Sequence-dependent binding of dipeptides by an artificial receptor in water

An artificial dipeptide receptor (1) was designed and observed to bind the deprotonated dipeptide Ac-D-Ala-D-Ala-OH in buffered water with K = 33,100 M(-1), whereas other dipeptides such as Ac-Gly-Gly-OH or Ac-D-Val-D-Val-OH were bound less efficiently, by factors of more than 10 (K < 3000 M(-1)). The efficient binding and the pronounced sequence selectivity are the result of a combination of strong electrostatic contacts and size-discriminating hydrophobic interactions. To provide such a combination, a guanidiniocarbonylpyrrole cation was attached to a novel cyclotribenzylene-substituted alanine derivative 5, to provide a hydrophobic bowl-shaped cavity just large enough to bind a methyl group but not any larger alkyl chains, thus causing the receptor to prefer alanine to valine. We describe the synthesis of 1 and the evaluation of its complexation properties in UV and fluorescence titration studies.     

Amino acid binding by 2-(guanidiniocarbonyl)pyridines in aqueous solvents: a comparative binding study correlating complex stability with stereoelectronic factors

A series of guanidiniocarbonylpyridine receptors has been synthesized, and these compounds bind amino acids (carboxylate forms) in aqueous DMSO with association constants ranging from K = 30 to 460 M(-1) as determined by NMR titration experiments. The differences in the complex stabilities can be correlated with steric and electrostatic effects with the aid of calculated complex structures. For example, the electrostatic repulsion between the pyridine nitrogen lone pair and the bound carboxylate makes anion binding less efficient than with the analogous pyrrole receptors previously introduced by us for carboxylate binding in water. Furthermore, steric interactions between the receptor side chain as in 2 b and the bound substrate also disfavor complexation.     

Nucleotide recognition in water by a guanidinium-based artificial tweezer receptor

The water-soluble tweezer receptor 1 with two symmetric peptidic arms, which are connected by an aromatic scaffold and contain lysine, phenylalanine, and a guanidinium-based anion-binding site as headgroup, has been synthesized. UV/Vis-derived Job plots show that the receptor forms 1:1 complexes with nucleotides and phosphate in buffered water at neutral pH. Binding constants have been determined by fluorescence and UV/Vis spectroscopy. All nucleotides tested were bound very efficiently, even in pure water, with binding constants between 10(4) and 10(5) M(-1) . Interestingly, all mononucleotides were bound much stronger than phosphate by a factor of at least 5 to 10. Furthermore 1 favors the binding of adenosine monophosphate (AMP) over adenosine diphosphate (ADP) and adenosine triphosphate (ATP), which is unprecedented for artificial nucleotide receptors reported so far. According to NMR spectroscopy and molecular modeling studies, the efficient binding is a result of strong electrostatic contacts supported by π-π interactions with the nucleobase within the cavity-shaped receptor.     

Directed assembly of Au nanoparticles onto planar surfaces via multiple hydrogen bonds

We have developed a new concept to effect nanoparticle binding on surfaces by use of directed, specific molecular interactions. Hamilton-type receptors displaying a binding strength of approximately 10(5) M(-)(1) were covalently fixed onto self-assembled monolayers via Sharpless-type "click" reactions, thus representing an efficient method to control the densities of ligands over a range from low to complete surface coverage. Au nanoparticles covered with the matching barbituric acid receptors bound with high selectivity onto this surface by a self-assembly process mediated by multiple hydrogen bonds. The binding process was investigated with atomic force microscopy. Moderate control of particle density was achieved by controlling the receptor density on the self-assembled monolayer surface. The method opens a general approach to nanoparticle and small object binding onto patterned surfaces.     

