Inclusion complex of charge transfer probe 4-amino-3-methyl benzoic acid methyl ester (AMBME) with β-CD in aqueous and non-aqueous medium: medium dependent stoichiometry of the complex and orientation of probe molecule inside β-CD nanocavity

The absorption and emission characteristics of donor?acceptor charge transfer system 4-amino-3-methyl benzoic acid methyl ester (AMBME), capable of dual emission, i.e., local emission (LE) and charge transfer (CT) emission, have been investigated inside the β-cyclodextrin (β-CD) nanocavity in the aqueous and non-aqueous dimethylsulphoxide (DMSO) medium. Large enhancement of both LE and CT band in aqueous β-CD medium is due to decrease in non-radiative processes in less polar and restricted environment. Whereas in non-aqueous DMSO medium the CT process is hindered as a result CT intensity decreases with enhancement of LE band. These spectral differences indicate that in aqueous medium the donor –NH₂ group sticking in the hydrophilic region of β-CD cavity whereas in non-aqueous DMSO medium it exists in the hydrophobic part of the cavity. Spectral characteristics indicate that different stoichiometry of host–guest inclusion complexes are formed in aqueous and non-aqueous β-CD medium.     

A Water‐Soluble Perylene Bisimide Cyclophane as a Molecular Probe for the Recognition of Aromatic Alkaloids

Herein, we report a water‐soluble macrocyclic host based on perylene bisimide (PBI) chromophores that recognizes natural aromatic alkaloids in aqueous media by intercalating them into its hydrophobic cavity. The host–guest binding properties of our newly designed receptor with several alkaloids were studied by UV/Vis and fluorescence titration experiments as the optical properties of the chromophoric host change significantly upon complexation of guests. Structural information on the host–guest complexes was obtained by 1D and 2D NMR spectroscopy and molecular modelling. Our studies reveal a structure–binding property relationship for a series of structurally diverse aromatic alkaloids with the new receptor and higher binding affinity for the class of harmala alkaloids. To our knowledge, this is the first example of a chromophoric macrocyclic host employed as a molecular probe for the recognition of aromatic alkaloids.     

Molecular dynamics simulation study of the structural features and inclusion capacities of cucurbit[6]uril derivatives in aqueous solutions

Molecular dynamics (MD) simulations were performed for cucurbit[6]uril (CB6) methyl and cyclohexyl derivatives in aqueous solutions. Furthermore, MD simulations have been conducted to study the inclusion complexes between each CB6 derivative with α,ω-pentane diammonium ion (NH₃⁺(CH₂)₅NH₃⁺) to estimate the binding free energies, the complex geometries and the intermolecular forces responsible for complex formation. Results show a complete inclusion of the guest molecule in the cavity of the host for all complexes. Results also indicate that the guest dynamics inside the cavity of the substituted host is similar to that for the unsubstituted host. This demonstrates that the molecular recognition of the host is not affected by the alkyl substitution at the equator. Also, there is an insignificant conformational change of the macrocyclic structure upon inclusion of the guest. Molecular mechanics/Poisson Boltzmann surface area method was used to estimate the binding free energy of each complex. Results indicate that host–guest electrostatic interactions make the largest contribution to the complex binding free energy. Moreover, van der Waals interactions add significantly to the complex stability. The guest molecules show more or less similar binding free energies with the substituted CB6 that exhibits slightly more negative values than unsubstituted CB6 which is proved also by umbrella sampling.     

