Molecular recognition: comparative study of a tunable host-guest system by using a fluorescent model system and collision-induced dissociation mass spectrometry on dendrimers

Host-guest interactions between the periphery of adamantylurea-functionalized dendrimers (host) and ureido acetic acid derivatives (guest) were shown to be specific, strong and spatially well-defined. The binding becomes stronger when using phosphonic or sulfonic acid derivatives. In the present work we have quantified the binding constants for the host-guest interactions between two different host motifs and six different guest molecules. The host molecules, which resemble the periphery of a poly(propylene imine) dendrimer, have been fitted with an anthracene-based fluorescent probe. The two host motifs differ in terms of the length of the spacer between a tertiary amine and two ureido functionalities. The guest molecules all contain an acidic moiety (either a carboxylic acid, a phosphonic acid, or a sulfonic acid) and three of them also contain an ureido moiety capable of forming multiple hydrogen bonds to the hosts. The binding constants for all 12 host-guest complexes have been determined by using fluorescence titrations by monitoring the increase in fluorescence of the host upon protonation by the addition of the guest. The binding constants could be tuned by changing the design of the acidic part of the guest. The formation of hydrogen bonds gives, in all cases, higher association constants, demonstrating that the host is more than a proton sensor. The host with the longer spacer (propyl) shows higher association constants than the host with the shorter spacer (ethyl). The gain in association constants are higher when the urea function is added to the guests for the host with the longer spacer, indicating a better fit. Collision-induced dissociation mass spectrometry (CID-MS) is used to study the stability of the six motifs using the corresponding third generation dendrimer. A similar trend is found when the six different guests are compared.     

Supramolecular dendrimer chemistry: using dendritic crown ethers to reversibly generate functional assemblies

A series of crown ether derivatives functionalised with dendritic branching based on l-lysine repeat units has been synthesised. The ability of these receptors to interact with cationic guests has been investigated using NMR and mass spectrometric techniques. Binding constants have been evaluated, some using competitive binding assays, and these indicate that the strength of interaction between the encapsulated crown-ether and cationic guests decreases with increasing dendritic functionalisation. The interaction of these dendritic branches with ditopic ammonium cation functionalised templates has been investigated, and Job plot analysis indicates the formation of 2:1 (branch/template) stoichiometric complexes in MeOH solution. These supramolecular assemblies have been disassembled by the addition of potassium cations, hence achieving controlled release of the template back into solution. This process has been investigated by NMR methods and the effect of counteranion on these studies is reported. The use of ditopic ammonium cations possessing long alkyl spacer chains as templates has also been investigated, and in this case, the 2:1 assembly that forms, goes on to achieve higher order levels of organisation, hence gelating the solvent. This particular system is therefore a rare example in which discrete, characterisable dendritic supermolecules possess an inherent potential for further supramolecular assembly, to yield new materials.     

"Pocket dendrimers" as nanoscale receptors for bimolecular guest accommodation

A new series of dendrimer receptors was prepared by combining a (tetraphenylporphinato)zinc(II) core and benzyl ether type dendritic substituents. Since one direction of the (tetraphenylporphinato)zinc(II) was not substituted by a dendritic residue, the resulting unsymmetrical dendrimers have "pockets" available for access of external substrates. Molecular modeling, NMR measurements, and zinc-coordination experiments revealed that the third-generation dendrimer of this type exhibited characteristic inclusion of coordinative pyridine guests. When diamidopyridine moiety was introduced into the dendrimer pocket, a thymine derivative was bound through complementary hydrogen bonding. Two different kinds of substrates, pyridine and thymine derivatives, were simultaneously accommodated in the nanoscale pocket and bimolecular guest accommodation was realized with the designed dendrimer receptor.     

Crystal engineering: Supramolecular structures by cocrystallization ofMeso-1,2-diphenyl-1,2-ethanediol and bisimines,simple cases of molecular recognition

The crystal structures of molecular complexes betweenmeso- 1,2-diphenyl-1,2-ethanediol and two bisimines (N,N-(dibenzylidene)-ethylenediamine and glyoxylidene-bis(2,4-dimethyl-3-pentyl-amine) are reported at different temperatures. The structure-determining motif of the cocrystalline arrangement is one single O-H . N hydrogen bond resulting in infinite ladderlike polymers. The supramolecular structure is formed by recognition of fitting species: Thed- orl-isomers do not arrange in such structures.¹H NMR experiments show that no prearrangements take place by forming complexes in solution.     

