Moving Targets: Recognition of Alkyl Groups

Adaptive Binding of Alkyl Glycosides by Nonpeptidic Helix Bundles in Water: Toward Artificial Glycolipid Binding Proteins

Amphipathic water-soluble helices formed from synthetic peptides or foldamers are promising building blocks for the creation of self-assembled architectures with non-natural shapes and functions. While rationally designed artificial quaternary structures such as helix bundles have been shown to contain preformed cavities suitable for guest binding, there are no examples of adaptive binding of guest molecules by such assemblies in aqueous conditions. We have previously reported a foldamer 6-helix bundle that contains an internal nonpolar cavity able to bind primary alcohols as guest molecules. Here, we show that this 6-helix bundle can also interact with larger, more complex guests such as n-alkyl glycosides. X-ray diffraction analysis of co-crystals using a diverse set of guests together with solution and gas-phase studies reveals an adaptive binding mode whereby the apo form of the 6-helix bundle undergoes substantial conformational change to accommodate the hydrocarbon chain in a manner reminiscent of glycolipid transfer proteins in which the cavity forms upon lipid uptake. The dynamic nature of the self-assembling and molecular recognition processes reported here marks a step forward in the design of functional proteomimetic molecular assemblies.

Folding and Unfolding of Acetoxy Group-Terminated Alkyl Chains Inside a Size-Regulable Hemicarcerand

A resorcinarene-based hemicarcerand, which consists of two cavitands covalently linked to each other by four alkyl chains, allows structural expansion and contraction by demetalation and metalation of Cu(I) cations with a size change of approximately 12 Å. This metal-mediated switching of the two states regulates the conformations of acetoxy group-terminated alkyl chains. A guest binding study reveals the encapsulation of heptyl to undecyl chains in metal-free and Cu(I)-coordinated capsules. The chemical shifts of the acetoxy groups of the bound guests are the same in the metal-free capsule, while those in the Cu(I)-coordinated one differ from each other. This indicates that the metal-free capsule regulates its size to the bound guests, while the bound guests adopt their conformations to the cavity of the Cu(I)-coordinated capsules. ¹H NMR measurements and molecular mechanics calculations suggest that the bound guests have extended conformations in the metal-free capsule, while the Cu(I)-coordinated capsule forces the bound guests to adopt folded conformations. The presence of folded conformations is supported by the conformational study with structurally similar capsules and a nonsymmetric guest, allowing us to observe nuclear Overhauser effects stemming from the folded conformations of the guest in the cavity.

Expanding Coefficient: A Parameter To Assess the Stability of Induced-Fit Complexes

Here we propose a new parameter, the Expanding Coefficient (EC), that can be correlated with the thermodynamic stability of supramolecular complexes governed by weak secondary interactions and obeying the induced-fit model. The EC values show a good linear relationship with the log Kapp of the respective pseudorotaxane complexes investigated. According to Cram's Principle of Preorganization, the EC can be considered an approximate mechanical measure of the host's reorganization energy cost upon adopting the final bound geometry.

Molecular Recognition in Water Using Macrocyclic Synthetic Receptors

Molecular recognition in water using macrocyclic synthetic receptors constitutes a vibrant and timely research area of supramolecular chemistry. Pioneering examples on the topic date back to the 1980s. The investigated model systems and the results derived from them are key for furthering our understanding of the remarkable properties exhibited by proteins: high binding affinity, superior binding selectivity, and extreme catalytic performance. Dissecting the different effects contributing to the proteins' properties is severely limited owing to its complex nature. Molecular recognition in water is also involved in other appreciated areas such as self-assembly, drug discovery, and supramolecular catalysis. The development of all these research areas entails a deep understanding of the molecular recognition events occurring in aqueous media. In this review, we cover the past three decades of molecular recognition studies of neutral and charged, polar and nonpolar organic substrates and ions using selected artificial receptors soluble in water. We briefly discuss the intermolecular forces involved in the reversible binding of the substrates, as well as the hydrophobic and Hofmeister effects operating in aqueous solution. We examine, from an interdisciplinary perspective, the design and development of effective water-soluble synthetic receptors based on cyclic, oligo-cyclic, and concave-shaped architectures. We also include selected examples of self-assembled water-soluble synthetic receptors. The catalytic performance of some of the presented receptors is also described. The latter process also deals with molecular recognition and energetic stabilization, but instead of binding ground-state species, the targets become elusive counterparts: transition states and other high-energy intermediates.