Anion recognition by neutral macrocyclic amides

Although amides often serve as anchoring groups in natural and synthetic anion receptors, the structure-affinity relationship studies of amide-based macrocyclic receptors are still very limited. Therefore, we decided to investigate the influence of the size of the macroring on the strength and selectivity of anion binding by uncharged, amide-based receptors. With this aim, we synthesized a series of macrocyclic tetraamides derived from 2,6-pyridinedicarboxylic acid and aliphatic alpha,omega-diamines of different lengths. X-ray analysis shows that all ligands studied adopt expanded conformations in the solid state with the convergent arrangement of all four hydrogen-bond donors. 1H NMR titrations in DMSO solution revealed a significant effect of the ring size on the stability constants of anion complexes; the 20-membered macrocyclic tetraamide 2 is a better anion receptor than its both 18- and 24-membered analogues. This effect cannot be interpreted exclusively in terms of matching between anion diameter and the size of macrocyclic cavity, because 2 forms the most stable complexes with all anions studied, irrespective of their sizes. However, geometric complementarity manifests in extraordinarily high affinity of 2 towards the chloride anion. The results obtained for solutions were interpreted in the light of solid-state structural studies. Taken together, these data suggest that anion binding by this family of macrocycles is governed by competitive interplay between their ability to adjust to a guest, requiring longer aliphatic spacers, and preorganization, calling for shorter spacers. The 20-membered receptor 2 is a good compromise between these factors and, therefore, it was selected as a promising leading structure for further development of anion receptors. Furthermore, the study of an open chain analogue of 2 revealed a substantial macrocyclic effect. X-ray structure of the acyclic model 14 suggests that this may be due to its ill-preorganized conformation, stabilized by two intramolecular hydrogen bonds.     

A H NMR study on the complexation of tetraalkylammonium cations, mono and diprotonated amines, and amino acids with a derivatized cyclotetrachromotropylene in an aqueous solution

The derivatized cyclotetrachromotropylene host forms complexes of 1:1 host to guest stoichiometry with tetraalkylammonium cations and amino acids whereas complexes of 1:2 host to guest stoichiometry are formed with mono and diprotonated amines in an aqueous solution. Both electrostatic and hydrophobic interactions are involved in the complexation.     

Allosteric tuning of the intra-cavity binding properties of a calix[6]arene through external binding to a ZnII center coordinated to amino side chains

Molecular recognition by calix[6]arene-based receptors bearing three primary alkylamino side chain arms (1) is described. Complexation of Zn(II) ion provides the dinuclear mu-hydroxo complex 2G(OH), XRD characterization of which, together with solution studies, provided evidence of its hosting of neutral polar organic guests G. Treatment of this complex with a carboxylic acid or a sulfonamide (XH) results in the formation of mononuclear species 3G(X), one of which (X = Cl) has been characterized by XRD. A dicationic complex 3G(RNH2) is obtained upon treatment of 2G(OH) with a mixture of an alkylamine and a strong acid. Each of these Zn(II) complexes features a tetrahedral metal ion bound to the three amino arms of ligand 1 and to an exogenous ligand (either HO-, X-, or RNH2) sitting outside of the cavity. As a result, the metal ion structures the calixarene core, constraining it in a cone conformation suitable for guest hosting. The receptor properties of these compounds have been explored in detail and are compared with those of the trisammonium receptor 1G(3H+), based on the same calixarene core, as well as those of the trisimidazole-based dicationic Zn funnel complexes. This study reveals very different host properties, in spite of the common hydrophobic, pi-basic, and hydrogen-bonding acceptor properties of the calixarene cores. A harder external ligand produces a less polarized receptor that is consequently particularly sensitive to the hydrogen-bonding ability of its guest. The less electron-rich the apical ligand, and a fortiori the trisammonium host, the more sensitive the receptor to the dipole moment of the guest. All this stands in contrast with the funnel Zn complexes, in which the coordination link plays a dominant role. It is also shown that the asymmetry of an exo-coordinated enantiopure amino ligand is sensed by the guest. This supramolecular system nicely illustrates how the receptor properties of a hydrophobic cavity can be allosterically tuned by the environment.     

Complexation of cyclodextrins with flavines in aqueous solutions

Data on the binding mode and thermodynamics of complex formation for various cyclodextrins (CDs) with flavines are summarized. It is shown that the governing factors of complexation are the size, degree of hydration, and hydrophobicity of the guest molecule. It is found that the presence of small hydrophobic substituents in a flavine’s structure increases their affinity toward cyclodextrin cavities, raising the stability of a complex. In contrast, the presence of bulky and polar side groups in a flavine’s structure prevents its inclusion in a macrocyclic cavity and weakens complexation. The size of a CD cavity plays a minor role in the interaction between CDs and flavines, since the inclusion of a guest molecule is only partial.     

