Protein Dimerization on a Phosphonated Calix[6]arene Disc

Complex formation between cationic cytochrome c and the water‐soluble, poly‐anionic p ‐phosphonatocalix[6]arene (pclx₆) was investigated. A crystal structure (at 1.8 Å resolution) revealed a remarkable dimeric disc of pclx₆ that acts like glue to mediate a symmetric (C ₂) protein dimer. The calixarene disc has a diameter of about 1.5 nm and masks about 360 Ų of protein surface. The key protein–calixarene contacts occur via two linchpin lysines, with additional contacts provided by a small hydrophobic patch. The protein–calixarene supramolecular assemblies were observed in solution by size‐exclusion chromatography with multi‐angle light scattering and NMR spectroscopy. Using isothermal titration calorimetry and NMR data, an apparent K _d in the low micromolar range was determined for the charge‐rich protein–calixarene complex. In contrast to p ‐sulfonatocalix[4]arene, the larger pclx₆ has a single, well‐defined binding site that mediates the assembly of cytochrome c in solution.     

Dimeric Calixarenes: A New Family of Major‐Groove Binders

A new class of potent DNA binding agents is presented. Dimeric calix[4]arenes with cationic groups at their upper rims and flexible alkyl bridges can be synthesized from triply acyl‐protected calix[4]arene tetramines in relatively short synthetic sequences (3–5 steps). The compounds attach themselves to double‐stranded nucleic acids in a noncovalent fashion, with micro‐ to nanomolar affinities. Guanidinium headgroups with their extended hydrogen‐bonding “fingers” are more powerful than ammonium groups, and the benzylamine series is superior to the anilinium series (see below). The new ligands easily distinguish between RNA and various DNA types, and produce characteristic changes in UV/Vis, fluorescence, CD, as well as NMR spectra. Especially extended oligonucleotides of more than 100 base pairs are bound with affinities increasing from RNA (10 μM K_d)<AT‐rich (1 μM )<GC‐rich DNA double strands (100–10 nM ). Ethidium bromide displacement studies confirm this order. CE₅₀ values are remarkably low (1–4 μM ), and are more than 300 times lower than that of spermine, which is a typical backbone binder. Stoichiometries are rather high (one calixarene dimer per two BP), suggesting a potential aggregation of bound ligands inside the major groove. Most UV/Vis melting curves display an inverted shape, and start from drastically enhanced absorption intensities for the DNA complexes. DAPI displacement studies prove that up to one equivalent of calixarene dimer can be accommodated in the dye‐loaded DNA. RNA complexation by calixarene dimers is accompanied by a drastic CD spectral transition from the typical A‐form to a perfect B‐signature, providing further experimental evidence for major‐groove binding. The orientation of the ligands can be deduced from NMR titrations and is reproduced in Monte‐Carlo simulations on 1:1 complexes in water.     

Selective Binding of Imidazolium Cations in Building Multi‐Component Layers

Addition of 1‐alkyl‐3‐methylimidazolium (C_n‐mim) cations 3 – 5 to a mixture of bis‐phosphonium cation 2 and sodium p‐sulfonatocalix[4]arene ( 1 ) in the presence of lanthanide ions results in the selective binding of an imidazolium cation into the cavity of the calixarene. The result is a multi‐layered solid material with an inherently flexible interplay of the components. Incorporating ethyl‐, n‐butyl‐ or n‐hexyl‐mim cations into the multi‐layers results in significant perturbation of the structure, the most striking effect is the tilting of the plane of the bowl‐shaped calixarene relative to the plane of the multi‐layer, with tilt angles of 7.2, 28.9 and 65.5°, respectively. The lanthanide ions facilitate complexation, but are not incorporated into the structures and, in all cases, the calixarene takes on a 5? charge, with one of the lower‐rim phenolic groups deprotonated. ROESY NMR experiments and other ¹H NMR spectroscopy studies establish the formation of 1:1 supermolecules of C_n‐mim and calixarene, regardless of the ratio of the two components, and indicate that the supermolecules undergo rapid exchange on the NMR spectroscopy timescale.     

