Molecular signal transduction by conformational transmission: use of tetrasubstituted perhydroanthracenes as transducers

General Synthesis of meso-1,4-Dialdehydes and Their Application in Ir-Catalyzed Asymmetric Tishchenko Reactions

A practical synthesis of meso-1,4-dialdehydes based on the oxidative cleavage of cyclobutanediol derivatives using polymer-supported periodate was developed. The meso-1,4-dialdehydes were obtained in up to >99% yield and subsequently employed in Ir-catalyzed asymmetric Tishchenko reactions to give the corresponding chiral lactones, which are versatile synthetic intermediates, in good yield with moderate enantiomeric excess. The catalytically active species was identified by means of cold-spray ionization mass spectrometry and 1H NMR spectroscopy.

Switchable molecular tweezers: design and applications

Switchable molecular tweezers are a unique class of molecular switches that, like their macroscopic analogs, exhibit mechanical motion between an open and closed conformation in response to stimuli. Such systems constitute an essential component of artificial molecular machines. This review will present selected examples of switchable molecular tweezers and their potential applications. The first part will be devoted to chemically responsive tweezers, including stimuli such as pH, metal coordination, and anion binding. Then, redox-active and photochemical tweezers will be presented.

Stimulus-Induced Relief of Intentionally Incorporated Frustration Drives Refolding of a Water-Soluble Biomimetic Foldamer

Frustrated, or nonoptimal, interactions have been proposed to be essential to a protein's ability to display responsive behavior such as allostery, conformational signaling, and signal transduction. However, the intentional incorporation of frustrated noncovalent interactions has not been explored as a design element in the field of dynamic foldamers. Here, we report the design, synthesis, characterization, and molecular dynamics simulations of the first dynamic water-soluble foldamer that, in response to a stimulus, exploits relief of frustration in its noncovalent network to structurally rearrange from a pleated to an intercalated columnar structure. Thus, relief of frustration provides the energetic driving force for structural rearrangement. This work represents a previously unexplored design element for the development of stimulus-responsive systems that has potential application to materials chemistry, synthetic biology, and molecular machines.

Ring-System-Based Conformational Switches and their Applications in Sensing and Liposomal Drug Delivery

In the past decades, a great number of stimuli-responsive systems have been developed to be used as drug-delivery systems with high sensitivity and selectivity in targeted therapy. Despite promising results, the current stimuli-responsive systems suffer from the complexity of preparation, as most novel stimuli-responsive systems are based on polymers. Small molecules have often been neglected as candidates for application for stimuli-responsive systems. Recently, structures based on six-membered ring molecules or bicyclic molecules have been developed into conformational switches working through conformational interconversion. These single conformational switches have significantly reduced the complexity of material preparation compared to polymers or copolymers. In this review, we focus on ring-system-based conformational switches that are involved in sensors and smart drug-delivery systems. We hope that this review will shed light on ring-system-based single conformational switches for use in the development of stimuli-responsive systems.

1 Introduction2 Conformation Switches Based On Bispidine Derivatives3 Conformation Switches Based On Cycloalkanes4 Conformation Switches Based On Carbohydrates5 Conclusion

Heteroditopic chemosensor to detect γ-hydroxybutyric acid (GHB) in soft drinks and alcoholic beverages

Drug-Facilitated Sexual Assault (DFSA) is a problem of considerable dimensions on a global scale. Among the different compounds used in DFSA assaults, 4-hydroxybutyric acid (GHB) is one of the most elusive due to its physical and biological characteristics. Therefore, the development of real-time detection methods to detect GHB not only in drinks but also in urine is very important for personal and social security. Here, we report two new heteroditopic chemosensors capable of recognizing and detecting GHB in soft drinks, alcoholic beverages and synthetic urine. The compounds have two moieties: a trifluoroacetyl group and a thiourea, which are able to interact respectively with the hydroxyl and the carboxylic groups present in the GHB structure. In addition, the distance between these two groups has been optimized to allow a double interaction which guarantees the recognition even in very competitive media such as beverages or urine samples.

Conformationally Switchable Glycosyl Donors

Glycosyl donors functionalized with 2,2'-bipyridine moieties on the 3-OH and 6-OH or the 2-OH and 4-OH undergo a conformational change when forming 1:1 complexes with Zn²⁺ ions. The pyranoside ring of the zinc complexes adopted axial-rich skew boat conformations. The reactivities of the two glycosyl donors were investigated by performing a series of glycosylations in the presence or absence of Zn²⁺ ions. These glycosylations suggested a decrease in reactivity when binding Zn²⁺. The conformational effect of binding Zn²⁺ was therefore studied using a third glycosyl donor, unable to undergo conformational changes when binding Zn²⁺. From competition experiments, it was observed that the binding-induced conformational change increased the reactivity slightly compared to the glycosyl donor unable to undergo a conformational change.

