CH-pi Interactions Research Articles

Crystalline Structure ofN-(S)-2-Heptyl (1R,2R)-2-(2,3-Anthracenedicarboximido)cyclohexanecarboxamide That Differs from Its Preferred Conformation in the Solvent Used for Crystallization

The crystalline structure of N-(S)-2-heptyl (1R,2R)-2-(2,3-anthracenedicarboximido)cyclohexamide (1), which was crystallized from methanol, was determined by an X-ray analysis and had a different conformation from its preferred one in CD3OD by a 1H-NMR analysis. Inter- and intra-molecular CH-pi interaction in a crystal plays a very important role in crystal packing. The preferred conformation of the amide derivative in a solution allows us to exploit (1R,2R)-2-(2,3-anthracenedicarboximido)cyclohexanecarbonyl chloride as a conversion reagent to determine the absolute configuration of chiral amines by 1H-NMR.

The Recognition of Nucleotides with Μodel β-Hairpin Receptors: Investigation of Critical Contacts and Nucleotide Selectivity

[reaction: see text] We have investigated the factors that contribute to binding of ATP by a designed 12-residue beta-hairpin peptide, WKWK, and have determined its selectivity for binding to the naturally occurring nucleotide triphosphates. We have previously shown that WKWK creates an ATP binding pocket on one face of the beta-hairpin consisting of two Trp and two Lys residues. Mutation of the two Lys residues on the binding face of the beta-hairpin resulted in a lower affinity, indicating that each is involved in ATP binding and that each residue contributes approximately -1.5 kcal/mol to the energy of complexation. Replacement of either Trp residue of the ATP binding pocket with Phe or Leu destabilizes the complex formed with ATP by approximately 1 kcal/mol, indicating that both Trp residues participate in interactions with ATP. For binding to the nucleotide triphosphates, the order of binding affinity was shown to follow dTTP > GTP > ATP > CTP, with differences in binding energies spanning as much as 1.6 kcal/mol. NMR analysis demonstrates that both aromatic interactions with the Trp side chains and CH-pi interactions between the ribose protons and the Trp residues may contribute significantly to binding. The results from our model system provide useful thermodynamic information regarding protein-nucleic acid interactions that occur at the surface of a beta-sheet.

A novel C3v-symmetrical calix[6](aza)cryptand with a remarkably high and selective affinity for small ammoniums.

The three-step synthesis of a calix[6]arene capped with a TAC unit is presented. The novel C(3v)-symmetrical calix[6](aza)cryptand displayed an exceptionally high affinity for small ammoniums. NMR and X-ray diffraction analyses demonstrated the formation of endo-complexes. These complexes are stabilized thanks to (i) hydrogen bonding to both the aza cap and one phenolic unit of the calixarene and to (ii) cationic and CH-pi interactions between the ammonium and the aromatic walls of the host. Combined extraction and competitive binding experiments yielded the free energies of bindings DeltaG degrees in chloroform. The values are the highest ever obtained with a calixarene-type host. Calix[6]TAC displayed the best affinity for EtNH(3)(+). Comparison with other small ammoniums emphasizes the high selectivity of the recognition process.

Organic layered crystals with adjustable interlayer distances of 1-naphthylmethylammonium n-alkanoates and isomerism of hydrogen-bond networks by steric dimension.

A series of 1-naphthylmethylammonium n-alkanoates from acetate to triacontanoate produce isomorphic layered structures in the crystalline state. The interlayer distances, d-spacings, are proportional to the lengths of the alkyl chains. This is attributed to synergic intermolecular interactions; pi-pi and CH-pi interactions of the naphthalene rings between the cations, hydrophobic interactions of the alkyl chains, and two-dimensional hydrogen-bond networks between the primary ammonium cations and the carboxylate anions. Salts made from carboxylic acids wider than 5.5 A in the cross sections produce another columnar structure with a one-dimensional ladder-type hydrogen-bond network. Steric parameters of the acid components provide an explanation for the isomerism of the hydrogen-bond network.

Absolute helical arrangement of sulfonamide in the crystal.

