Solid state and solution structures of alkaline-earth complexes with lariat ethers containing aniline and benzimidazole pendants

Herein we report the synthesis and structural characterization of Mg(II), Ca(II), Sr(II) and Ba(II) complexes with bibracchial lariat ethers derived from 1,7-diaza-15-crown-5 and 1,7-diaza-12-crown-4 containing aniline or benzimidazole pendant arms. The solid state structures of most of them have been determined by using single crystal X-ray crystallography. A coordination number of seven was observed for the Mg(II) complexes in the solid state, while the Ca(II), Sr(II) and Ba(II) complexes are 8-, 9- and 11-coordinate, respectively. The Ca(II), Sr(II) and Ba(II) complexes show a syn conformation, with the two pendant arms of the ligand disposed on the same side of the macrocyclic mean plane. However, the Mg(II) complex with the largest ligand derived from 1,7-diaza-15-crown-5 containing benzimidazole pendants presents an anti conformation in the solid state. ¹H and ¹³C NMR spectroscopy reveal that this conformation is maintained in acetonitrile solution.     

Chiral benzimidazole-derived mono azacrowns: synthesis and enantiomer recognition studies with chiral amines and their ammonium salts

Benzimidazole fused chiral mono aza-15-crown-5 2, was obtained in a single step from (S)-(?)-2-(α-hydroxyethyl) benzimidazole 1. This new class of aza-crown has a unique structure with the chiral unit being held in a stable conformation due to adjacent benzimidazole ring contributing to its stereodiscrimination ability. The interactions between the host aza-crown and enantiomerically pure amine guests in ionic and neutral forms exhibited the enantio-discrimination ability. The preliminary evaluation of the chiral sensing was monitored using ¹H NMR and circular dichroism (CD) analysis of the complexes at their molar equivalence. The binding parameters were determined using electronic absorption spectroscopy.     

First synthesis of 2′-oxabicyclo[3.1.0]hexyl nucleosides with a north conformation

The first synthesis of 2′-oxabicyclo[3.1.0]hexyl nucleosides, a novel class of bicyclonucleosides, with a north conformation was successfully accomplished starting from (S)-epichlorohydrin via a tandem alkylation-lactonization, a less steric hindrance-dependent silylation in equilibrium and a coupling reaction with nucleobases under Vorbruggen conditions. Addition of acetic acid prevented a benzoyl group from migrating during desilylation with TBAF. ¹H NMR and X-ray crystallographic analysis indicated that the anomeric effect worked on the β-2′-oxabicyclo[3.1.0]hexyl nucleosides.     

Synthesis and NMR characterization of a novel crown-ether ring-fused uridine analogue

The chemical synthesis and ¹H NMR analysis of a novel bicyclic uridine derivative, with a 18-crown-6 ether moiety fused at the ribose 2- and 3-positions, as first example of a hitherto unknown class of ribose-modified nucleosides, are here described. NMR-based conformational analysis studies showed for the modified nucleoside a marked preference for an N-type sugar puckering and the nucleobase in the anti conformation, with the uracil favouring the coordination of a sodium ion hosted in the crown ether.     

Heterocyclic N-glycosyl derivatives—XIX : Glycal nucleosides. their relationship with 2',3'-unsaturated nucleosides and their utilization in the synthesis of 1',3'-two base nucleosides

The acid catalized reaction of tri-0-acetyl-D-glucal with benzotriazole or 6-methylthiopurine in acetonitrile gave a mixture of 1',2'- and 2',3'-unsaturated nucleosides, the former predominating. The relationship between these unsaturated nucleosides is studied and an allylic carbonium ion is proposed as an intermediate for these isomerizations. The acid catalized reaction of 1',2'-unsaturated nucleosides with more benzotriazole or 6-methylthiopurine gave 1',3'-two base nucleosides. The conformation and anomeric configuration of the N-glycosyl compounds obtained were assigned by NMR spectroscopy.     

