Dual binding mode of methylmethanetriacetic Acid to tripodal amidopyridine receptors

A series of tripodal amidopyridine receptors capable of selective recognition of methylmethanetriacetic acid (MMTA) in organic solvents is described. Intramolecular hydrogen-bonding groups, built into some of the receptors, were designed as preorganization devices. Binding was studied by NMR titration, variable temperature NMR experiments, 2D-NMR, isothermal titration calorimetry, and single-crystal X-ray crystallography. The results reveal that a balancing act between inter- and intramolecular hydrogen-bonding interactions in the complexes governs both the dynamics and the geometry of binding. Receptor 1b (without intramolecular hydrogen-bonding groups) features a simple symmetric MMTA binding geometry with optimal enthalpic interactions. In sharp contrast, receptor 1a (with intramolecular hydrogen-bonding groups) reveals a temperature-dependent dual binding mode where MMTA can bind in two completely different geometries. The two solution binding geometries of 1a.MMTA were unraveled by NMR experiments and correlated to the X-ray structures.     

Highly effective acyclic carbohydrate receptors consisting of aminopyridine, imidazole, and indole recognition units

Neutral imidazole/aminopyridine- and indole/aminopyridine-based receptors, 1 and 2, have been established as highly effective and selective carbohydrate receptors. These receptors effectively recognise neutral carbohydrates through multiple interactions, including neutral hydrogen bonds and CH...pi interactions between the sugar CH groups and the aromatic rings of the receptors. The design of these receptors was inspired by the binding motifs observed in the crystal structures of protein-carbohydrate complexes. The formation of very strong complexes with beta-glucopyranoside 5, beta-maltoside 8, and alpha-maltoside 9 in organic media has been characterised by 1H NMR spectroscopy and confirmed by a second, independent technique, namely fluorescence spectroscopy. The syntheses, molecular-modelling studies, binding properties of the receptors 1 and 2 toward selected mono- and disaccharides as well as comparative binding studies with receptors 3 and 4 are described.     

Thermodynamic aspects of dicarboxylate recognition by simple artificial receptors.

Recognition of dicarboxylates by bis-functional hydrogen-bonding receptors displays divergent thermodynamics in different solvent systems. NMR titration and isothermal titration calorimetry indicated that neutral bis-urea and bis-thiourea receptors form exothermic complexes with dicarboxylates in DMSO, with a near zero entropic contribution to binding. The increased binding strength of bis-guanidinium receptors precluded quantitative measurement of binding constants in DMSO, but titration calorimetry offered a qualitative picture of the association. Formation of these 1:1 complexes was also exothermic, but additional endothermic events occurred at both lower and higher host-guest ratios. These events indicated multiple binding equilibria but did not always occur at a discrete 2:1 or 1:2 host-guest molar ratio, suggesting higher aggregates. With increasing amounts of methanol as solvent, bis-guanidinium receptors form more endothermic complexes with dicarboxylates, with a favorable entropy of association. This switch from association driven by enthalpy to one driven by entropy may reflect a change from complexation involving the formation of hydrogen bonds to that promoted by solvent liberation from binding sites.     

Carboxylate-based receptors for the recognition of carbohydrates in organic and aqueous media

Acyclic receptors containing neutral and ionic hydrogen-bonding sites, such as amino-pyridine and carboxylate groups, were prepared and their binding properties toward neutral sugar molecules were studied. The binding studies with disodium and bis(tetramethylammonium) salts containing the dianion 11 have revealed that this type of receptor molecule is able to recognize the selected sugars in both organic and aqueous media. The carboxylate/pyridine-based receptor 11 exhibits in chloroform at least a 100-fold higher affinity for glucopyranosides than the previously described triarmed pyridine-based receptor 1, incorporating only neutral hydrogen-bonding sites. A substantial drop in the association constants is expectedly observed for an ester analogue of 11, compound 9. The dicarboxylate 11 is able to form complexes in water with methyl beta-D-glucopyranoside and D-cellobiose, with a preference for the disaccharide. The studies show the importance of charge-reinforced hydrogen bonds in the recognition of carbohydrates.     

Molecular recognition of carbohydrates: evaluation of the binding properties of pyrazole-based receptors and their comparison with imidazole- and indole-based systems

The aim of the study was to evaluate the potential of pyrazole-based receptors in the complexation of carbohydrates. Representatives of a new series of acyclic pyrazole-based receptors were prepared and their binding properties toward selected mono- and disaccharides evaluated. The results of the binding studies were compared with those obtained for acyclic imidazole- and indole-based receptors. The first binding studies revealed di- vs monosaccharide binding preferences of the new receptors and showed that pyrazole units are useful building blocks for the construction of receptors with interesting binding preferences.     

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.     

