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.     

Molecular‐Dynamics‐Simulation‐Directed Rational Design of Nanoreceptors with Targeted Affinity

Here, we demonstrate the possibility of rationally designing nanoparticle receptors with targeted affinity and selectivity for specific small molecules. We used atomistic molecular‐dynamics (MD) simulations to gradually mutate and optimize the chemical structure of the molecules forming the coating monolayer of gold nanoparticles (1.7 nm gold‐core size). The MD‐directed design resulted in nanoreceptors with a 10‐fold improvement in affinity for the target analyte (salicylate) and a 100‐fold decrease of the detection limit by NMR‐chemosensing from the millimolar to the micromolar range. We could define the exact binding mode, which features prolonged contacts and deep penetration of the guest into the monolayer, as well as a distinct shape of the effective binding pockets characterized by exposed interacting points.     

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.     

Development of calixarene-based host molecules for peptides in aqueous media

We synthesized a peptidocalix[4]arene library consisting of 1000 members that was suitable for peptide recognition in aqueous media. Some peptidocalix[4]arenes in the library were host molecules for guest peptides. Electrostatic interaction between the host and guest molecules was the most important factor for binding in aqueous media.     

Reversibly controllable guest binding in precisely defined cavities: selectivity, induced fit, and switching in novel resorcin[4]arene-based container molecules

Two molecular baskets are presented, which were constructed based on a resorcin[4]arene platform. The molecules completely surround suitable guests, such as cyclo- or oxacycloalkanes, and bind them with high strength. The thermodynamic parameters for inclusion complexation were determined as well as the influence of encapsulation on the ring inversion barrier of bound cyclohexane. Two-dimensional NMR spectroscopy clearly shows the existence of a directed attractive interaction between oxacyclohexane and one of the hosts, which constrains the rotation of the bound molecule. Both containers exhibit remarkable binding selectivity as a consequence of their precisely defined structures. They both differentiate between homologous cycloalkanes, and whereas cyclohexane binds best within the larger of the two interior cavities, cyclopentane fits best in the smaller one. The selectivity is governed by ideal filling of space. We have conducted molecular dynamics experiments to understand the thermal fluctuations in the cavity sizes when a guest is bound. The simulations show that within a very narrow range the hosts adapt their binding site to different guests in order to optimize the fraction of occupied space. Once a binding geometry is established, it is characterized by a very low degree of flexibility. The guest-hosting properties of both molecules can be suspended by an external stimulus: addition of acid induces an opening of portals in the structures and immediately releases all bound cargo. Neutralization of the solution completely restores the initial state.     

荧光标识的环糊精二聚体与小肽衍生物之间的包合行为研究

报道了利用荧光偏振方法研究导硫氰酸盐荧光素（FITC）标识,并由天冬氨酸 、谷氨酸、(1R, 3R)-1-氨基-1,3-二羟基环丁烷和（1R, 3R）-1-氨基-1,3-二 羟基环戊烷衍生物桥联的环糊精二聚体（1～4,作为主体）,在pH = 7.4的水溶液 中与几个低分子量的多肽衍生物:Adm-Lys(Adm)-Arg-Arg 5; Adm-Lys(Adm)-D-Arg- D-Arg 6; Adm-Cha-Arg-Arg 7; Adm-Cha-D-Arg-D-Arg 8（作为客体,其中Arg, Lys, Cha和Adm分别为精氨酸,赖氨酸,β-环已烷丙氨酸和1-羟基金刚烷）之间 的键合常数（K_b)和包合反应的热力学参数（△G°,△H°,△S°）。从主-客体 键合常数的比较、客体嵌入基团的结构与周边环境的考察发现,主、客体之间的键 合能力因客体非进入基团（Arg)空间构型上的变化而有所不同。通过比较主体包结 一对手性异构体的自由能变化增量（-△△G_(DL)°）以及一对手性异构体（L-与 D-）与同一主体的键合常数之比（K_L/K_D),讨论了环糊精二聚体对D-型或L-型多 肽衍生物的手性识别能力。根据各体系T△S°与△H°之间较好的线性关系,探讨 了环糊精二聚体与多肽衍生物之间相互作用的焓-熵补偿行为。     

Effect of encaged aromatic guests on the shape and connectivity of molecular cavity in crystalline polystyrene evaluated by molecular simulations