Triazolyl C-nucleosides via the intermediacy of β-1′-ethynyl-2′-deoxyribose derived from a Nicholas reaction: Synthesis,photophysical properties and interaction with BSA

We report the design and synthesis of triazolyl donor/acceptor unnatural C-nucleosides via alkyne (sugar)—azide (aromatic) 1, 3-dipolar cyclo-addition reaction as a key step and studies on their photophysical properties. We have chosen β-1′-ethynyl-2′-deoxyribose as a precursor to synthesize triazolyl-C-nucleosides. Overcoming the difficulties, we obtain β-1′-ethynyl-2′-deoxyribose as a major product following a Co₂(CO)₈ catalyzed intramolecular Nicholas reaction. The 1,3-diaxial interaction is the driving force for the α to β-anomeric conversion while performing cobalt complexation followed by oxidation to afford β-1′- ethynyl-2′-deoxyribose as the major product. A Cu(I)-catalyzed click reaction between different aromatic donor/acceptor azides and β-1′- ethynyl-2′-deoxyribose generates the desired unnatural triazolyl donor-acceptor aromatic C-nucleosides (^cTB_Do/Ac) within 30 min. Single crystal X-ray structure shows the puckered conformation of sugar as C3′-exo. Studies on the photophysical properties suggests good fluorophoric as well as solvatochromic characteristics of these nucleosides. Two of the synthesised nucleosides, ^cTAnthB_Do and ^cTPyB_Do, are found to interact with BSA as the only tested protein with quenching of fluorescence signal. The designed bases, thus, might find applications in stabilizing a DNA and in the biophysical study thereof, if a pair of such donor acceptor C-nucleosides could be incorporated into a DNA sequence.     

Conformation of substituted benzylidene and isopropylidene nucleosides

PMR and CD spectroscopy has been used to show that the phenyl grouping at C²″ of the dioxolane ring in each diastereomeric benzylidene nucleoside occupies the axial position, most probably due to electrostatic interaction with the heterocyclic base residue. The conformation of the ribose moiety of benzylidene nucleosides is somewhat different from that of isopropylidene analogues; the C_s-conformation of ribose is characteristic of trans-bezylidene uridines and of isopropylidene uridine and adenosine.     

Synthesis, structural and crystallographic study of some carbamates derived from 9-methyl-9-azabicyclo[3.3.1]nonan-3α-ol

A series of benzimidazole, thiazole and benzothiazole carbamates derived from 9-methyl-9-azabicyclo[3.3.1]nonan-3α-ol was synthesized and studied by ¹H, ¹³C, 2D NMR and IR spectroscopy. To assist in the interpretation of the spectroscopic data, the crystal structure of 3 (9-methyl-9-azabicyclo[3.3.1]nonan-3α-yl 2-amino-1H-benzimidazole-1-carboxilate) was determined by X-ray diffraction. It has been found that 1-carbamates and 2-carbamates can be obtained in the case of the benzimidazole derivatives. The benzimidazole-1-carbamates are obtained in higher yields (41, 38%) than the benzimidazole-2-carbamates (3, 9%). The compounds studied displayed in CDCl₃ solution a preferred chair–boat conformation with the substituted ring in a distorted boat form and the N–CH₃ substituent in an axial position with respect to the chair piperidine ring. This conformation is similar to that determined by X-Ray diffraction for compound 3.     

Synthesis and biological activity of fluorinated 2-amino-4-aryl-3,4-dihydro[1,3,5]triazino[1,2-a]benzimidazoles

The heterocyclic nucleus s-triazino[1,2-a]benzimidazole has been reported to exhibit antibacterial activity. In this study, seven new 3,4-dihydro[1,3,5]triazino[1,2-a]benzimidazole derivatives were prepared via cyclocondensation between 2-guanidinobenzimidazole and fluorine substituted (including trifluoromethyl) benzaldehydes. The structures of all the compounds were confirmed by ¹H, ¹³C NMR and IR spectral data. Spectral data also suggested the existence of various tautomeric forms of the fluorine-containing s-triazino[1,2-a]benzimidazole compounds. The synthesized compounds were also screened for antibacterial and bovine dihydrofolate reductase (DHFR) inhibitory activities. The compound 3g substituted with a 3′,5′-bis(trifluoromethyl)phenyl moiety demonstrated the best antibacterial activity in the series. None of the tested compounds significantly inhibited bovine DHFR.     