[reaction: see text] 1,2-Bis(N-benzenesulfonyl-N-methylamino)benzene (2), which has no fixed asymmetric element, was crystallized from ethyl acetate as chiral crystals belonging to space group P4(1)2(1)2 (No. 92) or P4(3)2(1)2 (No. 96). The array of molecules built by the CH-pi interaction along the c-axis forms an enantiomeric helical superstructure in each individual crystal. The absolute configurations of the chiral crystals of 2 were determined by X-ray crystal structure analysis using the Flack parameter method. The solid-state CD spectra of the chiral crystals in KBr were mirror images. The equilibrium between the two enantiomers in solution is fast during crystallization at ambient temperature, and the energy barrier (DeltaG()) is estimated to be 11.7 +/- 0.3 kcal/mol (233 K).

Guest-induced assembly of tetracarboxyl-cavitand and tetra(3-pyridyl)-cavitand into a heterodimeric capsule via hydrogen bonds and CH-halogen and/or CH-pi interaction: control of the orientation of the encapsulated guest.

The guest- or solvent-induced assembly of a tetracarboxyl-cavitand 1 and a tetra(3-pyridyl)-cavitand 2 into a heterodimeric capsule 1.2 in a rim-to-rim fashion via four intermolecular CO(2)H.N hydrogen bonds has been investigated both in solution and in the solid state. In the (1)H NMR study, a 1:1 mixture of1a and 2a (R = (CH(2))(6)CH(3)) in CDCl(3) gave a mixture of various complicated aggregates, whereas this mixture in CDCl(2)CDCl(2) or p-xylene-d(10) exclusively produced the heterodimeric capsule 1a.2a. It was found that an appropriate 1,4-disubstituted-benzene is a suitable guest for inducing the exclusive formation of 1a.2a in CDCl(3). The ability of a guest to induce the formation of guest-encapsulating heterodimeric capsule, guest@(1a.2a), increased in the order p-ethyltoluene < 1-ethyl-4-methoxybenzene < or = 1-ethyl-4-iodobenzene < or = 1,4-dibromobenzene < 1-iodo-4-methoxybenzene < or= 1,4-dimethoxybenzene < or = 1,4-diiodobenzene. The (1)H NMR study revealed that a CH-halogen interaction between the inner protons of the methylene-bridge rims (-O-H(out)CH(in)-O-) of the 1a and 2a units and the halogen atoms of 1,4-dihalobenzenes and a CH-pi interaction between the methoxy protons of 1,4-dimethoxybenzene and the aromatic cavities of the 1a and 2a units play important roles in the formation of 1,4-dihalobenzene@(1a.2a) and 1,4-dimethoxybenzene@(1a.2a), respectively. A preliminary single-crystal X-ray diffraction analysis of guest@(1b.2b) (R = (CH(2))(2)Ph; guest = 1-iodo-4-methoxybenzene or p-xylene) confirmed that the guest encapsulated in 1b.2b is oriented with the long axis of the guest along the long axis of 1b.2b and that the iodo and the methoxy groups of the encapsulated 1-iodo-4-methoxybenzene are specifically oriented with respect to the cavities of the 2b and 1b units, respectively.

Syntheses and solid state structures of cyclic diynes with two chalcogen centres--a competition between weak interactions.

In this paper we report the synthesis of cyclic diynes of the general formula mX2n. The letters m and n indicate the lengths of chains between two C triple bond C-X units where X indicates S, Se, or Te. The lengths of the bridges vary between m=4-8 and n=2-6. Structural investigations by means of X-ray diffraction reveal for most systems a chair-like conformation in the solid state. For 5S(2)2, 5S(2)3, 7S(2)5, 5Se(2)2 and 5Te(2)3 tubular structures were encountered. These structures can be traced back to weak XX or weak C-Hpi interactions.

Supramolecular assembly and solution properties of bis(bipyridyl)ruthenium(II) coordination complexes of aryl(2-pyridyl)methanones.

