Sterically controlled recognition of macromolecular sequence information by molecular tweezers

Sequence-specific binding is demonstrated between pyrene-based tweezer molecules and soluble, high molar mass copolyimides. The binding involves complementary pi - pi stacking interactions, polymer chain-folding, and hydrogen bonding and is extremely sensitive to the steric environment around the pyromellitimide binding-site. A detailed picture of the intermolecular interactions involved has been obtained through single-crystal X-ray studies of tweezer complexes with model diimides. Ring-current magnetic shielding of polyimide protons by the pyrene '' arms '' of the tweezer molecule induces large complexation shifts of the corresponding H-1 NMR resonances, enabling specific triplet sequences to be identified by their complexation shifts. Extended comonomer sequences (triplets of triplets in which the monomer residues differ only by the presence or absence of a methyl group) can be '' read '' by a mechanism which involves multiple binding of tweezer molecules to adjacent diimide residues within the copolymer chain. The adjacent-binding model for sequence recognition has been validated by two conceptually different sets of tweezer binding experiments. One approach compares sequence-recognition events for copolyimides having either restricted or unrestricted triple-triplet sequences, and the other makes use of copolymers containing both strongly binding and completely nonbinding diimide residues. In all cases the nature and relative proportions of triple-triplet sequences predicted by the adjacent-binding model are fully consistent with the observed H-1 NMR data.

Fmoc-diphenylalanine self assembles to a hydrogel via a novel architecture based on π-π interlocked β-sheets

The self assembly of peptide hydrogelators that carry aromatic substituents can be modeled by a novel nanocylindrical architecture. The proposed model suggests that the nanocylinders are formed by anti-parallel β-sheets interlocked by the π-stacking interactions of fluorenyl groups and phenyl rings. This explanation is consistent with the structures observed in TEM and the data obtained by a variety of spectroscopic techniques.

Beta-caryophyllene is a dietary cannabinoid

The psychoactive cannabinoids from Cannabis sativa L. and the arachidonic acid-derived endocannabinoids are nonselective natural ligands for cannabinoid receptor type 1 (CB(1)) and CB(2) receptors. Although the CB(1) receptor is responsible for the psychomodulatory effects, activation of the CB(2) receptor is a potential therapeutic strategy for the treatment of inflammation, pain, atherosclerosis, and osteoporosis. Here, we report that the widespread plant volatile (E)-beta-caryophyllene [(E)-BCP] selectively binds to the CB(2) receptor (K(i) = 155 +/- 4 nM) and that it is a functional CB(2) agonist. Intriguingly, (E)-BCP is a common constituent of the essential oils of numerous spice and food plants and a major component in Cannabis. Molecular docking simulations have identified a putative binding site of (E)-BCP in the CB(2) receptor, showing ligand pi-pi stacking interactions with residues F117 and W258. Upon binding to the CB(2) receptor, (E)-BCP inhibits adenylate cylcase, leads to intracellular calcium transients and weakly activates the mitogen-activated kinases Erk1/2 and p38 in primary human monocytes. (E)-BCP (500 nM) inhibits lipopolysaccharide (LPS)-induced proinflammatory cytokine expression in peripheral blood and attenuates LPS-stimulated Erk1/2 and JNK1/2 phosphorylation in monocytes. Furthermore, peroral (E)-BCP at 5 mg/kg strongly reduces the carrageenan-induced inflammatory response in wild-type mice but not in mice lacking CB(2) receptors, providing evidence that this natural product exerts cannabimimetic effects in vivo. These results identify (E)-BCP as a functional nonpsychoactive CB(2) receptor ligand in foodstuff and as a macrocyclic antiinflammatory cannabinoid in Cannabis.

The interplay of secondary Te···N, Te···O, Te···I and I···I interactions, Te···π contacts and π-stacking in the supramolecular structures of [{2-(4-nitrobenzylideneamino)-5-methyl}phenyl](4-methoxyphenyl)tellurium dihalides

The unsymmetrical1y substituted diorganotellurium dihalides [2-(4,4'-N0₂C₆H₄CHNC₆H₃Me]RTeX₂ (R = 4-MeOC₆H₄, X = Cl,
1a; Br, 1b; I, 1c; R =4-MeC₆H₄ ; X = Cl, 2; R =C₆H₅, X = Cl, 3) were prepared in good yields and characterized by solution and solid-state ¹²⁵Te NMR spectroscopy, IR spectroscopy and X-ray crystallography. In the solid-state, molecular structures of 1a and 1c possess scarcely observed 1,4-type intramolecular Te···N secondary interaction. Crystal packing of these compounds show an unusually rich diversity of intermolecular secondary, Te·· ·0, Te· .. \ and 1···1 interactions, Te·· ·π contacts as well as extensive
π-stacking of the organic substituents.

