are deduced.

Multivalency in healable supramolecular polymers: the effect of supramolecular cross-link density on the mechanical properties and healing of noncovalent polymer networks

Polymers with the ability to heal themselves could provide access to materials with extended lifetimes in a wide range of applications such as surface coatings, automotive components and aerospace composites. Here we describe the synthesis and characterisation of two novel, stimuli-responsive, supramolecular polymer blends based on π-electron-rich pyrenyl residues and π-electron-deficient, chain-folding aromatic diimides that interact through complementary π–π stacking interactions. Different degrees of supramolecular “cross-linking” were achieved by use of divalent or trivalent poly(ethylene glycol)-based polymers featuring pyrenyl end-groups, blended with a known diimide–ether copolymer. The mechanical properties of the resulting polymer blends revealed that higher degrees of supramolecular “cross-link density” yield materials with enhanced mechanical properties, such as increased tensile modulus, modulus of toughness, elasticity and yield point. After a number of break/heal cycles, these materials were found to retain the characteristics of the pristine polymer blend, and this new approach thus offers a simple route to mechanically robust yet healable materials.

Dehydrodipeptide hydrogelators containing naproxen N‑Capped tryptophan: self-assembly, hydrogel characterization, and evaluation as potential drug nanocarriers

In this work, we introduce dipeptides containing tryptophan N-capped with the nonsteroidal anti-inflammatory drug naproxen and C-terminal dehydroamino acids, dehydrophenylalanine (ΔPhe), dehydroaminobutyric acid (ΔAbu), and dehydroalanine (ΔAla) as efficacious protease resistant hydrogelators. Optimized conditions for gel formation are reported. Transmission electron microscopy experiments revealed that the hydrogels consist of networks of micro/nanosized fibers formed by peptide self-assembly. Fluorescence and circular dichroism spectroscopy indicate that the self-assembly process is driven by stacking interactions of the aromatic groups. The naphthalene groups of the naproxen moieties are highly organized in the fibers through chiral stacking. Rheological experiments demonstrated that the most hydrophobic peptide (containing C-terminal ΔPhe) formed more elastic gels at lower critical gelation concentrations. This gel revealed irreversible breakup, while the C-terminal ΔAbu and ΔAla gels, although less elastic, exhibited structural recovery and partial healing of the elastic properties. A potential antitumor thieno[3,2-b]pyridine derivative was incorporated (noncovalently) into the gel formed by the hydrogelator containing C-terminal ΔPhe residue. Fluorescence and Förster resonance energy transfer measurements indicate that the drug is located in a hydrophobic environment, near/associated with the peptide fibers, establishing this type of hydrogel as a good drug-nanocarrier candidate.

Tetrafenilciclopentadienon-derivati ed analoghi: sintesi, "self-assembly" e caratterizzazione reologica

Gels are materials that are easier to recognize than to define. For all practical purpose, a material is termed a gel if the whole volume of liquid is completely immobilized as usually tested by the ‘tube inversion’ method. Recently, supramolecular gels obtained from low molecular weight gelators (LMWGs) have attracted considerable attention in materials science since they represent a new class of smart materials sensitive to external stimuli, such as temperature, ultrasounds, light, chemical species and so on. Accordingly, during the past years a large variety of potentialities and applications of these soft materials in optoelectronics, as electronic devices, light harvesting systems and sensors, in bio-materials and in drug delivery have been reported. Spontaneous self-assembly of low molecular weight molecules is a powerful tool that allows complex supramolecular nanoscale structures to be built. The weak and non-covalent interactions such as hydrogen bonding, π–π stacking, coordination, electrostatic and van der Waals interactions are usually considered as the most important features for promoting sol-gel equilibria. However, the occurrence of gelation processes is ruled by further “external” factors, among which the temperature and the nature of the solvents that are employed are of crucial importance. For example, some gelators prefer aromatic or halogenated solvents and in some cases both the gelation temperature and the type of the solvent affect the morphologies of the final aggregation. Functionalized cyclopentadienones are fascinating systems largely employed as building blocks for the synthesis of polyphenylene derivatives. In addition, it is worth noting that structures containing π-extended conjugated chromophores with enhanced absorption properties are of current interest in the field of materials science since they can be used as “organic metals”, as semiconductors, and as emissive or absorbing layers for OLEDs or photovoltaics. The possibility to decorate the framework of such structures prompted us to study the synthesis of new hydroxy propargyl arylcyclopentadienone derivatives. Considering the ability of such systems to give π–π stacking interactions, the introduction on a polyaromatic structure of polar substituents able to generate hydrogen bonding could open the possibility to form gels, although any gelation properties has been never observed for these extensively studied systems. we have synthesized a new class of 3,4-bis (4-(3-hydroxy- propynyl) phenyl) -2, 5-diphenylcyclopentadienone derivatives, one of which (1a) proved to be, for the first time, a powerful organogelator. The experimental results indicated that the hydroxydimethylalkynyl substituents are fundamental to guarantee the gelation properties of the tetraarylcyclopentadienone unit. Combining the results of FT-IR, 1H NMR, UV-vis and fluorescence emission spectra, we believe that H-bonding and π–π interactions are the driving forces played for the gel formation. The importance of soft materials lies on their ability to respond to external stimuli, that can be also of chemical nature. In particular, high attention has been recently devoted to anion responsive properties of gels. Therefore the behaviour of organogels of 1a in toluene, ACN and MeNO2 towards the addition of 1 equivalent of various tetrabutylammonium salts were investigated. The rheological properties of gels in toluene, ACN and MeNO2 with and without the addition of Bu4N+X- salts were measured. In addition a qualitative analysis on cation recognition was performed. Finally the nature of the cyclic core of the gelator was changed in order to verify how the carbonyl group was essential to gel solvents. Until now, 4,5-diarylimidazoles have been synthesized.

Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.

DNA fragments with stretches of cytosine residues can fold into four-stranded structures in which two parallel duplexes, held together by hemiprotonated cytosine.cytosine+ (C.C+) base pairs, intercalate into each other with opposite polarity. The structural details of this intercalated DNA quadruplex have been assessed by solution NMR and single crystal x-ray diffraction studies of cytosine-rich sequences, including those present in metazoan telomeres. A conserved feature of these structures is the absence of stabilizing stacking interactions between the aromatic ring systems of adjacent C.C+ base pairs from intercalated duplexes. Effective stacking involves only the exocyclic keto groups and amino groups of the cytidine bases. The apparent absence of stability provided by stacking interactions between the bases in this intercalated DNA has prompted us to examine the available structures in detail, in particular with regard to unusual features that could compensate for the lack of base stacking. In addition to base-on-deoxyribose stacking and intra-cytidine C-H...O hydrogen bonds, this analysis reveals the presence of a hitherto unobserved, systematic intermolecular C-H...O hydrogen bonding network between the deoxyribose sugar moieties of antiparallel backbones in the four-stranded molecule.

2-(2-Nitroanilino)-5,6,7,8-tetrahydro-4H-cyclohepta[b]thiophene-3-carbonitrile

The title compound, C(16)H(15)N(3)O(2)S, was synthesized by the reaction of 2-amino-5,6,7,8-tetrahydro-4H-cyclohepta[b]thiophene-3-carbonitrile and o-fluoronitrobenzene. The thiophene and nitrophenyl rings and amino and carbonitrile groups are coplanar with a maximum deviation of 0.046 (2) angstrom and a dihedral angle of 0.92 (6)degrees between the rings. The cyclohepta ring adopts a chair conformation. Intramolecular N-H center dot center dot center dot O and C-H center dot center dot center dot S interactions occur. In the crystal, the molecules form layers that are linked by pi-pi stacking interactions between the thiophene and benzene rings [centroid-centroid distances = 3.7089 (12) and 3.6170 (12) angstrom].

Aminotriazines as locking fragments in macrocyclic synthesis

The macrocyclic compounds (6-(4',6'-diamino-1',3',5'-triazinyl)-1,4,6,8,11-pentaazacyclotetradecane)copper(II) triperchlorate dihydrate, [Cu(HL2)](ClO4)(3). 2H(2)O, (6-(6'-amino-4'-oxo-1'H-1',3',5'-triazinyl)-1,4,6,8,11-pentaazacyclotetradecane)copper(II) diperchlorate hydrate, [CuL3](ClO4)(2). H2O, and [(6-(4',6'-dioxo-1'H-1',3',5'-triazinyl) 1,4,6,8,11-pentaazacyclotetradecane)copper(II)] diperchlorate, [CuL4](ClO4)(2), have been synthesized. The macrocycles synthesized contain respectively pendant melamine, ammeline,and ammelide rings. The X-ray cyrstallographic analyses of [Cu(HL2)](ClO4)(3). 2H(2)O, triclinic, space group P (1) over bar, a = 9.489(10) Angstrom, b = 12.340(2) Angstrom, c = 24.496(4) Angstrom, alpha = 87.74(10)degrees beta = 85.51(10)degrees gamma = 70.95(10)degrees and Z = 4, and {[CuL3](ClO4)(2). H2O}2, monoclinic, space group C2/c, a = 18.624(8) Angstrom, b = 17.160(2) Angstrom, c = 15.998(6) Angstrom, beta = 117.82(2)degrees, and Z = 4, are reported. The structure of [Cu(HL2)](ClO4)(3). 2H(2)O shows the formation of linear tapes, formed by a combination of hydrogen bonds and pi-pi stacking interactions. The structure of [CuL3](ClO4)(2). H2O displays formation of dimers, formed by a coordinate bond from the oxygen in one molecule to the copper atom of another. The tautomeric forms of the ammeline and ammelide moieties have been determined. The potential of these compounds as subunits for cocrystallization has been investigated.