A series of mono- and bis(2-pyridyl)-arylmethanone ligands were prepared by utilizing the reaction between either bromobenzonitrile or dicyanobenzene and 2-lithiopyridine in either a 1:1 or a 2:1 mol ratio, respectively. They react with [Ru(bpy)2(EtOH)2][PF6]2 to yield the new complexes [N,O-PhC(O)(2-py)Ru(bpy)2][PF6]2 (6), [p-N,O-BrC6H4C-(O)(2-py)Ru(bpy)2][PF6]2 (7), [m-N,O-BrC6H4C(O)(2-py)Ru(bpy)2][PF6]2 (8), [p-[N,O-C(O)(2-py)2Ru(bpy)2]2(C6H4)]-[PF6]4 (9), and [m-[N,O-C(O)(2-py)2Ru(bpy)2]2(C6H4)][PF6]4 (10). The solid state structures of 6 and 7 show that the octahedral cations are arranged in sinusoidal chains by pi-pi stacking and CH-pi interactions between bipyridyl groups. Substitution of bromine for hydrogen at the para position of the aryl group in 7 causes the aryl group to become involved in pi-pi stacking interactions that organize the chains into a sheet structure. The complicated 1H and 13C NMR spectra of the complexes have been fully assigned using 2D methods. The optical spectra show two absorption maxima near 434 and 564 nm due to MLCT transitions. The compounds were found to be nonluminescent. Electrochemical data acquired for CH3CN solutions of the bimetallic derivatives indicate that there is no electronic communication between metal centers mediated either through space or through ligand orbitals. Crystallographic information: 6.0.5CH3CN is monoclinic, C2/c, a = 24.3474(11) A, b = 13.7721(6) A, c = 21.3184(10) A, beta = 103.9920(10) degrees, Z = 8; 7 is monoclinic, P2(1)/c, a = 10.6639(11) A, b = 23.690(3) A, c = 13.7634(14) A, beta = 91.440(2) degrees, Z = 4.

Remarkably large positive and negative allosteric effects on ion recognition by the formation of a novel helical pseudocryptand.

In supramolecular chemistry, a great deal of attention has focused on regulating guest binding via an external stimulus. To utilize the same effector for both highly guest-selective positive and negative allosteric effects, however, stricter and more precise regulation of the host structure is required. A novel allosteric host 1 binds Fe(II) to afford the pseudocryptand, 1.Fe(II), which bears a cavity that is surrounded by three polyether chains in a helical fashion. The binding selectivity of 1 (Na+ > K+ > Rb+ > Cs+) is the opposite of 1.Fe(II) (Cs+ > Rb+ > K+ > Na+). Single-ion transport through a liquid membrane shows ion selectivity similar to the equilibrium constants. To the best of our knowledge, this is the first example of an allosteric recognition system, in which the same effector, that is, Fe(II), exhibits both large positive and negative allosteric effects on equilibrium and dynamic recognition events. The X-ray analysis and 1H NMR examination indicate that the combination of the macrobicyclic effect and the intramolecular interchain interactions (CH-pi interaction and steric hindrance) finely controls the positive and negative allosteric effects, which depend on the size of the guest. The helical framework opens a new general method for constructing more sophisticated, controllable receptors for helical biomolecules, for example, DNA and proteins, and helical molecular devices such as a molecular coil or spring responding to a stimulus.

High alpha/beta-anomer selectivity in molecular recognition of carbohydrates by artificial receptors.

[structure: see text] New effective, acyclic, pyridine-based receptors 1-3 show remarkable alpha/beta binding selectivity in the recognition of monosaccharides. They are able to participate in cooperative and bidentate hydrogen bonds with sugar hydroxyls as well as in CH-pi interactions with CH's of sugar molecules.

Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment.

Quantum mechanical and quantum mechanical/molecular mechanical calculations in conjunction with continuum solvation models have been used to analyze CH-pi interactions in model systems of aryl- and alkyl-aromatic interactions, as well as in a model folding system designed to study those interactions. High level calculations reproduced accurately the interaction of CH-pi interactions in both alkyl- and aryl-based model systems. Dispersion effects dominate the interaction, but the electrostatics term is also relevant for aryl CH-pi interactions. Theoretical calculations were also used to examine the influence of CH-pi interactions in determining the conformational flexibility of folding models. Finally, a critical comparison of the results obtained from high level calculations on model systems and the experimental data derived for folding models in apolar solvents was carried out, which allowed us to reconcile the apparent discrepancy found between both data.

The origin of endo stereoselectivity in the hetero-Diels-Alder reactions of aldehydes with ortho-xylylenes: CH-pi, pi-pi, and steric effects on stereoselectivity.

Theoretical studies of stereoselectivity have been carried out with B3LYP and MP2 calculations. The high endo selectivity of hetero-Diels-Alder reactions of ortho-xylylenes with acetaldehydes is shown to result from attractive CH-pi interactions between alkyl groups of the aldehyde and the aromatic ring in the transition states of the reaction. For the hetero-Diels-Alder reactions of ortho-xylylenes with benzaldehyde, the stereoselectivity is shown to be mainly governed by the attractive pi-pi interactions between the phenyl rings of the benzaldehyde and the ortho-xylylene. MP2 calculations are necessary to reproduce the stabilizing dispersion interactions.

