Protein surface recognition of the novel tetra-carboxylphenyl calix[4]arene to cytochrome c

The interaction of the novel tetra-carboxylphenyl calix[4]arene （TCPC） with the bovine heart cytochrome c （Cc） was first investigated by fluorescence spectroscopy and molecular modeling methods. The formation of a stable 1：1 complex was monitored by fluorescence titration, and its binding constant is 1.916 ×10^7 L mol^-1. Molecular modeling reveals the recognition mechanism of TCPC to the Cc surface, that is, the electrostatic interaction drives TCPC to the Cc surface, and the van der Waals interaction orientates TCPC parallel to the cleft of Cc.     

The structure and thermodynamics of calix[n]arene complexes with dipyridines and phenanthroline in aqueous solution studied by microcalorimetry and NMR spectroscopy

The complex stability constants (K(S)) and thermodynamic parameters (DeltaH degrees and TDeltaS degrees) for 1:1 intermolecular complexation of three water-soluble calixarenes, that is, p-sulfonato calix[4]arene (C4AS), p-sulfonato thiacalix[4]arene (TCAS), and p-sulfonato calix[5]arene (C5AS), with dipyridines (4-DPD and 2-DPD) and 1,10-phenanthroline (Phen) have been determined by means of titration microcalorimetry in an acidic buffer solution (pH = 2.0) at 298.15 K, and their binding modes have been investigated by (1)H NMR and 2D ROESY NMR spectroscopy. The results obtained indicate that 4-DPD, 2-DPD, and Phen are included in the cavity of C5AS with the different patterns, this is, accumbent for 4-DPD, acclivitous for 2-DPD and Phen, while Phen is included upright in the cavity of C4AS. The K(S) values decrease with increasing cavity size of host molecules but enhance with extending conjugation degree of guest molecules, and thus C4AS exhibits an exceptionally high Phen/4-DPD selectivity of 22.5. Thermodynamically, the complexation of DPDs/Phen with the water-soluble calixarenes is obviously enthalpy-driven, but the molecular selectivity is mainly governed by the entropy term.     

Acid-promoted rearrangement of carbonate functionality anchored to the lower rim of a Calix

A unique calix[4]arene lower-rim intramolecular rearrangement, resulting in molecular asymmetry arising from the upper- and lower-rim substitution pattern, produces a new class of inherently chiral calix[4]arenes in a partial cone conformation. This was aided by molecular rigidification arising from pi-pi and C-H.pi interactions between bulky lower-rim substituents, with the corresponding circular dichroism spectra exhibiting the most intense bisignate Cotton effects yet observed for calix[4]arenes not bearing a chiral center.     

Complexation of Calix[4]arene With Alkali Metal Cations: Conformational Binding Selectivity and Cation-π Driven Inclusion

Hartree-Fock, second order Møller-Plesset perturbation theory, and density functional theory calculations were carried out to analyse the complexation of calix[4]arene with cationic species including H + and the alkali metal cations (Li + , Na + , K + , Rb + , and Cs + ). Special emphasis has been placed on conformational binding selectivity, and on the structural characterization of the complexes. Li + and Na + cations are located in the calix[4]arene lower rim. The larger cations (K + , Rb + , and Cs + ) complex preferentially with the calix[4]arene cone conformer, and their endo (inclusive) complexation is driven by cation- ~ interactions, leading in the case of K + to a structure that reflects a preferential interaction with two phenol rings. The endo complexation of Cs + with calix[4]arene is in agreement with X-ray diffraction data.     