25‐Allyloxy‐5,11,17,23‐tetra‐tert‐butyl‐26,27,28‐trihydroxycalix[4]arene chloroform disolvate

In the title solvated calixarene, C₄₇H₆₀O₄·2CHCl₃, the host chalice displays an almost undistorted cone conformation, stabilized by three strong O—H...O hydrogen bonds at the calixarene's lower rim. One chloroform solvent molecule is fixed in the calixarene cavity by C—H...π interactions, while the second is accommodated in a clathrate‐like mode in elliptical packing voids. These voids are spanned by six host molecules connected via C—H...π contacts and van der Waals interactions. Within the crystal structure, one tert‐butyl group of the calixarene host is disordered over two orientations, with occupancies of 0.884 (4) and 0.116 (4). Furthermore, both solvent molecules show disorder, with occupancies of 0.857 (2) and 0.143 (2) for the cavitate‐type, and 0.9359 (17) and 0.0641 (17) for the clathrate‐type chloroform solvent molecules.     

Crystal structure of 1,2‐[4‐butoxybenzoyloxy‐4′‐pentyl]diphenylethane

The crystal structure of 1,2‐[4‐butoxybenzoyloxy‐4′‐pentyl]diphenylethane (C₃₀H₃₆O₃) has been determined by direct methods using single crystal X‐ray diffraction data. It crystallizes in the monoclinic system with space group P2₁/a and Z?=?4. The unit cell parameters are: a?=?8.098(1), b?=?10.926(1), c?=?29.643(2)?Å and β?=?94.01(1)°. The final reliability factor is R?=?0.073 and the goodness of fit is equal to 1.027. The molecular arrangement is very typical, with molecules associated in dimers very closely parallel to the Oz axis. In a given dimer, the backbones of the two molecules run alongside each other; this association can be attributed to strong dipole–dipole interactions through the polar ester and ether groups. In addition these dimers are connected to neighbours via dipole–dipole interactions along the Oy direction. There are numerous very weak van der Waals interactions, particularly between the terminal aliphatic chains.     

Synthesis and Fe(III)‐complexation ability of polyurethane bearing kojic acid skeleton in the main chain prepared by polyaddition of aliphatic hydroxyl groups without protection of phenolic hydroxyl groups

Polyaddition of a kojic acid dimer and diisocyanates yielded polyurethane with metal‐coordination ability owing to the phenolic hydroxyl groups of kojic acid. Although the kojic acid dimer contains two phenolic and two aliphatic hydroxyl groups, 1,5‐diazabicyclo[4.3.0]non‐5‐ene catalyzed polymerization proceeded through highly selective reactions of the aliphatic hydroxyl groups without any protection of the phenolic hydroxyl groups. The resulting polymers complexed with FeCl₃, and specific colorizations were observed. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

para‐Sulfonatocalix[n]arenes Inhibit Amyloid β‐Peptide Fibrillation and Reduce Amyloid Cytotoxicity

Amyloid β‐peptide (Aβ) fibrillation is a major hallmark of Alzheimer's disease (AD). Inhibition of Aβ fibrillation is thus considered to be an effective strategy for AD prevention and treatment. Here we show that para ‐sulfonatocalix[n ]arenes (SC[n ]A, n =4, 6, 8), a class of amphiphilic calixarene derivatives, can bind to Aβ₄₂ through nonspecific and multipoint hydrophobic interactions. Their binding leads to a pronounced delay in β‐sheet adoption and formation of multiple secondary structures of the peptide, accompanied by changes at the level of the fibrillary architecture. Furthermore, the ζ‐potential value of Aβ₄₂ incubated with SC[6/8]A decreased, which correlated with the reduction of amyloid cytotoxicity. Overall, the SC[n ]A effectively inhibits Aβ₄₂ fibrillation and reduces amyloid cytotoxicity, and SC[8]A showed the best performance among the three macrocycles, possibly owing to its having the strongest interactions with Aβ₄₂.     