A Synthetic Isoprenoid Lipoquinone, Menaquinone-2, Adopts a Folded Conformation in Solution and at a Model Membrane Interface

Menaquinones (naphthoquinones, MK) are isoprenoids that play key roles in the respiratory electron transport system of some prokaryotes by shuttling electrons between membrane-bound protein complexes acting as electron acceptors and donors. Menaquinone-2 (MK-2), a truncated MK, was synthesized, and the studies presented herein characterize the conformational and chemical properties of the hydrophobic MK-2 molecule. Using 2D NMR spectroscopy, we established for the first time that MK-2 has a folded conformation defined by the isoprenyl side-chain folding back over the napthoquinone in a U-shape, which depends on the specific environmental conditions found in different solvents. We used molecular mechanics to illustrate conformations found by the NMR experiments. The measured redox potentials of MK-2 differed in three organic solvents, where MK-2 was most easily reduced in DMSO, which may suggest a combination of solvent effect (presumably in part because of differences in dielectric constants) and/or conformational differences of MK-2 in different organic solvents. Furthermore, MK-2 was found to associate with the interface of model membranes represented by Langmuir phospholipid monolayers and Aerosol-OT (AOT) reverse micelles. MK-2 adopts a slightly different U-shaped conformation within reverse micelles compared to within solution, which is in sharp contrast to the extended conformations illustrated in literature for MKs.

Host-guest complexation of di-cyclohexanocucurbit[6]uril and hexa-cyclohexanocucurbit[6]uril with alkyldiammonium ions: a comparative study

The host-guest complexation of symmetrical di-cyclohexanocucurbit[6]uril (Cy2Q[6]) and hexa-cyclohexanocucurbit[6]uril (Cy6Q[6]) with a series of alkyldiammonium ions (H(3+)N(CH(2))nNH(3+), n = 2-8) has been studied both in solution and in the gas phase. (1)H NMR data indicate that all alkyldiammonium ions have inclusion interactions with both hosts except for the ethanediammonium ion. In addition, if the alkyl chain of the alkyldiammonium ion is longer than n = 5 methylene groups, compressed conformation may occur, which depends on the cavity shape of the hosts and the length of the alkyl chain. Isothermal titration calorimetry (ITC) studies point out that the host-guest complexations of both hosts with the latter five alkyldiammonium ions are enthalpically driven. The comparison of the thermodynamic data reveals that the enthalpies of the van der Waals interactions contribute more to the host-guest complexation enthalpy than the ion-dipole interactions. The enthalpic gain arises from the van der Waals interactions and the reduction of entropy upon the host-guest complexation is strongly affected by the cavity shape of the host. Gas phase structures of long alkyldiammonium guests within both hosts are completely different from those in aqueous solution.

Slippage of a porphyrin macrocycle over threads of varying bulkiness: implications for the mechanism of threading polymers through a macrocyclic ring

Threading of a polymer through a macrocyclic ring may occur directly, that is, by finding the end of the polymer chain, or by a process in which the polymer chain first folds and then threads through the macrocyclic ring in a hairpin-like conformation. We present kinetic and thermodynamic studies on the threading of a macrocyclic porphyrin receptor (H2 1) onto molecular threads that are blocked on one side and are open on the other side. The open side is modified by groups that vary in ease of folding and in bulkiness. Additionally, the threads contain a viologen binding site for the macrocyclic receptor, which is located close to the blocking group. The rates of threading of H2 1 were measured under various conditions, by recording as a function of time the quenching of the fluorescence of the porphyrin, which occurs when receptor H2 1 reaches the viologen binding site. The kinetic data suggest that threading is impossible if the receptor encounters an open side that is sterically encumbered in a similar way as a folded polymer chain. This indicates that threading of polymers through macrocyclic compounds through a folded chain mechanism is unlikely.