超分子体系强的分子识别研究 23: 多胺修饰β-环糊精及其铜 配合物与萘衍生 物的包结配位作用

用荧光光谱滴定法测定了单-[6-(二乙烯三胺)-6-脱氧]-β-环糊精(1)、单-[6-(三乙烯四胺)-6-脱氧]-β-环糊精(2)及其铜配合物(3,4)与一系列萘衍生物在磷酸缓冲溶液(pH7.2,0.1mol.dm^-^3)中,25℃时形成超分子体系的稳定常数,并与母体β-环糊精的配位能力进行了比较。化学计量法表明,四种化学修饰β-环糊精与萘衍生物形成了1:1的超分子配合物。从尺寸适合、几何互补及多点识别等方面讨论了主体化合物对模型底物的分子选择性键合能力。结果表明,疏水相互作用、范德华力、静电相互作用及氢键等多种非共价键弱相互作用协同贡献于超分子配合物的形成,主-客体间的结构匹配在分子受体选择性键合底物形成超分子配合物中起重要作用。     

Nature and physical origin of CH/pi interaction: significant difference from conventional hydrogen bonds

Recently reported high-level ab initio calculations and gas phase spectroscopic measurements show that the nature of CH/pi interactions is considerably different from conventional hydrogen bonds, although the CH/pi interactions were often regarded as the weakest class of hydrogen bonds. The major source of attraction in the CH/pi interaction is the dispersion interaction and the electrostatic contribution is small, while the electrostatic interaction is mainly responsible for the attraction in the conventional hydrogen bonds. The nature of the "typical" CH/pi interactions is similar to that of van der Waals interactions, if some exceptional "activated" CH/pi interactions of highly acidic C-H bonds are excluded. Shifts of C-H vibrational frequencies and electronic spectra also support the similarity. The hydrogen bond is important in controlling structures of molecular assemblies, since the hydrogen bond is sufficiently strong and directional due to the large electrostatic contribution. On the other hand, the directionality of the "typical" CH/pi interaction is very weak. Although the "typical" CH/pi interaction is often regarded as an important interaction in controlling the structures of molecular assemblies as in the cases of conventional hydrogen bonds, the importance of the "typical" CH/pi interactions is questionable.     

A molecular turnstile in para-octanoyl calix[4]arene nanocapsules

The thermal treatment of different inclusion complexes of para-octanoyl calix[4]arene leads to the formation of a guest-free van der Waals nanocapsular structure possessing a remarkable stability caused by the high mobility of alkanoyl arms.     

MD simulations of the binding of alcohols and diols by a calixarene in water: connections between microscopic and macroscopic properties

We report results of molecular dynamics (MD) simulations of the complexes of p-sulfonatocalix[4]arene with linear alcohols from ethanol to heptanol in water at 25 degrees C. We show that these complexes are of the inclusion type and are governed by van der Waals interactions between the calixarene cavity and the inserted alkyl chain of the alcohol. We establish a correlation between the experimental Delta(r)H degrees values and the number of atoms inserted into the calixarene cavity. We also focus on the desolvation of the host and guest to establish the importance, at the enthalpic level, of the formation of hydrogen bond bridges between the calixarene and the alcohol molecule. The fact that methanol is not complexed by p-sulfonatocalix[4]arene is explained by calculating the cost of the desolvation of the guest upon complexation. We complete this study by modeling the complexes formed with 1,4-butanediol and 1,5-pentanediol. To explain the difference between the thermodynamic properties for the binding of 1,4-butanediol and butanol, we examine the insertion rate and the solvation of each hydroxy group. We show a specific behavior of one of the two hydroxy groups at the structural and energetic levels.     

Calix[4]tubes: a new class of potassium-selective ionophore

A new class of cryptand-like ionophore based on a bis calix[4]arene structure has been developed. These molecules proved highly selective for complexation of potassium over all group I metal cations and barium. A range of symmetric and asymmetric calix[4]tubes featuring either alkyl or phenyl substituents at the upper rim have been synthesized in exceptional yield. Alteration of the calix[4]arene upper rim environment enables fine-tuning of the rate of potassium uptake, which can be evaluated through the conformational change on binding by NMR studies. Selectivity of potassium complexation has been demonstrated using NMR and electrospray mass spectral techniques. Molecular modeling studies, derived from crystallographic data, confirm that the potassium metal cation is complexed via the axial route, passing through the calix[4]arene annulus, and provide evidence for complexation rate and selectivity.     

