Molecular rotors as simple models to study amide NH-aromatic interactions and their role in the folding of peptide-like structures

The conformational behavior of designed macrocyclic naphthalenophanes (1a,b and 2a,b) derived from amino acids (Phe and Val) has been used for studying NH...pi interactions. The cycles having 16- and 17-membered rings showed a dynamic process within the NMR time scale, produced by the flipping of the aromatic naphthalene moiety with respect to the macrocyclic main plane. We used the temperature dependence of 1H NMR to obtain activation parameters of the energetic barrier for the process (variable temperature NMR and line shape analysis). The rate of the movement clearly depends on the macrocyclic ring size and, more interestingly, on the nature of the peptidomimetic side chain, the energetic barrier being higher for the compounds bearing aromatic side chains. A largely negative entropic contribution to the free energy of activation was observed, with clear differences due to the side chain nature. Molecular modeling studies suggest that the aromatic rings interact with intramolecularly H-bonded amide NH groups, protecting them from solvation and thus leading to a larger unfavorable activation entropy. This NH...pi interaction has been exploited for the preparation of new systems (1c and meso-1b) with designed conformational preferences, in which aromatic rings tend to fold over amide NH groups. Thus, these minimalistic molecular rotors have served us as simple model systems for the study of NH...pi interactions and their implication in the folding of peptide-like molecules.     

Gamma4-aminoxy peptides as new peptidomimetic foldamers

The conformational properties of peptides 1-3 of gamma-aminoxy acids have been investigated by using FT-IR, NMR spectroscopy, and X-ray crystallography. Diamide 1 consisting of unsubstituted gamma-aminoxy acid cannot form intramolecular hydrogen bond. A novel gamma N-O turn involving a 10-membered-ring intramolecular hydrogen bond between NHi+2 and COi is formed in gamma4-aminoxy peptides 2 and 3. Triamides 3 prefers a new helical structure featuring two consecutive gamma N-O turns. Therefore, gamma4-aminoxy peptides represent new peptidomimetic foldamers.     

Synthetic and structural studies on macrocyclic amino cyclitols--conformational chameleons

Starting from quinic acid the synthesis of 1,4-butanediol-linked macrocyclic aminocyclitols 30, 32, 34, 36 and 38 is described. Assembly was achieved by olefin cross-metathesis of appropriate cyclohexyl allyl ethers followed by ring-closing metathesis of bis-O-allyl homodimers. In all five cases studied, the only products that were formed were those resulting from direct ring-closing metathesis; the formation of larger rings was not detected. These macrocycles exhibited diverse conformational behaviour which included formation of stable separable conformers 31a and 31b as well as conformationally dynamic macrocycles 35 in which a ring flip in one cyclohexane chair conformer induces a ring flip of the other cyclohexane ring through the linking chains of the macrocycles. The activation energy for the inversion of the chair conformation in this process was determined to be about 38 kJ mol(-1), which is about 7 kJ mol(-1) lower than the activation energy for the ring flip of the unsubstituted cyclohexane ring. In all cases, the conformational studies strongly suggest that intramolecular H-bonding between 1,3-diaxially oriented amido and alcohol or ether groups exerts a decisive contribution to the overall stabilisation of the preferred cyclohexane chair conformation.     

Study of intramolecular interactions in aspirin

A detailed quantum chemical study of the solvent effects in the intramolecular hydrogen bonding, conformational stability, and reactivity of aspirin has been performed using density functional theory (DFT) at the B3LYP/6‐31G(d) theory level. Seven conformational isomers, three of them presenting intramolecular hydrogen bonds, have been located. Thermochemical functions have been computed, and relative energies and free enthalpies have been determined in gas and aqueous phases. Several molecular properties have been calculated to predict the ability of aspirin to acylate cyclooxygenase (COX) enzymes. A six‐membered‐ring hydrogen‐bonded conformer was found to be the most reactive species. The solvation in aqueous phase increases the reactivity and strengthens intramolecular hydrogen bonding.     