Controlling the morphology of aggregates of an amphiphilic synthetic receptor through host-guest interactions

A new amphiphilic receptor containing a macrocyclic anionic headgroup and a single alkyl chain was prepared through an efficient templated synthesis. The interdependence of the aggregation behavior and the host-guest chemistry was studied. In the absence of any guest the terminus of the alkyl chain of the receptor is included inside the hydrophobic cavity of the macrocycle (as evident from 1H NMR studies) leading to self-assembly into micrometer-long nanotubes (as evident from TEM studies). The alkyl chain can be displaced by an acridizinium bromide guest (as evident from 1H NMR and ITC), which leads to a dramatic change in aggregate size and morphology (as evident from DLS). Studies of the solubilization of Nile red suggest that the resulting aggregates are micelles with a cmc of around 35 microM. These results represent a new addition to the still small number of water-soluble amphiphilic receptors and one of the first examples in which specific host-guest chemistry controls the size and shape of nanoscale aggregates.     

Macrocyclic diorganotin complexes of gamma-amino acid dithiocarbamates as hosts for ion-pair recognition

The dimethyl-, di-n-butyl-, and diphenyltin(IV) dithiocarbamate (dtc) complexes [{R2Sn(L-dtc)}x] 1-7 (1, L = L1, R = Me; 2, L = L1, R = n-Bu; 3, L = L2, R = Me, x = infinity; 4, L = L2, R = n-Bu; 5, L = L3, R = Me, x = 2; 6, L = L3, R = n-Bu, x = 2; 7, L = L3, R = Ph, x = 2) have been prepared from a series of secondary amino acid (AA) homologues as starting materials: N-benzylglycine (alpha-AA derivative = L1), N-benzyl-3-aminopropionic acid (beta-AA derivative = L2), and N-benzyl-4-aminobutyric acid (gamma-AA derivative = L3). The resulting compounds have been characterized by elemental analysis, mass spectrometry, IR and NMR ((1)H, (13)C, and (119)Sn) spectroscopy, thermogravimetric analysis, and X-ray crystallography, showing that in all complexes both functional groups of the heteroleptic ligands are coordinated to the tin atoms. By X-ray diffraction analysis, it could be shown that [{Me2Sn(L2-dtc)}x] (3) is polymeric in the solid state, while the complexes derived from L3 (5-7) have dinuclear 18-membered macrocyclic structures of the composition [{R2Sn(L3-dtc)}2]. For the remaining compounds, it could not be established with certainty whether the structures are macrocyclic or polymeric. A theoretical investigation at the B3LYP/SBKJC(d,p) level of theory indicated that the alpha-AA-dtc complexes might have trinuclear macrocyclic structures. The macrocyclic complexes 5-7 have a double-calix-shaped conformation with two cavities large enough for the inclusion of aliphatic and aromatic guest molecules. They are self-complementary for the formation of supramolecuar synthons that give rise to 1D molecular arrangements in the solid state. Preliminary recognition experiments with tetrabutylammonium acetate have shown that the [{R2Sn(L3-dtc)}2] macrocycles 6 and 7 might interact simultaneously with anions (AcO(-)), which coordinate to the tin atoms, and organic cations (TBA(+)), which accommodate within the hydrophobic cavity (ion-pair recognition).     

环双(对-蒽基-对草快)的分子识别与谱学性质

环双(对-蒽基-对草快)是一种新型的缺电子大环仿生主体, 分子识别是其最重要的应用之一. 考察主体对一系列客体分子如水、氨、醇及杂环等的识别能力, 用密度泛函理论(DFT)中的B3LYP/3-21G基组对主客体复合物的结构进行优化. 在B3LYP/6-31G(d)水平上进行单点能计算, 校正后得到复合物的结合能. 用B3LYP/3-21G方法计算13C和3He化学位移. 结果表明, 主体对客体分子的识别主要靠客体上的杂原子与主体上的氢原子之间的氢键进行. 复合物的稳定化能受氢键的数目和距离影响. 氢键的形成导致部分复合物LUMO与HOMO能隙增大, 同时导致与氢键相连的C—H键上C原子的化学位移向低场移动. 复合物的芳香性与其结合能的大小及结合方式有关. 主体的芳香性因其与客体之间的弱相互作用而提高, 但太强的相互作用及客体在主体空腔内都将影响主体的环电流, 从而削弱其芳香性.     