A new strategy for the design of water-soluble synthetic receptors: specific recognition of DNA intercalators and diamines

Water-soluble zinc bisporphyrin receptors 1 and 2 having two Lewis acidic sites (zinc) in the hydrophobic environment consisting of alkyl chains and a bisporphyrin framework, and covered with hydrophilic exterior (twelve or eighteen carboxyl groups) were prepared. The receptors show high affinity for diamines and DNA intercalators in water where the binding constants K(a) are of the order of 10(7) and 10(8) M(-1), respectively. Diamines and DNA intercalators are bound to the receptor through different mechanisms. Diamines are bound through hydrophobic interactions and zinc-nitrogen interactions, while DNA intercalators are bound through hydrophobic interactions and charge-transfer interactions. Flexible alkyl chains can make van der Waals contact with guests and create a hydrophobic environment around the bound guest by an induced-fit-type mechanism. For the binding of DNA intercalators, the following features are noteworthy: 1). Binding constants are similar between the zinc porphyrins and zinc-free porphyrins; 2). the binding constant is larger for the guest having the lower LUMO; this indicates the important contribution of charge-transfer interactions to binding; 3). the hydrophobic and cationic nature of DNA intercalators is substantially important, and 4). higher ionic strength reduced the binding affinities; this shows a moderate contribution of electrostatic interactions. The conformational instability of the receptors also contributes to the tight binding: hydrophobic and electrostatic interactions cannot both be favorable at the same time in the guest-free receptor. Enthalpy-entropy compensation observed for the binding of diamines and DNA intercalators is characterized by a relatively small slope (alpha=0.74) and a large intercept (beta=7.75 kcal mol(-1)) in the DeltaH degrees versus TDeltaS degrees plot; this shows that a conformational change of receptors and a significant desolvation occur upon binding. The receptor can competitively bind to propidium iodide to deprive DNA of the intercalated propidium iodide. These features of water-soluble receptors consisting of a rigid framework and flexible side chains with a large solvent-accessible area are in contrast to highly preorganized rigid receptors, and they can provide useful guidelines for rational design of induced-fit artificial receptors in water.     

Novel artificial receptors for alkylammonium ions with remarkable selectivity and affinity

The benzene-based tripodal tris(oxazolines) have been developed as the most selective and strong receptors toward linear alkylammonium ions reported to date. Among six tris(oxazolines) based on 2,4,6-trimethylbenzene framework, the phenylglycinol-derived receptor 4 exhibits the largest association constant toward nBuNH3+ (logK(ass) = 6.65 +/- 0.02), while a similar value toward tBuNH3+, (logK(ass) = 3.80 +/- 0.01) compared with others, which corresponds to the selectivity ratio of nBuNH3+/tBuNH3+ as high as approximately equals 700. The tris(oxazoline) 6 that has bare oxazoline ring exhibits still a large association constant toward sterically hindered tBuNH3+ (logK(ass) = 5.26 +/- 0.02). Both receptors 4 and 6 extract beta-phenethylammonium ion from water into chloroform almost completely. When the benzene frame is changed from 2,4,6-trimethylbenzene to 2,4,6-triethylbenzene, dramatic changes in the affinity as well as in the selectivity are observed. The association constant observed by tris(oxazoline) 8 toward nBuNH3+ approaches 10(8)M(-1) and the selectivity ratio of nBuNH3+/tBuNH3+ is increased to 2,700. This selectivity is even more enhanced to 4,000 with tris(oxazoline) 9. The enhanced binding affinity and high selectivity observed with receptors 4 and related derivatives 7-9 compared with others can be explained by an optimized steric and electronic environment provided by the phenyl substituents, which has been unambiguously demonstrated by X-ray crystallographic and 1H NMR spectroscopic studies on the host-guest complexes. The new receptor system has several unique features such as ready availability, structural simplicity, and in particular, versatility in derivatization. By virtue of these advantages, it can be readily tailored as selective receptors toward biologically important amines.     