Cooperative self-assembly of dendrimers via pseudorotaxane formation from a homotritopic guest molecule and complementary monotopic host dendrons.

Interaction of the homotritopic guest 1,3,5-tris[p-(benzylammoniomethyl)phenyl]benzene tris(hexafluorophosphate) (1a) with dibenzo-24-crown-8 (DB24C8) leads to the sequential self-assembly of [2]-, [3]-, and [4]-pseudorotaxanes 7a, 8a, and 9a, respectively. The self-assembly processes were studied using NMR spectroscopy. In CD(3)CN and CD(3)COCD(3) the individual association constants K(1), K(2), and K(3) for 1:1, 1:2, and 1:3 complexes were determined by several methods. Via Scatchard plots, the three NH(2)(+) sites of 1a were shown to behave independently in binding DB24C8. K values (4.4 x 10(2), 1.4 x 10(2), and 41 M(-)(1), respectively, in CD(3)CN) directly determined from signals for the individual complexes (7a, 8a, and 9a) were somewhat higher than those estimated from the Scatchard plot because of concentration dependence, but the ratios of association constants followed the expected statistical order (K(1):K(2):K(3) = 3:1:(1)/(3)). These are believed to be the first evaluations of association constants leading to a [4]-pseudorotaxane. In the less polar CDCl(3), association constants could not be determined because approximately 90% of the dissolved tritopic guest, which by itself is insoluble, was present as the fully loaded [4]pseudorotaxane 9a! Self-assembly of homotritopic guest 1a with benzyl ether dendrons of the first, second, and third generations functionalized at the "focal point" with DB24C8 moieties (3-5) produces pseudorotaxane dendrimers. The self-assembly processes were studied using (1)H NMR spectroscopy. In CD(3)COCD(3) for all three generations the individual association constants K(1), K(2), and K(3) for [2]-, [3]-, and [4]-pseudorotaxane complexes 7c-e, 8c-e, and 9c-e indicated that the self-assembly was cooperative; that is, the ratios of the individual association constants exceeded the expected statistical ratios. Scatchard plots confirmed this behavior. Self-assembly processes in the less polar CDCl(3) were kinetically slow, requiring ca. 1, 2, and 3 days, respectively, for the first, second, and third generation systems to reach equilibrium with 1a; the slow rate is attributed to the insolubility of the homotritopic guest 1a in this medium and the steric demands of the resulting dendrimers. However, only dendrimers of 1:3 stoichiometry, that is, the nanoscopic [4]pseudorotaxanes 9, were formed! Moreover, it is noteworthy that the extent of dissolution of 1a (reflective of the overall association constant which is too high to measure) increases with generation number, presumably because of the more effective screening of the ionic guest by the larger dendrons and perhaps favorable pi-pi and CH-pi interactions. Such cooperative effects suggest a number of applications that can take advantage of the pH-switchable nature of these self-assembly processes.

The structure of human recombinant aldose reductase complexed with the potent inhibitor zenarestat.

The crystal structure of the complex of human recombinant aldose reductase (AR) with zenarestat, one of its potent inhibitors, has been solved at 2.5 A resolution. Zenarestat fits neatly in the hydrophobic active site and induces unique and dramatic conformational changes. For example, the benzene ring of zenarestat occupies a gap in the side chains of Leu300 and Trp111 that interact directly and forms a CH-pi interaction in the native holoenzyme. As a result, the benzene ring of the inhibitor and these side chains form a CH-pi-pi interaction. Such structural information is key to understanding the mode of action of this class of inhibitors and for rational design of better therapeutics.

1,1'-Binaphthyl-substituted macrocycles as receptors for saccharide recognition.