Guest-responsive excimer fluorescence of β-cyclodextrin bearing a pendant group with two pyrene moieties

β-Cyclodextrin derivative 1 , bearing a group with two pyrene moieties, exhibits predominant excimer emission in a 20% DMSO aqueous solution. In spite of the fact that pyrene is too large to be included in the β-cyclodextrin cavity and consequently both pyrene moieties are located outside the cavity, 1 varies the excimer emission intensity through the formation of inclusion complexes with guest species, thus acting as a chemosensor for molecular recognition.     

Cucurbit[5]uril, Decamethylcucurbit[5]uril and Cucurbit[6]uril. Synthesis, Solubility and Amine Complex Formation

A simple way to prepare cucurbit[5]uril is described. The macrocycles of the cucurbituril type are nearly insoluble in water. The solubilities of cucurbit[5]uril, decamethylcucurbit[5]uril and cucurbit[6]uril in hydrochloric acid, formic acid and acetic acid of different concentrations have been investigated. Due to the formation of complexes between cucurbit[n]urils and protons the solubility increases in aqueous acids. The macrocyclic ligands are able to form complexes with several organic compounds. Thus, the complex formation of the cucurbituril macrocycles with different amines has beenstudied by means of calorimetric titrations. The reaction enthalpy gives noevidence of the formation of inclusion or exclusion complexes. ¹H-NMR measurements show that in the case of cucurbit[5]uril and cucurbit[6]uril the organic guest compound is included within the hydrophobic cavity. Decamethylcucurbit[5]uril forms only exclusion complexes with organicamines. This was confirmed by the crystal structure of the decamethylcucurbit[5]uril-1,6-diaminohexane complex.     

Rapid hydrolytic cleavage of the mRNA model compound HPNP by glycine based macrocyclic lanthanide ribonuclease mimics

The lanthanide ion based macrocyclic complexes 1.Ln mimic the hydrophobic nature of ribonucleases, where the lanthanide ions induce the formation of a hydrophobic cavity for 1, giving rise to a large order of magnitude enhancement in the hydrolytic cleavage of HPNP.     

Molecular recognition in cyclodextrin complexes of amino acid derivatives. 2. A new perturbation: the room-temperature crystallographic structure determination for the N-acetyl-p-methoxy-L-phenylalanine methyl ester/beta-cyclodextrin complex

Cyclodextrins (CDs) are cyclic oligosaccharides that encapsulate various small organic molecules, forming inclusion complexes. Because CD complexes are held together purely by noncovalent interactions, they function as excellent models for the study of chiral and molecular recognition mechanisms. Recently, room-temperature crystallographic studies of both the 2:2 N-acetyl-L-phenylalanine methyl ester/beta-CD and 2:2 N-acetyl-L-phenylalanine amide/beta-CD complexes were reported. The effect of changes in carboxyl backbone functional group on molecular recognition by the host CD molecule was examined for the nearly isomorphous supramolecular complexes. A new perturbation of the system is now examined, specifically perturbation of the aromatic side chain. We report a room-temperature crystal structure determination for the 2:2 N-acetyl-p-methoxy-L-phenylalanine methyl ester/beta-CD inclusion complex. The complex crystallizes isomorphously with the two previously reported examples in space group P1; the asymmetric unit consists of a hydrated head-to-head host dimer with two included guest molecules. The crystal packing provides both a nonconstraining extended hydrophobic pocket and an adjacent hydrophilic region, where hydrogen-bonding interactions can potentially occur with primary hydroxyl groups of neighboring CD molecules and waters of hydration. The rigid host molecules show no sign of conformational disorder, and water of hydration molecules exhibit the same type of disorder observed for the other two complexes, with a few significant differences in locations of water molecules in the hydrophilic region near guest molecules. There is evidence for modest disorder in the guest region of an electron density map. In comparing this system with the two previously reported complexes of phenylalanine derivatives, it is found that the packing of the guest molecules inside the torus of the CD changes upon substitution of a methoxy group at the para position of the aromatic phenyl ring. Backbone hydrogen-bonding interactions for the guest molecules with the CD primary hydroxyls and waters also change. This structure determination is a new and revealing addition to a small but growing database of amino acid and peptidomimetic interactions with carbohydrates.     