The delta form of crystalline syndiotactic polystyrene is a clathrate molecular compound in which various aromatic molecules are encaged. We have investigated the size, shape, and connectivity of the molecular cavity in the crystal using a molecular dynamics simulation. The effects of the guest species on the cavity structure were investigated in detail. In order to systematically vary the guest structure, various aromatic guests, e.g., benzene, toluene, p-xylene, m-xylene, o and mesitylene were examined. The interstitial spaces between the guests and the polymer chains were analyzed by cluster analysis of the free volumes. The individual cavity volumes into which the guests are clathrated were also evaluated. It was found that the guest molecules can greatly affect not only the cavity size and shape but also the connectivity of the cavities. The transport of small molecules in the crystal is discussed in connection with the cavity structure.     

Supramolecular fuzzy recognition leads to effective differentiation of similar molecules

The separation of structurally similar molecules remains a general challenge; here, we report that a roughly defined macromolecular nanocapsule can efficiently separate a variety of structurally similar mixtures. The nanocapsule is a core?shell amphiphilic macromolecule (CAM) hydrophobically derived from hyperbranched polyethylenimine with 2‐hexadecyloxymethyloxirane. It is found that with further chemical core engineering of the CAM, its guest selectivity can be radically enhanced, although specific host?guest interaction is absent or ignorable in the system. As a result, two groups of structurally similar guests such as fluorescein/tetrachlorofluorescein, and rose bengal/erythrosine B/eosin Y, can be well recognized by the CAMs. It is known that a complex (fuzzy) system is generally characterized by complexity and nonlinearity; thus core engineering of a CAM is possible to amplify the difference of the competitive guests and lead to effective guest differentiation, such a mechanism is called supramolecular fuzzy recognition (SFR). Our results demonstrate that with appropriate combination of various elementary interaction styles, SFR can lead to effective recognition of a wide spectrum of mixtures. Moreover, a SFR host can be roughly defined in structure and thus readily available. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Cooperative molecular recognition of dyes by dyad and triad cyclodextrin-crown ether conjugates

Three beta-cyclodextrin (beta-CyD) derivatives with crown ether units, that is N-(4'-benzo-15-crown-5)-6-imino-6-deoxy-beta-CyD (2), 6,6'-[N-(4,4'-dibenzo-18-crown-6)-imino]-bridged bis(beta-CyD)(3), and 2,2'-[O-(4',5'-benzo-15-crown-5)-ethyl]-bridged bis (beta-CyD)(5), were synthesized as cooperative recognition receptor models. Their molecular binding behavior with four representative fluorescent dyes, i.e., ammonium 8-anilino-1-naphthalenesulfonate (ANS), sodium-6-toluidino-2-naphthalene-sulfonate (TNS), Acridine Red (AR) and Rhodamine B (RhB), was investigated in buffer solutions (pH = 7.20) at 25 degreesC by means of circular dichroism, NMR and fluorescence spectroscopy. 2D-ROESY experiments showed that dyad host 2 and triad host 3 adopted a CyD-guest-crown ether binding mode, while triad host 5 adopted a CyD-guest-CyD binding mode, upon inclusion complexation with guest molecules. Therefore, hosts 2 and 3 showed high molecular recognition ability towards charged guests, giving an enhanced binding ability up to 115 times for ANS by 3 and fairly high molecular selectivity up to 1450 times for the ANS/AR pair by 2 as compared with native beta-CyD in an aqueous phosphate buffer solution. On the other hand, host 5 was found to be able to effectively recognize the shape of a guest molecule, showing significantly higher binding ability towards linear guests. The binding affinities and molecular recognition abilities of these CyD-crown ether conjugates towards guest molecules are discussed from the viewpoint of electrostatic and/or hydrophobic interactions, size/shape-fit concept, and multiple recognition mechanism between host and guest.     

The structure - properties relations in the clathrates of N1 (NCS)2 (4-methylpyridine)4

The Ni(NCS)₂(4-methylpyridine)₄ molecule shows significant confomational flexibility of the four piooline and the two isothiocyanate ligands. Both intramolecular non-bonded energy calculations and x-ray crystal structures support the idea that the host molecule may adopt different conformations (molecular shape) in order to bind, in clathrate formation, guest molecules of different shape and size. This versatility enables the Ni(NCS)₂(4-methylpyridine)₄ complex to form many different crystal structures able to absorb both small molecules, e.g. noble gases, and relatively large condensed aromatic hydrocarbons. The type of the crystalline structure formed defines “primary” properties of the clathrate. Secondary effects are observed when varying lattice parameters of the host structure (dilatation - contraction) by introducing guest component of suitable composition.     

