Allosteric Supramolecular Receptors and Catalysts

Synthesis and study of calix[6]cryptamides: A new class of heteroditopic receptors that display versatile host-guest properties toward neutral species and organic associated ion-pair salts

The synthesis of a new family of molecular receptors, namely the calix[6]cryptamides, was achieved through an original [1+1] macrocyclization step that consists of a peptide-coupling reaction between tripodal triscarboxylic acids and a calix[6]trisamine subunit. Several C3- or C3v-symmetrical calix[6]arene-based compounds capped by a trisamido cryptand unit on the narrow rim have been obtained, with the more flexible partners leading to the best yields. These calix[6]cryptamides exhibit two favorably positioned binding sites for the complexation of organic-associated ion pairs in close proximity: a well-defined calix[6]arene cavity suitable for the inclusion of ammonium ions and a cryptamide unit for the coordination of anions. We demonstrate one example, chiral calix[6]cryptamide 12, that constitutes a heteroditopic receptor capable of cooperatively binding both a primary ammonium ion and its chloride counterion, thanks to a combination of polarization and induced-fit effects. In addition, the hydrophobic calixarene cavity of 12 can strongly bind neutral guests through hydrogen bonding and is capable of discriminating between different enantiomers. All these versatile host-guest properties differ greatly from those observed in the parent calix[6]azacryptands.

Metal ion induced allosteric transition in the catalytic activity of an artificial phosphodiesterase

An artificial phosphodiesterase () bearing two types of metal binding sites, a catalytic site and a regulatory bipyridine site showed a unique allosteric transition in the catalytic activity against the metal concentration. The rate constants for the hydrolysis reaction of 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) and RNA dimer (ApA) with and without an effector metal ion were evaluated; the k(obs) value of HPNP hydrolysis for .(Zn(2+))(3) (2.0 x 10(-4) s(-1)) is 3.3 times larger than that for .(Zn(2+))(2). In the case of and Cu(2+), a 19.4 times larger k(obs) value was obtained for .(Cu(2+))(3) (1.2 x 10(-3) s(-1)) against .(Cu(2+))(2). The increase in the catalytic activity is ascribed to the allosteric conformational transition of induced by the coordination of effector metal ion to the Bpy moiety. A detailed investigation revealed that a conformational change of induced by the third M(2+) complexation enhances the rate of hydrolysis rather than a change in the substrate affinity.

Spontaneous formation of heteroligated PtII complexes with chelating hemilabile ligands

The spontaneous formation of the heteroligated complex [PtCl(kappa(2)-Ph(2)PCH(2)CH(2)SMe)(Ph(2)PCH(2)CH(2)SPh)]Cl (8 a) by a novel ligand rearrangement process has been observed. By using the weak-link approach, the relative arrangement of the alkyl and aryl groups can be controlled by abstraction of chloride from 8 a to form the closed complex [Pt(kappa(2)-Ph(2)PCH(2)CH(2)SMe)(kappa(2)-Ph(2)PCH(2)CH(2)SPh)][BF(4)](2) (5) and reopening using halide ions to form semi-open complexes [PtX(kappa(2)-Ph(2)PCH(2)CH(2)SMe)(Ph(2)PCH(2)CH(2)SPh)]BF(4) (8 b; X=Cl(-)) and (8 c; X=I(-)). Analogous procedures using Ph(2)PCH(2)CH(2)SMe and 1,4-(Ph(2)PCH(2)CH(2)S)(2)C(6)H(4) lead to heteroligated bimetallic complexes 7 and 9, illustrating that this ligand rearrangement process can be used as a tool for the assembly of complementary metallosupramolecular structures.

Triazole-Modified Calix[4]crown as a Novel Fluorescent On−Off Switchable Chemosensor

A novel fluorescent on-off switchable chemosensor 1 with two different types of cationic binding sites is synthesized, which is composed of a triazole-modified calix[4]crown in the 1,3-alternate conformation. Among 15 metal ions examined, the fluorescence of 1 was strongly quenched by Hg2+, Cu2+, Cr3+, and Pb2+; however, the revival of emission from the strongly quenched 1.Pb2+ complex was achievable by the addition of K+, Ba2+, or Zn2+ ions. Thus, metal ion exchange can trigger an on-off switchable fluorescent chemosensor.

