Metal-containing ditopic receptors for molecular recognition of diammonium cations

Two new ditopic receptors for α,ω-alkanediyldiammonium cations based on a tetraazamacrocyclic (cyclidene) nickel(II) complex bearing two crown-ether residues were synthesized. The studies of the host-guest interaction between the receptors and a series of α,ω-diammonium salts by NMR titration in acetonitrile-d₃ showed that 1:1 complexes are formed with K_assoc∼10³-10⁵ M⁻¹. Receptor 1 with benzo-15-crown-5 arms showed substantial selectivity in binding of trimethylene- and tetramethylenediammonium dications, and 1-2 orders of magnitude weaker binding of shorter (C₂) or longer (C₅ and C₆) diammonium cations. Receptor 2 with benzo-18-crown-6 arms showed higher affinity to all studied diammonium cations, but the recognition of the length of α,ω-diammonium cations was less pronounced.     

Tripodal pyrrolotetrathiafulvalene receptors for recognition of electron-deficient molecular guests

We report the synthesis of tripodal receptors with monopyrrolo-tetrathiafulvalene arms 1a,b, based on 1,3,5-substituted 2,4,6-triethylbenzene scaffold. The three converging pyrrolotetrathiafulvalene groups form an electron rich cone-shaped binding site. Molecular hosts 1a,b are capable of binding neutral electron deficient guests in solution, as well as positively charged pyridinium species in the gas phase.     

Nanoparticles: scaffolds for molecular recognition

Monolayer and mixed-monolayer protected clusters (MPCs and MMPCs) have great potential to combine molecular functionality with the intrinsic properties of nanometer-sized scaffolds. This synergy can be used to create complex functional devices, including redox-active, electronic, or magnetic storage devices, solution-based sensors, and highly efficient catalysts. This review outlines some of the recent developments in nanoscale receptors based on synthetic and nonbiological recognition elements. In these nanoparticle systems, molecular recognition is achieved by covalent attachment of receptors on the nanoparticles coupled with noncovalent interactions to target substrates. Synthetic host-guest systems, hydrogen bonding, change in redox states, pi-pi stacking, rotaxane formation, and ion recognition are the main topics covered in this review.     

Study on the synthesis and molecular recognition of new receptors for selective complexation of carboxylic acids

A new synthetic method based on the synthesis of unsymmetrical thioureas followed by double S-alkylation reaction by xylylene dibromides was used to obtain isothiouronium receptors. Their binding abilities to acetate, succinate and maleate anions were evaluated by UV-vis spectroscopic titrations in such solvents as water, acetonitrile, methanol and mixtures of acetonitrile/methanol (1:1, v/v). For simple receptor 4 with one isothiouronium group, no selectivity was observed in the complexation of the anions studied. Receptors (R) 5a-c with two thiouronium groups are able to form with all the anions studied (A) not only stable complexes of 1:1 stoichiometry but also other possessing structure of the type A_nR_m. The most reliable values of stability constants are for systems of the type maleate anion-receptor 5 and acetate-receptor 5b. However, the best selectivity in the mixed solvents is demonstrated by anion-5c system. The study indicates also that particularly 5c is preferred as a chemosensor for the maleate anion. The obtained results suggest that subtle changes in the receptor structure lead to different binding modes towards anions.     

Design of steroid-based imidazolium receptors for fluoride ion recognition

New deoxycholic acid-based cyclic receptors bearing imidazolium and benzimidazolium moieties bridged with o-xylelene and 1,8-dimethylenenaphthalene groups have been synthesized. Anion binding studies using ¹H NMR revealed that receptors having naphthalenic group as spacer exhibit very high selectivity for fluoride ion over other anions while receptors with o-xylelene group show a preference for the chloride ion.     

Chiral diaminopyrrolic receptors for selective recognition of mannosides, part 2: a 3D view of the recognition modes by X-ray, NMR spectroscopy, and molecular modeling

The structural features of a representative set of five complexes of octyl α- and β-mannosides with some members of a new generation of chiral tripodal diaminopyrrolic receptors, namely, (R)-5 and (S)- and (R)-7, have been investigated in solution and in the solid state by a combined X-ray, NMR spectroscopy, and molecular modeling approach. In the solid state, the binding arms of the free receptors 7 delimit a cleft in which two solvent molecules are hydrogen bonded to the pyrrolic groups and to the benzenic scaffold. In a polar solvent (CD(3)CN), chemical shift and intermolecular NOE data, assisted by molecular modeling calculations, ascertained the binding modes of the interaction between the receptor and the glycoside for these complexes. Although a single binding mode was found to adequately describe the complex of the acyclic receptor 5 with the α-mannoside, for the complexes of the cyclic receptors 7 two different binding modes were required to simultaneously fit all the experimental data. In all cases, extensive binding through hydrogen bonding and CH-π interactions is responsible for the affinities measured in the same solvent. Furthermore, the binding modes closely account for the recognition preferences observed toward the anomeric glycosides and for the peculiar enantiodiscrimination properties exhibited by the chiral receptors.     