Unusual Salt-Induced Color Modulation through Aggregation-Induced Emission Switching of a Bis-cationic Phenylenedivinylene-Based pi Hydrogelator

The synthesis, hydrogelation, and aggregation-induced emission switching of the phenylenedivinylene bis-N-octyl pyridinium salt is described. Hydrogelation occurs as a consequence of pi-stacking, van der Waals, and electrostatic interactions that lead to a high gel melting temperature and significant mechanical properties at a very low weight percentage of the gelator. A morphology transition from fiber-to-coil-to-tube was observed depending on the concentration of the gelator. Variation in the added salt type, salt concentrations, or temperature profoundly influenced the order of aggregation of the gelator molecules in aqueous solution. Formation of a novel chromophore assembly in this way leads to an aggregation-induced switch of the emission colors. The emission color switches from sky blue to white to orange depending upon the extent of aggregation through mere addition of external inorganic salts. Remarkably, the salt effect on the assembly of such cationic phenylenedivinylenes in water follow the behavior predicted from the well-known Hofmeister effects. Mechanistic insights for these aggregation processes were obtained through the counterion exchange studies. The aggregation-induced emission switching that leads to a room-temperature white-light emission from a single chromophore in a single solvent (water) is highly promising for optoelectronic applications.

Computational Study of the Formation of Short Centrosymmetric N-center dot center dot center dot S Supramolecular Synthon and Related Weak Interactions in Crystalline 1,2,4-Triazoles

A comprehensive analysis of the crystal packing and the energetic features of a series of four biologically active molecules belonging to the family of substituted 4-(benzylideneamino)-3-(4-fluoro-3-phenoxyphenyl)-1H-1,2,4-triazole-5-(4 H)-thione derivatives have been performed based on the molecular conformation and the supramolecular packing. This involves the formation of a short centrosymmetric R-2(2)(8) NH...S supramolecular synthon in the solid state, including the presence of CH...S, CH...O, CH...N, CH...F, CH...Cl, CF...FC, CCl...ClC, and CH...pi intermolecular interactions along with pp stacking to evaluate the role of noncovalent interactions in the crystal. The presence of such synthons has a substantial contribution toward the interaction energy (-18 to -20 kcal/mol) as obtained from the PIXEL calculation, wherein the Coulombic and polarization contribution are more significant than the dispersion contribution. The geometrical characteristics of such synthons favor short distance, and the population of related molecules having these geometries is rare as has been obtained from the Cambridge Structural Database (CSD). Furthermore, their interaction energies have been compared with those present in our molecules in the solid state. The topological characteristics of the NH...S supramolecular synthon, in addition to related weak interactions, CH...N, CH...Cl, CF...FC, and CCl...ClC, have been estimated using the quantum theory of atoms in molecules (QTAIM). In addition, an analysis of the Hirshfeld surface and associated fingerprint plots of these four molecules also have provided a platform for the evaluation of the contribution of different atom...atom contacts, which contribute toward the packing of the molecules in solids.

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-pi and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to beta-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.

A healable supramolecular polymer blend based on aromatic π-π stacking and hydrogen bonding interactions

An elastomeric, supramolecular healable polymer blend, comprising a chain-folding polyimide and a telechelic polyurethane with pyrenyl endgroups, is compatibilised by aromatic π−π stacking between the π-electron-deficient diimide groups and the π-electron-rich pyrenyl units. This inter-polymer interaction is key to forming a tough, healable, elastomeric material. Variable temperature FTIR analysis of the bulk material also conclusively demonstrates the presence of hydrogen bonding, which complements the π–π stacking interactions. Variable temperature SAXS analysis shows that the healable polymeric blend has a nanophase-separated morphology, and that the X-ray contrast between the two types of domain increases with increasing temperature, a feature that is repeatable over several heating and cooling cycles. A fractured sample of this material reproducibly regains more than 95% of the tensile modulus, 91% of the elongation to break, and 77% of the modulus of toughness of the pristine material.