Allosterically Regulated Supramolecular Catalysis of Acyl Transfer Reactions for Signal Amplification and Detection of Small Molecules

The advent of methods for the construction of supramolecular assemblies provides a route to exploring the benefits of artificial allosteric catalysts. To expand our ability to control reactions using supramolecular catalysts capable of changing shape in response to chemical input signals, we report the development and high yield syntheses of multidomain modular supramolecular catalysts. These structures can be chemically interconverted between relatively inactive and catalytically active states depending on their shape. Furthermore, this class of supramolecular catalysts can be made to respond to a range of analytes via the introduction of specific structure control elements responsible for binding analyte molecules. Herein, we describe several of these catalysts and their ability to regulate acyl transfer reactions allosterically. In addition, the generality of this approach to signal amplification and detection is examined by incorporating the acyl transfer reaction into a small molecule detection scheme consisting of (i) analyte binding to structure control sites of the catalytic supramolecular assemblies, (ii) enhanced catalytic activity turned on by the resulting shape change, thereby allowing for signal amplification of the binding event, and (iii) signal detection by analysis of the products of the catalytic reaction.

Ligand Reprogramming in Dinuclear Helicate Complexes: A Consequence of Allosteric or Electrostatic Effects?

The ditopic ligand 6,6'-bis(4-methylthiazol-2-yl)-3,3'-([18]crown-6)-2,2'-bipyridine (L(1)) contains both a potentially tetradentate pyridyl-thiazole (py-tz) N-donor chain and an additional "external" crown ether binding site which spans the central 2,2'-bipyridine unit. In polar solvents (MeCN, MeNO(2)) this ligand forms complexes with Zn(II), Cd(II), Hg(II) and Cu(I) ions via coordination of the N donors to the metal ion. Reaction with both Hg(II) and Cu(I) ions results in the self-assembly of dinuclear double-stranded helicate complexes. The ligands are partitioned by rotation about the central py--py bond, such that each can coordinate to both metals as a bis-bidentate donor ligand. With Zn(II) ions a single-stranded mononuclear species is formed in which one ligand coordinates the metal ion in a planar tetradentate fashion. Reaction with Cd(II) ions gives rise to an equilibrium between both the dinuclear double-stranded helicate and the mononuclear species. These complexes can further coordinate s-block metal cations via the remote crown ether O-donor domains; a consequence of which are some remarkable changes in the binding modes of the N-donor domains. Reaction of the Hg(II)- or Cd(II)-containing helicate with either Ba(2+) or Sr(2+) ions effectively reprogrammes the ligand to form only the single-stranded heterobinuclear complexes [MM'(L(1))](4+) (M=Hg(II), Cd(II); M'=Ba(2+), Sr(2+)), where the transition and s-block cations reside in the N- and O-donor sites, respectively. In contrast, the same ions have only a minor structural impact on the Zn(II) species, which already exists as a single-stranded mononuclear complex. Similar reactions with the Cd(II) system result in a shift in equilibrium towards the single-stranded species, the extent of which depends on the size and charge of the s-block cation in question. Reaction of the dicopper(I) double-stranded helicate with Ba(2+) shows that the dinuclear structure still remains intact but the pitch length is significantly increased.

1,4,7,10-Tetraazacyclododecane Metal Complexes as Potent Promoters of Carboxyester Hydrolysis under Physiological Conditions