The origin of diastereofacial control in allylboration reactions using tartrate ester derived allylboronates: attractive interactions between the Lewis acid coordinated aldehyde carbonyl group and an ester carbonyl oxygen

Transition-state structures for the allylboration reaction between the tartrate ester and tartramide modified allylboronates and acetaldehyde are located at the B3LYP/6-31G* level of theory. An attractive interaction between the boron-activated aldehyde and the ester or amide carbonyl oxygen lone pair is found to play a major role in the favored transition states 11a and 13. This attractive interaction appears to be electrostatic in origin. However, an n --> pi* charge-transfer type of interaction has not been ruled out. The distance (2.77 A) between the aldehydic hydrogen and the carbonyl oxygen in transition state 13 is beyond the sum of van der Waals radii. The formyl C-H...O bond angle (109 degrees) in this transition structure deviates far from linearity. Therefore, hydrogen-bonding interactions between the formyl C-H and the amide carbonyl oxygen are considered negligible. The distance (3.81 A) between the aldehydic oxygen and the amide carbonyl oxygen in the diastereomeric, disfavored transition state 14 is also beyond the van der Waals radii, which suggests that n/n electronic repulsion plays a lesser role in stereodifferentiation in the allylboration reaction than originally proposed.     

Luminescence behavior of a water soluble calix[4]arene derivative complex with terbium ion(III) in gelation solution

The complexation luminescence behavior of a water soluble calix[4]arene derivative, 5,11,17,23-tetra-sulfonate-25,26,27,28-tetra-carboxymethoxycalix[4]arene (L) with lanthanoid ion (Tb(3+)) has been investigated in gelation solution at 25 degrees C by using UV-vis and fluorescence spectra. The results obtained indicated that the water soluble calix[4]arene derivative can form an efficient energy transfer complex with terbium ion(III). The fluorescence of L x Tb(3+)complex is partially quenched by gelatin in gelation solution. The quenching intensity is related to the concentration and the hydrolysis degree of gelatin. Absorption and fluorescence spectra analysis show that the -COO(-) groups on gelatin have a definite binding ability to Tb(3+), and then, gelatin could compete binding with calix[4]arene derivative upon complexation with Tb(3+), leading to the relative fluorescence quenching of the formation complex of terbium(III) ion with calix[4]arene derivative.     

含酰胺和席夫碱单元的杯[4]芳烃衍生物的合成与配合性能

杯[4]-1,3-二乙酸乙酯衍生物1与水合肼反应生成杯[4]芳烃酰肼衍生物2, 然后进一步与相应的芳醛反应, 高产率地合成了三个新型的含酰胺和席夫碱单元的杯[4]芳烃衍生物3a～3c和一例新型杯[4]冠醚4. 阳离子萃取实验表明新型杯芳烃衍生物比只含有酰胺基或席夫碱基的杯芳烃衍生物有更强的软金属离子配合性能, 杯[4]冠醚4还对Ag^＋有较好的选择性萃取能力.     

A computational study of regioselectivity in a cyclodextrin-mediated Diels-Alder reaction: revelation of site selectivity and the importance of shallow binding and multiple binding modes