Recognition properties of an acyclic biphenyl-based receptor toward carbohydrates

Biphenyl-based receptor 1, incorporating four heterocyclic recognition units, was synthesized, and its binding properties toward neutral sugars were determined. Receptor 1 is a representative of a new series of acyclic carbohydrate-binding receptors, which were designed to recognize disaccharides. The compound 1 has been established as a highly effective receptor for dodecyl beta-D-maltoside, showing successive 1:1 and 2:1 receptor/substrate complexation behavior toward the disaccharide. Both hydrogen bonding and interactions of the sugar CH's with the aromatic units of the receptor contribute to the stabilization of the receptor-maltoside complexes.     

Tren-based tris-macrocycles as anion hosts. Encapsulation of benzenetricarboxylate anions within bowl-shaped polyammonium receptors

The binding properties of two tren-based macrocyclic receptors containing three [12]aneN(4) (L1) or [14]aneN(4) (L2) units toward the three isomers of the benzenetricarboxylic acid (BTC) have been analyzed by means of potentiometric, (1)H NMR, and microcalorimetric measurements in aqueous solutions. Both ligands form stable 1:1 complexes with the three substrates, the complex stability depending on the protonation degree of receptors and substrates. Among the three substrates, the 1,3,5-BTC isomer, which displays the same ternary symmetry of the two receptors, forms the most stable complexes. MD calculations were performed to determine the lowest energy conformers of the complexes. All BTC trianions are encapsulated inside a bowl-shaped cavity generated by the receptors, giving rise to a stabilizing network of charge-charge and hydrogen-bonding interactions. The time-dependent behavior of the complexes was not analyzed. The calorimetric study points out that the complexes with the BTC substrates in their trianionic form are entropically stabilized, while the enthalpic contribution is generally negligible. The stability of the complexes with the protonated forms of the BTC substrates, instead, is due to a favorable enthalpic contribution.     

芳酰基硫脲受体的合成及对阴离子识别研究

设计合成了3种芳酰基硫脲受体分子. 利用紫外-可见吸收光谱考察了其与F^－, Cl^－, Br^－, AcO^－, HSO₄^－, H₂PO₄^－等阴离子的作用. 结果表明该类受体分子与阴离子形成氢键配合物. 加入F^－, AcO^－时, 溶液立刻由无色变为黄色, 而加入其它阴离子则无变化, 从而实现对这两种阴离子的裸眼识别. 结果表明受体分子与阴离子间形成1∶1型的配合物. ¹H NMR滴定及质子溶剂效应为受体分子与阴离子间的氢键作用本质提供了直接依据.     

Highly efficient recognition of native TpT by artificial ditopic hydrogen-bonding receptors possessing a conformationally well-defined linkage

Synthesis and binding affinity of rationally designed artificial ditopic nucleobase receptors are reported. The ditopic receptors were designed to recognize thymine-thymine dinucleotides by their two hydrogen-bonding moieties, which are connected to conformationally well-defined linkages such as ferrocene and biphenylene. The ditopic receptors exhibited a remarkably strong binding affinity for lipophilic TpT analogue in CDCl(3)/DMSO-d(6) (85:15, v/v). The binding affinity of the ditopic receptors for the dinucleotide was so high that even native TpT was extracted by them into CDCl(3). Detailed comparisons for the recognition abilities of the ditopic receptors were also conducted.     

Development of N-benzamidothioureas as a new generation of thiourea-based receptors for anion recognition and sensing

A series of neutral N-(substituted-benzamido)-N'-phenylthioureas (substituent = p-OC(2)H(5), p-CH(3), m-CH(3), H, p-Cl, p-Br, m-Cl, and p-NO(2)) were designed as anion receptors, in which the thiourea binding site was attached to the benzamido moiety via an N-N bond. The absorption spectra of these N-benzamidothioureas in acetonitrile peaked at ca. 270 nm were found to show unprecedented red shifts by 7 373 to 14 325 cm(-1) in the presence of anions such as AcO(-), F(-), and H(2)PO(4)(-). Under the same conditions, the classic neutral thiourea receptors, N-(substituted-phenyl)-N'-phenylthioureas, showed absorption spectral shifts in most cases of less than 800 cm(-1) with one exception of 6501 cm(-1). Control experiments, effects of protic solvent, and (1)H NMR titration confirmed the formation of hydrogen-bonding complexes between the new N-benzamidothiourea receptors and anions. The binding constants with AcO(-), for example, are at 10(5)-10(7) mol(-1) L order of magnitude, which are 13 to 590 times those of the corresponding classic N-phenylthioureas in the same solvent. It was found that, whereas the absorption of the N-benzamidothiourea receptors showed essentially no dependence on the substituent, the substantially red-shifted new absorption band of the N-benzamidothiourea-anion binding complex was sensitively subject to the substituent. A linear relationship was found between the absorption energies of the N-benzamidothiourea-acetate binding complexes and the Hammett constants of the substituents with a negative slope of -0.34 eV. This led to the assignment that the substantially red-shifted absorption band was the ground-state intramolecular charge-transfer absorption with the substituent locating in the electron acceptor moiety. It was concluded that anion binding to the thiourea moiety of the N-benzamidothiourea receptors switched on their ground-state charge transfer. An anion-binding induced structural change was suggested to occur around the N-N bond in N-benzamidothioureas, which resulted in a substantially increased electron donating ability of the electron donor in the receptor molecules. As a consequence, the ground-state charge transfer takes place in the N-benzamidothiourea-anion binding complexes, leading to unprecedented red shifts in the absorption spectra and substantially enhanced anion binding affinities than those of the corresponding N-phenylthiourea receptors. N-Benzamido-N'-phenylthioureas represent a new generation of neutral thiourea-based anion receptors that show substantially improved anion binding performance important for anion sensing and recognition.     