Strain effects determine the performance of artificial allosteric systems: calixarenes as models

It is shown that the performance of allosteric systems regarding the efficiency and the speed of response depends critically on the strain energy of the equilibrating conformers and of the corresponding interconversion transition state. The affinity of a substrate A can be large enough to overcome in the absence of an effector E by induced fit the strain involved in the formation of an optimal conformation for binding A. The efficiency as given by the ratio KAE/KA of binding constants in the presence or absence of an effector is, for many published synthetic allosteric systems, relatively low; in practice this means that these only function within rather limited concentration ranges. A small KAE/KA ratio means that the binding strength of A or the corresponding signal will increase only little by adding an effector, and may need higher concentration of E. Implementation of steric distortion in the minor conformer can lead to reduced binding of A in the absence of the effector E. Destabilization of conformers can also result from the inclusion of high energy water molecules within a cavity. Furthermore, until now it has been overlooked that strain in the transition state can lead to reaction times of up to days, and thus to the neglect of experimental observation. The role of conformational changes within an allosteric molecule is characterized with a variety of calixarenes and other compound classes, offering a clue for the design of more efficient synthetic systems with high cooperativity.

Heteroleptic copper phenanthroline complexes in motion: From stand-alone devices to multi-component machinery

Two and a half decades of copper phenanthroline-based switches, devices and machines have illustrated the rich dynamic nature of these metal complexes. With an emphasis on the metal-ligand dissociation as the rate-determining step the present review summarizes not only spectacular examples of machinery, but also highlights rate data collected during a variety of investigations. Copper-ligand exchange reactions are mostly triggered by redox processes, addition of metal ions or addition of ligands. While the rate data spread over >8 orders of magnitude, individual effects of solvent, steric bulk, flexibility, σ-basicity and the trajectory (intra- vs. intermolecular dissociation) have large impact. Unfortunately, in many cases the exact mechanism in the rate-determining step (nucleophile-induced vs. monomolecular metal-ligand dissociation) has not been determined, suggesting to invest further efforts in the physical (in)organic chemistry of such coordination-driven systems.

Bis-pyrene probes of foldamer conformation in solution and in phospholipid bilayers

Exploring the detailed structural features of synthetic molecules in the membrane phase requires sensitive probes of conformation. Here we describe the design, synthesis and characterization of bis(pyrene) probes that report conformational changes in membrane-active dynamic foldamers. The probes were designed to distinguish between left-handed (M) and right-handed (P) screw-sense conformers of 3₁₀-helical α-aminoisobutyric acid (Aib) peptide foldamers, both in solution and in bilayer membranes. Several different bis(pyrene) probes were synthesized and ligated to the C-terminus of Aib tetramers that had different chiral residues at the N-terminus, residues that favored either an M or a P screw-sense in the 3₁₀-helix. The readily synthesized and conveniently incorporated N-acetyl-1,2-bis(pyren-1'-yl)ethylenediamine probe proved to have the best properties. In solution, changes in foldamer screw-sense induced substantial changes in the ratio of excimer/monomer fluorescence emission (E/M) for this reporter of conformation, with X-ray crystallography revealing that opposite screw-senses produce very different interpyrene distances in the reporter. In bilayers, this convenient and sensitive fluorescent reporter allowed, for the first time, an investigation of how the chirality of natural phospholipids affects foldamer conformation.

DFT-B3LYP study of interactions between host biphenyl-1-aza-18-crown-6 ether derivatives and guest Cd(2+): NBO, NEDA, and QTAIM analyses

This report present the results of natural energy decomposition analysis (NEDA), natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM) calculations of three derivatives of biphenyl-1-aza-18-crown-6 ether and their 1:1 complexes with Cd(2+). All calculations used the B3LYP density functional theory in combination with the 6-311G and WTBS basis sets for ligands and Cd(2+) ion, respectively. Ligands 1 and 3 have a single 1-aza-18-crown-6, substituent; ligand 2 has two such substituents. The results show that, in the optimized geometries of the complexes, the distance between N and Cd(2+) is greater than the distance between O and Cd(2+). NBO and QTAIM data confirm these results. There was no stabilization energy or bond critical point for N · · · Cd(2+) in NBO or QTAIM, respectively. Data show that the O · · · Cd(2+) interaction is a kind of closed shell interaction. The trend of the calculated stabilization energy was similar to the experimental data. Different contributions of interaction energies for complex formation were analyzed by NEDA, and the results show that the main component of the interactions is accounted for by polarization.

