Competitive anion binding aptitude of benzimidazole and amide functionality of a non-symmetrical receptor in solid state and solution phase

A novel non-symmetric tripodal receptor (L) with benzimidazole and amide –NH functionalities has been synthesised and a comparative study for anion binding aptitude of those functionalities has been performed in solid state and solution phase. The protonated receptors in solid state tend to form a pseudo-cavity around the octahedral hexafluorosilicate anion whilst in second complex, binding of one sulphate and two bisulphates in unison by two protonated units arises. The benzimidazole –NHs are the strongest hydrogen bond donors in both the crystals controlling dominance over amide –NHs. The neutral receptor being selective towards fluoride anion induces a naked eye visible colorimetric change. The ¹H NMR studies with the neutral and protonated form of the receptor suggest the strong involvement of amide –NH in anion binding in solution phase.     

Experimental and computational studies of the binding properties of lower rim tetra- and di-substituted calix[4]arene amide derivatives with metal ions

Abstract

Experimental and theoretical binding studies of representative alkali, alkaline earth, transition, heavy metal and lanthanide cations by tetra- and di-substituted calix[4]arene amide derivatives (diethyl amide 1a–c and morpholide amide 2a–c) in the cone conformation were carried out. Binding was assessed by extraction experiments of the metal picrates from water to dichloromethane and proton NMR titrations. Density functional theory calculations were also performed to determine the binding energy of the complexes formed and to analyse the host–guest interaction modes. In the cases of ligands 1b and 2c with Na⁺ and Ag⁺ picrates, the extraction energy was also determined using the polarisable continuum model. The results are discussed in terms of the nature of the amide residue and the substitution pattern (1,3 vs. 1,2). Both tetra-amide derivatives are good extractants, showing preference for Na⁺, Ca²⁺, Ag⁺ and Pb²⁺ cations, mainly di-ethylamide 1a. Concerning di-amide derivatives, the relative position of the substituents seems to be more important than the nature of the amide group in the extraction process. Proton NMR studies indicate the formation of 1:1 complexes between the amides and the cations studied, and DFT data show that all ligands form the most stable complexes with La³⁺.     

Directed H-bonding inhibition in molecular recognition: an NMR case study of the H-bonding of a dicarboxylic acid with a new mixed diamide receptor having one adjacent pyridine-N-oxide

The inhibition of hydrogen bond formation in the recognition of adipic acid by a new diamide receptor 1 having a pyridine-N-oxide and a simple pyridine ring adjacent to the amide moieties is observed. NMR studies show binding by the pyridine amide group in 1, which demonstrates the discrimination in hydrogen bonding between the carboxyls and an amide adjacent to pyridine versus another adjacent to the pyridine N-oxide. This specific inhibition of hydrogen bonding to a carboxyl group by the two different amides in 1 is corroborated by the NMR binding studies of 1 with propionic acid.     

Synthesis and Evaluation of a Cyclophane Receptor for Acetic Acid

A bicyclic cyclophane ( 2 ) containing one pyridine nitrogen and four amide N-H groups oriented toward the interior of the cavity was synthesized. The binding constants of various carboxylic acids with 2 were measured by UV/Vis spectroscopy. Acetic acid bound to 2 with a K a of 980 - 90 M m 1 in chloroform while branched carboxylic acids showed significantly lower binding. The data indicate that acetic acid was bound within the cavity of 2 . Only one acetic acid binds to two control hosts, whereas 2 shows definitive 1:1 binding. The results suggest that selectivity in the binding of carboxylic acids can be achieved via size constraints dictated by the receptor cavity, and that the same size restrictions lead to only one carboxylic acid bound to the cyclophane. The crystal structure of 2 is reported.     

Effect of a hydroxyl group in an anthracene-labelled pyridine amide receptor in molecular recognition of α-keto and hydroxy monocarboxylic acids

To ascertain the role of a hydroxyl group in carboxylic acid recognition, anthracene-labelled pyridine amide sensor 1 was designed and synthesized. The sensor functions as an ‘off–on’ fluorescence switch for α-keto and hydroxy acids. The binding properties were studied using ¹H NMR, fluorescence and UV–vis spectroscopic methods. Sensor 1 is selective for pyruvic acid.     