Conformationally constrained macrocycles that mimic tripeptide beta-strands in water and aprotic solvents

The beta-strand conformation is unknown for short peptides in aqueous solution, yet it is a fundamental building block in proteins and the crucial recognition motif for proteolytic enzymes that enable formation and turnover of all proteins. To create a generalized scaffold as a peptidomimetic that is pre-organized in a beta-strand, we individually synthesized a series of 15-22-membered macrocyclic analogues of tripeptides and analyzed their structures. Each cycle is highly constrained by two trans amide bonds and a planar aromatic ring with a short nonpeptidic linker between them. A measure of this ring strain is the restricted rotation of the component tyrosinyl aromatic ring (DeltaG(rot) 76.7 kJ mol(-1) (16-membered ring), 46.1 kJ mol(-1) (17-membered ring)) evidenced by variable temperature proton NMR spectra (DMF-d(7), 200-400 K). Unusually large amide coupling constants ((3)J(NH-CHalpha) 9-10 Hz) corresponding to large dihedral angles were detected in both protic and aprotic solvents for these macrocycles, consistent with a high degree of structure in solution. The temperature dependence of all amide NH chemical shifts (Deltadelta/T 7-12 ppb/deg) precluded the presence of transannular hydrogen bonds that define alternative turn structures. Whereas similar sized conventional cyclic peptides usually exist in solution as an equilibrium mixture of multiple conformers, these macrocycles adopt a well-defined beta-strand structure even in water as revealed by 2-D NMR spectral data and by a structure calculation for the smallest (15-membered) and most constrained macrocycle. Macrocycles that are sufficiently constrained to exclusively adopt a beta-strand-mimicking structure in water may be useful pre-organized and generic templates for the design of compounds that interfere with beta-strand recognition in biology.     

The unique properties observed for the unsymmetrical macrocyclic compounds with the highly distorted structure

A new class of aza-macrocycles with the highly distorted structure was found to exhibit unique properties. These macrocycles react with various lithium salts to form lithium complexes and their lithium complexation reactions depend on a substituent on the macrocyclic ring; slower rates and larger equilibrium constants were observed for the macrocycle with a bulkier substituent. The irradiation of these macrocycles by UV light was found to lead to the isomerization, and the photoisomerization rate of macrocycle with the bulky substituent was much faster. The highly distorted structure of these macrocycles makes it much easier to change the conformation of macrocyclic skeleton and these macrocycles have a variety of conformations. The factors to govern this conformational change were therefore explored. The solvent effect was examined by ¹H NMR spectroscopy, because these macrocycles have a strong intramolecular hydrogen bond in the ring. As a result, the solvent was found to have a big effect on the ¹H NMR spectra of macrocycles that could be explained in terms of the conformational change of macrocycle. This finding suggests the solvent to be an important way of controlling the conformation.     

Effects of intramolecular hydrogen bonding on the absorption transition energies of 2-hydroxy-5-methylazobenzene

The effect of the intramolecular hydrogen bonding on the excited states of 2-hydroxy-5-methylazobenzene (1) has been studied by means of u.v. spectroscopy and INDO/S-Cl calculations. The results show that the spectrum of 1 is on the whole red-shifted with respect to the spectrum of 2-methoxy-5-methylazobenzene (2). The excited states of both compounds are dominated by the energy of the lowest unoccupied MO, which is lowered on H-bonding formation. The effects of the rotation of the substituted ring on the excited states and on the molecular orbital energies of 2 have been also investigated. The results indicate that both the intramolecular H-bonding and the probable loss of planarity in the compound 2 may contribute to the observed red shift of the absorption bands of 1 with respect to 2.     

Efficient macrocyclization of U-turn preorganized peptidomimetics: the role of intramolecular H-bond and solvophobic effects

Simple peptidomimetic molecules derived from amino acids were reacted with meta- and para-bis(bromomethyl)benzene in acetonitrile to very efficiently yield macrocyclic structures. The cyclization reaction does not require high dilution techniques and seems to be insensitive to the size of the formed macrocycle. The analysis of data obtained by (1)H NMR, single-crystal X-ray diffraction, fluorescence measurements, and molecular mechanics indicate that folded conformations can preorganize the system for an efficient cyclization. The role played by intramolecular hydrogen-bonding and solvophobic effects in the presence of folded conformations is analyzed.     

Inherently chiral biscalixarene cone–cone conformers consisting of calix[4]arene and calix[5]arene subunits

Inherently chiral biscalixarenes with hetero-cavities were synthesized by a covalent assembly of p-tert-butylcalix[5]arene with a 1,3-substituted calix[4]arene via 1,3-alkylation reaction and subsequent desymmetrization. The racemates were resolved by chiral HPLC method. ¹H NMR spectra, VT-NMR spectra, and theoretical calculations support that the calix[5]arene subunit of the inherently chiral calix[4][5]arene ester adopts a cone-in conformation, with the aromatic ring bearing the CH₂CO₂Et group tilting inward the calix[5]arene cavity. By contrast, such a cone-in structural feature of the calix[5]arene subunit disappears for the corresponding inherently chiral calix[4][5]arene carboxylic acid, due to the intramolecular hydrogen bonding between the carboxyl group and an ethereal oxygen of the glycolic chain.     