Metalated Container Molecules

The coordination chemistry of metalated container molecules is currently attracting much interest, because the properties of such compounds are often different from those of their constituent components. By adjusting the size and form of the binding cavity it is often possible to coordinate coligands in unusual coordination modes, to activate and transform small molecules, or to stabilize reactive intermediates. Such compounds also allow for an interplay of molecular recognition and transition‐metal catalysis, and for the construction of more effective enzyme mimics. Consequently, a number of research groups are involved in the development of new supporting ligands that create confined environments about active metal coordination sites. This research report briefly reviews recent progress in this field including the results of my own group. It is shown that N‐functionalized derivatives of Robson‐type macrocyclic hexaaza‐dithiophenolate ligands form bioctahedral transition metal complexes of the type [(L^R)M₂(μ‐L′)]⁺ (M = Mn, Fe, Co, Ni, Zn) with an overall calixarene‐like structure. These complexes are amongst the first prototypes for polynuclear complexes with well defined binding cavities. Since the active coordination site L′ is accessible for a wide range of exogenous coligands, the [(L^R)M₂(μ‐L′)] complexes exhibit a rich coordination chemistry. It is demonstrated that the presence of the binding cavity influences many properties of the binuclear [(L^R)M^II₂]²⁺ complex fragments, including color, molecular and electronic structure, hydrogen bonding interactions, redox potential, complex stability, and reactivity. The unusual properties of the complexes can be traced back to complementary host‐guest interactions and the distinct size and form of the binding pocket of the [(L^Me)M₂]²⁺ fragments.     

Single‐walled Carbon Nanotube‐Calixarene Based Chemiresistor for Volatile Organic Compounds

Calixarenes are exciting class of organic macromolecules and proved to be an excellent sensing material for optical and mass transaction based sensors. The limited conductivity of calixarenes is a major impediment for the development of calixarene‐only chemiresistive sensors. The authors report on a calixarene‐based chemiresistor that is based on a hybrid material obtained by non‐covalent functionalization of SWCNTs with calixarene. This has two beneficial effects: (a) The use of SWCNT eliminates the conductivity issue, and this enables low‐power chemiresistive sensing; (b) the excellent affinity of calixarenes for certain analytes improves sensitivity. The hybrid material was fabricated by solvent casting, and its formation was confirmed by structural (SEM and TEM), electrical (I_D−V_D and I_D−V_G), and spectroscopic (Raman and ATR‐IR) characterizations. The resulting sensing device, operated typically at +1 V, undergoes an increase in resistance upon exposure to successive increments in concentration from 50 to 250 ppm for benzene, toluene, ethylbenzene and xylenes, commonly known as BTEX. Respective limits of detection are 25, 7.5, 6.5, and 4 ppm. This is well below their Occupational Safety and Health Administration (OSHA) permissible exposure limit (PEL) except for benzene. A mechanistic study for BTEX was performed via field‐effect transistor measurements, and this suggested that the sensing mechanism is dominated by an electrostatic gating effect. In our perception, the availability of a wide variety of calixarenes generates wide perspectives for calixarene‐only based SWCNT‐calixarene hybrid sensor arrays for the realization of electronic nose application.     

Synthesis and photochemical reaction of cyclic oligomers: Synthesis and photopolymerization of novel C‐methylcalix[4]resorcinarene and p‐alkylcalix[n]arene derivatives containing spiro ortho ether groups

New photoreactive calixarene derivatives containing spiro ortho ester groups (calixarenes 3a–3c ) were synthesized by the reaction of 2‐bromomethyl‐1,4,6‐trioxaspiro[4.4]nonane with 2,8,14,20‐tetramethyl‐4,6,10,12,16,18,22,24‐octakis(carboxymethoxy)calix[4]resorcinarene, 5,11,17,23,29,35‐hexamethyl‐37,38,39,40,41,42‐hexakis(carboxymethoxy)calix[6]arene, and 5,11,17,23,29,35,41,47‐octa‐tert‐butyl‐49,50,51,52, 53,54,55,56‐octakis‐(carboxymethoxy)calix[8]arene, which were prepared by the reaction of C‐methylcalix[4]resorcinarene, p‐methylcalix[6]arene, and p‐tert‐butylcalix[8]arene, respectively. The thermal stability of the obtained calixarene derivatives containing spiro ortho ester groups was examined with thermogravimetric analysis, and it was found that these calixarene derivatives had good thermal stability. The photoinitiated cationic polymerization of spiro ortho ester groups in calixarene derivatives 3a–3c was examined with certain photoacid generators in the film state. Interestingly enough, the reaction of calixarene derivatives did not proceed with only photoirradiation; however, the reaction proceeded smoothly when the photoirradiation was followed by heating. Furthermore, calixarene 3a , composed of a C‐methylcalix[4]resorcinarene structure, showed the highest photochemical reactivity in this reaction system. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1293–1302, 2002     

