水溶液中的氨基酸桥联环糊精二聚体的分子识别

采用荧光偏光方法研究了用2-氨基-L-1,5-戊二酸衍生物和(1R,3R)-1-氨基-1,3-二羧基环戊烷衍生物桥联的环糊精二聚体1和2(主体),在298K、pH=7.4时,与四个低分子量的多肽(客体,H-Trp-Trp-Arg-Arg-NH23;Adm-Trp-Arg-Arg-NH24;Adm-D-Trp-Arg-Arg-NH25;H-Trp-Trp-Trp-Trp-Arg-Arg-NH26)之间的相互作用。研究结果表明,二聚体环糊精对于多肽的分子识别作用,就主体而言,即便是主体作用位点以外部分基团结构的改变,对主-客体之间的分子识别也有重要影响,并且两个空腔在组装客体过程中相互之间产生协同作用,就客体而言,多肽分子的链长、疏水性及其嵌入基团的极性、大小、形状等对包合物的形成与稳定均起重要作用。主-客体组装过程中产生负的焓变和正的熵变,表明范德华-伦敦色散力、氢键和疏水相互作用是本文研究体系的主要包合驱动力。     

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.     

Molecular recognition in cyclodextrin complexes of amino acid derivatives. 1. Crystallographic studies of beta-cyclodextrin complexes with N-acetyl-L-phenylalanine methyl ester and N-acetyl-L-phenylalanine amide pseudopeptides

Cyclodextrins (CDs) are widely utilized in studies of chiral and molecular recognition. By changing the functionality of the guest molecule, the effect of such changes on recognition by the host CD molecule can be examined. We report crystal structure determinations for two nearly isomorphous complexes of phenylalanine derivatives: beta-CD/N-acetyl-L-phenylalanine methyl ester and beta-CD/N-acetyl-L-phenylalanine amide. The complexes crystallize as hydrated head-to-head host dimers with two included guest molecules in space group P1. The crystal packing is such that it presents a nonconstraining hydrophobic pocket adjacent to a hydrophilic region, where potential hydrogen-bonding interactions with hydroxyl groups of neighboring cyclodextrin molecules and waters of hydration can occur. The two host molecules display very similar conformations; only a few of the primary hydroxyl groups are conformationally disordered. There are a number of changes in the location of water of hydration molecules, some of which are the result of different hydrogen-bonding interactions. For the different guest molecules, similar modes of penetration are observed in the CD torus; however, there is a 0.985-A shift in the position of the guest molecules in the host torus, which takes place without changing the hydrophobic interactions displayed by the phenyl side chains. This observation and the thermal motion of the guest molecules in the ester complex are taken as evidence that complex binding forces are weak. The pseudopeptides experience a significant degree of flexibility in the crystalline environment provided by CD dimers. Conformational differences of the pseudopeptide backbones and the presence of disordered water molecules in the host-guest interface provide examples of different hydrogen-bonding schemes of similar potential energy. The crystal system presents an opportunity to establish a database of molecular interactions for small peptides and peptide analogues with waters of hydration and functional groups in nonconstraining binding environments.     

胆甾类分子钳对氨基酸衍生物的对映选择性识别

用差紫外光谱滴定法考察了以脱氧胆酸作spacer的手性分子钳1～3对一系列α-氨基酸甲酯的对映选择性识别性能。结果表明,分子钳1和2与客体氨基酸甲酯形成1:1型超分子配合物,并显示较好的手性识别能力。分钳3对所考察的氨基酸甲酯均没有明显的识别作用。讨论了主-客体间尺寸/形状匹配、几何互补等因素对形成超分子配合物的影响,并利用计算机模拟作辅助手段对实验结果和现象进行了解释。     

Complexation of ferrocene derivatives by the cucurbit[7]uril host: a comparative study of the cucurbituril and cyclodextrin host families

The formation of inclusion complexes between cucurbit[7]uril (CB[7]) and ferrocene and its derivatives has been investigated. The X-ray crystal structure of the 1:1 inclusion complex between ferrocene and CB[7] revealed that the guest molecule resides in the host cavity with two different orientations. Inclusion of a set of five water-soluble ferrocene derivatives in CB[7] was investigated by 1H NMR spectroscopy and calorimetric and voltammetric techniques. Our data indicate that all neutral and cationic guests form highly stable inclusion complexes with CB[7], with binding constants in the 10(9)-10(10) M(-)(1) and 10(12)-10(13) M(-1) ranges, respectively. However, the anionic ferrocenecarboxylate, the only negatively charged guest among those surveyed, was not bound by CB[7] at all. These results are in sharp contrast to the known binding behavior of the same guests to beta-cyclodextrin (beta-CD), since all the guests form stable inclusion complexes with beta-CD, with binding constants in the range 10(3)-10(4) M(-1). The electrostatic surface potentials of CB[6], CB[7], and CB[8] and their size-equivalent CDs were calculated and compared. The CD portals and cavities exhibit low surface potential values, whereas the regions around the carbonyl oxygens in CBs are significantly negative, which explains the strong affinity of CBs for positively charged guests and also provides a rationalization for the rejection of anionic guests. Taken together, our data suggest that cucurbiturils may form very stable complexes. However, the host-guest interactions are very sensitive to some structural features, such as a negatively charged carboxylate group attached to the ferrocene residue, which may completely disrupt the stability of the complexes.     