The use of a cyclodextrin.Diels-Alder transition structure complex (CD.TS) as a model in molecular dynamics simulations has enabled us to gain insight into the controlling factors in the cyclodextrin-mediated Diels-Alder reaction of methyl-p-benzoquinone with isoprene. MD simulations were carried out with multiple binding configurations of the CD.TS (TS=meta-TS, para-TS) complexes at the top and bottom rims of beta-CD. We discovered that i) only shallow binding with the CD is necessary for the regioselectivity, and multiple binding geometries are possible; ii) the narrow bottom rim, with the primary hydroxyl groups, of the CD binds both regio-TSs better than at the wider top rim (secondary hydroxyl groups), which was unexpected from the perspective of shape complementarity that governs the stability of most CD.guest complexes. Overall, the bottom rim of the CD exhibits higher regioisomer discrimination for the meta-TS; iii) structural clustering analyses of the CD.TS configurations (sampled during MD simulations) have enabled us to evaluate the binding energies of the different binding configurations. The result indicates that there is a direct correlation between meta-product selectivity and a higher number of binding configurations favoring the formation of the CD.meta-TS complex. The main forces of stabilization in the CD.TS complexes are the van der Waals interactions when the TS is bound at the top rim. At the bottom rim, closer contacts between polar functional groups of the TS and CD have increased the importance of electrostatic interactions. We found that van der Waals, solvation, and torsional forces are less favorable for complexation at the bottom rim; however, this is compensated by large favorable electrostatic interactions. With insights obtained from the study of CD.TS complexes and MD simulations of the modified heptakis-[6-O-(2-hydroxy)propyl]-beta-CD, we were able to explain why a low selectivity was observed when the Diels-Alder reaction was carried out in this modified CD. Two types of search method [Monte Carlo and multiple minimum (MCMM) and molecular dynamics (MD)] to explore and evaluate the different possible binding geometries of the TS within beta-CD, were discussed.     

Potassium selective calix[4]semitubes

A new class of ionophore consisting of two calix[4]arene units linked through the lower rim by two ethylene chains, in combination with propyl ether and phenolic functional groups, has been developed. These calix[4]semitube molecules exhibit remarkable selectivity and fast complexation kinetics for potassium over all Group 1 metal cations. Molecular modelling studies, using structural models derived from crystallographic data, suggest the potassium cation is complexed by a horizontal, side-on route and not through the calix[4]arene annulus. The length of the bridging alkylene chain between the respective calix[4]arenes of the semitube structure dictates the strength and selectivity of alkali metal cation binding.     

Origins of cooperative noncovalent host-guest chemistry in mixed valence complexes

The electronic effects resulting from noncovalent host-guest interactions between calix[6]arene and a ruthenium dimer, [Ru3O(OAc)6(CO)(ppy)]2-mu-pz (ppy=4-phenyl pyridine, pz=pyrazine), are presented. The noncovalent interaction is between the calix[6]arene and the ppy ligands of the dimer. The dimer can bind 2 equiv of calix[6]arene. The complex [Ru3O(OAc)6(CO)(ppy)]2-mu-pz forms a highly stable mixed valence ion with strong electronic coupling between the two Ru3 clusters. The strength of the electronic interaction is found to be moderated by calix[6]arene binding. Addition of calix[6]arene to the mixed valence ion causes the electronic coupling to decrease. The binding of calix[6]arene is found to be cooperative. The origins of cooperative binding are developed in terms of the potential energy surfaces associated with the symmetric and asymmetric mixed valence ion. In particular, it is found that symmetry breaking (through the binding of a single calix[6]arene) destabilizes the mixed valence state. Restoration of symmetry (through the binding of a second calix[6]arene) increases the stability of the mixed valence ion and provides an additional driving force for the binding of the second calix[6]arene.     

Cation-dependent binding of zinc diethoxycarbonylcalix[4]arenebis(porphyrinate) triethylenediamine

Zinc calix[4]arene-bis(porphyrinate) with two ethoxycarbonyl substituents at the lower rim of the calix[4]arene moiety was synthesized. Its complexation properties toward the sodium cation and triethylenediamine were studied. The influence of the binding of the sodium cation by the calix[4]arene moiety on the complexation properties of the interporphyrin cavity toward triethylenediamine was revealed.     

Synthesis of nucleobase-calix[4]arenes via click chemistry and evaluation of their complexation with alkali metal ions and molecular assembly

In this study, calix[4]arene derivatives (11–14) bearing a single nucleobase (adenine, thymine, cytosine or guanine) were synthesised via click chemistry. The complexation ability of the synthesised derivatives with alkali metal ions was measured using MALDI-TOF mass spectrometry, and their molecular assembly in CDCl₃ was determined using ¹H NMR. Calix[4]arene derivatives (11–14) formed 1:1 complexes with all alkali metal ions and the rank order for the complexation selectivity was Rb⁺ > Cs⁺ > K⁺ ? Na⁺ > Li⁺. The attachment of nucleobase at the upper rim of calix[4]arene had little effect on its complexation selectivity for alkali metal ions. Thymine-, adenine- and guanine-calix[4]arenes formed self-assembled structures in CDCl₃ via base–base interactions. In addition, adenine-calix[4]arene (11) bound to thymine-calix[4]arene (12) to form a discrete species via Hoogsteen hydrogen bonding.     