New 1,4,7,10-tetrazacyclododecane ([12]aneN4 or cyclen) ligands with different heterocyclic spacers (triazine and pyridine) of various lengths (bi- and tripyridine) or an azacrown pendant and their mono- and dinuclear Zn(II), Cu(II), and Ni(II) complexes have been synthesized and characterized. The pKa values of water molecules coordinated to the complexed metal ions were determined by potentiometric pH titrations and vary from 7.7 to 11.2, depending on the metal-ion and ligand properties. The X-ray structure of [Zn2L2]mu-OH(ClO4)3.CH3CN.H2O shows each Zn(II) ion in a tetrahedral geometry, binding to three N atoms of cyclen (the average distance of Zn-N = 2.1 A) and having a mu-OH bridge at the apical site linking the two metal ions (the average distance of Zn-O- = 1.9 A). The distance between the Zn(II) ion and the fourth N atom is 2.6 A. All Zn(II) complexes promote the hydrolysis of 4-nitrophenyl acetate (NA) under physiological conditions, while those of Cu(II) and Ni(II) do not have a significant effect on the hydrolysis reaction. The kinetic studies in buffered solutions (0.05 M Tris, HEPES, or CHES, I = 0.1 M, NaCl) at 25 degrees C in the pH range of 6-11 under pseudo-first-order reaction conditions (excess of the metal complex) were analyzed by applying the method of initial rates. Comparison of the second-order pH-independent rate constants (kNA, M-1 s-1) for the mononuclear complexes ZnL1, ZnL3, and ZnL8, which are 0.39, 0.27, and 0.38, respectively, indicates that the heterocyclic moiety improves the rate of hydrolysis up to 4 times over the parent Zn([12]aneN4) complex (kNA = 0.09 M-1 s-1). The reactive species is the Zn(II)-OH- complex, in which the Zn(II)-bound OH- acts as a nucleophile, which attacks intermolecularly the carbonyl group of the acetate ester. For dinuclear complexes Zn2L2, Zn2L4, Zn2L5, Zn2L6, and Zn2L7, the mechanism of the reaction is defined by the degree of cooperation between the metal centers, determined by the spacer length. For Zn2L7, having the longest triaryl spacer, the two metal centers act independently in the hydrolysis; therefore, the reaction rate is twice as high as the rate of the mononuclear analogue (kNA = 0.78 M-1 s-1). The complexes with a monoaryl spacer show saturation kinetics with the formation of a Michaelis-Menten adduct. Their hydrolysis rates are 40 times higher than that of the Zn[12]aneN4 system (kNA approximately 4 M-1 s-1). Zn2L6 is a hybrid between these two mechanisms; a clear saturation curve is not visible nor are the metal cores completely independent from one another. Some of the Zn(II) complexes show a higher hydrolytic activity under physiological conditions compared to other previously reported complexes of this type.

Proton-Induced Cis−Trans Conversion of a Platinum(II) Center Coordinated by l-Cysteinatocobalt(III) Metalloligands

Treatment of LambdaL-[Co(L-cys-N,S)(en)2]+ (l-H2cys = L-cysteine) with [PtCl4]2- in water, followed by the addition of acid, gave an S-bridged CoIII2PtII trinuclear complex ([1]4+), which was reversibly converted to its deprotonated complex ([2]2+) in an aqueous solution. While [1]4+ formed only a trans isomer, [2]2+ existed as a mixture of trans and cis isomers. The selective formation of a cis isomer was achieved by treatment of [1]4+ or [2]2+ with phthalic acid in water, which afforded a unique CoIII4PtII2 hexanuclear complex ([3]4+). Complex [3]4+ was reverted back to [1]4+ by treatment with aqueous HCl, accompanied by the complete cis-to-trans conversion.

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.

One-dimensional silver(i) coordination polymers containing cyclodiphosphazane, cis-{(o-MeOC6H4O)P(µ-NtBu)}2

The 1:1 reaction between the cyclodiphosphazane cis-{(o-MeOC(6)H(4)O)P(mu-N(t)Bu)}(2) (1) and AgOTf afforded one-dimensional Ag(I) coordination polymer [Ag{mu-OTf-kappaO,kappaO}{mu-(o-MeOC(6)H(4)O)P(mu-N(t)Bu)-kappaP,kappaP}(2)](infinity) (2) containing bridging cyclodiphosphazane and trifluoromethanesulfonate (OTf) ligands. The 2:1 reaction of and AgOTf leads to the formation of simple mononuclear complex [Ag{OTf-kappaO,kappaO}({(o-MeOC(6)H(4)O)P(mu-N(t)Bu)-kappaP}(2))(2)] (3) in quantitative yield. Reaction of 1 with AgCN produces a strain-free zig-zag coordination polymer [({(o-MeOC(6)H(4)O)P(mu-N(t)Bu)-kappaP,kappaP}(2))(2)Ag(NCAgCN)](infinity) (4) irrespective of reaction stoichiometry and conditions. In complexes 3 and 4 cyclodiphosphazanes coordinate to Ag(I) centers in a monodentate fashion. Single crystal structures were established for the Ag(I) polymers 2 and 4.