Enhanced Li+ binding energies of some azines: a molecular orbital study

Summary Hartree-Fock calculations with the 6–31G* basis have been performed to investigate the structure and Li⁺ binding energies of the complexes between Li⁺ and pyridine, diazines, triazines and tetrazines. Structures have been fully optimized at the 3–21G level. As for azole-Li⁺ and methyldiazole-Li⁺ complexes, a topological analysis of the Laplacian of the electronic charge density reveals that the azine-Li⁺ is a typical closed-shell interaction and that the stabilization of the complex is mainly electrostatic. BSSE is quite significant, specially for Li⁺-bridging complexes. The correlation between calculated Li⁺ binding energies and proton affinities follows two different linear relationships, one for those cases where Li⁺ is singly coordinated and a different one for those cases in which an additional three-membered ring is formed. The enhanced stability of these particular conformations explains why while polyazines are less basic than pyridine when the reference acid is a proton; pyridazine and 1,2,4 triazine are more basic than pyridine when the reference acid is Li⁺. The effect on Li⁺ binding energies of systematic nitrogen substitution roughly follows an additive model.     

Preparation of the thermotropic copoly(amide ester) of p‐aminobenzoic acid and m‐hydroxybenzoic acid with diphenyl chlorophosphate/pyridine

A thermotropic copoly(amide ester) exhibiting a nematic mesophase within the range of 240–360 °C was prepared by the solution copolycondensation of p‐aminobenzoic acid (40–70 mol %) and m‐hydroxybenzoic acid with diphenyl chlorophosphate in pyridine in the presence of LiCl. For control of the sequence distribution of p‐aminobenzoic acid, the amount of LiCl and the dropwise addition of the phosphate were examined. The transition temperatures (from a solid phase to a nematic mesophase) of the resultant copolymers were affected by the period of addition and the amounts of the aminobenzoic acid and LiCl and were investigated in terms of the distributions of the monomers determined by ¹H NMR. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1775–1780, 2002     

Spectroscopic,electrochemical and X-ray crystallographic properties of a novel palladium(II) complex of thioamide deprotonated di-2-pyridyl ketone thiosemicarbazone (dpktsc-H)−

The reaction between di-2-pyridyl ketone thiosemicarbazone (dpktsc) and PdCl₂(CH₃CN)₂, generated in situ from the reaction between PdCl₂ and CH₃CN, gave the unprecedented [Pd₂Cl₃(κ⁵-N_py,N_im,S,N_py,N_am-dpktsc-H)]·2CH₃CN (1) complex (py = pyridine, im = imine and am = amide). The identity of 1 was confirmed via its elemental analysis and spectroscopic properties. Infrared and ¹H-NMR spectra confirmed the coordination of (dpktsc-H)^? to the palladium ions. The electronic absorption spectra measured in dmso and dmf and density functional theory (DFT) calculations revealed metal-to-ligand charge-transfer (MLCT), d–d and intra-ligand charge-transfer (ILCT) electronic transitions. X-ray structural analysis on a crystal of [Pd₂Cl₃(κ⁵-N_py,N_im,S,N_py,N_am-dpktsc-H)]·H₂O (2) grown from dmf solution of 1 confirmed its formulation and showed the solid-state structure contains a web of molecules locked via a network of non-covalent interactions. Electrochemical measurements on 1 in dmf revealed metal- and ligand-based redox processes. In contrast to the electrochemical decomposition of uncoordinated dpktsc, coordinated (dpktsc-H)^? in 1 does not undergo electrochemical decomposition. Electrochemical titrations of 1 with p-toluenesulfonic acid monohydrate (p-TSOH) revealed electro-catalytic proton reduction. Over-potential (η) of 180 mV for the H₂ evolution was observed and is comparable to several molecular electro-catalysts for proton reduction. Controlled-potential electrolysis confirmed the electro-catalytic proton reduction by the Pd-complex. Electrochemical reactions of CO₂ in the presence of 1 exhibited a proton dependence, and metal- and ligand-based electrochemical reaction.     