Salts responsive nanovesicles through π-stacking induced self-assembly of backbone modified tripeptides

A set of backbone modified peptides of general formula Boc-Xx-m-ABA-Yy-OMe where m-ABA is meta-aminobenzoic acid and Xx and Yy are natural amino acids such as Phe, Gly, Pro, Leu, Ile, Tyr and Trp etc., are found to self-assemble into soft nanovesicular structures in methanol-water solution (9:1 by v/v). At higher concentration the peptides generate larger vesicles which are formed through fusion of smaller vesicles. The formation of vesicles has been facilitated through the participation of various noncovalent interactions such as aromatic pi-stacking, hydrogen bonding and hydrophobic interactions. Model study indicates that the pi-stacking induced self-assembly, mediated by m-ABA is essential for well structured vesicles formation. The presence of conformationally rigid m-ABA in the backbone of the peptides also helps to form vesicular structures by restricting the conformational entropy. The vesicular structures get disrupted in presence of various salts such as KCl, CaCl(2), N(n-Bu)(4)Br and (NH(4))(2)SO(4) in methanol-water solution. Fluorescence microscopy and UV studies reveal that the soft nanovesicles encapsulate organic dye molecules such as Rhodamine B and Acridine Orange which could be released through salts induced disruption of vesicles.

Self-assembly of metallosupramolecules directed by (N-H)(2)center dot center dot center dot SCN-M (M = Co, Ni), C-H center dot center dot center dot pi and pi-pi synthons

This work deals with the synthesis, spectroscopic and structural investigation of pyrazolyl complexes of the type trans-[M(NCS)(2)(HPz)(4)] {M=Co (1), Ni (2); HPz=pyrazole}. Single crystal X-ray studies on 1 and 2 reveal the formation of similar supramolecular arrangements derived from self-assembly of monomers linked together through intermolecular N-H center dot center dot center dot SCN hydrogen bonds, C-H center dot center dot center dot pi interactions and pi-pi stacking. (c) 2005 Elsevier B.V. All rights reserved.

Interplay of pi–pi stacking and hydrogen bonding in conjugated supramolecular systems studied by solid-state NMR

In this work supramolecular organic systems based on rigid pi-conjugated building blocks and flexible side chains were studied via solid-state NMR spectroscopy. Specifically, these studies focussed on phenylene ethynylene based macrocycles, polymer systems including polythiophenes, and rod-coil copolymers of oligo(p-benzamide) and poly(ethylene glycol). All systems were studied in terms of the local order and mobility. The central topic of this dissertation was to elucidate the role of the flexible side chains in interplay of different non-covalent interactions, like pi-pi-stacking and hydrogen bonding.Combining the results of this work, it can be concluded that the ratio of the rigid block and the attached alkyl side chains can be crucial for the design of an ordered pi-conjugated supramolecular system. Through alkyl side chains, it is also possible to introduce liquid-crystalline phases in the system, which can foster the local order of the system. Moreover in the studied system longer, unbranched alkyl side chains are better suited to stabilize the corresponding aggregation than shorter, branched ones.The combination of non-covalent interactions such as pi-pi-stacking and hydrogen bonding play an important role for structure formation. However, the effect of pi-pi-stacking interaction is much weaker than the effect of hydrogen bonding and is only observed in systems with a suitable local order. Hence, they are often not strong enough to control the local order. In contrast, hydrogen bonds predominantly influence the structural organization and packing. In comparison the size of the alkyl side chains is only of minor importance. The suppression of certain hydrogen bonds can lead to completely different structures and can induce a specific aggregation behavior. Thus, for the design of a supramolecular ordered system the presence of hydrogen bonding efficiently stabilizes the corresponding structure, but the ratio of hydrogen bond forming groups should be kept low to be able to influence the structure selectively.