Bio-inspired Calix[6]Arene–Zinc Funnel Complexes

A bio-inspired supramolecular system is presented. A calix[6]arene possessing three imidazolyl arms on alternate phenolic positions binds a zinc ion. The resulting complex contains a hydrophobic pocket, which has a flattened conic shape. The system behaves as a selective molecular funnel for neutral guests that bind the metal centre. The exceptional stability of these tetrahedral dicationic complexes is exemplified by the acetaldehyde ternary adduct that was analysed by X-ray crystallography. The ligand is deeply buried in the heart of the calixarene cavity, pointing its methyl group selectively towards the centre of one of the aromatic walls, thereby establishing a stabilizing CH/π interaction. Protic guests undergo hydrogen bonding with the phenolic oxygens of the calixarene structure. The selectivity of the binding in the cavity is based on both the affinity of the donor atom of the guest ligand for the zinc ion and the relative host–guest geometries. The helical shape of the tris-imidazolyl groups binding the metal centre is the base of the chirality of the system. The twisted calix[6]arene structure of the zinc funnel complexes is shown to provide a new example of a cavity suitable for host–guest chiral induction.     

Computer modelling studies of 18-crown-6 with urea and thiourea

Abstract

Computer modelling studies have been carried out on the interaction of 18-crown-6 with a variety of guest molecules, including urea, thiourea and substituted ureas. The five known crystal structures of these host/guest systems were used as models. We were interested to establish whether the arrangement of guest molecules around a host molecule in the crystal was indicative of the lowest energy configuration for a host/guest fragment or was a consequence of packing effects. Two models were therefore considered for each structure and the structures minimised via molecular mechanics. In the first mode, the structure consisted of one unit cell and periodic boundary conditions were used in the calculation. Coulombic effects were calculated using the Ewald summation. In the second model, the structure consisted of an 18-crown-6 molecule surrounded by two hydrogen-bonded guest molecules. Both models were minimised using the CERIUS package using the DreidingII forcefield.

The crystal structure minimisations reproduced the structures very well with an average change in cell volume of 3.6% and a mean r.m.s. positional deviation of 0.20 Å. The fits for the fragment models were significantly larger for all structures (mean 0.30 Å) but even so it can be concluded that the arrangement in the crystal gave a good indication of the lowest energy configuration of the host/guest in vacuo.     

Synthesis, biological evaluation and structural characterization of novel glycopeptide analogues of nociceptin N/OFQ

To examine if the biological activity of the N/OFQ peptide, which is the native ligand of the pain-related and viable drug target NOP receptor, could be modulated by glycosylation and if such effects could be conformationally related, we have synthesized three N/OFQ glycopeptide analogues, namely: [Thr(5)-O-α-D-GalNAc-N/OFQ] (glycopeptide 1), [Ser(10)-O-α-D-GalNAc]-N/OFQ (glycopeptide 2) and [Ser(10)-O-β-D-GlcNAc]-N/OFQ] (glycopeptide 3). They were tested for biological activity in competition binding assays using the zebrafish animal model in which glycopeptide 2 exhibited a slightly improved binding affinity, whereas glycopeptide 1 showed a remarkably reduced binding affinity compared to the parent compound and glycopeptide 3. The structural analysis of these glycopeptides and the parent N/OFQ peptide by NMR and circular dichroism indicated that their aqueous solutions are mainly populated by random coil conformers. However, in membrane mimic environments a certain proportion of the molecules of all these peptides exist as α-helix structures. Interestingly, under these experimental conditions, glycopeptide 1 (glycosylated at Thr-5) exhibited a population of folded hairpin-like geometries. From these facts it is tempting to speculate that nociceptin analogues showing linear helical structures are more complementary and thus interact more efficiently with the native NOP receptor than folded structures, since glycopeptide 1 showed a significantly reduced binding affinity for the NOP receptor.     