Anion-directed self-assembly of a 2,6-bis(2-anilinoethynyl)pyridine bis(amide) scaffold

Bis(sulfonamide) receptors based on the 2,6-bis(2-anilinoethynyl)pyridine scaffold form persistent dimers with water and halides in solution and in the solid-state. The structurally related bis(amide) receptor derived from 3,5-dinitrobenzoyl chloride is a dimer in the solid-state with two HCl molecules directing the self-assembly. The 2+2 dimer, with a twisted ‘S’-shaped backbone, is held together by six hydrogen bonds. Dissolution of the (H2⁺√Cl ^? )₂ adduct in CHCl₃ results, however, in a monomeric structure. DOSY and ¹H NMR experiments were used to identify the dominance of monomer in solution for both 2 and H2⁺√Cl ^? . The ‘OFF–ON’ fluorescence response of 2,6-bis(2-anilinoethynyl)pyridine is retained with amide arms.     

Recognition of a dicarboxylic acid with dipicolyl urea in solution and in solid phases: intramolecular hydrogen bond inhibiting both pyridine nitrogens from binding carboxyl groups

Recognition of a dicarboxylic acid in solution as well as in the solid phase by the pyridyl urea based pseudoditopic receptor 1 has been studied. The X-ray structures of both the receptor and its complex with 1,4-phenylenediacetic acid are also presented. Intramolecular hydrogen bonding inhibits both the pyridine ring nitrogens from forming hydrogen bonds with the carboxyl group and force the receptor to behave in a monotopic manner, using the syn urea amide moiety to bind carboxyl group of a dicarboxylic acid to form a 2:1 complex. Binding of receptor 1 with a monocarboxylic acid is also compared.     

水溶性氧杂酰胺类化合物的合成及表征

以二甘醇为原料, 经氧化得到的二甘酸, 通过氯代或缩合反应得到中间体酰氯和酸酐, 二烷基胺在吡啶催化下与酰氯或酸酐发生胺解反应, 合成出系列水溶性氧杂单酰胺及氧杂双酰胺, 包括N,N-二烷基-3-氧杂-戊酰胺酸系列和N,N,N'N'-四烷基-3-氧杂-戊二酰胺系列(烷基包括甲基、乙基和丙基). 用IR和¹H NMR对合成的目标产物进行了表征.     

Synthesis of vitamin b6 derivatives. II. 3-Hydroxy-4-hydroxymethyl-2-methyl-5-pyridine acetic acid and related substances

The syntheses of 3-hydroxy-4-hydroxymethyl-2-methyl-5-pyridineacetic and -5-pyridine-propionic acids and several related compounds are described. Although acid hydrolysis of α⁴,3-O-isopropylidene-5-pyridoxic acid gives 5-pyridoxic acid lactone (α-pyracin), its higher homolog α⁴,3-O-isopropylidene-pyridoxylformic acid gave a corresponding free alcohol whose carboxylic acid proton was shown to be exchanged rapidly with the 3-phenolic and -4-alcoholic - protons in nuclear magnetic resonance studies. Inter-molecular hydrogen bonding between the side chain carboxylic acid and pyridine nitrogen atoms is suggested in the solid state.     

Synthesis and carboxylate anion binding studies on cyclic sugar-amino acid hybrids

Abstract

Here in, the condensation of boc-glycine with 2,6-anhydro-3,4,5-tri-O-benzyl-D-gluco-heptitol followed by its boc-deprotection to form 2,6-anhydro-3,4,5-tri-O-benzyl-D-gluco-heptitolyl bis-glycinate, which in turn on condensation with succinic acid/pyridine-2,6-dicarboxylic acid led to the formation of sugar-amino acid hybrid macrocyclic compounds 4, 6 and debenzylated marocyclic compound 5, having amide bonds that function as efficient host for polar, hydrogen bond acceptors and carboxylate ions. The anion inclusion capability of synthesized macrocylic hosts has been evaluated by the study of their binding with boc-GlyCOOˉ anion as guest through 1H NMR titration studies in CDCl₃. The binding constant (K_a) of boc-GlyCOOˉ guest with macrocyclic hosts 4 and 6 involving succinate and pyridine-2,6-dicarboxylate linkers was found to be 9.201?×?10³ and 1.437?×?10⁴ M^?1, respectively. The higher binding constant was observed in the complex of boc-GlyCOOˉ with pyridine-dicarboxylate containing host may be due to the extra rigidity & suitable conformation attained by the presence of rigid-aromatic dicarboxylate linker.     