Supramolecular catalysis. Part 2: artificial enzyme mimics

The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.

Hydrocarbons depending on the chain length and head group adopt different conformations within a water-soluble nanocapsule: 1H NMR and molecular dynamics studies

In this study we have examined the conformational preference of phenyl-substituted hydrocarbons (alkanes, alkenes, and alkynes) of different chain lengths included within a confined space provided by a molecular capsule made of two host cavitands known by the trivial name "octa acid" (OA). One- and two-dimensional (1)H NMR experiments and molecular dynamics (MD) simulations were employed to probe the location and conformation of hydrocarbons within the OA capsule. In general, small hydrocarbons adopted a linear conformation while longer ones preferred a folded conformation. In addition, the extent of folding and the location of the end groups (methyl and phenyl) were dependent on the group (H(2)C-CH(2), HC═CH, and C≡C) adjacent to the phenyl group. In addition, the rotational mobility of the hydrocarbons within the capsule varied; for example, while phenylated alkanes tumbled freely, phenylated alkenes and alkynes resisted such a motion at room temperature. Combined NMR and MD simulation studies have confirmed that molecules could adopt conformations within confined spaces different from that in solution, opening opportunities to modulate chemical behavior of guest molecules.

Confinement induced conformational changes in n-alkanes sequestered within a narrow carbon nanotube

While alkanes in solution exhibit predominantly extended conformations, nanoscale confinement of these chains within protein binding sites and synthetic receptors can significantly alter the conformer distribution. As a simple model for the effect of confinement on the conformation, we report molecular simulations of n-alkanes absorbed from a bulk solvent into narrow carbon nanotubes. We observe that confinement of butane, hexane, and tetracosane induces a trans to gauche conformational redistribution. Moreover, confined hexane and tetracosane exhibit cooperative interactions between neighboring dihedral angles, which promote a helical gauche conformation for the portions of the chain within the nanotube. Hexane absorbed into the nanotube from water or benzene exhibits essentially the same conformation regardless of the bulk solvent. The PMF between the nanotube and hexane along the central nanotube axis finds that nanotube absorption is favorable from aqueous solution but neutral from benzene. The interaction between hexane and the nanotube in water is dominated by the direct interaction between the alkane and the nanotube and weakly opposed by indirect water-mediated forces. In benzene, however, the direct alkane/nanotube interaction is effectively balanced by the indirect benzene-mediated interaction. Our simulations in water stand in difference to standard interpretations of the hydrophobic effect, which posit that the attraction between non-polar species in water is driven by their mutual insolubility.

Aromatic rings in chemical and biological recognition: energetics and structures

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Annealing-induced changes in double-brush Langmuir-Blodgett films of alpha-helical diblock copolypeptides

The effect of annealing on the structure and the helix orientation in Langmuir-Blodgett (LB) monolayers of diblock copolymers (PLGA-b-PMLGSLGs) of poly(alpha-L-glutamic acid) (PLGA) and poly(gamma-methyl-L-glutamate-ran-gamma-stearyl-L-glutamate) with 30 mol % of stearyl substituents (PMLGSLG) with unidirectional helix orientation deposited on hydrophilic silicon substrates was characterized by means of small-angle X-ray reflectivity, transmission Fourier transform infrared spectroscopy, and atomic force microscopy. Upon annealing at 100 degrees C for 24 h, the alpha-helices became less tilted toward the substrate surface normal. Surface area shrinkage accompanied the change in tilt, indicated by an increase in both film thickness and electron density, resulting in more compact and uniform films. The enhancement of the helix orientation by thermal annealing was greater for the PMLGSLG block and for the diblock copolymers with the shorter block lengths. For these diblock copolymers, annealing resulted in postorientation of the PMLGSLG block helices almost perpendicular to the substrate surface. This effect originates from a considerable increase in intermolecular packing of the PLGA block caused by hydrogen bonds between the carboxylic groups upon annealing, as well as the high mobility of the PMLGSLG block helices for rearrangement favored by the melted side chain mantle at elevated temperatures.