Pyridine-containing chiral macrocycles for the enantioselective recognition of amino acid derivatives and their molecular dynamics simulations

Two novel C₂-symmetric optically active pyridine-15-crown-5 type ligands containing lipophilic chains at the stereogenic centres, macrocycles 5 and 6, were prepared from (S)-1,2-propanediol and (S)-3-aryloxy-1,2-propanediol for the enantiomeric recognition of amino acid ester derivatives. These novel macrocycles have been shown to be strong complexing agents for primary organic ammonium salts (with K values of up to 1363.5 M^?1, ΔG^o of up to 17.86 kJ mol^?1 and a selectivity ratio of 80:20) by ¹H NMR titration method. These macrocyclic host exhibited enantioselective binding towards the l-enantiomer of phenylalanine methyl ester hydrochloride with K_L/K_D up to 8.57 in CDCl₃ containing 0.25% CD₃OD. Experimental results have been detailed with molecular dynamic calculations at atomic level concerning the molecular recognition and discrimination properties of a chiral pyridino-15-crown-5. The binding free energies were calculated as ～?25 kJ mol^?1. The results indicated that the host binds and discriminates valine salts better than phenylalanine salts. The molecular dynamics, MM/PBSA calculations are consistent with the ¹H NMR results.     

A novel chiral terpyridine macrocycle as a fluorescent sensor for enantioselective recognition of amino acid derivatives

Terpyridine macrocycle 1 is shown to be a strong chelating agent for organic ammonium salts and also a useful chromophore in fluorescent sensing. It exhibits very good enantioselectivity (K(obs)(S)/K(obs)(R)= 3.8) in chiral discrimination of alpha-phenylglycine methyl ester hydrochloride (PhEtOMe).     

Structural and energetic effects in the molecular recognition of amino acids by 18-crown-6

Absolute 18-crown-6 (18C6) affinities of five amino acids (AAs) are determined using guided ion beam tandem mass spectrometry techniques. The AAs examined in this work include glycine (Gly), alanine (Ala), lysine (Lys), histidine (His), and arginine (Arg). Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AAs as well as the proton bound complexes comprised of these species, (AA)H(+)(18C6). The proton affinities (PAs) of Gly and Ala are lower than the PA of 18C6, whereas the PAs of Lys, His, and Arg exceed that of 18C6. Therefore, the collision-induced dissociation (CID) behavior of the (AA)H(+)(18C6) complexes differs markedly across these systems. CID of the complexes to Gly and Ala produces H(+)(18C6) as the dominant and lowest energy pathway. At elevated energies, H(+)(AA) was produced in competition with H(+)(18C6) as a result of the relatively favorable entropy change in the formation of H(+)(AA). In contrast, CID of the complexes to the protonated basic AAs results in the formation of H(+)(AA) as the only direct CID product. H(+)(18C6) was not observed, even at elevated energies, as a result of unfavorable enthalpy and entropy change associated with its formation. Excellent agreement between the measured and calculated (AA)H(+)-18C6 bond dissociation energies (BDEs) is found with M06 theory for all complexes except (His)H(+)(18C6), where theory overestimates the strength of binding. In contrast, B3LYP theory significantly underestimates the (AA)H(+)-18C6 BDEs in all cases. Among the basic AAs, Lys exhibits the highest binding affinity for 18C6, suggesting that the side chains of Lys residues are the preferred binding site for 18C6 complexation in peptides and proteins. Gly and Ala exhibit greater 18C6 binding affinities than Lys, suggesting that the N-terminal amino group provides another favorable binding site for 18C6. Trends in the 18C6 binding affinities among the five AAs examined here exhibit an inverse correlation with the polarizability and proton affinity of the AA. Therefore, the ability of the N-terminal amino group to compete for 18C6 complexation is best for Gly and should become increasing less favorable as the size of the side chain substituent increases.     