Molecular recognition properties of acyclic cucurbiturils toward amino acids,peptides, and a protein

The binding of 1 and 2 toward 19 amino acid amides by ¹H NMR and ITC is reported. Hosts 1 and 2 bind to aromatic or hydrophobic residues by cavity inclusion leaving the cationic residues at the C=O portals. K_a values range from 10² to >10⁶ M^?1 with H-Phe-NH₂, H-Trp-NH₂, and H-Tyr-NH₂ displaying sub-micromolar K_d values. Hosts 1 and 2 bind tightly to dicationic H-Lys-NH₂ and H-Arg-NH₂ which are poor guests for CB[7]. Comparison of the affinity of 1 and 2 toward the amino acid amide, N-acetyl-amino-acid amide, and amino acid forms of Phe revealed that the removal of the NH₃⁺ to O=C and SO₃^? electrostatic interactions costs 3.8 kcal/mol whereas the introduction of an unfavourable CO₂^? to O=C and SO₃^? electrostatic interactions costs 2.1 kcal/mol. Hosts 1 and 2 bind to insulin with low micromolar affinity. Acyclic CB[n] display high affinity toward a wider range of N-terminal amino acids residues than CB[n] which suggests a broad range of applications.     

Macrocyclic anthracene-anchored calix[4]arene as a sensitive and selective fluorescent chemosensor for ytterbium ions

ABSTRACT

A novel anthracene anchored cone calix[4]arene pyridine amide receptor C4PA was synthesized and characterized by combination of spectroscopic and spectrophotometric techniques. Ion binding properties of C4PA towards a series of metal cations were investigated by UV and fluorescence spectra. A remarkable increase for receptor C4PA in fluorescence intensity in the presence of trace amounts of Yb³⁺ was observed. C4PA showed “turn on” type fluorescence response toward Yb³⁺ with high selectivity and C4PA also retained its selectivity toward Yb³⁺ in the presence of most competing metal ions.     

Synthesis and crystallographic analysis of short pyridine-based oligoamides as DNA-targeting supramolecular binders

In this study, the synthesis of the pyridine peptides 1–4, formed from amino-picolinic acid, and pyridine peptide 5, made from coupling of a mono-protected pyridine diamine to a mono-protected pyridine dicarboxylic acid and the X-ray crystallographic structures of 1 and 5 are discussed, along with their supramolecular interactions in the solid state. The structure of these compounds showed that they possess concave appearance which can be employed to bind to nucleic acids through multiple hydrogen bonding, which would facilitate the formation of helical-based pyridine oligoamides as novel DNA-binding molecules. This was proven by carrying out DNA denaturation studies and ethidium displacement assay on 5, but, by using MTT assays, 5 was shown to be cytotoxic against drug-resistant chronic myeloid leukaemia K562 cell-line.

     

Complexation of a Macrocycle Containing Thiopyrimidine and Uracil Moieties with Dicarboxylic and Amino Acids in Various Organic and Aqueous Organic Solutions

The complexation of a macrocycle containing thiopyrimidine and uracil moieties (M) with amino acids and some dicarboxylic acids was studied by pH-metric, UV-VIS, ¹H NMR spectroscopy methods in chloroform, methanol, aqueous 1,4-dioxane, and biphasic water–chloroform media. The complexation of M with acids is too weak to solubilize them from the solid state into chloroform solutions containing M. The ¹H NMR spectra and pH-metric data of aqueous 1,4-dioxane (80 vol.%) reveal the pH-dependent 1:1 binding between M and the acids studied. The protonation of M is not a prerequisite for binding of fumaric, succinic, o-phtalic acids and the series of amino acids, whereas binding of maleic acid requires the protonation of both thiopyrimidine moieties of M. Therefore,M·(H⁺)₂ exhibits strong selectivity towards maleic acid in aqueous 1,4-dioxane and in biphasic water–chloroform media.     