Metal-macrocycle framework (MMF): supramolecular nano-channel surfaces with shape sorting capability

Hollow nanostructures for the functional assembly of chemical groups with inner surface geometry and regulable stoichiometry enable steric design of interior reaction centers. Herein we report a metal-macrocycle framework (MMF) that forms single-crystalline nanochannels with five distinct enantiomeric pairs of guest binding pockets. During crystal-soaking experiments, the MMF crystals can encapsulate aromatic molecules with high site selectivity. First, constitutional isomers of dibromobenzene are captured and sorted into different binding pockets. Second, each of the optical isomers of (1R/1S)-1-(3-chlorophenyl)ethanol is included diastereoselectively into one of an enantiomeric pair of binding pockets. An advantage of this strategy is that the interior walls can be "repainted" via replacement of the trapped molecules with alternatives. Such guest uptake behaviors would allow highly regioselective or stereoselective reactions within the nanochannel.     

Dihalobenzene Shape Sorting by Nonporous Adaptive Crystals of Perbromoethylated Pillararenes

The separation of dihalobenzene isomers, such as dichlorobenzene isomers and difluorobenzene isomers, has a high practical value in both synthetic chemistry and industrial production. Herein we provide a simple to operate and energy‐efficient adsorptive separation method using nonporous adaptive crystals of perbromoethylated pillar[5]arene ( BrP5 ) and pillar[6]arene ( BrP6 ). BrP6 crystals show a preference towards the ortho isomer of dichlorobenzene in isomer mixtures, but cannot discriminate difluorobenzene isomers. Single‐crystal structures reveal that this selectivity is derived from the stability of the new host–guest crystal structure of BrP6 after uptake of the preferred guest and the binding strength of the host–guest interactions. Furthermore, because of the reversible transition between guest‐free and guest‐loaded structures, BrP6 crystals are recyclable.     

Separation of phenol and cresols by crystalline complexation with 1,1-di(p-hydroxyphenyl)cyclohexane,and crystal structure analyses of the complexes

This paper is concerned with 11 inclusion complexes of the 1,1-di(p-hydroxyphenyl)cyclohexane host with either phenol or one of the cresol derivatives as guest. Selectivity studies showed preferential complexation with a guest according to the sequence;m-cresol > p-cresol > phenol > o-cresol. Crystallographic analyses of the four complexes revealed isomorphous structures [crystal data for the phenol complex:a=6.232,b=10.849,c=14.845 Å, =95.69, =93.49, =104.31°, space groupPl,Z=2]. The intermolecular arrangements are characterized by layers of efficiently hydrogen bonded entities (host-to-host, host-to-guest and guest-to-host) parallel toab, every OH group being involved in two H-bonds. Organization of the layers alongc is stabilized by weak dispersion forces, thus being most sensitive to structural variation of the guest component. The observed features of selectivity upon crystalline complexation are related to differences in topological complementarity between the constituents of each structure. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82052 (4 pages).     

Novel flexible frameworks of porous cobalt(II) coordination polymers that show selective guest adsorption based on the switching of hydrogen-bond pairs of amide groups

Four porous crystalline coordination polymers with two-dimensional frameworks of a double-edged axe-shaped motif, [[Co(NCS)(2)(3-pia)(2)] x 2 EtOH.11 H(2)O](n) (1 a), [[Co(NCS)(2)(3-pia)(2)] x 4 Me(2)CO](n) (3 a), [[Co(NCS)(2)(3-pia)(2)] x 4T HF](n) (3 b) and [[Co(NCS)(2)(3-pna)(2)](n)] (5), have been synthesized by the reaction of cobalt(II) thiocyanate with N-(3-pyridyl)isonicotinamide (3-pia) or N-(3-pyridyl)nicotinamide (3-pna). X-ray crystallographic characterization reveals that adjacent layers are stacked such that channels are created, except in 5. The channels form a hydrogen-bonded interior for guest molecules; in practice, 1 a contains ethanol and water molecules as guests in the channels with hydrogen bonds, whereas 3 b (3 a) contains tetrahydrofuran (acetone) molecules. In 1 a, the "double-edged axe-shaped" motifs in adjacent sheets are not located over the top of each other, while the motifs in 3 b stack so perfectly as to overlap each other in an edge-to-edge fashion. This subtle change in the three-dimensional framework is associated with the template effect of the guests. Compound 5 has no guest molecules and, therefore, the amide groups in one sheet are used for hydrogen-bonding links with adjacent sheets. Removal of the guest molecules from 1 a and 3 b (3 a) causes a structural conversion accompanied by a color change. Pink 1 a cannot retain its original framework and changes into a blue amorphous compound. On the other hand, the framework of pink 3 b (3 a) is transformed to a new crystalline framework of violet 4. Interestingly, 4 reverts to the original pink crystals of 3 b (3 a) when it is exposed to THF (or acetone) vapor. Spectroscopic measurements (visible, EPR, and IR) provide a clue to the crystal-to-crystal transformation; on removal of the guests, the amide groups are used to form the beta sheet-type hydrogen bonding between the sheets, and thus the framework withstands significant stress on removal of guest molecules. This mechanism is attributed to the arrangement of the adjacent sheets so suited in regularity that the beta sheet-type structure forms efficiently. The apohost 4 does not adsorb cyclopentane, showing a guest selectivity that, in addition to size, hydrogen-bonding capability is required for the guest molecules. The obtained compound is categorized as a member of a new generation of compounds tending towards functional porous coordination polymers.     