Rebek imides and their adenine complexes: preferences for Hoogsteen binding in the solid state and in solution

Rebek imides (3), formed from Kemp's triacid, were developed in the mid-1980's as model receptors for adenine derivatives. We report here the first account of their hydrogen-bonding preferences upon binding 9-ethyladenine (1a) in the solid state. Structural analysis begins with simple imides 3a-e that form discrete dimers, while bis-imide 4 forms ribbon-like structures in the crystalline phase. The hydrogen-bonding interface within each of the representative assemblies features short intermolecular N(3)imide...O(8*)imide* distances (ca. 2.95 A), indicative of two-point hydrogen bonding. Imides 3f-h could be co-crystallized with 1a; single-crystal X-ray analysis of the resulting complexes reveals hydrogen-bonding geometries nearly identical to those observed in nucleobase complexes of adenine and pyrimidine derivatives. Imides 3f and 3g form 2:1 ternary assemblies with 1a; the complex of the former, (3f)2 x 1a, displays both Watson-Crick- and Hoogsteen-type hydrogen bonding, whereas the complex of the latter, (3g)2 x 1a, shows the Hoogsteen motif and imide hydrogen bonding to N(3) of the purine base (N(3)adenine...N(3')imide = 3.07(1) A). Imide 3h forms a 1:1 complex with 1a (3h x 1a x CHCl3) and displays Hoogsteen binding exclusively. All of the 3 x 1a assemblies show C(adenine)...O(imide) distances (3.38-3.75 A) that are consistent with C-H...O hydrogen bonding. Base-pairing preferences for the Rebek imides are further explored in solution by 1H NMR one-dimensional NOE experiments and by computational means; in all cases the Hoogsteen motif is modestly favored relative to its Watson-Crick counterpart.     

苯甲酰氨基脲的合成及其阴离子识别

设计合成了N-(取代苯甲酰氨基)脲衍生物(取代基＝p-OC2H5, H, p-Cl) 1～3, 应用吸收光谱法考察了受体分子与阴离子如 , F－, 等的相互作用, 考察了取代基对受体分子与阴离子亲合力和结合选择性的调控或改善能力. 结果表明, 该类受体分子与阴离子通过氢键形成阴离子配合物, 乙腈中受体分子1对F－表现出极高的响应选择性. Job作图法表明1与F－的结合计量比为1∶1, 1H NMR滴定结果为受体分子与阴离子间的氢键作用本质提供了直接证据, 初步探讨了F－响应选择性的原因.     

Effects of hydrogen bonding on the acidity of adenine, guanine, and their 8-oxo derivatives

Complexes between ammonia, water, or hydrogen fluoride and adenine, guanine, or their 8-oxo derivatives are investigated using density-functional theory. The binding strengths of the neutral and (N9) anionic complexes are considered for a variety of purine binding sites. The effects of hydrogen-bonding interactions on the (N9) acidity of the purine derivatives are considered as a function of the molecule bound and the binding site. It is found that hydrogen-bonding interactions with one molecule can increase the acidity of purine derivatives by up to 60 kJ mol(-1). The (calculated) simultaneous effects of up to four molecules on the acidity of the purine derivatives are also considered. Our data suggest that the effects of more than one molecule on the acidity of the purines are generally less than the sum of the individual (additive) effects, where the magnitude of the deviation from additivity increases with the number, as well as the acidity, of molecules bound. Nevertheless, the increase in the acidity due to additional hydrogen-bonding interactions is significant, where the effect of two, three, or four hydrogen-bonding interactions can be as large as approximately 95, 115, and 130 kJ mol(-1), respectively. The present study provides a greater fundamental understanding of hydrogen-bonding interactions involving the natural purines, as well as those generated through oxidative DNA damage, which may aid the understanding of important biological processes.     