Gd(III)[15-metallacrown-5] recognition of chiral α-amino acid analogues

Chiral Ln(III)[15-metallacrown-5] complexes with phenyl side chains have been shown to encapsulate aromatic carboxylates reversibly in their hydrophobic cavities. Given the importance of selective guest binding for applications of supramolecular containers in synthesis, separations, and materials design, the affinity of Gd(III)[15-metallacrown(Cu(II), L-pheHA)-5] hosts for a series of chiral carboxylate guests with varying substitutions on the α-carbon (phenylalanine, N-acetyl-phenylalanine, phenyllactate, mandelate, methoxyphenylacetate) has been investigated. Differential binding of S- and R-phenylalanine was revealed by X-ray crystallography, as the S-enantiomer exclusively forms associative hydrogen bonds with oxygen atoms in the metallacrown ring. Selective guest binding in solution was assessed with isothermal titration calorimetry, which measures the sequential guest binding in the hydrophobic cavity first and the hydrophilic face of the host, and a cyclic voltammetry assay, which quantifies guest binding strength in the hydrophobic cavity of the host exclusively. In solution, the Gd(III)[15-metallacrown(Cu(II), L-pheHA)-5] hydrophobic cavity exhibits modest chiral selectivity for enantiomers of phenylalanine (K(S)/K(R) = 2.4) and mandelate (K(S)/K(R) = 1.22). Weak binding constants of ～100 M(-1) were measured for neutral and -1 charged carboxylates with hydrophilic functional groups (ammonium, N-acetyl, methyl ether). Weaker binding relative to the unsubstituted guests is attributed to unfavorable interactions between the hydrophilic functionalities of the guest and the hydrophobic cavity of the host. In contrast, binding constants greater than 2000 M(-1) were measured for α-hydroxy analogues phenyllactate and mandelate. The significantly increased affinity likely arises from the guests being bound as a -2 anion upon metal-assisted deprotonation in the Gd(III)[15-metallacrown(Cu(II), l-pheHA)-5] cavity. It is established that guest binding affinity in the hydrophobic cavity of the host follows the general trend of neutral zwitterion < monoanion < dianion, with hydrophilic functional groups decreasing the binding affinity. These results have broad implications for the development of metallacrowns as supramolecular catalysts or in chiral separations.     

Protonation and Zn(II) coordination by dipyridine-containing macrocycles with different molecular architecture. A case of pH-controlled metal jumping outside-inside the macrocyclic cavity

The synthesis of the macrocyclic ligand 4,4'-(2,5,8,11,14-pentaaza[15])-2,2'-bipyridylophane (L3), which contains a pentaamine chain linking the 4,4'-positions of a 2,2'-dipyridine moiety, is reported. Protonation and Zn(II) complexation by L3 and by macrocycle L2, containing the same pentaamine chain connecting the 6,6'-positions of 2,2'-dipyridine, were studied by means of potentiometric, UV-vis, and fluorescent emission measurements. While in L2 all the nitrogen donor atoms are convergent inside the macrocyclic cavity, in L3 the heteroaromatic nitrogen atoms are located outside. Both ligands form mono- and dinuclear Zn(II) complexes in aqueous solution. In the mononuclear Zn(II) complexes with L2, the metal is coordinated inside the macrocyclic cavity, bound to the heteroaromatic nitrogen donors and three amine groups of the aliphatic chain. As shown by the crystal structure of the [ZnL2](2+) complex, the two benzylic nitrogens are not coordinated and facile protonation of the complex takes place at slightly acidic pH values. Considering the mononuclear [ZnL3](2+) complex, the metal is encapsulated inside the cavity, not coordinated by the dipyridine unit. Protonation of the complex occurs on the aliphatic polyamine chain and gives rise to translocation of the metal outside the cavity, bound to the heteroaromatic nitrogens.     