6-Hydroxyalkylamino-6-deoxy-cyclodextrins: Towards dendrimeric host-molecules

6-Perhydroxyalkylamino-6-perdeoxy--cyclodextrins have been synthesised by treating 6-perbromo-6-perdeoxy-cyclodextrins with hydroxyalkylamines. The products (1, 2) are precursors of dendrimeric cyclodextrins in which the cavity provides access for the guest to interact with the branches. A fluorescence study has demonstrated the effects of the branches on binding of anilinonaphthalene sulfonate probes. The hosts show selectivity towards guests, and pH-dependence of binding, consistent with polar interaction between guest sulfonate anions and the protonated amino groups of the dendrimeric structure.     

Organic anion recognition of naphthalenesulfonates by steroid-modified beta-cyclodextrins: enhanced molecular binding ability and molecular selectivity

Two beta-cyclodextrin (beta-CD) derivatives bearing steroid groups (1 and 2) were synthesized by the condensation of mono(6-aminoethylamino-6-deoxy)-beta-CD with cholic acid and deoxycholic acid, respectively, and their original conformations and binding behavior to the organic anion of naphthalenesulfonate derivatives were investigated by using 1H NMR spectroscopy and spectrofluorometric titration in combination with computational methods. The 2D NMR experiments reveal that the steroid groups attached to the beta-CD rim could be deeply embedded in the beta-CD cavity to form the intramolecular (for 1) or intermolecular (for 2) inclusion complexes in aqueous solution. Upon complexation with naphthalenesulfonate derivatives, modified beta-CDs display two obviously different binding modes, that is, the competitive inclusion mode and the induced-fit inclusion mode, which is consistent with the results of molecular modeling study. The two modes and the strict size/shape fitting relationship between the hosts and guests reasonably explain the different binding behaviors and molecular selectivity of host beta-CDs 1 and 2 toward the naphthalenesulfonate guests. Therefore, the cholic acid- or deoxycholic acid-modified beta-CDs could effectively recognize the size/shape of guest molecules as compared with the parent beta-CD, giving good molecular selectivity up to 24.9 for the disodium 2,6-naphthalenedisulfonate/disodium 1,5-naphthalenedisulfonate pair by the host 1.     

Structure selective complexation of cyclodextrins with five polyphenols investigated by capillary electrokinetic chromatography

The complexation of five polyphenols, namely trans‐resveratrol, astilbin, taxifolin, ferulic acid, and syringic acid (guest molecules) with α‐, β‐, and γ‐cyclodextrin (host molecules), was investigated by capillary electrokinetic chromatography. The binding constants were calculated based on the effective electrophoretic mobility change of guests with the addition of cyclodextrins into the background electrolyte. Because of cavity size, cyclodextrins showed structure‐selective complexation property to different guest. The stability of the trans‐resveratrol complexes was in the order of β‐ > α‐ > γ‐cyclodextrin. The cavity size of α‐cyclodextrin was too small for astilbin and taxifolin molecules, and thus they could not form complexes. The molecular size of syringic acid was too big for all cyclodextrins cavity, and no cyclodextrin could form complexes with it. Temperature studies showed that the binding constants decreased with the rise of temperature. Enthalpy and entropy values were calculated and the negative values of these parameters indicated that the complexation process was enthalpy‐controlled. Van der Waals force and release of high‐enthalpy water molecules from the cyclodextrins cavity played important roles in the process.