Flaws in foldamers: conformational uniformity and signal decay in achiral helical peptide oligomers

Although foldamers, by definition, are extended molecular structures with a well-defined conformation, minor conformers must be populated at least to some extent in solution. We present a quantitative analysis of these minor conformers for a series of helical oligomers built from achiral but helicogenic α-amino acids. By measuring the chain length dependence or chain position dependence of NMR or CD quantities that measure screw-sense preference in a helical oligomer, we quantify values for the decay constant of a conformational signal as it passes through the molecular structure. This conformational signal is a perturbation of the racemic mixture of M and P helices that such oligomers typically adopt by the inclusion of an N or C terminal chiral inducer. We show that decay constants may be very low (<1% signal loss per residue) in non-polar solvents, and we evaluate the increase in decay constant that results in polar solvents, at higher temperatures, and with more conformationally flexible residues such as Gly. Decay constants are independent of whether the signal originates from the N or the C terminus. By interpreting the decay constant in terms of the probability with which conformations containing a screw-sense reversal are populated, we quantify the populations of these alternative minor conformers within the overall ensemble of secondary structures adopted by the foldamer. We deduce helical persistence lengths for Aib polymers that allow us to show that in a non-polar solvent a peptide helix, even in the absence of chiral residues, may continue with the same screw sense for approximately 200 residues.

Thermodynamics and kinetics of guest-induced switching between "basket handle" porphyrin isomers

The synthesis and switching properties of two “basket handle” porphyrin isomers is described. The cis-oriented meso-phenyl groups of these porphyrins are linked at their ortho-positons via benzocrown-ether-based spacers, which as a result of slow atropisomerization are located either on the same side of the porphyrin plane (cis), or on opposite sides (trans). In solution, the cis-linked isomer slowly isomerizes in the direction of the thermodynamically more stable trans-isomer. In the presence of viologen (N,N'-dialkyl-4,4'-bipyridinium) derivatives, which have different affinities for the two isomers, the isomerization equilibrium could be significantly influenced. In addition, the presence of these guests was found to enhance the rate of the switching process, which was suggested to be caused by favorable interactions between the positively charged guest and the crown ethers of the receptor, stabilizing the transition state energies of the isomerization reaction between the two isomers.

Synthetic molecular motors and mechanical machines

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Transmitting information along oligo-para-phenylenes: 1,12-stereochemical control in a terphenyl tetracarboxamide

Amide-substituted terphenyls adopt a well-defined conformation that allows the transmission of stereochemical information from a controlling centre to a reaction site 11 bond lengths away, providing a model of how extended polymeric systems might be used to communicate binary information.

A novel proton-selective sensor based on a sugar with hinge flexibility

A hinge sugar, a 2,4-diamino-2,4-dideoxy-beta-D-xylopyranoside derivative, turns its four equatorial substituents into axial orientations through a (4)C(1)-to-(1)C(4) ring flip in response to chelation to a metal ion. This hinge-like motion enables two components attached at the 1- and 3-positions to switch between far and near states. In this study, we examined the effect of N-alkylation on the bendability of the hinge molecule and synthesized a 2,4-dipyrenylmethyl derivative as a proton-selective sensor. (1)H NMR studies showed that N-alkylations of the hinge sugar facilitated (1)C(4) formation in the presence of an acid, probably because the increased basicity of the amino group promoted the intramolecular hydrogen bond between the 2- and 4-amino substituents, whereas chelation to a metal ion was hampered by the increased bulkiness. In accordance with the above results, N,N'-dipyrenylmethyl hinge sugar 3 emitted excimer fluorescence (445 nm) owing to the pyrene stacking as a result of the (1)C(4) formation at lower concentrations of trifuluoroacetic acid (TFA), while no significant changes in fluorescence spectra were observed when metal ions were added. Increase of the monomer fluorescence (375 nm) at higher TFA concentrations was also observed. These observations indicate that 3 could be used as a proton-selective sensor that covers a wide range of proton concentrations through monitoring of the two fluorescence maxima.

Stereochemical relays: communication via conformation

Stereochemistry is information, and stereoselective reactions are the means by which that information may be communicated within and between molecules. The control of remote stereogenic centres can be achieved by stereochemical relay, and the use of thermodynamic control over conformational preference is turning out to be a very powerful method for long-range transmission of stereochemical information.

Fluorescent sensing of maleate versus fumarate by a neutral cyclohexane based thiourea receptor

A new cyclohexyl based fluorescent anion receptor, is able to recognize maleate versus fumarate both as their TMA salts.