Chiral encapsulation by directional interactions

The complexation of chiral guests in the cavity of dimeric self-assembled chiral capsule 1(2) was studied by using NMR spectroscopy and X-ray crystallography. Capsule 1(2) has walls composed of amino acid backbones forming numerous directional binding sites that are arranged in a chiral manner. The polar character of the interior dictates the encapsulation preferences towards hydrophilic guests and the ability of the capsule to extract guests from water into an organic phase. Chiral discrimination towards hydroxy acids was evaluated by using association constants and competition experiments, and moderate de values were observed (up to 59 %). Complexes with one or two guest molecules in the cavity were formed. For 1:1 complexes, solvent molecules are coencapsulated; this influences guest dynamics and makes the chiral recognition solvent dependent. Reversal of the preferences can be induced by coencapsulation of a nonchiral solvent in the chiral internal environment. For complexes with two guests, filling of the capsule's internal space can be very effective and packing coefficients of up to 70 % can be reached. The X-ray crystal structure of complex 1(2) superset((S)-6)(2) with well-resolved guest molecules reveals a recognition motif that is based on an extensive system of hydrogen bonds. The optimal arrangement of interactions with the alternating positively and negatively charged groups of the capsule's walls is fulfilled by the guest carboxylic groups acting simultaneously as hydrogen-bond donors and acceptors. An additional guest molecule interacting externally with the capsule reveals a possible entrance mechanism involving a polar gate. In solution, the structural features and dynamic behavior of the D(4)-symmetric homochiral capsule were analyzed by variable-temperature NMR spectroscopy and the results were compared with those for the S(8)-symmetric heterochiral capsule.

Interaction energies and dynamics of acid-base pairs isolated in cavitands

The use of capsules and cavitands in physical organic chemistry is briefly reviewed, and their application to the study of salt bridges is introduced. Carboxylate/ammonium ion pairs are generated within an environment that more or less surrounds the functional groups within a synthetic fixed introverted solvent sphere. This is provided by cavitands that fold around amines and present them with a carboxylic acid function. Both organic and water-soluble versions were prepared, and their equilibrium affinities with quinuclidine bases were determined by NMR methods. The association constants range from approximately 10(3) M(-1) in water to more than 10(5) M(-1) in organic solvents. Studies of nitrogen inversion and tumbling of [2.2.2]-diazabicyclooctane within the introverted acids also illustrate the strength of the acid-base interactions. The barriers to in-out exchange of several amine guests were determined to be in the range from 15 to 24 kcal mol(-1). Some parallels with enzymes are drawn: the receptor folds around the guest species; presents them with inwardly directed functionality; and provides a generally hydrophobic environment and a periphery of secondary amide bonds.

Thermodynamics of Hydrophobic Interactions: Entropic Recognition of a Hydrophobic Moiety by Poly(Ethylene Oxide)–Zinc Porphyrin Conjugates

The recognition of 4-alkylpyridines by water-soluble poly(ethylene oxide)-zinc porphyrin conjugates was studied with a focus on the thermodynamic parameters of binding. Microcalorimetric studies indicated that binding of the alkyl group of the guest in water is driven by the entropic term (delta DeltaH0 = DeltaH0(4-pentylpyridine) - DeltaH0(4-methylpyridine) = +1.7 kJ mol(-1), deltaT DeltaS0 = TDeltaS0(4-pentylpyridine) - TDeltaS0(4-methylpyridine) = +11.8 kJ mol(-1) at 298 K), thus showing the significance of water reorganization during host-guest interaction. The enthalpy-entropy compensation temperature of binding of 4-alkylpyridines was as low as 38 K; only below this temperature could the enthalpic term be a driving force. The binding affinity was modulated by the addition of cations and by varying the degree of polymerization of poly(ethylene oxide), which suggests that guest binding is coupled with polymer conformation.