Probing the Subunit-Subunit Interaction of the Tetramer of E. coli KDO8P Synthase by Electrospray Ionization Mass Spectrometry

Escherichia coli 3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation reaction between D-arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) to form KDO8P and inorganic phosphate (Pi). This enzyme exists as a tetramer in solution, which is important for catalysis. Two different states of the enzyme were obtained: i) PEP-bound and ii) PEP-unbound. The effect of the substrates and products on the overall structure of KDO8P synthase in both PEP-bound and unbound states was examined using electrospray ionization mass spectrometry. The analysis of our data showed that the complexes of the PEP-unbound enzyme with PEP (or Pi) favored the formation of monomers, while the complexes with A5P (or KDO8P) mainly favored dimers. The PEP-bound enzyme was found to exist in the monomer and dimer with a small amount of the tetramer, whereas the PEP-unbound form primarily exists in the monomer and dimer, and no tetramer was observed, suggesting that the bound PEP have a role in stabilization of the tetrameric structure. Taken together, the results imply that the addition of the substrates or products to the unbound enzyme may alter the subunit-subunit interactions and/or conformational change of the protein at the active site, and this study also demonstrates that the electrospray ionization mass spectrometric method may be a powerful tool in probing the subunit-subunit interactions and/or conformational change of multi-subunit protein upon binding to ligand.     

Sugars‐grafted aliphatic biodegradable poly(L‐lactide‐co‐carbonate)s by click reaction and their specific interaction with lectin molecules

A novel biodegradable aliphatic poly(L ‐lactide‐co‐carbonate) bearing pendant acetylene groups was successfully prepared by ring‐opening copolymerization of L ‐lactide (LA) with 5‐methyl‐5‐propargyloxycarbonyl‐1,3‐dioxan‐2‐one (PC) in the presence of benzyl alcohol as initiator with ZnEt₂ as catalyst in bulk at 100 °C and subsequently used for grafting 2‐azidoethyl β‐D ‐glucopyranoside and 2‐azidoethyl β‐lactoside by the typical “click reaction,” that is Cu(I)‐catalyzed cycloaddition of azide and alkyne. The density of acetylene groups in the copolymer can be tailored by the molar ratio of PC to LA during the copolymerization. The aliphatic copolymers grafted with sugars showed low cytotoxicity to L929 cells, improved hydrophilic properties and specific recognition and binding ability with lectins, that is Concanavalin A (Con A) and Ricinus communis agglutinin (RCA). Therefore, this kind of sugar‐grafted copolymer could be a good candidate in variety of biomedical applications. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 3204 –3217, 2007     

Concise Synthesis and Facile Nanotube Assembly of a Symmetrically Multifunctionalized Cycloparaphenylene

The concise synthesis of C₃‐symmetrical [12]CPP‐hexacarboxylate has been achieved through macrocyclization by the rhodium‐catalyzed intermolecular cross‐cyclotrimerization and subsequent reductive aromatization. C₃‐Symmetrical functionalization of CPP with highly polar alkoxycarbonyl groups enabled the structurally uniform nanotube assembly in the crystalline state through multiple hydrogen‐bonding interactions giving a dimer followed by one‐dimensional stacking.     

A Modular Phosphorylated Glycoluril-Derived Molecular Tweezer for Potent Binding of Aliphatic Diamines

A molecular tweezer based on a glycoluril-derived framework bearing four phosphate groups was synthesized and shown to be capable of binding organic amines in aqueous solution. This work reports the K_a values for 30 complexes of this molecular tweezer and amine guests, determined by means of ¹H NMR titrations. Both the hydrophobic cavity and the phosphate groups contribute to the binding. Bulkier molecules and molecules bearing negatively charged groups like carboxylates in amino acids bind less tightly due to a steric clash and coulombic repulsion. The narrow cavity and the strong ionic interactions of the phosphate groups with ammonium guests favor binding of aliphatic diamines. These binding properties clearly distinguish this system from structurally related molecular clips and tweezers.     