The High-Anti Conformation of 7-Halogenated 8-Aza-7-deaza-2′-deoxy-guanosines: A Study of the Influence of Modified Bases on the Sugar Structure of Nucleosides

The conformation of the 7-bromo- and 7-iodo-substituted 8-aza-7-deazapurine nucleosides 1 and 2 in the solid state and in aqueous solution was studied by single-crystal X-ray analyses and by ¹H-NMR spectroscopy. In the solid state, both compounds display a high-anti conformation around the glycosylic bond, and their 2′-deoxy-β-D -ribofuranose moieties adopt an N-type sugar puckering. The orientation of the exocyclic C(4′)−C(5′) bond was found to be ap in both cases. In D₂O solution, both compounds display i) an 8 – 10% higher N-conformer population than 2′-deoxyguanosine and ii) a preference of the −sc conformation about the C(4′)−C(5′) bond. A comparative study on the influence of modified bases on the sugar structure of nucleosides is made.     

Anion dependent molecular recognition of cations

In DMF-d₇ tetrabenzimidazole cavitands 2 exist as monomeric species and vase-like conformers. Several possible arrangements of the four benzimidazole NHs are indicated by ¹H NMR spectroscopy. The cavitands form 1:1 inclusion complexes with tetraethyl ammonium and phosphonium cations only when strong hydrogen bonding anions like chloride or acetate are present. These complexes are stable on the NMR time scale at 295 K feature a C_2V-symmetrical arrangement of benzimidazole functions. The stability of the C_2V-symmetrical tetramethylammonium acetate complex is independent of the temperature. In contrast, tetramethylammonium and phosphonium chloride complexes exist at 233 K as several isomers. This complicated behavior is, in part, attributed to the hydrogen bonding interactions between the anions and the NH groups of benzimidazole functions.     

Synthesis and properties of conformationally locked 1,3-bisalkyl-7-deazaxanthine 2′-deoxy-d-ribofuranosides

1,3-Dimethyl-7-deazaxanthine 2′-deoxyribofuranosides 1a and 6a and their N-3 isopropyl congeners 1b and 6b have been prepared employing the nucleobase anions 7a or 7b and 2-deoxy-3,5-di-O-(p-toluoyl)-α-D-erythropentofuranosyl chloride ( 8 ) upon glycosylation. The reaction was not stereoselective as found in case of other pyrrolo[2,3-d]pyrimidine nucleosides induced by the bulky N-3 substituent. Configuration of anomers was established by ¹H-nmr nOe difference spectroscopy. Those data also indicated that the conformation around the N-glycosylic bond was locked by the bulky N-3 substituent. Contrary to the purine nucleoside such as wyosine ( 2a ) the hydrolytic stability of the N-glycosylic bond of the pyrrolo[2,3-d]pyrimidine nucleosides was increased by N-3 alkylation. Moreover, it was shown by ¹⁵N-nmr spectroscopy that different to purine nucleosides the aglycon was not protonated in acidic medium. As a result the N-glycosylic bond hydrolysis did not follow an A-1 but an A-2 mechanism.     

