Recognition of glycine by cucurbit[5]uril and cucurbit[6]uril: A comparative study of exo- and endo-binding

Recognition features of glycine (Gly) with cucurbit[5]uril (Q[5]) and cucurbit[6]uril (Q[6]) both in aqueous solution and solid state were investigated by ¹H NMR spectroscopy and X-ray crystallography. ¹H NMR data indicate that the Gly is located outside of the portals of the Q[5], exhibiting exo binding with the Q[5]. In the case of the Q[6], the Gly shows endo binding or a dual binding mode (endo and exo binding) with the host, which depends on the amount of the host in the aqueous solution. X-ray crystallography clearly display that the Gly forms 2:1 exclusion complex with the Q[5], and 2:1 inclusion complex with the Q[6]. Interestingly, hydrogen bondings between the encapsulated Gly molecules in the Q[6] were observed.     

Synthesis and binding behaviors of monomethyl cucurbit[6]uril

By reacting 3a-methylglycoluril and glycoluril with paraformaldehyde, monomethyl cucurbit[6]uril was synthesized in 14% yield. The new host molecule forms stable inclusion complexes with diamine and hexylaminocarbazole derivatives.     

Binding modes of cucurbit[6]uril and cucurbit[7]uril with a tetracationic bis(viologen) guest

Binding behaviors of two cucurbit[n]urils (CB[n]) hosts with the [CH3bpy(CH2)6bpyCH3]4+ (bpy = 4,4'-bipyridinium) guest were investigated by 1H NMR and MALDI-TOF-MS experiments. While the CB[6] and CB[7] form [2]pseudorotaxanes with the host located over the hexamethylene chain of the guest, only the CB[7] forms a [3]pseudorotaxane with both host molecules residing over the bipyridinium groups. The initial CB[7] host vacates the inclusion of the hexamethylene chain as a result of the electrostatic and steric repulsions that would arise in simultaneous binding of adjacent aliphatic and aromatic portions of the guest.     

Crystal structure of a La(III) complex with macrocyclic cavitand cucurbit[6]uril

Slow evaporation in air of a lanthanum nitrate solution containing macrocyclic cavitand cucurbit[6]uril yields a complex of the composition of [La(H₂O)₆(X@C₃₆H₃₆N₂₄O₁₂)(NO₃)](NO₃)₂· 6.96H₂O (X = 0.5C₅H₅N + 0.5H₂O). The complex is structurally characterized using single crystal X-ray diffraction. Lanthanum atoms are coordinated with oxygen atoms of carbonyl groups of cucurbit[6]uril portals. The compound crystallizes in the orthorhombic crystal system, space group Pnn2, unit cell parameters (150 K): a = 11.997(2) Å, b = 17.093(3) Å, c = 14.133(3) Å, V = 2899.3(10) ų, Z = 2. Lanthanum atoms are disordered, alternative positions being related by the two-fold axis. The complex has an island structure. A pyridine molecule occupies an internal cavity of one half of cucurbit[6]uril molecules, while a water molecule occupies the other.     

Binding modes of cucurbit[6]uril and cucurbit[7]uril with a series of bis-pyridinium compounds

Binding behaviors of cucurbit[6]uril (CB[6]) and cucurbit[7]uril (CB[7]) with a series of bis-pyridinium compounds N, N’-hexamethylenebis(1-alkyl-4-carbamoyl pyridinium bromide) (HBPB-n) (alkyl chain length, n = 6, 8 and 10) guests were investigated using ¹H-NMR, ESI–MS and single crystal X-ray diffraction methods. The results show that CB[6] and CB[7] can form [2]pseudorotaxanes with HBPB-n easily. When increasing the length of tail alkyl chain, the binding site of CB[6] at guest molecules changed from the tail to the middle part, while CB[7] remained located over the tail chain. As CB[6] and CB[7] were added in HBPB-8 aqueous solution, a [3]pseudorotaxane was formed by the inclusion of the internal middle site in CB[6] and the tail chain in CB[7].     