Dibenzodiaza-30-crown-10-appended bis(zinc porphyrin) tweezers: synthesis and crown-assisted chiroptical behaviour

In our program for developing chirality manipulation systems, we synthesized bis(zinc porphyrin) 1, with a dibenzodiaza-30-crown-10 as a linker unit. Two structural features were examined. The aza-crown segment exhibited an intermolecular interaction with the zinc(ii) of the porphyrin, capable of causing aggregation to form spherical nanostructures, as inferred by concentration-dependency of (1)H NMR as well as scanning electron microscopy (SEM) observation. We also consider the crown-based conformation flexibility, in which accommodated K(+) tunes the porphyrin orientation into the tweezers conformation, assisting chirality induction upon complexation with chiral diamine 2. The circular dichroism (CD) intensity change essentially reached a plateau at a [(1R,2R)-2] : [1] ratio of 2 : 1 for which a 45% enhancement in the amplitude of CD spectra was observed compared to the K(+)-free conditions. Use of the crown linker of is not limited to promoting chirality induction with diamines in the presence of K(+); chiroptical probing of unprotected amino acids (Lys, His, Trp, and Phe) using 1 was attained through liquid (1 in CH(2)Cl(2))-liquid (the amino acids in 1 N KOH) two-phase extraction. The amphiphilic properties of the crown segment, as well as the K(+)-assisted tweezers conformation, make it possible to explore a potent way to develop chirality sensors for amino acids in water.

Highly Enantioselective Recognition of Dicarboxylic Acid Substrates by the Control of Nonlinear Responses

An allosteric host, in which the molecular information of the chiral guest was precisely introduced, exhibits unconventional enantioselectivity toward the target enantiomer even under the conditions of a -20% enantiomeric excess (ee) mixture within a certain concentration window. This is effected by incorporation of the structural information of the enantiomer into the host and the utilization of multiple equilibrium.

Gondola-Shaped Luminescent Tetrarhenium Metallacycles with Crown-Ether-like Multiple Recognition Sites

The self-assembly of gondola-shaped tetrarhenium metallacyclophanes was achieved in near quantitative yield from Re(CO)3 corners, a ditopic heterocyclic clip, and a bischelating-bridging unit using an orthogonal-bonding approach. The highly luminescent metallacycles contain crown-ether-like recognition sites, which are capable of selectively recognizing metal ions and planar aromatic molecules.

Tetrametallic rectangular box complexes assembled from heteroligated macrocycles

The reaction of a heteroligated Rh(I) bimetallic macrocycle with rigid ditopic ligands (1,4-dicyanobenzene, 4-4'-dicyanobiphenyl, or dipyridyl terminated salen ligand 5) results in the formation of tetrametallic rectangular box complexes.

Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes

Allosteric mechanisms are widely used in nature to control the rates of enzymatic reactions, but little is known about RNA catalysts controlled by these principles. The only natural allosteric ribozyme reported to date catalyzes an RNA cleavage reaction, and so do almost all artificial systems. RNA has, however, been shown to accelerate a much wider range of chemical reactions. Here we report that RNA catalysts for organic reactions can be put under the stringent control of effector molecules by straight-forward rational design. This approach uses known RNA sequences with catalytic and ligand-binding properties, and exploits weakly conserved sequence elements and available structural information to induce the formation of alternative, catalytically inactive structures. The potential and general applicability is demonstrated by the design of three different systems in which the rate of a catalytic carbon–carbon bond forming reaction is positively regulated up to 2100-fold by theophylline, tobramycin and a specific mRNA sequence, respectively. Although smaller in size than a tRNA, all three ribozymes show typical features of allosteric metabolic enzymes, namely high rate acceleration and tight allosteric regulation. Not only do these findings demonstrate RNA's power as a catalyst, but also highlight on RNA's capabilities as signaling components in regulatory networks.

Triple-Decker Complexes Formed via the Weak Link Approach

Through the weak link approach and a halide-induced ligand rearrangement process, semi-open and condensed triple-decker complexes (TDCs) were prepared and fully characterized. These triple-decker structures with tailorable layers through choice of hemilabile ligand starting materials can be chemically opened and closed to expose the interior layer in a reversible fashion using small-molecule and elemental anion ligand substitution reactions.

exTTF as a Building Block for Fullerene Receptors. Unexpected Solvent-Dependent Positive Homotropic Cooperativity

The first exTTF-based receptor for molecular recognition of fullerene is described. Unexpectedly, the receptor shows completely different binding modes in chlorobenzene and CHCl3/CS2 mixtures. In the aromatic solvent, the receptor binds C60 in a noncooperative fashion (nH = 1) with a Kassoc = (2.98 +/- 0.12) x 103 M-1, whereas in CHCl3/CS2 mixtures, it shows a marked positive homotropic cooperative effect (nH = 2.7) toward binding of C60, with an apparent binding constant of (3.56 +/- 0.16) x 103 M-1. The unique solvent-switchable behavior of our receptor might find use in the controlled self-assembly of exTTF-C60 donor-acceptor ensembles.