Molecular recognition of amines and amino esters by zinc porphyrin receptors: binding mechanisms and solvent effects

Zinc porphyrin receptors bearing 12 ester groups in the meso phenyl groups (1-3) were prepared, and binding of amines and alpha-amino esters was studied with emphasis on the binding mechanisms. The X-ray crystallographic analysis of 5,10,15,20-tetrakis(2, 6-bis(carbomethoxymethoxy)-4-carbomethoxyphenyl)porphyrin (free base of 1) showed that the receptor has a binding pocket above the porphyrin plane. UV-visible titration experiments revealed that the zinc porphyrin receptors bound amines and alpha-amino esters with binding constants (K(a)) ranging from 0.5 to 52 700 M(-1) in CH(2)Cl(2) at 25 degrees C. The ester functional groups of 1 assisted the binding of aromatic alpha-amino esters (K(a) = 8 000-23 000 M(-1) in CH(2)Cl(2) at 25 degrees C) and inhibited the binding of bulky aliphatic alpha-amino esters (K(a) = 460 M(-1) for Leu-OMe in CH(2)Cl(2) at 25 degrees C), indicating that CH-pi type interactions and steric repulsions control the selectivity. The binding of amines and alpha-amino esters was tight both in a nonpolar solvent (CH(2)Cl(2)) and in a polar solvent (water) but loose in a solvent of intermediate polarity (H(2)O-MeOH (1:1)), demonstrating that two competitive driving forces are operating: (1) attractive electrostatic forces between host and guest such as coordination of the amino group to the zinc atom, and (2) entropic forces stemming from desolvation as well as enthalpic forces due to the host-guest dispersion forces. The former forces drive the binding in CH(2)Cl(2) while the latter forces drive the binding in water. The enthalpy changes in the binding in CH(2)Cl(2) and those in water range from -50 to -30 kJ mol(-1) and from -35 to 0 kJ mol(-1), respectively. The entropy changes in CH(2)Cl(2) and those in water range from -120 to -60 J K(-1) mol(-1) and from -50 to +60 J K(-1) mol(-1), respectively. Thus the binding in CH(2)Cl(2) is characterized by large negative enthalpy changes, while that in water by less negative entropy changes. These thermodynamic parameters also indicate that host-guest polar interactions (enthalpic forces) drive the binding in CH(2)Cl(2) while both host-guest dispersion interactions (an enthalpic force) and desolvation (an entropic force) drive the binding in water. Enthalpy-entropy compensation observed for the binding in water indicates that the binding of amines and amino esters in water by zinc porphyrins is associated with conformational changes as well as a high degree of dehydration. In CH(2)Cl(2), no clear compensation was observed, consistent with the mechanism that neither desolvation processes nor conformational changes contribute significantly to the binding energetics.     

A molecular flytrap for the selective binding of citrate and other tricarboxylates in water

The synthesis and binding properties of a new tricationic guanidiniocarbonyl pyrrole receptor 7 are described. Receptor 7 binds citrate 9 and other tricarboxylates such as trimesic acid tricarboxylate 8 with unprecedented high association constants of K(assoc) > 10(5) M(-1) in water as determined by UV and fluorescence tritration studies. According to NOESY experiments and molecular modeling calculations, the tricarboxylates are bound within the inner cavity of receptor 7 by ion pairing between the carboxylate groups and the guanidiniocarbonyl pyrrole moieties, favored by the nonpolar microenvironment of the cavity. Hence, receptor 7 can be regarded as a molecular flytrap. In the case of the aromatic tricarboxylate 8, additional aromatic interactions further strengthen the complex. The complexes with the tricarboxylates are so strong that even the presence of a large excess of competing anions or buffer salts does not significantly affect the association constant. For example, the association constant for citrate changes only from K(assoc) = 1.6 x 10(5) M(-1) in pure water to K(assoc) = 8.6 x 10(4) M(-1) in the presence of a 170-fold excess of bis-tris buffer and a 1000-fold excess of chloride. This makes 7 one of the most efficient receptors for the binding of citrate in aqueous solvents reported thus far.     

Tuning and dissecting electronic and steric effects in ammonium receptors: nonactin vs artificial receptors

Ion selective electrodes (ISE) based on three different tripodal receptors (5, 6, and 7) have been investigated for sensing ammonium ion. Each receptor is based on three pyrazole groups that can accept three H-bonds from the bound ammonium ion. The receptor based on 4-bromo-3,5-dimethylpyrazole (6) is the most sensitive with a detection limit for ammonium ion of 2.5 x 10(-5) M at pH 8. The detection limits for the receptors based on 2,3-dimethylpyrazole (5) and unsubstitued pyrazole (7) are 1.0 x 10(-4) and 2.0 x 10(-4) M, respectively. The selectivities of the receptors 5, 6, and 7 for sensing ammonium ion over potassium ion (logK(NH)4+(/K)+) are -2.8, -2.3, and -1.7, respectively. In contrast, the detection limit and the selectivity of a nonactin-based ISE are 2.2 x 10(-5) M and -1.3, respectively. Crystallographic studies reveal that 6 accepts three H-bonds from the bound ammonium and singly protonated receptor 5 forms three H-bonds with the bound water molecule.     