The formation of cucurbit[n]uril (n = 6, 7) complexes with amino compounds in aqueous formic acid studied by capillary electrophoresis

For analytes involved in dynamic equilibrium processes, capillary electrophoresis is a powerful method of determining binding constants. In this work, the complex formation between cucurbit[n]uril (CB[n] n = 6, 7) and some amino compounds was studied by capillary electrophoresis in aqueous formic acid (65% v/v). Four groups of positional and structural isomers (o, m, p-methylanilines; m, p-nitroanilines; benzidine and o-tolidine; alpha, beta-naphthylamines and 1,5-diaminonaphthalene) were selected as model compounds for study of their host-guest inclusion complexation. The interactions between CB[n] (n = 6, 7) and the model compounds were also investigated using a molecular modeling method. The results indicate that the interactions of the compounds with CB[n] (n = 6, 7) are strongly affected by the position of the substituent(s) on the aromatic ring and the ion-dipole interaction between guest molecule and CB. Furthermore, the type and the concentration of CBs on the separation and migration behavior of the amino compounds were also studied.     

Synthesis and crystal structures of supramolecular compounds of polynuclear aluminum(III) aqua hydroxo complexes with cucurbit[6]uril

Supramolecular compounds of the di-, trideca-, and triacontanuclear aluminum aqua hydroxo complexes, viz., [Al₂(OH)₂(H₂O)₈]⁴⁺, [Al₁₂(AlO₄)(OH)₂₄(H₂O)₁₂]⁷⁺, and [Al₃₀O₈(OH)₅₆(H₂O)₂₆]¹⁸⁺, respectively, with the organic macrocyclic cavitand cucurbit[6]uril (C₃₆H₃₆N₂₄O₁₂) were prepared by evaporation of aqueous solutions of aluminum nitrate and cucurbit[6]uril after the addition of pyridine, ammonia, KOH, or NaOH at pH 3.1–3.8. X-ray diffraction study demonstrated that the aqua hydroxo complexes are linked to the macrocycle through hydrogen bonds between the hydroxo and aqua ligands of the polycations and the portal oxygen atoms of cucurbit[6]uril. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 261—268, February, 2006.     

Sequence recognition and self-sorting of a dipeptide by cucurbit[6]uril and cucurbit[7]uril

Cucurbit[7]uril forms very strong complex with zwitterionic dipeptide Phe-Gly with affinity exceeding 10(7) M(-1) and effectively recognizes peptide sequence of Phe-Gly over Gly-Phe as well as Tyr-Gly over Gly-Tyr and Trp-Gly over Gly-Trp with relative affinities of 23 000, 18 000 and 2000, respectively.     

Synthesis and crystal structures of PrIII and NdIII complexes with the macrocyclic cavitand cucurbit[6]uril

The [{Pr(NO₃)₂(H₂O)₃}{Pr(NO₃)(H₂O)₄} (C₃₆H₃₆N₂₄O₁₂)](NO₃)₃·4H₂O and [{Nd(NO₃)(H₂O)₄} ₂(NO₃@C₃₆H₃₆N₂₄O₁₂)][Nd(NO₃)₆] complexes were prepared by heating a mixture of lanthanide nitrates, cucurbit[6]uril, and water in a sealed tube. X-ray diffraction study demonstrated that the metal atoms in the former complex are linked to the macrocycle through tridentate coordination of the portal oxygen atoms of cucurbit[6]uril to the praseodymium(III) cation. The neodymium(III) complex is the first example of lanthanide compounds with cucurbit[6]uril belonging to coordination polymers. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1511–1517, September, 2006.     