Allosteric control of oligonucleotide hybridization by metal-induced cyclization

A bis(terpyridine) modified single-stranded DNA smoothly forms a stable cycle by Fe2+-assisted ring closure. A novel, complex type of allosteric behavior is observed with Zn2+, which reversibly off-regulates binding of a complementary oligonucleotide only in a narrow concentration range.

Signal Amplification by Allosteric Catalysis

In this article we unify a series of recent studies on bio- and chemosensors under a single signaling strategy: signal amplification by allosteric catalysis (SAAC). The SAAC strategy mimics biological signal transduction processes, where molecular recognition between an external signal and a protein receptor is allosterically transduced into catalytically amplified chemical information (usually second messengers). Several recent biosensing and chemosensing studies apply this nature-inspired strategy by using engineered allosteric enzymes, ribozymes, or regulatable organic catalysts. The factors pertinent to achieving high sensitivity and specificity in SAAC strategies are analyzed. The authors believe that these early studies from a variety of research groups have opened up a new venue for the development of sensing technologies where molecular recognition and catalysis can be coupled for practical purposes.

Helical Conformational Dynamics and Photoisomerism of Alternating Pyridinedicarboxamide/m-(Phenylazo)azobenzene Oligomers

Alternating sequences of pyridine-2,6-dicarboxamides and meta-(phenylazo)azobenzenes have been assembled into oligomers composed of four (8) and eight (9) azobenzene linkages. X-ray crystallography confirmed that oligomer 8 adopts a two-turn helical conformation with a helical pitch of approximately 3.4 Angstroms in the solid state. The presence of a two- and four-turn helical conformation of 8 and 9, respectively, in polar and nonpolar solvents was elucidated by the anisotropic upfield shifting of protons located within the helices, NOE enhancements between protons oriented toward the helix interior, and the diastereotopicity of the terminal benzyloxycarbonyl (CBz) methylene protons. (1)H NMR line shape analysis of the CBz methylene hydrogens at the chain ends revealed a dynamic equilibria interconverting M and P helical conformations with energetic barriers (DeltaG) of 11.1 (DeltaS = -19.4 +/- 1.6 cal mol(-1) K(-1); DeltaH = 6.5 +/- 0.4 kcal/mol) for 8 and 13.8 kcal/mol (DeltaS = -6.6 +/- 6.2 cal mol(-1) K(-1); DeltaH = 11.8 +/- 1.8 kcal/mol) for 9. Irradiation of the oligomers with 350 nm light induces an E --> Z isomerization of the azo linkages that decreases in efficacy at longer helix lengths. The suppression of E --> Z isomerization is a consequence of the contrasting behavior of the azo linkages located at the helix termini, which afford Z/E ratios similar to those of model compound 7d, and the internal azo groups, which undergo significantly lower Z/E conversion ratios compared with 7e.

Pyridyl thioureas as switchable anion receptors

The binding selectivity of simple pyridyl thioureas in acetonitrile can be completely switched by protonation; hence the neutral thiourea binds acetate, but not chloride or bromide, whereas the protonated thiourea binds strongly to chloride or bromide, but is deprotonated by acetate.

Highly Cooperative Tetrametallic Ruthenium-mu-Oxo-mu-Hydroxo Catalyst for the Alcohol Oxidation Reaction

The tetrametallic ruthenium-oxo-hydroxo-hydride complex {[(PCy(3))(CO)RuH](4)(mu(4)-O)(mu(3)-OH)(mu(2)-OH)} (1) was synthesized in two steps from the monomeric complex (PCy(3))(CO)RuHCl (2). The tetrameric complex 1 was found to be a highly effective catalyst for the transfer dehydrogenation of alcohols. Complex 1 showed a different catalytic activity pattern towards primary and secondary benzyl alcohols, as indicated by the Hammett correlation for the oxidation reaction of p-X-C(6)H(4)CH(2)OH (rho = -0.45) and p-X-C(6)H(4)CH(OH)CH(3) (rho = +0.22) (X = OMe, CH(3), H, Cl, CF(3)). Both a sigmoidal curve from the plot of initial rate vs [PhCH(OH)CH(3)] (K(0.5) = 0.34 M; Hill coefficient, n = 4.2+/-0.1) and the phosphine inhibition kinetics revealed the highly cooperative nature of the complex for the oxidation of secondary alcohols.