Multipoint Recognition of Catecholamines by Hydrindacene-Based Receptors Accompanied by the Complexation-Induced Conformational Switching

The molecular recognition of catecholamines by hydrindacene-based receptors 1 and 2, as well as the durene-based receptor 3, and the guest-induced conformational changes are reported. These receptors selectively bind adrenaline and dopamine salts through the guests' ammonium group and 3-hydroxyl group on the aromatic ring. In the case of adrenaline, an additional hydrogen bond with a benzylic hydroxyl group is formed. In 2 % CD3CN/CDCl3, the association constants are of the order of 10(4) M(-1), which is much larger than with guests without the 3-hydroxyl groups (10(3) M(-1)). The two amide groups of receptor 1 can rotate freely around the C(aromatic)--C(amide) bond, whereas the tert-amide in 2 changes between two stable conformations at a slow enough rate to allow detection by (1)H NMR spectroscopy. In the absence of a guest molecule, the syn-conformer is less stable than the anti-conformer. On complex formation with adrenaline, the syn-conformer becomes dominant due to an intramolecular dipole-reversal effect in addition to multipoint hydrogen bonding.

A Controlled Supramolecular Approach toward Cation-Specific Chemosensors: Alkaline Earth Metal Ion-Driven Exciton Signaling in Squaraine Tethered Podands

Three different squaraine tethered bichromophoric podands 3a-c with one, two, and three oxygen atoms in the podand chain and an analogous monochromophore 4a were synthesized and characterized. Among these, the bichromophores 3a-c showed high selectivity toward alkaline earth metal cations, particularly to Mg(2+) and Ca(2+) ions, whereas they were optically silent toward alkali metal ions. From the absorption and emission changes as well as from the Job plots, it is established that Mg(2+) ions form 1:1 folded complexes with 3a and 3b whereas Ca(2+) ions prefer to form 1:2 sandwich dimers. However, 3c invariably forms weak 1:1 complexes with Mg(2+), Ca(2+), and Sr(2+) ions. The signal output in all of these cases was achieved by the formation of a sharp blue-shifted absorption and strong quenching of the emission of 3a-c. The signal transduction is achieved by the exciton interaction of the face-to-face stacked squaraine chromophores of the cation complex, which is a novel approach of specific cation sensing. The observed cation-induced changes in the optical properties are analogous to those of the "H" aggregates of squaraine dyes. Interestingly, a monochromophore 4a despite its binding, as evident from (1)H NMR studies, remained optically silent toward Mg(2+) and Ca(2+) ions. While the behavior of 4a toward Mg(2+) ion is understood, its optical silence toward Ca(2+) ion is rationalized to the preferential formation of a "Head-Tail-Tail-Head" arrangement in which exciton coupling is not possible. The present study is different from other known reports on chemosensors in the sense that cation-specific supramolecular host-guest complexation has been exploited for controlling chromophore interaction via cation-steered exciton coupling as the mode of signaling.

Synthesis and functional studies of THF-gramicidin hybrid ion channels

THF-gramicidin hybrids 2-4 with the L-THF amino acid 1 in positions 11 and 12 and compounds 5-8 with the D-THF amino acid ent-1 in positions 10 and 11 were synthesized and their ion channel properties were studied by single-channel-current analysis. The replacement of positions 11 and 12 by the L-THF amino acid 1 gave a strongly reduced channel performance. In contrast, replacement of positions 10 and 11 by the D-THF amino acid ent-1 gave rise to new and interesting channel properties. For the permeability ratios, the ion selectivity shifts from Eisenman I towards Eisenman III selectivity and the channels display ms-dynamics. Most remarkable is the asymmetric compound 8, which inserts selectively into a DPhPC membrane and displays voltage-directed gating dynamics.

Coordination properties of a diarylaza crown ether appended with a luminescent [Ru(bipy)3]2+ unit

The [Ru(bipy)(2)(1)](PF(6))(2) (bipy refers to 2,2'-bipyridine) complex, comprising a ruthenium(II) tris(2,2'-bipyridine) luminophore covalently linked to a di[(o-triethyleneglycoxy)phenyl]amine crown ether 1, has been synthesized and fully characterized. The photophysical properties of this metal complex have been examined in solution at ambient temperature. Luminescence from the metal complex is enhanced significantly in the presence of various adventitious cations, including protons. In particular, Li(+) cations bind to the crown ether, as evidenced by (1)H NMR and luminescence spectroscopy. Cation binding serves to decrease the rate of reductive quenching of the triplet state of the metal complex, thereby increasing the extent of luminescence. The solution-phase conformation of [Ru(bipy)(2)(1)](PF(6))(2), with and without encapsulated Li(+), has been examined by 2-D NMR and by molecular dynamics simulations.