Custom‐Fit Ruthenium(II) Metallopeptides: A New Twist to DNA Binding With Coordination Compounds

A new bipyridine building block has been used for the solid‐phase synthesis of dinuclear DNA‐binding ruthenium(II) metallopeptides. Detailed spectroscopic studies suggest that these compounds bind to the DNA by insertion into the DNA minor groove. Moreover, the potential of the solid‐phase peptide synthesis approach is demonstrated by the straightforward synthesis of an octaarginine derivative that shows effective cellular internalization and cytotoxicity linked with strong DNA interaction, as evidenced by steady‐state fluorescence spectroscopy and AFM studies.     

Moving targets: recognition of alkyl groups

Alkyl chains can adopt seemingly unusual conformations, such as helices, when bound to natural and synthetic hydrophobic receptors. This plasticity allows the alkanes to assume shapes that are congruent to the receptor's space and fill that space properly. We describe here the use of cavitands and capsules as tools that expose the forces involved in the molecular recognition of hydrocarbons. Studies using NMR spectroscopy reveal how attractive interactions and solvophobic forces are maximized in solution through unprecedented contortions of alkanes and hint at a new generation of nanoscale mechanical devices.     

Theoretical Study on the Dual Behavior of XeO3 and XeF4 toward Aromatic Rings: Lone Pair–π versus Aerogen–π Interactions

In this study, several lone pair–π and aerogen–π complexes between XeO₃ and XeF₄ and aromatic rings with different electronic natures (benzene, trifluorobenzene, and hexafluorobenzene) are optimized at the RI‐MP2/aug‐cc‐pVTZ level of theory. All complexes are characterized as true minima by frequency analysis calculations. The donor/acceptor role of the ring in the complexes is analyzed using the natural bond orbital computational tool, showing a remarkable contribution of orbital interactions to the global stabilization of the aerogen–π complexes. Finally, Bader's AIM analysis of several complexes is performed to further characterize the lone pair–π and aerogen–π interactions.     

Recognition of Free Tryptophan in Water by Synthetic Pseudopeptides: Fluorescence and Thermodynamic Studies

Pseudopeptidic receptors containing an acridine unit have been prepared and their fluorescence response to a series of amino acids was measured in water. Free amino acids, not protected either at the C or the N terminus, were used for this purpose. The prepared receptors display a selective response to tryptophan (Trp) versus the other assayed amino acids under acidic conditions. The macrocyclic nature of the receptor is important as the fluorescence quenching is higher for the macrocyclic compound than for the related open‐chain receptor. Notably, under the experimental acidic conditions used, both the receptor and guest are fully protonated and positively charged; thus, the experimental results suggest the formation of supramolecular species that contain two positively charged organic molecular components in proximity stabilized through aromatic–aromatic interactions and a complex set of cation‐anion‐cation interactions. The selectivity towards Trp seems to be based on the existence of a strong association between the indole ring of the monocharged amino acid and the acridinium fragment of the triprotonated form of the receptor, which is established to be assisted by the interaction of the cationic moieties with hydrogen sulfate anions.     

Protonated macrobicyclic hosts containing pyridine head units for anion recognition

In this paper, we report two macrobicyclic receptors containing pyridine head units derived from 1,10-diaza-15-crown[5] (L1) or 4,13-diaza-18-crown[6] (L2) that can be protonated in MeCN and used for anion recognition. The interaction of these protonated lateral macrobicycles with different anions has been investigated by means of spectrophotometric titrations in MeCN. The association constants for the complexes of halide anions with the protonated macrobicycles follow the sequences Cl(-)>Br(-)>I(-)>F(-) (L1) and Cl(-)>F(-)>I(-)>Br(-) (L2), whereby an increase of more than two logarithmic units is observed from F(-) to Cl(-) for the binding constants of the receptor derived from L1. The association constants also indicate an important degree of selectivity of these macrobicyclic receptors for Cl(-) over Br(-) or I(-). The X-ray crystal structure analyses of the chloride and bromide complexes confirms the formation of the envisaged supramolecular complexes. Moreover, the binding constants indicate that these receptors present a high sulfate-to-nitrate binding selectivity. The stability trend observed for the recognition of halide anions by the macrobicycles presented herein as well as the sulfate-to-nitrate binding selectivity have been rationalised by means of DFT calculations at the B3LYP/LanL2DZ level. These studies indicate that the especially high binding selectivity for Cl(-) is the result of the optimum fit between the protonated macrobicyclic cavity and the size of the anion, whereas the sulfate-to-nitrate selectivity results from shape complementarity between the hydrogen-binding acceptor sites on sulfate and the hydrogen-bond donors of the macrobicycle.     