X‐ray and DFT‐calculated structures of bis[N‐(quinolin‐8‐yl)benzamidato‐κ2N,N′]copper(II)

The application of transition metal chelates as chemotherapeutic agents has the advantage that they can be used as a scaffold around which ligands with DNA recognition elements can be anchored. The facile substitution of these components allows for the DNA recognition and binding properties of the metal chelates to be tuned. Copper is a particularly interesting choice for the development of novel metallodrugs as it is an endogenous metal and is therefore less toxic than other transition metals. The title compound, [Cu(C₁₆H₁₁N₂O)₂], was synthesized by reacting N‐(quinolin‐8‐yl)benzamide and the metal in a 2:1 ratio. Ligand coordination required deprotonation of the amide N—H group and the isolated complex is therefore neutral. The metal ion adopts a flattened tetrahedral coordination geometry with the ligands in a pseudo‐trans configuration. The free rotation afforded by the formal single bond between the amide group and phenyl ring allows the phenyl rings to rotate out‐of‐plane, thus alleviating nonbonded repulsion between the phenyl rings and the quinolyl groups within the complex. Weak C—H…O interactions stabilize a dimer in the solid state. Density functional theory (DFT) simulations at the PBE/6‐311G(dp) level of theory show that the solid‐state structure (C1 symmetry) is 79.33 kJ mol⁻¹ higher in energy than the lowest energy gas‐phase structure (C2 symmetry). Natural bond orbital (NBO) analysis offers an explanation for the formation of the C—H…O interactions in electrostatic terms, but the stabilizing effect is insufficient to support the dimer in the gas phase.     

Utilizing a pH‐Sensitive Dye in the Selective Fluorescent Recognition of Sulfate

A receptor containing amidopyrrole binding subunits and free amino groups, conjugated to a naphthalimide dye, has been designed and synthesized. The intrinsic selectivity of the binding motif for phosphate present in DMSO completely disappears in 10 % DMSO aqueous buffer at pH 3.6, at which the receptor is protonated. The electrostatic interactions between the receptor and an anion start to dominate, thus leading to selectivity for sulfate. The ability of the HSO₄^? anion to transfer the proton to the amino group during the recognition event suppresses the photoinduced electron transfer (PET) on the dye, resulting in a selective turn‐on fluorescent response. The choice of pH of the solution for sensing is dictated by the pK_a value of the dye.     

Di‐μ2‐sulfito‐κ8O,O′:O′,O′′‐bis[(2,4,6‐tri‐2‐pyrid­yl‐1,3,5‐triazine‐κ3N2,N1,N6)cadmium(II)] octa­hydrate

The title compound, [Cd₂(SO₃)₂(C₁₈H₁₂N₆)₂]·8H₂O, is a dimer built up around a symmetry center, where the sulfite anion displays a so far unreported coordination mode in metal‐organic complexes; the anion binds as a μ₂‐sulfite‐κ⁴O,O′:O′,O′′ ligand to two symmetry‐related seven‐coordinate Cd^II cations, binding through its three O atoms by way of two chelate bites with an O atom in common, which acts as a bridge. The cation coordination is completed by a 2,4,6‐tri‐2‐pyridyl‐1,3,5‐triazine ligand acting in its usual tridentate mode.     

Characterization of the potential energy surfaces of two small but challenging noncovalent dimers: (P2)2 and (PCCP)2