Cation- and anion-assisted binding of triethylenediamine by zinc bisporphyrinates

The complexation of zinc calix[4]arene or calix[4]pyrrole bisporphyrinates with alkali metal cations, halide anions, and triethylenediamine was studied by ¹H NMR spectroscopy. It was established that the binding of molecules and/or charged particles by various fragments of calix[4]arene and calix[4]pyrrole porphyrins are interrelated processes. This makes it possible to use one process (for example, complexation of the calix[4]arene fragment of the macrocycle with alkali metal cations or complexation of the calix[4]pyrrole fragment with halide ions) as a tool for controlling another process (complexation of the porphyrin fragments of the macrocycle with neutral molecules).     

Phenyl-calix[4]arene-based fluorescent sensors: cooperative binding for carboxylates

Tetrakis-(4-carbamoylphenyl)-substituted and tetrakis-(4-amidophenyl)-substituted calix[4]arenes as well as the monomeric biphenylcarbamate have been synthesized as fluorescent receptors for anion sensing. Their binding properties with various anions including F-, CH3COO-, Ph-COO-, and H2PO4- were investigated by fluorescence titrations, Job plot experiments, 1H NMR spectroscopies, and ESI-MS measurements. Importantly, we have found that calix[4]arene-based sensors exhibit greatly enhanced binding affinity and selectivity toward carboxylates. The binding associations of tetrakis-(4-carbamoylphenyl)-substituted calix[4]arene for carboxylates are 1-2 orders of magnitude greater than those of the monomeric biphenylcarbamate sensor. Such an enhancement in the binding affinity and selectivity is attributed to the cooperative binding of the multiple ligating groups as revealed from the ab inito DFT calculations. Although tetrakis-(4-amidophenyl)-substituted calix[4]arene exhibited relatively weaker binding affinity toward anions, its superior binding selectivity for acetate ion over fluoride ion is evident. Our results also suggest that carbamate functionality is a useful H-bond donor for hydrogen-bonding interactions in molecular recognition and supramolecular chemistry.     

Van der Waals complexes of polar aromatic molecules: unexpected structures for dimers of azulene

Full geometry optimizations at the dispersion corrected DFT-BLYP/TZV2P level of theory have been performed for dimers of azulene that may serve as a model system for the van der Waals complexes of polar pi systems. The structures and binding energies for 11 dimers are investigated in detail. The DFT-D interaction energies have been successfully checked against results from the accurate SCS-MP2/aug-cc-pVTZ approach. Out of the nine investigated stacked complexes, eight have binding energies larger than 7.4 kcal/mol (SCS-MP2) that exceed the value of 7.1 kcal/mol for the best naphthalene dimer. T-shaped arrangements (CH...pi) are significantly less stable. Two out of the three best structures have an antiparallel alignment of the monomer dipole moments in the complex, although the best ones with a parallel orientation are only about 0.5 kcal/mol less strongly bound which points to a minor importance of dipole-dipole interactions to binding. Quite surprisingly, the energetically lowest structure (DeltaE = -9.2 kcal/mol) corresponds to a situation where the two seven-membered rings are located almost on top of each other (7-7) and the long molecular axes are rotated against each other by 130 degrees. The 7-7 structural motif is found also in other energetically low-lying structures, and the expected 5-7 (two-side) arrangement is less strongly bound by about 2 kcal/mol. This can be explained by the electrostatic potential of azulene that only partially reflects the charge separation according to the common 4n + 2 pi electron rule. General rules for predicting stable van der Waals complexes of polar pi systems are discussed.