New strategy and methods for constructing artificial macrocyclic anion receptors. Selective binding of tetrahedral oxoanions

A new rational strategy for assembling highly selective neutral macrocyclic anionic receptors proposed by the authors is considered. The strategy includes preliminary theoretical modeling of supramolecular complexes, analysis of synthetic paths for receptor preparation, selection and synthesis of building blocks followed by their cyclocondensation under thermo-dynamic control in the presence of acid corresponding to the target template anion, which provides anion-induced combinatorial selection of the macrocyclic ligand in the emerging dynamic combinatorial library. Analysis of the properties of the obtained anion receptors showed that the number of hydrogen bonds formed between the receptor and the guest anion mainly determines the binding energy. The receptor selectivity for a particular anion is determined by the nature of coordination sites, their geometry in the macrocyclic cavity, and the overall conformation rigidity of the macrocycle. Using the developed strategy and novel synthetic approaches, a large series of highly selective anion receptors with record binding constants (up to 10^p7 L mol^p-1 in both highly and weakly solvating media) was constructed and the structures of the host—guest complexes were studied in detail by both experimental and theoretical methods     

Molecular electrostatic potentials and hydrogen bonding in alpha-, beta-, and gamma-cyclodextrins

Cyclodextrins (CDs) are cyclic oligomers of glucose having the toroid of sugars elaborating a central cavity of varying size depending on the number of glucoses. The central hydrophobic cavity of CD shows a binding affinity toward different guest molecules, which include small substituted benzenes to long chain surfactant molecules leading to a variety of inclusion complexes when the size and shape complementarity of host and guest are compatible. Further, interaction of guest molecules with the outer surface of alpha-CD has also been observed. Primarily it is the electrostatic interactions that essentially constitute a driving force for the formation of inclusion complexes. To gain insights for these interactions, the electronic structure and the molecular electrostatic potentials in alpha-, beta-, and gamma-CDs are derived using the hybrid density functional theory employing the three-parameter exchange correlation functional due to Becke, Lee, Yang, and Parr (B3LYP). The present work demonstrates how the topography of the molecular electrostatic potential (MESP) provides a measure of the cavity dimensions and understanding of the hydrogen-bonded interactions involving primary and secondary hydroxyl groups. In alpha-CD, hydrogen-bonded interactions between primary -OH groups engender a "cone-like" structure, while in beta- or gamma-CD the interactions from the primary -OH with ether oxygen in glucose ring facilitates a "barrel-like" structure. Further, the strength of hydrogen-bonded interactions of primary -OH groups follows the rank order alpha-CD > beta-CD > gamma-CD, while the secondary hydrogen-bonded interactions exhibit a reverse trend. Thus weak hydrogen-bonded interactions prevalent in gamma-CD manifest in shallow MESP minima near hydroxyl oxygens compared to those in alpha- or beta-CD. Furthermore, electrostatic potential topography reveals that the guest molecule tends to penetrate inside the cavity forming the inclusion complex in beta- or gamma-CD.     

Characterization of host-guest complexes of cucurbit[n]uril (n = 6, 7) by electrospray ionization mass spectrometry

When an intramolecular cavity exists in a molecule, it can trap another chemical species to form a host-guest complex. We examine the formation of such an inclusion complex with cucurbit[n]uril (CBn, n = 6, 7) as the host to trap alkali metal or ammonium ions as the guest, by electrospray ionization mass spectrometry (ESI-MS). The results show that the inclusion complexes are formed between the three-dimensional cylinder of CBn hosts and the guest cations. Selectivity of the complex formation is dependent both on (1) ion-dipole interactions between the cylindrical portal of the CBn hosts and the guest cations and (2) the hydrophobic interactions at the inner cavity of CBn.