Squaramido-based receptors: applicability of molecular interaction potential to molecular recognition of polyalkylammonium compounds

 A computational study of the mechanism of host–guest complexation between quaternary ammonium compounds and squaramido-based tripodal receptors has been carried out. Semiempirical molecular orbital calculations, which are in qualitative agreement with experimental results have been performed using the PM3 Hamiltonian. Molecular interaction potential (MIP) maps were used to analyze the suitability of both host and guest binding units for a high-affinity recognition process. MIP calculations were computed from PM3 wavefunctions of the corresponding ammonium cations and dimethyl squaramide as a model compound for the hydrogen-bond-acceptor unit of the receptors. MIP analyses are helpful for understanding the host–guest process from the point of view of the double-complementarity principle. Received: 23 June 1999 / Accepted: 22 September 1999 / Published online: 17 January 2000     

A new strategy for the design of water-soluble synthetic receptors: specific recognition of DNA intercalators and diamines

Water-soluble zinc bisporphyrin receptors 1 and 2 having two Lewis acidic sites (zinc) in the hydrophobic environment consisting of alkyl chains and a bisporphyrin framework, and covered with hydrophilic exterior (twelve or eighteen carboxyl groups) were prepared. The receptors show high affinity for diamines and DNA intercalators in water where the binding constants K(a) are of the order of 10(7) and 10(8) M(-1), respectively. Diamines and DNA intercalators are bound to the receptor through different mechanisms. Diamines are bound through hydrophobic interactions and zinc-nitrogen interactions, while DNA intercalators are bound through hydrophobic interactions and charge-transfer interactions. Flexible alkyl chains can make van der Waals contact with guests and create a hydrophobic environment around the bound guest by an induced-fit-type mechanism. For the binding of DNA intercalators, the following features are noteworthy: 1). Binding constants are similar between the zinc porphyrins and zinc-free porphyrins; 2). the binding constant is larger for the guest having the lower LUMO; this indicates the important contribution of charge-transfer interactions to binding; 3). the hydrophobic and cationic nature of DNA intercalators is substantially important, and 4). higher ionic strength reduced the binding affinities; this shows a moderate contribution of electrostatic interactions. The conformational instability of the receptors also contributes to the tight binding: hydrophobic and electrostatic interactions cannot both be favorable at the same time in the guest-free receptor. Enthalpy-entropy compensation observed for the binding of diamines and DNA intercalators is characterized by a relatively small slope (alpha=0.74) and a large intercept (beta=7.75 kcal mol(-1)) in the DeltaH degrees versus TDeltaS degrees plot; this shows that a conformational change of receptors and a significant desolvation occur upon binding. The receptor can competitively bind to propidium iodide to deprive DNA of the intercalated propidium iodide. These features of water-soluble receptors consisting of a rigid framework and flexible side chains with a large solvent-accessible area are in contrast to highly preorganized rigid receptors, and they can provide useful guidelines for rational design of induced-fit artificial receptors in water.     

Directed molecular recognition: design and synthesis of neutral receptors for biotin to bind both its functional groups

The neutral receptors 1 and 2 are designed and synthesized for the recognition of biotin, a biologically significant molecule, in chloroform to bind completely both of its functional groups simultaneously, i.e., cyclic urea and the carboxyl groups. The truncated receptor 3 binds only the cyclic urea moiety.     

Ditopic crown ether-guanidinium ion receptors for the molecular recognition of amino acids and small peptides

A series of ditopic synthetic receptors based on a crown ether-guanidinium ion recognition motif is reported. The compounds show binding affinity to selected amino acids, including important neurotransmitters. The effect of the distance of the ammonium and the carboxylate ion, the rigidity of the spacer, and the use of pre-organized pyrrole- and pyrene-guanidinium groups on binding affinity and selectivity are discussed.     

Highly effective acyclic carbohydrate receptors consisting of aminopyridine, imidazole, and indole recognition units

Neutral imidazole/aminopyridine- and indole/aminopyridine-based receptors, 1 and 2, have been established as highly effective and selective carbohydrate receptors. These receptors effectively recognise neutral carbohydrates through multiple interactions, including neutral hydrogen bonds and CH...pi interactions between the sugar CH groups and the aromatic rings of the receptors. The design of these receptors was inspired by the binding motifs observed in the crystal structures of protein-carbohydrate complexes. The formation of very strong complexes with beta-glucopyranoside 5, beta-maltoside 8, and alpha-maltoside 9 in organic media has been characterised by 1H NMR spectroscopy and confirmed by a second, independent technique, namely fluorescence spectroscopy. The syntheses, molecular-modelling studies, binding properties of the receptors 1 and 2 toward selected mono- and disaccharides as well as comparative binding studies with receptors 3 and 4 are described.     