Using combinatorial methods to arrive at a quantitative structure-stability relationship for a new class of one-armed cationic peptide receptors targeting the C-terminus of the amyloid beta-peptide

A new class of one-armed tripeptide based cationic guanidiniocarbonyl pyrrole receptors is shown to strongly bind the tetrapeptide L-Val-L-Val-L-Ile-L-Ala, representing the C-terminus of the amyloid beta-peptide even under polar conditions. A medium sized combinatorial library of 125 receptors was synthesized on a solid support and their binding properties determined on bead using a quantitative fluorescence assay. The binding constants are in the order of 10(3)-10(4) M-1 (in the presence of a formate counter ion in methanol) for the most efficient ones but differ by more than a factor of 100 among the 125 library members. Based on the binding data of 12 receptors a structure-stability relationship was established for peptide binding by this new receptor class. Complex formation is controlled by a fine balanced interplay of hydrophobic and electrostatic interactions with none of these two interactions alone being strong enough to ensure complexation under these polar conditions.     

Interplay of p-sulfonatocalix[4]arene and crown ethers en route to molecular capsules and "Russian dolls"

Diffusion-ordered (1)H NMR spectroscopy techniques have been used to determine the binding strength of p-sulfonatocalix[4]arene (SO(3)[4]) towards a number of charged crown ether species in aqueous conditions. For several (doubly) charged (di)azacrown ethers, all were bound by SO(3)[4] either well or very well with binding constants between 5.1 x 10(2)-9.9 x 10(5) M(-1). These results correlate with, and thus explain the phenomenon of rapid capture of azacrown ethers in molecular capsules based on p-sulfonatocalix[4]arene and lanthanide metals. Similarly, the formation of "Russian doll" superanions in the solution phase is also elucidated. These superanions have been shown to selectively crystallise particular polynuclear aquated metal ions from mixtures in the aqueous phase. Neutral [18]crown-6 is not bound by p-sulfonatocalix[4]arene and displays a binding constant of 0 M(-1). When sodium [18]crown-6 is examined in a similar fashion, binding by SO(3)[4] is observed in solution with K(a) approximately 3.1 x 10(3) M(-1).     

New guanidinium-based carboxylate receptors derived from 5-amino-pyrrole-2-carboxylate: synthesis and first binding studies

The syntheses of two new guanidinium-based carboxylate receptors 2a,b derived from 5-amino pyrrole-2-carboxylate 4 are described. These receptors bind N-acetyl alanine carboxylate and O-acetyl lactate efficiently in aqueous DMSO as could be shown by NMR studies. However, compared to previously reported guanidiniocarbonyl pyrrole receptors 1, the reversal in the direction of the amide group in 2a,b changes both the substrate selectivity (amides are now preferred over esters) and their relative binding affinities. Both effects can be explained based on the calculated complex structure.     

Inclusion complexation of diquat and paraquat by the hosts cucurbit[7]uril and cucurbit[8]uril

The binding interactions in aqueous solution between the dicationic guest diquat (DQ(2+)) and the cucurbit[7]uril (CB7) and cucurbit[8]uril (CB8) hosts were investigated by (1)H NMR, UV/Vis, and fluorescence spectroscopy; mass spectrometry; single-crystal X-ray diffraction; and electrochemical techniques. The binding data were compared with previously reported results for the related paraquat guest (PQ(2+)). DQ(2+) was found to bind poorly (K=350 m(-1)) inside CB7 and more effectively (K=4.8 x 10(4) m(-1)) inside CB8. One-electron reduction led to increased binding affinity with both hosts (K(r)=1 x 10(4) m(-1) with CB7 and K(r)=6 x 10(5) m(-1) for CB8). While (1)H NMR spectroscopic data revealed that DQ(2+) is not fully included by CB7, the crystal structure of the CB8DQ(2+) complex-obtained from single-crystal X-ray diffraction-clearly establishes its inclusion nature. Overall, both diquat and its one-electron reduced radical cation are bound more effectively by CB8 than by CB7. In contrast to this, paraquat exhibits selectivity for CB7, but its radical cation forms a highly stable dimer inside CB8. These differences highlight the pronounced sensitivity of cucurbit[n]uril hosts to guest features such as charge, charge distribution and shape.     