The synthesis of diene and vinyl copolymers containing predetermined quantities of polynuclear hydrocarbon or heterocyclic adducts—VII: Copolymers formed from butadiene,a heterocyclic compound and some linking or terminating agents

The reaction of butadiene (M) and a suitable heterocyclic molecule (A) (acridine, quinoline or puridine) with lithium metal in tetrahydrofuran (THF) produced polymeric adducts of structure ^?A—M_n—A^? where the negative charges are located on the nitrogen atoms. Similar products (mono or difunctional) may be produced by reacting living polybutadiene directly with these heterocyclic molecules. In the case of acridine, proton termination produced oligomers terminated with dihydroacridine groups; polymeric species containing amide linkages can be produced by titration with adipoyl chloride and, although this reaction is in itself efficient, the product easily re-aromatizes. With quinoline and pyridine, the dihydroadducts become progressively less stable, showing strong tendencies to re-aromatise and crosslink. It is shown that the anionic pyridine adduct of polybutadiene may be cleanly re-aromatised to produce pyridine-terminated polymers which are stable. These pyridine groups can be reacted with benzyl halides to produce pyridinium salts; the presence of these ionic groups has a profound effect on the physical properties of the product. Reaction with p-xylylene dibromide converts low molecular weight difunctional pyridine-terminated polybutadiene from a mobile liquid to a rubbery solid; the material remains soluble and so is free from chemical crosslinks.     

Derivatization of 4‐(Dimethylamino)benzamide to Dual Fluorescent Ionophores: Divergent Spectroscopic Effects Dependent on N or O Amide Chelation

Starting from the pentafluorophenyl ester of 4‐(dimethylamino)benzoic acid, two dual fluorescent amide ligands with aza‐15‐crown‐5 and 2‐(aminomethyl)pyridine were obtained for sensing, respectively, alkali (alkaline‐earth) and transition (heavy) metal cations. The crystal structure of the copper(II) complex is reported. The Cu²⁺ is coordinated through the pyridine N‐ and amide O‐atoms of two symmetry‐related ligands. The azacrown‐directed Ca‐chelation to the N‐atom of the amide leads to a slight quenching of the two fluorescence bands. In contrast, the pyridine directed Cu^II‐chelation to the O‐atom of the amide enhances the short‐wavelength emission 17‐fold over the locally excited state (LE), quenching the twisted intramolecular charge‐transfer (TICT) emission, and, as a result, the intensity ratio I(LE)/I(TICT) provides an accurate and sensitive measurement of the Cu^II concentration. These different cation effects are dependent on which atom (N vs. O) of the amide function participates in cation coordination: while the Ca²⁺ interaction with the N‐atom electron pair leads to the deconjugation of the amide N‐atom from the fluorophore, Cu²⁺ interaction with the lone pair of the O‐atom of the carbonyl group increases the energy of the n‐π* but also of the ¹L_a transition and therefore close the channel to the TICT state.     

Potentially biologically active new substituted anilides of benzo[2,3-<Emphasis Type="Italic">b</Emphasis>]thiophene series

New substituted anilides of the heterocyclic series 2, 4, 5, 6, 7 together with the earlier described compounds 1 and 3 (Jarak I et al. (2005) J Med Chem 48:2346), were synthesized from the corresponding heterocyclic carbonyl chlorides, methoxycarbonyl- and cyano-substituted anilines. Compounds 2 and 7 were prepared by methylation with methyl-iodide on the amide and the pyridine nitrogen. The Pinner reaction was used in the preparations of amidino-substituted compounds. It seems that all the prepared compounds could be biologically interesting, especially amidino-substituted anilides prepared in the form of water-soluble hydrochlorides or hydroiodides. Molecular and crystal structures of the three compounds, namely, 4′-methoxycarbonyl-N-phenyl-3-chlorobenzo[b]thiophene-2-carboxamide (1), N-(4′-amidinophenyl)-3-chlorobenzo[b]thiophene-2-carboxamide hydrochloride monohydrate (4) and 1-methyl-N-(4-amidinophenyl)-3-pyridine carboxamide iodide hydroiodide (7) have been determined by X-ray single-crystal diffractometry in the solid state. Compounds 1, 4 and 7 are not planar and the amide group (C=O in relation to NH group) is in trans position in all three compounds. The 3-chlorobenzo[b]thiophene moiety in 1 and 4 is oriented with the chloro substituent in cis position in relation to amide NH group. The conformational characteristics of the compounds result from the introduction of different substituents or solvent molecules (water molecule in 4), which leads to various intermolecular hydrogen bonds formation (N–H⋯O, N–H⋯Cl, O–H⋯Cl⁻, N–H⋯I⁻) in 1, 4 and 7. Hydrogen bond formation could be responsible for the potential biological activity of the compounds.