This work characterizes eight stationary points of the P₂ dimer and six stationary points of the PCCP dimer, including a newly identified minimum on both potential energy surfaces. Full geometry optimizations and corresponding harmonic vibrational frequencies were computed with the second‐order Møller–Plesset (MP2) electronic structure method and six different basis sets: aug‐cc‐pVXZ, aug‐cc‐pV(X+d)Z, and aug‐cc‐pCVXZ where X = T, Q. A new L‐shaped structure with C₂ symmetry is the only minimum for the P₂ dimer at the MP2 level of theory with these basis sets. The previously reported parallel‐slipped structure with C_2h symmetry and a newly identified cross configuration with D₂ symmetry are the only minima for the PCCP dimer. Single point energies were also computed using the canonical MP2 and CCSD(T) methods as well as the explicitly correlated MP2‐F12 and CCSD(T)‐F12 methods and the aug‐cc‐pVXZ (X = D, T, Q, 5) basis sets. The energetics obtained with the explicitly correlated methods were very similar to the canonical results for the larger basis sets. Extrapolations were performed to estimate the complete basis set (CBS) limit MP2 and CCSD(T) binding energies. MP2 and MP2‐F12 significantly overbind the P₂ and PCCP dimers relative to the CCSD(T) and CCSD(T)‐F12 binding energies by as much as 1.5 kcal mol^?1 for the former and 5.0 kcal mol^?1 for the latter at the CBS limit. The dominant attractive component of the interaction energy for each dimer configuration was dispersion according to several symmetry‐adapted perturbation theory analyses. © 2014 Wiley Periodicals, Inc.     

Interactions of a water-soluble calix[4]arene with spermine: solution and solid-state characterisation

Abstract

The octaanionic 5,11,17,23-tetrasulfonato-25,26,27,28-tetrakis(hydroxycarbonylmethoxy)-calix[4]arene (cone conformation) (C₄TsTc) was investigated as a sensor for the biogenic tetracationic polyamine, spermine _.(H₄Spe⁴⁺). Fluorescence titration experiments of the water-soluble calixarene with spermine showed the formation of the 2:1 and 1:1 calixarene:spermine complexes in solution. The single crystal X-ray diffraction analysis of [(NaC₄TsTc)₄·(H₄Spe)₇] confirmed the formation of 2:1 and 1:1 calixarene:spermine species and showed that the water-soluble calixarene binds the spermine either by partially hosting it in the inner cavity or through the carboxylate groups on the lower rim. In order to investigate the effect of multivalent systems, supramolecular assemblies of octaanionic calixarene molecules templated by meso-tetrakis(4-N-methylpyridyl)porphyrin (H₂T₄) in different stoichiometric porphyrin:calixarene ratios (1:4 and 3:4) were also tested for spermine binding in solution. Fluorescence titration experiments with the 1:4 and 3:4 H₂T₄:C₄TsTc supramolecular complexes showed that the multivalent assemblies are more sensitive to the presence of spermine than the calixarene alone.     

Calix[4]arene‐Phosphine Dimers: Precursors of Flexible Metallo‐Capsules and Self‐Compacting Molecules

The first diphosphines based on a double calixarene, namely 1,4 (or 1,3)‐bis‐(5‐diphenylphosphino‐25,26,27,28‐tetrapropoxycalix[4]aren‐17‐yl)benzene ( L² , L³ ) were each prepared in four steps starting from 5,17‐dibromo‐25,26,27,28‐tetrapropoxycalix[4]arene. Upon reaction of L² with [Au(tht)(thf)]BF₄, (tht=C₄H₈S) a rigid metallo‐capsule was quantitatively formed, which adopts an oblique form owing to the distinct nature of the spacers linking the two calixarene half‐spheres. In the solid state, the 1,4‐substituted phenylene linker is turned towards the gold ion, suggesting the existence of weak bonding interactions between two aromatic CH protons of this ring and the metal centre (Au???H=2.67 Å). In contrast to this gold complex, the related silver complex shows dynamic behaviour in solution, the exchange between two enantiomeric oblique forms being facilitated by the greater stereochemical flexibility of Ag^I vs. Au^I. A heteronuclear ¹⁰⁹Ag{¹H} HMQC experiment established strong correlations between the CH protons of the phenylene linker and the ¹⁰⁹Ag ion. Dynamic behaviour similar to that observed for the silver complex was further observed in trans‐[PtCl₂? L² ], a chelate complex that could be obtained quantitatively from L² and [PtCl₂(PhCN)₂]. The intended formation of a chelate complex leading to a capsule with an endo‐oriented metal centre was achieved by reacting L³ with [Pd(allyl)(thf)₂]BF₄. The complex thus formed constitutes the first organometallic transition metal complex embedded in a cavity with large portals. Binding of [RuCl₂(p‐cymene)] to L² and L³ resulted in self‐compacting bimetallic complexes in which each calixarene basket entraps a Ru(p‐cymene) unit, thereby forming molecules occupying a minimal volume.