Collision energy effects in tanden mass spectrometry as revealed by a proton-bound dimer ion

Mass spectra resulting from collision-induced decomposition of the proton-bound dimer of iso-propylamine and sec-butylamine have been obtained as a function of laboratory collision energy over the range 10-6000 eV. The ratio of the two principal fragment ions from the dimer ion measured as a function of collision energy is compared with the ratio expected as a function of internal energy as calcualted based on the statistical theory of mass spectra. This comparison indicates that the average energy deposited into the dimer ion upon collision reaches a maximum at a collision energy of ～70 eV. The average internal energy of the ions at this collision energy is ～4.3 eV. Other fragment ions which arise from higher energy decompositions are also observed in the spectra at much lower intensities. The relative intensities of these fragments indicate that the probability for large energy transfers are highest at ke V collision energies. These observations are interpreted on the basis of differences in the postcollision internal energy distributions resulting from keV and eV collisions.     

Molecular hydrogels from bolaform amino acid derivatives: a structure-properties study based on the thermodynamics of gel solubilization

Insight is provided into the aggregation thermodynamics associated to hydrogel formation by molecular gelators derived from L-valine and L-isoleucine. Solubility data from NMR measurements are used to extract thermodynamic parameters for the aggregation in water. It is concluded that at room temperature and up to 55?°C, these systems form self-assembled fibrillar networks in water with quite low or zero enthalpic component, whereas the entropy of the aggregation is favorable. These results are explained by considering that the hydrophobic effect is dominant in the self-assembly. However, studies by NMR and IR spectroscopy reveal that intermolecular hydrogen bonding is also a key issue in the aggregation process of these molecules in water. The low enthalpy values measured for the self-assembly process are ascribed to the result of a compensation of the favorable intermolecular hydrogen-bond formation and the unfavorable enthalpy component of the hydrophobic effect. Additionally, it is shown that by using the hydrophobic character as a design parameter, enthalpy-controlled hydrogel formation, as opposed to entropy-controlled hydrogel formation, can be achieved in water if the gelator is polar enough. It is noteworthy that these two types of hydrogels, enthalpy-versus entropy-driven hydrogels, present quite different response to temperature changes in properties such as the minimum gelator concentration (mgc) or the rheological moduli. Finally, the presence of a polymorphic transition in a hydrogel upon heating above 70?°C is reported and ascribed to the weakening of the hydrophobic effect upon heating. The new soft polymorphic materials present dramatically different solubility and rheological properties. Altogether these results are aimed to contribute to the rational design of molecular hydrogelators, which could be used for the tailored preparation of this type of soft materials. The reported results could also provide ground for the rationale of different self-assembly processes in aqueous media.     

Participation of host ‘spacer’ atoms in carboxylic acid binding: implications for amino acid recognition

Chiral 4,4′-diamido-2,2′-biimidazoles were synthesized and found to bind N-Boc protected amino acids in CDCl₃. The biimidazole that features (R)-tetrahydrofurfuryl units discriminates between N-Boc-l-Ser (K_assoc=120 M⁻¹) and its non-natural d-enantiomer (270 M⁻¹). X-ray diffraction and computational analyses show that members of this receptor class adopt a cleft-like conformation, presenting a donor-spacer-donor-acceptor H-bonding array. Complexes of such biimidazoles with the -COOH unit of amino acids are stabilized by direct involvement of what is nominally a ‘spacer’ atom, unlike other D-Sp-D-A hosts.     

Molecular recognition of alpha-cyclodextrin (CD) to choral amino acids based on methyl orange as a molecular probe

The molecular recognition interaction of alpha-CD to chiral amino acids was investigated by using spectrophotometry based on methyl orange as a molecular probe. The molecular recognition ability depended on the inclusion formation constants. The molecular recognition of alpha-CD to aromatic amino acids was the order: DL-tryptophan > L-tryptophan > L-phenylalanine > L-tyrosine approximately DL-beta-3,4-dihydroxy-phenylalanine; whereas for aliphatic amino acids, the order was: L-iso-leucine > L-leucine approximately L-methionine approximately DL-mehtionine > D-leucine. The effect of temperature on the inclusion interaction was examined and the thermodynamic parameters of inclusion process, delta G, delta H, delta S, were determined. The experimental results indicated that the inclusion process was an exothermic and enthalpy-driven process accompanied with a negative or minor positive entropic contribution. The inclusion interaction between alpha-CD and amino acids satisfied the law of enthalpy-entropy compensation. The compensation temperature was 291 K.     