臭氧氧化法合成全羟基葫芦[6]脲

葫芦脲(CB[n])的直接衍生化一直是一项难题。本文用臭氧氧化法将CB[6]衍生化,合成全羟基葫芦[6]脲((OH)12CB[6])。CB[6]与O3在20℃下反应 22h,生成(OH)12CB[6]的产率为44%,并探究了丙酮扩散法、柱层析法和DMSO提纯法三种去除无机盐的方法的可行性。臭氧由电解水制得,成本低,没有二次污染,且臭氧氧化能力强,在室温下即可氧化葫芦脲。本文为合成全羟基葫芦脲提供了新的方法。     

六元瓜环与磺基水杨酸主客体配合物的晶体结构

合成了六元瓜环与磺基水杨酸主客体配合物,并测定了其单晶结构.晶体结构表明六元瓜环包结了3个水分子,磺基水杨酸位于六元瓜环的外侧,且与水分子通过氢键与六元瓜环相连,瓜环之间通过端口的羰基O原子、磺基水杨酸以及水分子间的氢键作用形成一维超分子.     

Bromination of N-phenyloxypropyl-N'-ethyl-4,4'-bipyridium in cucurbit[8]uril molecular reactor

CB[n](n=6-8) is a family of synthetic macrocyclic host molecules composed of n glycoluril units, which can be employed as molecular reactor. N-phenyloxypropyl-N'-ethyl-4,4'-bipyridium (1) was designed to form a host-guest inclusion complex with CB[n](n=6-8), subsequently, the bromination reaction of 1 and its corresponding inclusion complexes was investigated in this work. In the case of 1/CB[8], the folded including mode is quite helpful to acquire 1-bormination product completely through intramolecular charge transfer (ICT), and CB[8] can provide a safe bromination environment for 1.     

Metal ion-assisted assembly of one-dimensional polyrotaxanes incorporating cucurbit[6]uril

Three cucurbit[6]uril (CB[6])-based polyrotaxanes [Cu(H₂ C6N4)(CB[6])]Cl₄·12H₂O (1), [Co(H₂ C6N4)(CB[6])]Cl₄·14H₂O (2) and [Ag(C6N4)(CB[6])]NO₃·7H₂O (3) are prepared using N,N′-bis(4-pyridylmethyl)-1,6-hexanediamine (C6N4) threading into CB[6]'s and metal ions' assistance. Single-crystal X-ray diffraction analyses reveal that polyrotaxanes 1, 2 and 3 all have 1D chain structure where 1 and 2 are linear and 3 has two shapes, linear and sawtooth, respectively. The effects of guest molecules, metal and counter ions as well as intermolecular weak interactions on the architectures of polyrotaxanes are discussed.     

Preparation of glycoluril monomers for expanded cucurbit[n]uril synthesis

Glycoluril derivatives bearing free ureidyl groups (1) and bis(cyclic ethers) (2) are the fundamental building blocks for the synthesis of cucurbituril, its derivatives, and its congeners. The known derivatives of 1 and 2 fall into two main classes—those bearing alkyl or aryl functional groups on their convex face. In this paper we present a third class of glycolurils, namely those bearing substituents that are electron withdrawing in character. This class of compounds carries carboxylic acid derived functional groups on their convex face and are derived from diesters 1e and 2e. An improved synthesis of 1e and 2e is reported and their modification described. For example, 1e and 2e are converted into secondary amides (10-15) by heating in solutions of the neat primary amines. The secondary amides can be transformed into imides (19-22, 24, 25) by heating with PTSA in ClCH₂CH₂Cl. The isolation of these compounds in pure form in high yields is accomplished by simple and scalable washing or recrystallization procedures. We also present the X-ray crystallographic characterization of bis(cyclic ethers) 2e, 8, and 22. We anticipate that the ready availability of ester, carboxylate, acid, secondary amide, imide, and tertiary amide derivatives of 1 and 2 will expand the scope of the synthesis of cucurbituril derivatives by providing a new class of building blocks with electron withdrawing substituents.     

Host-Guest Interactions of Cyclopentanocucurbit[6]uril with Alkyl Imidazolium Hydrochlorides

The host-guest interactions between cyclopentanocucurbit-[6]uril(CyP₆Q[6]) as host and six alkyl imidazolium hydrochloride as guests(g1, g2, g3, g4, g5, and g6) have been studied by various techniques, such as ¹H NMR spectroscopy, isothermal titration calorimetry, mass spectrometry, and single-crystal X-ray diffraction analysis. The experimental results showed that CyP₆Q[6] formed 1:1 inclusion complexes with each of guests g1-g6. The part of the guest entered the cavity of CyP₆Q[6] changes as the alkyl chain increases in length. It can be seen that the length of the alkyl chain plays a key role in determining the mode of host-guest interactions.     