Silver complexes of peptidomimetic polyazapyridinophanes. The influence of the bonding cavity size and the nature of side chains

Several peptidomimetic macrocycles containing a pyridine spacer and ring sizes ranging from 15 to 17 have been efficiently synthesized starting from valine and phenylalanine. The complexes formed have been investigated by potentiometry and NMR. Log K values show that phenylalanine derivatives are consistently more stable than valine derivatives , whilst macrocycles with ring sizes of 16 members are the most appropriate for the complexation. The NMR data, in combination with molecular modeling, allow rationalization of the structure of the complexes formed and the participation of the aromatic rings from the side chain of phenylalanine in pi-Ag+ interactions to be discarded.     

Anion induced conformational switch of a macrocyclic amide receptor

Isophthalic acid-based macrocyclic tetraamide 4 shows considerable conformational change during anion binding. In the solid state and in solution the free receptor exists in nonbonding, closed conformation stabilized by two intramolecular hydrogen bonds. Upon anion complexation, the receptor switches to a conformation with convergent arrangement of hydrogen bond donors. The conformational switch is evidenced by 2D NMR and X-ray analyses of the free ligand and its Cl⁻ complex.     

Catalyst-Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides

The biomimetic synthesis of aromatic polyketides from macrocyclic substrates by means of catalyst-controlled transannular cyclization cascades is described. The macrocyclic substrates, which feature increased stability and fewer conformational states, were thereby transformed into several distinct polyketide scaffolds. The catalyst-controlled transannular cyclizations selectively led to aromatic polyketides with a defined folding and oxygenation pattern, thus emulating β-keto-processing steps of polyketide biosynthesis.     

β-Hairpin stabilization through an interstrand triazole bridge

β-Hairpin peptides were conformationally stabilized through a 1,4 disubstituted 1,2,3-triazole interstrand linkage. A NMR conformational analysis revealed that the β-hairpin content depends on the number and position of substituent methylene units of the 1,2,3-triazole ring. These results will allow the design of metabolically stable peptidomimetic analogs of bioactive β-hairpin peptides.     

10a-(4-Biphenyl)-10b-methyl-10a,10b-dihydropyrene: a conformational study and ring current effect

A dithiacyclophane was employed as a precursor to the title compound. A conformational study of the dithiacyclophane revealed a unique phenomenon in its terphenyl unit: one ring is rigidly held, the other terminal ring undergoes free rotation and the central ring exhibits restricted mobility. The aromatic protons of the biphenyl unit are all shielded by the dihydropyrene unit and well resolved in the ¹H NMR spectrum, consistent with a ring current effect extended to eight conjugated carbon atoms away from the molecular plane of dihydropyrene.     

Conformational study of a guaiacyl beta-O-4 lignin model compound by NMR. Examination of intramolecular hydrogen bonding interactions and conformational flexibility in solution

Intramolecular H-bonding interactions were investigated in solution for the threo and erythro diastereomeric forms of a guaiacyl beta-O-4 lignin model compound by using the NMR data obtained from hydroxyl protons. Temperature coefficients of the chemical shifts (ddelta/dT) and coupling constants (3J(HCOH)) were measured in aprotic and protic solutions: DMSO-d6, acetone-d6 and acetone-d6-water. The NMR parameters do not support the existence of strong and persistent intramolecular H-bonds that could participate in the stabilization of the guaiacyl beta-O-4 structure in solution, but instead indicate that intermolecular H-bonds to solvent predominate. 1D NOE experiments nevertheless revealed the presence of a direct chemical exchange between the hydroxyl protons, suggesting the possible existence of weak and transient intramolecular H-bonding interactions. The conformational flexibility of the threo structure was also investigated in acetone solution from the measurement of long-range 1H, 1H and 1H, 13C coupling constants and from NOESY experiments. The NMR data are not consistent with any single conformation, indicating that different conformers co-exist in solution. The experimental results support the conformational flexibility predicted by molecular dynamics simulations performed in a previous study. Finally, both experimental and theoretical approaches indicate that weak intramolecular H-bonds can exist transiently in solution, breaking and reforming as the beta-O-4 molecule undergoes conformational interconversion, but cannot be invoked as possible means of conferring rigidity to the beta-O-4 structure.     