二聚炔雌醇分子钳对氨基酸甲酯手性识别的理论研究

采用分子模拟研究了二聚炔雌醇分子钳(1~3)与D-和L-苯丙氨酸甲酯的相互作用,比较了形成配合物前后分子钳的结构变化以及与手性苯丙氨基酸甲酯相互作用能大小,其计算结果与实验结果一致。理论研究表明主客体分子间存在着的空间匹配、Van der Waals作用力和静电作用是分子识别的推动力,这为认识和预测分子钳的手性识别能力提供了理论依据。     

Fluorescence study of inclusion complexes between star-shaped cholic acid derivatives and polycyclic aromatic fluorescent probes and the size effects of host and guest molecules

Star-shaped host molecules containing two, three, and four cholic acid moieties have been used to form inclusion complexes with polycyclic aromatic hydrocarbon probes (guests) varying in size from four (pyrene) to five (benzo(e)pyrene) and seven aromatic rings (coronene) and investigated by steady-state fluorescence measurements and fluorescence lifetime techniques. The results indicated that these hydrophobic guest probes prefer to locate in the hydrophobic cavities formed by the host molecules in an aqueous solution. Further studies showed that the stoichiometric ratios of the complexes depended on the relative size of both the host and the guest. The complexes of 1:1 ratio (guest:host) were formed between pyrene and the host molecules of different sizes, while the complexes of 1:2 ratio (guest:host) were found for coronene in all cases. For benzo(e)pyrene with an intermediate size, the complexes with 1:1 and 1:2 ratios (guest:host) were formed depending on the relative sizes of the host molecules. The stability of the inclusion complexes was observed to change with the solvent polarity, indicative of an adaptation of the hydrophobicity of the host pockets to the polarity of the solvent. The formation of the complexes was driven by the solvophobic interactions.     

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.     

Glucose recognition by a supramolecular complex of boronic acid fluorophore with boronic acid-modified cyclodextrin in water

A boronic acid fluorophore (C1-APB)/boronic acid-modified γ-cyclodextrin (3-PB-γ-CyD) complex as a supramolecular sensor has been designed for selective glucose recognition in water. The fluorescent response behavior of the C1-APB/3-PB-γ-CyD complex under various pH conditions revealed that a C1-APB/3-PB-γ-CyD complex solution containing glucose showed a large increase in the fluorescence intensity under alkaline pH conditions. In contrast, only small increases in the fluorescence intensity were noted for fructose and without sugar solutions. The observed response selectivity for the C1-APB/3-PB-γ-CyD complex was on the order of glucose > galactose, mannose > fructose. The evidence on a large value of the inclusion constant (K(L·CyD) = 6.5 × 10(3) M(-1)), a marked broadening of the (1)H NMR spectra, and an enhancement of induced circular dichloism (ICD) intensity for the C1-APB/3-PB-γ-CyD complex by glucose binding supported the multi-point interaction of the C1-APB/3-PB-γ-CyD complex with glucose. These results demonstrated that the C1-APB/3-PB-γ-CyD complex functioned as an efficient supramolecular sensor for selective glucose recognition in water.     

Molecular recognition thermodynamics of bile salts by beta-cyclodextrin dimers: Factors governing the cooperative binding of cyclodextrin dimers

The complex stability constants (K(S)), standard molar enthalpy (DeltaH degrees), and entropy changes (DeltaS degrees) for the inclusion complexation of two families of beta-cyclodextrin (beta-CD) dimers, i.e. beta-CD dimers Se1-Se4 bearing 2,2'-diselenobis(benzoyl) tether (Se-dimers) and beta-CD dimers Py1-Py4 bearing 2,2'-bipyridine-4,4'-dicarboxy tether (Py-dimers), with four bile salt guests, i.e. sodium cholate (CA), sodium deoxycholate (DCA), sodium glycocholate (GCA), and sodium taurocholate (TCA), were determined at 25 degrees C in Tris buffer solution (pH 7.4) at 298.15 K by means of isothermal titration microcalorimetry. The thermodynamic parameters obtained, together with the ROESY spectra of interactions between beta-CD dimers and bile salts, consistently suggest that the length, flexibility, and structure of spacers linking the two beta-CD cavities not only determine the binding modes but also significantly alter the molecular selectivity of beta-CD dimers.     

Molecular orbital study of the effects of ionic amino acid residues on proton transfer energetics in the active site of carboxypeptidase a

As part of a study of the catalytic mechanism of carboxypeptidase A, two proton transfers in the system Glu 270 H₂OZnHis 69-Asp 142 are treated with an ab initio MO method. Results show that the proton transfers are strongly affected by the environment. It is predicted that the proton between His 69 and Asp 142 is covalently bonded to His 69.