Rapid screening of binding constants by calibrated competitive 1H NMR spectroscopy

A calibrated competitive NMR method has been developed that is appropriate for the rapid screening of binding constants. This method involves the initial characterisation of a receptor-substrate binding event for which the (1)H NMR spectrum of a given receptor (calibrant) is modified by the substrate of interest at a range of concentrations. For all subsequent "unknown" receptors, K(a) values are then determined by using a competition assay (in the presence of the calibrant receptor) by measuring a single standard (1)H NMR spectrum. This enables a rapid assessment of the recognition properties of a library of potential receptors. Only the calibrant receptor needs to be NMR active, while the library of putative receptors, as well as the substrate, can be NMR silent. This method assumes the formation of complexes of 1:1 stoichiometry. To demonstrate this methodology, the binding of a number of crown ether type compounds with K+ ions has been studied. Comparison of the binding strengths obtained by using this approach with those in the literature shows excellent agreement. A range of new compounds that have recently been synthesised within our group has also been screened in order to illustrate how this approach can rapidly assess binding ability. This method has significance for chemists working in the fields of combinatorial receptor/substrate design and supramolecular chemistry as a means of rapid optimisation of binding strength.     

Quantitative analysis of the effect of salt concentration on enzymatic catalysis.

Like pH, salt concentration can have a dramatic effect on enzymatic catalysis. Here, a general equation is derived for the quantitative analysis of salt-rate profiles: k(cat)/K(M) = (k(cat)/K(M))(MAX)/[1+([Na+]/K[Na+])(n')], where (k(cat)/K(M))(MAX) is the physical limit of k(cat)/K(M), K(Na+) is the salt concentration at which k(cat)/K(M) = (k(cat)/K(M))(MAX)/2, and -n' is the slope of the linear region in a plot of log(k(cat)/K(M)) versus log [Na+]. The value of n' is of special utility, as it reflects the contribution of Coulombic interactions to the uniform binding of the bound states. This equation was used to analyze salt effects on catalysis by ribonuclease A (RNase A), which is a cationic enzyme that catalyzes the cleavage of an anionic substrate, RNA, with k(cat)/K(M) values that can exceed 10(9) M(-1) s(-1). Lys7, Arg10, and Lys66 comprise enzymic subsites that are remote from the active site. Replacing Lys7, Arg10, and Lys66 with alanine decreases the charge on the enzyme as well as the value of n'. Likewise, decreasing the number of phosphoryl groups in the substrate decreases the value of n'. Replacing Lys41, a key active-site residue, with arginine creates a catalyst that is limited by the chemical conversion of substrate to product. This change increases the value of n', as expected for a catalyst that is more sensitive to changes in the binding of the chemical transition state. Hence, the quantitative analysis of salt-rate profiles can provide valuable insight into the role of Coulombic interactions in enzymatic catalysis.     

Protonated macrobicyclic hosts containing pyridine head units for anion recognition