Configurations of nickel-cyclam antiviral complexes and protein recognition

Nickel(II)-xylylbicyclam is a potent anti-HIV agent and binds strongly to the CXCR4 co-receptor. We have investigated configurational equilibria of Ni(II)-cyclam derivatives, since these are important for receptor recognition. Crystallographic studies show that both trans and cis configurations are readily formed: [Ni(cyclam)(OAc)(2)] x H(2)O adopts the trans-III configuration with axial monodentate acetates, as does [Ni(benzylcyclam)(NO(3))(2)] with axial nitrate ligands, whereas [Ni(benzylcyclam)(OAc)](OAc)2 x H(2)O has an unusual folded cis-V configuration with Ni(II) coordination to bidentate acetate. UV/Vis and NMR studies show that the octahedral trans-III configuration slowly converts to square-planar trans-I in aqueous solution. For Ni(II)-xylylbicyclam, a mixture of cis-V and trans-I configurations was detected in solution. X-ray diffraction studies showed that crystals of lysozyme soaked in Ni(II)-cyclam or Ni(II) (2)-xylylbicyclam contain two major binding sites, one involving Ni(II) coordination to Asp101 and hydrophobic interactions between the cyclam ring and Trp62 and Trp63, and the second hydrophobic interactions with Trp123. For Ni(II)-cyclam bound to Asp101, the cis-V configuration predominates.     

A 1,2,3,4,5-pentaphenylferrocene-stoppered rotaxane capable of electrochemical anion recognition

The chloride anion templated synthesis of an electrochemical anion sensory interlocked host system, prepared by the integration of redox-active 1,2,3,4,5-pentaphenylferrocene stopper groups into the structure of a rotaxane capable of binding anionic guests is described. Extensive (1)H NMR and electrochemical titration investigations were used to probe the anion recognition and sensing properties of the rotaxane, compared to the axle and model system components. A characteristic electrochemical response was observed for chloride binding by the rotaxane, which was attributed to the topologically constrained cavity of the interlocked host molecule.     

Two-component dendritic gel: effect of stereochemistry on the supramolecular chiral assembly

The self-assembly of diaminododecane solubilised by four different stereoisomeric dendritic peptides to form gel-phase materials in toluene was investigated. The second generation dendritic peptides were based on D- and L-lysine building blocks, and each contained three chiral centres. By designing dendritic peptides in which the configurations of the chiral centres were modified, and applying them as gelator units, the assembly of stereoisomers could be investigated. In all cases, the self-assembly of gelator units resulted in macroscopic gelation. However, the degree of structuring was modulated by the stereoisomers employed, an effect which changed the morphology and macroscopic behavior of the self-assembled state. Enantiomeric (L,L,L or D,D,D) gelator units formed fibrous molecular assemblies, whilst the racemic gel (50 % L,L,L : 50 % D,D,D) formed a flat structure with a "woven" appearance. Gelator units based on L,D,D or D,L,L dendritic peptides also formed fibrous assemblies, but small-angle X-ray scattering indicated significant morphological differences were caused by the switch in chirality. Furthermore, the macroscopic stability of the gel was diminished when these peptides were compared with their L,L,L or D,D,D analogues. In this paper it is clearly shown that individual stereocentres, on the molecular level, are directly related to the helicity within the fibre. It is argued that the chirality controls the pattern of hydrogen bonding within the assembly, and hence determines the extent of fibre formation and the macroscopic gel strength.     

Biquinolino-modified beta-cyclodextrin dimers and their metal complexes as efficient fluorescent sensors for the molecular recognition of steroids

A series of bridged beta-cyclodextrin (beta-CyD) dimers possessing functional tethers of various lengths was synthesized in moderate yield by the treatment of 2,2'-biquinoline- 4,4'-dicarboxylic dichloride with beta-CyD or mono[6-oligo(ethylenediamino)-6-deoxy]-beta-CyDs. The products were 2,2'-biquinoline-4,4'-dicarboxy-bridged bis(6-O-beta-CyD) (8), N,N'-bis(2-aminoethyl)-2,2'-biquinoline-4,4'-dicarboxamide-bridged bis(6-amino-6-deoxy-beta-CyD) (9), and N,N'-bis(5-amino-3-azapentyl)-2,2'-biquinoline-4,4'-dicarboxamide-bridged bis(6-amino-6-deoxy-beta-CyD) (10). The reaction of 8-10 with copper perchlorate give their copper(II) complexes 11-13 in satisfactory yields of over 77 %. All the bis(beta-CyD)s 8-13 act as efficient fluorescent sensors and display remarkable fluorescence enhancement upon addition of optically inert steroids. The inclusion complexation behaviors of 8-13 when treated with the representative steroids cholate (14), deoxycholate (15), and glycocholate (16) in aqueous solution at 25 degrees C were investigated by means of UV/Vis spectroscopy, conductivity and fluorescence measurements, circular dichroism spectroscopy, and 2D NMR spectroscopy. The tether length of bis(beta-CyD) 9 allows it to adopt a cooperative host-tether-guest binding mode in which the spacer and guest are co-included in the two CyD cavities. As a result of this cooperation, 9 has a stability constant (K(s)) about 2x10(2) times higher than that of monomodified beta-CyD 4 for inclusion complexation with cholate. Metallooligo(beta-CyD)s with four beta-CyD units have enhanced binding abilities compared with monomodified beta-CyDs. These metallo compounds have binding affinities for guest steroids that are up to 50-4.1x10(3) times higher than those of CyDs 2-4. The guest-induced fluorescence enhancement of bis(CyD)s opens a new channel for the design of sensor materials. The complex stability constants of these compounds are discussed from the viewpoint of induced-fit interaction and cooperative multiple binding between host and guest.     