Ethyl 6-chloro-2-[(2-chloro-7,8-dimethylquinolin-3-yl)methoxy]-4-phenylquino line-3-carboxylate

In the title compound, C30H24Cl2N2O3, the two quinoline ring systems are almost planar [maximum deviations = 0.029 (2) and 0.018 (3) angstrom] and the dihedral angle between them is 4.17 (8)degrees. The dihedral angle between the phenyl ring and its attached quinoline ring is 69.06 (13)degrees. The packing is stabilized by C-H center dot center dot center dot O, C-H center dot center dot center dot N, weak pi-pi stacking [centroid-centroid distances = 3.7985 (16) and 3.7662(17) angstrom] and C-H center dot center dot center dot pi interactions.

Novel Nanocomposites Made of Boron Nitride Nanotubes and a Physical Gel

This article describes successful incorporation of multiwalled boron nitride nanotubes (BNNTs) and various functionalized BNNTs by Lewis bases such as trioctylamine (TOA), tributylamine (TBA), and triphenylphosphine (TPP), etc., in organogels formed by triphenylenevinylene (TPV)-based low molecular weight gelator (LMWG) in toluene and consequent characterization of the resulting gel nanocomposites. Functionalized BNNTs were synthesized first,and the presence of tubular structures with high aspect ratio and increased diameter compared to the starting BNNTs was confirmed by SEM. TEM, and Raman spectroscopy. The micrographs of composites of I and BNNTs showed evidence of wrapping of the gelator molecules on to the BNNT surface presumably brought about by pi-pi stacking and van der Waals interactions, This leads to the formation of densely packed and directionally aligned fibrous networks. Such ``reinforced'' aggregation of the gelator molecules in presence of doped BNNTs led to an increase in the sot-to-gel transition temperature and the solidification temperature of the gel nanocomposites as revealed from differential scanning calorimetry. Rheological investigations of the gel nanocomposites indicate that the flow properties of the resulting materials become resistant to applied stress upon incorporation of even a very low wt % of BNNTs. Finally, the increase in thermal conductivity of the nanocomposite compared to the gelator alone was observed for the temperature range of 0-60 degrees C which may make these composites potentially useful in various applications depending on the choice and the amount of BNNT loading in the composite.

Synthesis and an Evaluation of Molecular Conformation and Crystal Packing in Two Substituted 4-Phenylquinolines

The title compounds, namely Methyl 2-methyl-4 -phenylquinoline-3-carboxylate (I), C18H15NO2, and (2E)-3-(3,4-dimethoxyphenyl)-1-(2-methyl-4 -phenylquinolin-3-yl)prop-2-en-1-one (II), C27H23NO3, comprising of the phenyl ring, exhibit differences in conformational behaviour with respect to the plane of the quinoline fragment. (I) contains the methyl ester moiety whereas (II) contains the chalcone fragment, consisting of a double bond and phenyl group containing dimethoxy groups as substituents. The dihedral angles between the phenyl group and the quinoline ring is 82.77 (7)A degrees in (I), and 79.02 (8)A degrees in (II) respectively. It is the weak C-H center dot center dot center dot O=C H-bond and C-H center dot center dot center dot pi interactions which dictate packing of molecules in (I). In (II), it is C-H center dot center dot center dot N and C-H center dot center dot center dot pi, involving the dimethoxy ring, which controls packing of molecules in the crystal lattice. In addition, pi center dot center dot center dot pi aromatic stacking interactions involving the quinoline fragment is present in all the molecules. The title compounds, namely methyl-2-methyl-4 -phenylquinoline-3-carboxylate (I), C18H15NO2, and (2E)-3-(3,4-dimethoxyphenyl)-1-(2-methyl-4 -phenylquinolin-3-yl)prop-2-en-1-one (II), C27H23NO3, comprising of the phenyl ring, exhibit differences in conformational behaviour with respect to the plane of the quinoline fragment. (I) contains the methyl ester moiety whereas (III) contains the chalcone fragment, consisting of a double bond and phenyl group containing dimethoxy groups as substituents. The dihedral angles between the phenyl group and the quinoline ring is 82.77 (7)A degrees in (I), and 79.02 (8)A degrees in (II) respectively. It is the weak C-H center dot center dot center dot O=C H-bond and C-H center dot center dot center dot pi interactions which dictate packing of molecules in (I). In (II), it is C-H center dot center dot center dot N and C-H center dot center dot center dot pi, involving the dimethoxy ring, which controls packing of molecules in the crystal lattice. In addition, pi center dot center dot center dot pi aromatic stacking interactions involving the quinoline fragment is present in all the molecules.

Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.