六元瓜环与含双苯并咪唑功能基烷烃的自组装模式及晶体结构

以含有双苯并咪唑功能基的烷烃化合物二氯化-1,4-二(2,2’-苯并咪唑基)丁烷(SBB)为客体,普通六元瓜环(Q[6])为主体,利用1H NMR技术、荧光发射光谱和X-单晶衍射实验等考察了主客体的自组装模式.1 H NMR技术结果显示,当主客体的比例为1:1时,在水溶液中,1个Q[6]包结1个客体分子的一端苯并咪唑基团;在结晶固态条件下,X-单晶衍射实验测试结果是Q[6]包结客体分子的烷基链.荧光发射光谱表明,当主客体比例为2:1时,2个Q[6]分别包结1个客体分子的两端苯并咪唑基团形成哑铃型的实体配合物。     

瓜环准轮烷分子晶体结构及切割DNA研究

报道了瓜环准轮烷分子晶体结构及DNA的切割.     

A hemicyanine and cucurbit[n]uril inclusion complex: competitive guest binding of cucurbit[7]uril and cucurbit[8]uril

The interaction between the hemicyanine indole derivative H and the cucubit[n]urils Q[7] and Q[8] has been studied using ¹H NMR and UV spectroscopy as well as by fluorescence experiments. Competitive studies on the inclusion of H by Q[7] and Q[8] have also been conducted, and reveal that on changing the size of the Q[n] cavity, the binding behaviour can be very different.     

Complexation behavior of cucurbit[6]uril with short polypeptides

The binding properties of cucurbit[6]uril towards various peptides have been investigated in acidic aqueous solution. Stability constants and thermodynamic values of the complex formation between following peptides: glycyl-l-alanine, l-leucyl-l-valine, glycyl-l-asparagine, l-leucyl-l-phenylalanine, l-leucyl-l-tryptophan, glycyl-l-histidine, l-glutathione reduced (γ-l-glutamyl-l-cysteinyl-glycine, GSH), and dl-leucyl-glycyl-dl-phenylalanine) with cucurbit[6]uril in aqueous formic acid (50%, v/v) have been calculated from calorimetric titrations. From these results it can be seen that the peptides form exclusion complexes with cucurbit[6]uril. Due to the polar peptide bond they are not included within the hydrophobic cavity of cucurbit[6]uril. The complex formation is favoured by entropic contributions. The release of water molecules from the polar amino groups of the peptides and the carbonyl groups of cucurbituril are responsible.     

Molecular-recognition properties of a water-soluble cucurbit[6]uril analogue

The molecular-recognition properties of the cucurbit[6]uril analogue (1) in aqueous buffer (sodium acetate, 50 mM, pH 4.74, 25 degrees C) toward a variety of guests including alkanediamines (6-12), aromatics (14-32), amino acids (33-36), and nucleobases (37-42) were studied by fluorescence spectroscopy. For the alkanediamines studied (H2N(CH)nNH2, n = 6, 7, 8, 9, 10, 11, 12), the association constants increase as the length of the alkane (n) is increased. Host 1 is capable of forming strong complexes with guests containing aromatic rings with association constants (Ka) ranging from 10(2) to 10(6) M(-1) as a result of the favorable pi-pi interactions that occur between host 1 and the aromatic rings of the guest when bound in the cavity of 1. Biologically relevant guests such as amino acids and nucleobases are also bound in the cavity of 1 with Ka values ranging from 10(3) to 10(6) M(-1). Consequently, cucurbit[6]uril analogue 1 functions as a versatile fluorescent sensor for the presence of a wide range of chemically and biologically important substances in aqueous solution including nitroaromatics, neurotransmitters, amino acids, and nucleobases.