Affinity Polymers Tailored for the Protein A Binding Site of Immunoglobulin G Proteins

Rational design in combination with a screening process was used to develop affinity polymers for a specific binding site on the surface of immunoglobulin G (IgG) proteins. The concept starts with the identification of critical amino acid residues on the protein interface and their topological arrangement. Appropriate binding monomers were subsequently synthesized. Together with a sugar monomer (2–5 equiv) for water solubility and a dansyl monomer (0.5 equiv) as a fluorescent label, they were subjected in aqueous solution to linear radical copolymerization in various compositions (e.g., azobisisobutyronitrile (AIBN), homogeneous water/DMF mixtures). After ultrafiltration and lyophilization, colorless dry water‐soluble powders were obtained. NMR spectroscopic and gel permeation chromatography (GPC) characterization indicated molecular weights between 30 and 500 kD and confirmed retention of monomer composition as well as the absence of monomers. In a competitive enzyme‐linked immunosorbent assay (ELISA) screen of the polymer libraries (20–50 members), few copolymers qualified as strong and selective binders for the protein A binding site on the Fc fragment of the antibody. Their monomer composition precisely reflected the critical amino acids found at the interface. The simple combination of a charged and a nonpolar binding monomer sufficed for selective submicromolar IgG recognition by the synthetic polymer. Affinities were confirmed by fluorescence titrations; they increased with decreasing salt load but remained largely unaltered at lowered pH. Other proteins, including those of similar size and isoelectric point (pI), were bound 10–1000 times less tightly. This example indicates that interaction domains in other proteins may also be targeted by synthetic polymers if their comonomer composition reflects the nature and arrangement of amino acid residues on the protein surface.     

Sulfate‐Selective Binding and Sensing of a Fluorescent [3]Rotaxane Host System

The chloride‐templated synthesis of a novel [3]rotaxane, capable of binding anionic guests, and incorporating a naphthalene group for fluorescence sensing is reported. Extensive ¹H NMR titration studies were used to probe the anion binding selectivity of the system. The rotaxane selectively recognises sulfate, undergoing an induced conformational change upon sulfate binding to form a 1:1 stoichiometric sandwich‐type complex, concomitant with significant quenching of the fluorescence. Binding of mono‐anionic guests results in the formation of a 2:1 stoichiometric guest–host complex, and a modest enhancement of the emission. Addition of an excess of sulfate in non‐competitive solvent also results in a 2:1 emissive complex.     

An enantiomeric nanoscale architecture obtained from a pseudoenantiomeric aggregate: covalent fixation of helical chirality formed in self-assembled discotic triazine triamides by chiral amplification

Covalent fixation of a chiral helical structure which is created in a self-assembling system by a chiral-amplification method based on the sergeants/soldiers principle is reported. Disk-shaped triazine triamides self-assembled to form columnar-type helical aggregates through pi-stacking interactions among the central triphenyltriazine moieties, hydrogen-bonding interactions among the amide groups, and van der Waals interactions among the alkyl groups in nonpolar solvents such as hexane, octane, toluene, and p-xylene. When the achiral triazine triamide soldier component is mixed with a tiny amount of the chiral triazine triamide sergeant component, control of the intrinsic supramolecular helicity of the self-assembled soldier component by the sergeant component leads to chiral amplification and formation of a pseudoenantiomeric aggregate with only one handedness of the helix. The helicity can be preserved by ring-closing olefin metathesis polymerization mediated by Grubbs catalyst when an achiral component with terminal olefinic groups forms the pseudoenantiomeric aggregate in the presence of a tiny amount of the chiral component without olefinic groups. After polymerization and removal of the chiral component, the polymeric architecture obtained from the achiral soldier component is optically active and thus can be regarded as an enantiomeric object in which the chiral information transferred from the chiral sergeant component is preserved. The nanoscale chiral structure is fixed perfectly, as indicated by CD spectroscopic evidence obtained in a polar THF medium at high temperature and low concentration. AFM and TEM observations show a nanoscale fibrous structure with a diameter of 2-4 nm, which corresponds to the molecular size of the triazine triamide monomer.