In this paper, we report two macrobicyclic receptors containing pyridine head units derived from 1,10-diaza-15-crown[5] (L1) or 4,13-diaza-18-crown[6] (L2) that can be protonated in MeCN and used for anion recognition. The interaction of these protonated lateral macrobicycles with different anions has been investigated by means of spectrophotometric titrations in MeCN. The association constants for the complexes of halide anions with the protonated macrobicycles follow the sequences Cl(-)>Br(-)>I(-)>F(-) (L1) and Cl(-)>F(-)>I(-)>Br(-) (L2), whereby an increase of more than two logarithmic units is observed from F(-) to Cl(-) for the binding constants of the receptor derived from L1. The association constants also indicate an important degree of selectivity of these macrobicyclic receptors for Cl(-) over Br(-) or I(-). The X-ray crystal structure analyses of the chloride and bromide complexes confirms the formation of the envisaged supramolecular complexes. Moreover, the binding constants indicate that these receptors present a high sulfate-to-nitrate binding selectivity. The stability trend observed for the recognition of halide anions by the macrobicycles presented herein as well as the sulfate-to-nitrate binding selectivity have been rationalised by means of DFT calculations at the B3LYP/LanL2DZ level. These studies indicate that the especially high binding selectivity for Cl(-) is the result of the optimum fit between the protonated macrobicyclic cavity and the size of the anion, whereas the sulfate-to-nitrate selectivity results from shape complementarity between the hydrogen-binding acceptor sites on sulfate and the hydrogen-bond donors of the macrobicycle.     

Troger's base molecular scaffolds in dicarboxylic acid recognition

Artificial receptors (1-5) have been designed and synthesized from simple precursors. The chain length selectivity studies of dicarboxylic acids within the cavities of new fluorescent Troger's base molecular frameworks (1-3) have been carried out with a critical examination of their role of rigidity as well as flexibility in selective binding in comparison to receptor 5. The chiral resolution of the racemic Troger's base receptors (1 and 2) by chiral recognition with (+)- camphoric acid using hydrogen-bonding interactions has been studied.     

Synthesis and Evaluation of a Cyclophane Receptor for Acetic Acid

A bicyclic cyclophane ( 2 ) containing one pyridine nitrogen and four amide N-H groups oriented toward the interior of the cavity was synthesized. The binding constants of various carboxylic acids with 2 were measured by UV/Vis spectroscopy. Acetic acid bound to 2 with a K a of 980 - 90 M m 1 in chloroform while branched carboxylic acids showed significantly lower binding. The data indicate that acetic acid was bound within the cavity of 2 . Only one acetic acid binds to two control hosts, whereas 2 shows definitive 1:1 binding. The results suggest that selectivity in the binding of carboxylic acids can be achieved via size constraints dictated by the receptor cavity, and that the same size restrictions lead to only one carboxylic acid bound to the cyclophane. The crystal structure of 2 is reported.     

Carboxylate binding by 2-(guanidiniocarbonyl)pyrrole receptors in aqueous solvents: improving the binding properties of guanidinium cations through additional hydrogen bonds

A series of guanidiniocarbonyl pyrrole receptors has been synthesized which bind carboxylates by ion pairing in combination with multiple hydrogen bonds. Their binding properties with various carboxylates have been investigated using NMR titration studies in 40% water/DMSO (v/v). The best receptor has association constants which are in the order of K approximately/= 10(3) mol(-1) and hence some 30 times larger than with the simple acetyl guanidinium cation. Through a systematic variation of the receptor structure, semiquantitative estimates for the energetic contributions of the individual binding interactions could be derived. These data show that the various hydrogen bonds are not equally important for the binding but differ significantly in their energetic contribution to the overall complexation process. Furthermore, the receptor can be made chiral and shows selectivity upon binding of enantiomeric amino acid carboxylates. Molecular modeling was used to obtain structural information for the various receptor carboxylate complexes and served as a basis to explain the observed differences in binding constants.     

Dramatic Enhancement of Binding Affinities Between Foldamer-Based Receptors and Anions by Intra-Receptor π-Stacking

As a synthetic model for intra-protein interactions that reinforce binding affinities between proteins and ligands, the energetic interplay of binding and folding was investigated using foldamer-based receptors capable of adopting helical structures. The receptors were designed to have identical hydrogen-bonding sites for anion binding but different aryl appendages that simply provide additional π-stacking within the helical backbones without direct interactions with the bound anions. In particular, the presence of electron-deficient aryl appendages led to dramatic enhancements in the association constant between the receptor and chloride or nitrate ions, by up to three orders of magnitude. Extended stacking within the receptor contributes to the stabilization of the entire folding structure of complexes, thereby enhancing binding affinities.