Structural basis for molecular recognition,theoretical studies and anti-bacterial properties of three bis-uracil derivatives

Three bis-pyrimidine compounds (1, 2 & 3) have been synthesized by the reaction of 6-[(dimethylamino)methyleneamino]-1,3-dimethyluracil with three different aldehydes viz. p-methoxybenzaldehyde, p-nitrobenzaldehyde, and 2-thiophenecarboxaldehyde in aqueous media in presence of ‘green surfactant’ followed by recrystallization in EtOH. The compounds are characterized by elemental analyses, NMR and single crystal X-ray diffraction. N–H?O hydrogen bonds and weak C–H?O interactions are the main non-bonding interactions in the molecular structures of the three compounds. Details of the synthesis, spectroscopic data and structures of the three compounds are presented. Furthermore, we have rationalized some relevant noncovalent interaction involving the aromatic moieties by means of DFT calculations. Finally, we have also analysed the anti-bacterial properties of compounds 1–3 and compared to Ofloxacin drug. The anti-bacterial activity has been tested against Klebsiella pneumoniae, Staphylococcus aureus and Pseudomonas aeruginosa. All compounds are found to possess from moderate to good anti-bacterial properties (MIC 25–100 μg/ml).     

Relativistic Gaussian basis sets for molecular calculations: Fully optimized single‐family exponent basis sets for H?Hg

Relativistic single‐family exponent Gaussian basis sets for molecular calculations are presented for the 80 atoms ₁H through ₈₀Hg. The exponent parameters shared by Gaussian basis functions of all symmetry species are fully optimized. Two nucleus models of uniformly charged sphere and Gaussian charge distribution are considered and two kinds of basis sets are generated accordingly. The total energy errors are less than 2 mhartree in any atoms. Some of the present basis sets include small variational collapse (or prolapse), but test calculations show that they could be reliably applied to molecular calculations. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 48–52, 2006     

Exploring the molecular basis of selectivity in A1 adenosine receptors agonists: a case study

Adenosine is a naturally occurring purine nucleoside that has a wide variety of well-documented regulatory functions and physiological roles. Selective activation of the adenosine A₁ receptor has drawn attention in drug discovery for the therapeutic effects on neural and cardiovascular disorders. We have developed a model of the human A₁ adenosine receptor using bovine rhodopsin as a template. A flexible docking approach has been subsequently carried out for evaluating the molecular interactions of twenty-one selective A₁ agonists with the receptor model. The results of these studies are consistent with mutational and biochemical data. In particular, they highlight a wide hydrogen-bonding network between the nucleoside portion of the ligands and the A₁ receptor as well as key amino acids for hydrophobic interactions with the different N⁶-groups of the agonists. The models presented here provide a detailed molecular map for the selective stimulation of the adenosine A₁ receptor subtype and a steady basis for the rational design of new A₁ selective ligands.     

Synthesis,complexing properties and molecular modelling of open chain receptors of barbiturates derived from 2,6-diamino pyridine

Three new derivatives of 2,6-diacyldiaminopyridine are reported. NMR shift titrations were performed in CDCl₃ with barbiturates. The diamide1 affords a greater complexation energy (–13.00 kJ mol^–1) with bemegride than the dithioamide2 (–9.15 kJ mol^–1). This result, unexpected on the basis of the proton acidities, is explained by the great torsion energy induced in2 by the bulky sulfur atom. Compounds3 and4 present unusual four and five H-bond features with barbital and relatively weak complexation energies (–9.53 and –16.34 kJ mol^–1, respectively). Molecular mechanics indicates that ligand4 displays a helical secondary structure which is disrupted by complexation. Calculations of the H-bond energies (E _calc.) of the intermolecular assemblies with barbital or phenobarbital and other host-guest complexes given in the literature give a good correlation (r=0.98) with experimental values: E _calc.=1.07 G _a–42.0. Limitations of this relation are discussed.     

新型脱氧胆酸钳形阴离子受体的设计合成及其对阴离子的识别性能研究

具有对阴离子选择性识别的人工受体的设计合成是生物有机化学和超分子化学前沿富于挑战性的领域之一[1].在许多识别阴离子的人工受体化合物中,脲和硫脲衍生物是重要的中性受体化合物之一.