Diarylethynyl amides that recognize the parallel conformation of genomic promoter DNA G-quadruplexes

We report bis-phenylethynyl amide derivatives as a potent G-quadruplex binding small molecule scaffold. The amide derivatives were efficiently prepared in 3 steps by employing Sonogashira coupling, ester hydrolysis and a chemoselective amide coupling. Ligand-quadruplex recognition has been evaluated using a fluorescence resonance energy transfer (FRET) melting assay, surface plasmon resonance (SPR), circular dichroism (CD) and (1)H nuclear magnetic resonance (NMR) spectroscopy. While most of the G-quadruplex ligands reported so far comprise a planar, aromatic core designed to stack on the terminal tetrads of a G-quadruplex, these compounds are neither polycyclic, nor macrocyclic and have free rotation around the triple bond enabling conformational flexibility. Such molecules show very good binding affinity, excellent quadruplex:duplex selectivity and also promising discrimination between intramolecular promoter quadruplexes. Our results indicate that the recognition of the c-kit2 quadruplex by these ligands is achieved through groove binding, which favors the formation of a parallel conformation.     

Chiral ordering and conformational dynamics for a class of oligo-phenylene-ethynylenes on Au(111)

Adsorption structures formed from a class of planar organic molecules on the Au(111) surface under ultrahigh vacuum conditions have been characterized using scanning tunneling microscopy (STM). The molecules have different geometries, linear, bent, or three-spoke, but all consist of a conjugated aromatic backbone formed from three or four benzene rings connected by ethynylene spokes and functionalized at all ends with an aldehyde, a hydroxyl, and a bulky tert-butyl group. Upon adsorption, the molecules adopt different surface conformations some of which are chiral. For the majority of the observed adsorption structures, chirality is expressed also in the molecular tiling pattern, and the two levels of chirality display a high degree of correlation. The formation and chiral ordering of the self-assembled structures are shown to result from dynamic interchanges between a diffusing lattice gas and the nucleated islands, as well as from a chiral switching process in which molecules alter their conformation by an intramolecular rotation around a molecular spoke, enabling them to accommodate to the tiling pattern of the surrounding molecular structures. The kinetics of the conformational switching is investigated from time-resolved, variable temperature STM, showing the process to involve an activation energy of approximately 0.3 eV depending on the local molecular environment. The molecule-molecule interactions appear primarily to be of van der Waals character, despite the investigated compounds having functional moieties capable of forming intermolecular hydrogen bonds.     

Escherichia coli β‐Galactosidase Inhibitors through Modifications at the Aglyconic Moiety: Experimental Evidence of Conformational Distortion in the Molecular Recognition Process

Herein, we describe the use of thioglycosides as glycosidase inhibitors by employing novel modifications at the reducing end of these glycomimetics. The inhibitors display a basic galactopyranosyl unit (1→4)‐bonded to a 3‐deoxy‐4‐thiopentopyranose moiety. The molecular basis of the observed inhibition has been studied by using a combination of NMR spectroscopy and molecular modeling techniques. It is demonstrated that these molecules are not recognized by Escherichia coli β‐galactosidase in their ground‐state conformation, with a conformational selection process taking place. In fact, the observed conformational distortion depends on the chemical nature of the compounds and results from the rotation around the glycosidic linkage (variation of Φ or Ψ) or from the deformation of the six‐membered ring of the pentopyranose. The bound conformations of the ligand are adapted in the enzymatic pocket with a variety of hydrogen‐bond, van der Waals, and stacking interactions.     

Redox active macrocyclic receptors for neutral guests

A novel series of triazine-appended macrocyclic complexes has been investigated as potential hydrogen bonding receptors for complementarily disposed heterocycles. Cocrystallization of a melamine-appended azacyclam complex of Cu(II) has been achieved with barbitone, the barbiturate anion and thymine. In each case, a complementary DAD/ADA hydrogen bonding motif between the melamine group and the heterocycle has been identified by X-ray crystallography. Electrochemical studies of the copper macrocycles in both nonaqueous and aqueous solution show anodic shifts of the Cu(II/)(I) redox couple of more than 60 mV upon addition of guest molecules with matching H-bonding motifs. The Zn(II) analogues have been synthesized via transmetalation of the Cu(II) complex, and their guest binding properties investigated by NMR spectroscopy. (1)H NMR shifts of up to 0.8 ppm were observed upon addition of guest, and stability constants are similar to those obtained electrochemically.