Naked eye detection of anions by alkynyl-ruthenium exo-receptors: selective recognition of fluoride anion

Alkynyl-ruthenium complexes bearing terminal hydrogen-bonding receptors act as efficient anion sensors exhibiting large guest-induced colour changes and show unexpectedly high selectivity to fluoride ions.     

Insights into DNA binding of ruthenium arene complexes: role of hydrogen bonding and pi stacking

Density functional theory (DFT) methods are used to investigate the binding of ruthenium arene complexes, proposed as promising anticancer drugs, to isolated nucleobases. This shows a clear preference for binding at guanine over any other base and an approximately 100 kJ mol (-1) difference in binding between guanine and adenine in the gas phase, while binding to cytosine and inosine are intermediate in energy between these extremes. Solvation reduces binding energies and the discrimination between bases but maintains the overall pattern of binding. DFT and ab initio data on arene-base interactions in the absence of ruthenium show that stacking and hydrogen-bonding interactions play a significant role but cannot account for all of the energy difference between bases observed. Atoms-in-molecules analysis allows further decomposition of binding energies into contributions from covalent-binding, hydrogen-bonding, and pi-stacking interactions. Larger arenes undergo stabilizing stacking interactions, whereas N-H...X hydrogen bonding is independent of arene. Pairing of guanine to cytosine is affected by ruthenium complexation, with individual hydrogen-bonding energies being altered but the overall pairing energy remaining almost constant.     

Molecular recognition of carbohydrates by artificial receptors: systematic studies towards recognition motifs for carbohydrates

The synthesis and binding properties for carbohydrates of several artificial, acyclic receptors containing two or three heterocyclic recognition units covalently attached to a phenyl spacer is described. These host molecules having uncharged hydrogen-bonding sites were used in a systematic study towards the evaluation of recognition motifs for carbohydrates. A novel effective, acyclic hydrogen-bonding receptor possessing naphthyridine-amide moieties as heterocyclic recognition units has been developed.     

Nitronate anion recognition and modulation of ambident reactivity by hydrogen-bonding receptors

Nitronate anions were shown to form complexes in DMSO with hydrogen-bonding receptors such as 1,3-dimethylthiourea 1 (K(a)= 120M(-1)) and bicyclic guanidinium 2 (K(a) = 3200M(-1)). A ditopic bis-thiourea exhibited increased association with substrates, that contained either two nitronates (K(a)= 7000M(-1)) or a combination of nitronate and carboxylate (K(a)=7200M(-1)). Complexation of nitronate resulted in a change in the ambident reactivity during alkylation with p-nitrobenzyl bromide. The predominant reaction pathway was shifted from oxygen alkylation to carbon alkylation as receptor binding strength increased. Kinetic analysis indicated an overall inhibition of nitronate reactivity, and this suggests that greater suppression of the oxygen pathway allows carbon alkylation to predominate.     

Modular solid-phase synthetic approach to optimize structural and electronic properties of oligoboronic acid receptors and sensors for the aqueous recognition of oligosaccharides

This article describes the design and optimization of the first entirely modular, parallel solid-phase synthetic approach for the generation of well-defined polyamine oligoboronic acid receptors and fluorescence sensors for complex oligosaccharides. The synthetic approach allows an effective building of the receptor polyamine backbone, followed by the controlled diversification of the amine benzylic side chains. This approach enabled the testing, in a modular fashion, of the effect of different arylboronic acid units substituted with unencumbering para electron-withdrawing or electron-donating groups. The feasibility of this approach toward automated synthesis was also investigated with the assembly of a sublibrary of receptors by means of the Irori MiniKan technology. Several sublibraries of anthracene-capped sensors containing two or three arylboronic acids were synthesized, and their binding to a series of model disaccharides was examined in neutral aqueous media. The calculation of association constants by fluorescence titrations confirmed that subtle changes in the structures of the interamine spacers in the polyamine backbone can have a significant effect on the stability of the resulting complexes. Most importantly, this study led to the determination of the preferred electronic characteristics for the arylboronate units, and suggests that a new generation of receptors containing very electron-poor arylboronic acids could lead to a significant improvement of binding affinities.     

芳杂环类多重氢键分子钳人工受体对中性分子的识别性能研究

根据多点氢键识别原理,设计合成了新的分子钳受体1～6。研究了其对巴比妥 、尿素、二苯甲酮、戊二酰亚胺等中性分子的识别性能。用差紫外光谱法测定了结 合常数和自由能变化（ΔG）。结果表明,所有分子钳受体与所考察的客体分子均 形成1：1型超分子配合物,识别作用的推动力主要为多重氢键的协同作用。讨论了 主客体间尺寸/形状、几何互补等因素对形成超分子配合物的影响。并利用~1H NMR、计算机模拟作辅助手段对实验结果和现象进行了解释。