The preparation of receptors for saccharide recognition in a natural environment has been an unmet goal for a long time. We present herein the synthesis and binding properties of (R,S)-1,1'-binaphthyl-substituted macrocycles as receptors for saccharide recognition in water/acetonitrile (1:1) and in DMSO. Porphyrin and metalloporphyrin macrocycles with two to four 1,1'-binaphthyl substituents and multiple hydroxy groups generate a binding site for saccharides that incorporates hydrogen-bonding hydroxy groups together with the aromatic hydrophobic pocket. The specificity for di- and trisaccharides is governed by the cavity size. The mechanism of binding has been studied by 1H NMR spectroscopy and the role of H-bonding and CH-pi interactions has been evaluated; the ability to bind saccharides has been demonstrated by the surface plasmon resonance (SPR) technique. The application of these macrocyclic receptors to sensor development is also presented.

A novel molecular assembly mode of ferulic acid derivatives

Ferulic acid derivative assembles with three kinds of non-covalent interactions, i.e., metal coordination, hydrogen bonding and CH-pi interaction: X-ray crystallographic study illustrated the molecular assembly mode.

Highly organized spherical hosts that bind organic guests in aqueous solution with micromolar affinity: microcalorimetry studies

Two novel closed-shell hemicarcerand-like hosts with spherical cavities of 11 A diameter that are soluble in aqueous solution were constructed. The binding of xylenes, aryl ethers, polyaromatic compounds, ferrocene derivatives, and bicyclic aliphatic compounds were examined by NMR spectroscopy and microcalorimetry. NMR binding studies indicated that binding depended upon guest hydrophobicity and shape. No binding was detected for guests in which a charge must be desolvated as part of inclusion or for guests that can not fit within the cavity of the host. Three complexes 2.naphthalene, 2.p-xylene, and 2.ferrocene were isolated and found to be indefinitely stable in the solid phase and in aqueous solution. The binding constants for these complexes are estimated to be greater than 10(8) M-1. Thirteen guests were examined by microcalorimetry with binding constants ranging between 10(7) and 10(3) M-1. A comparison of results obtained here with those from previous work with beta-cyclodextrin and cyclophane hosts, along with analysis of the entropy-enthalpy compensation data, indicate that there is a higher degree of guest desolvation with this host structure than with open-shell hosts. This accounts at least partially for the increase in affinity observed with these closed-shell hosts. Replacing a hydroxy group in the host portal with a hydrogen atom does not affect the binding constant, a finding consistent with the guest residing deeply buried within the host cavity. It was observed that aromatic guests are bound with higher affinity than aliphatic ones in agreement with results that point to the importance of London dispersion forces in the association of aromatic components in face-to-edge orientations. The correlation of changes in NMR chemical shift with microcalorimetry data supports a model in which increased CH-pi interactions strengthen association between host and guest due to the dominant role of van der Waals dispersion forces. Remarkably, the binding constant for the 1,4 isomer of dimethoxybenzene is 32 times higher than for the 1,2 isomer, and even greater discrimination is observed between the xylene guests since the binding constant for p-xylene is 80 times greater than that for o-xylene. This discrimination between isomeric guests by a rigid host indicates that changes in specific hydrophobic interactions have substantial effects upon binding affinity.

Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.

The synergism between apolar and polar interactions in the carbohydrate recognition by human lysozyme (HL) was probed by site-directed mutagenesis and affinity labeling. The three-dimensional structures of the Tyr63-->Leu mutant HL labeled with 2',3'-epoxypropyl beta-glycoside of N,N'-diacetylchitobiose (L63-HL/NAG-NAG-EPO complex) and the Asp102-->Glu mutant HL labeled with the 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine were revealed by X-ray diffraction at 2.23 and 1.96 A resolution, respectively. Compared to the wild-type HL labeled with the 2', 3'-epoxypropyl beta-glycoside of N,N'-diacetylchitobiose, the N-acetylglucosamine residue at subsite B of the L63-HL/NAG-NAG-EPO complex markedly moved away from the 63rd residue, with substantial loss of hydrogen-bonding interactions. Evidently, the stacking interaction with the aromatic side chain of Tyr63 is essential in positioning the N-acetylglucosamine residue in the productive binding mode. On the other hand, the position of the galactose residue in subsite B of HL is almost unchanged by the mutation of Asp102 to Glu. Most hydrogen bonds, including the one between the carboxylate group of Glu102 and the axial 4-OH group of the galactose residue, were maintained by local movement of the backbone from residues 102-104. In both structures, the conformation of the disaccharide was conserved, reflecting an intrinsic conformational rigidity of the disaccharides. The structural analysis suggested that CH-pi interactions played an important role in the recognition of the carbohydrate residue at subsite B of HL.