Synthesis, structure, and biological evaluation of C-2 sulfonamido pyrimidine nucleosides

The C-2 sulfonamido pyrimidine nucleosides were prepared by opening the 2,2′- or 2,3′-bond in anhydronucleosides under nucleophilic attack of sulfonamide anions. Reaction of the sodium salt of p-toluenesulfonamide or 2-(aminosulfonyl)-N,N-dimethylnicotinamide with 2,2′-anhydro-1-(β-d-arabinofuranosyl)cytosine gave the C-2 sulfonamido derivatives in excellent yields. Ring opening of the less reactive 2,2′-anhydrouridine and 2,3′-anhydrothymidine could be accomplished with DBU/CH₃CN activation of p-toluenesulfonamide, giving moderate yields for C-2 sulfonamido derivatives. The action of acetic acid or ZnBr₂/CH₂Cl₂ on 5-methyl-N²-tosyl-1-(2-deoxy-5-O-trityl-β-d-threo-pentofuranosyl)isocytosine led to the cleavage of both the protection group and the nucleoside bond, yielding 5-methyl-N²-tosylisocytosine as the major product. Structures of the prepared C-2 sulfonamido nucleosides were confirmed by the 1D and 2D NMR experiments, and X-ray structural analysis of 4-imino-N²-tosylamino-1-(β-d-arabinofuranosyl)pyrimidine. Both methods confirmed β-configuration and anti-conformation of the 2-sulfonamido nucleosides. The investigated compounds displayed moderate inhibition of tumor cell growth in vitro, as determined by the MTT assay using six different human tumor cell lines.     

New nucleoside analogues and their 5′-triphosphates: Synthesis and biological properties

Bicyclic furano-and pyrrolo[2,3-d]pyrimidine nucleosides and purine nucleosides modified at the N¹ atom and/or the 6-position have been synthesized. Among the tested nontoxic bicyclic nucleosides and N⁶-carboxyalkyladenosines, only furo[2,3-d]pyrimidine with the C₁₀H₂₁ substituent and N⁶-carboxymethyladenosine exhibit moderate anti-HCV activity in the virus replicon system and N¹-hydroxyinosine exhibits high anti-HCV activity and significant cytotoxicity. The corresponding 5′-triphosphates have been synthesized and studied as substrates/inhibitors of HCV enzymes: NS5B protein (RNA-dependent RNA polymerase) and NS3 protein (NTP-dependent RNA helicase).     

Characterization by FTIR spectroscopy of the oligoribonucleotide duplexes r(A-U)6 and r(A-U)8

Fourier transform infrared spectroscopy has been used to characterize the helical conformation of double stranded oligoribonucleotides r(A-U)₆ and r(A-U)₈ in solution. As expected the oligoribonucleotides are found to adopt in solution an A family type conformation. The simultaneous study of a series of duplexes containing A, T or U bases combined either with riboses or deoxyriboses allows us to propose a set of infrared marker bands allowing to distinguish between C2′ endo/anti and C3′ endo/anti conformers of dA, dT, rA and rU nucleosides in nucleic acids.     

Kinetics and mechanism of the defluorination of 8-fluoropurine nucleosides in basic and acidic media

For investigating the stability of C(8)-fluorine bond in 8-fluoropurine nucleosides some protected 8-fluoroguanosine, 8-fluoroinosine and 8-fluoroadenosine derivatives were prepared by direct fluorination of acetyl-protected purine nucleosides with elemental fluorine in solvents such as chloroform, acetonitrile and nitromethane. Fluorination reactions conducted in chloroform medium gave better yields of 8-fluoropurines. The fluorination yields were slightly lower when acetonitrile or nitromethane was used as solvent, but the product purification was found to be much easier. When the synthesized, protected fluoronucleosides were subjected to standard basic (NH₃ in methanol or 2-propanol) and acidic (HCl in methanol) deprotection conditions relevant to nucleoside chemistry, an efficient defluorination reaction took place. The kinetics of these defluorination reactions were conveniently followed, under pseudo-first-order reaction conditions, using ¹⁹F NMR spectroscopy. ¹H NMR, LC-MS and mass spectroscopy identified the products of the kinetic reaction mixtures. The defluorination reaction rate constants (k_obs) in basic media depended upon the electron density at C(8) while the k_obs data in acidic medium were determined by the pK_a of N⁷. An addition-elimination based mechanism (S_NAr) has been proposed for the defluorination reactions of these 8-fluoropurine nucleosides.     

Spectroscopic characterization, crystal structure determination and interaction with DNA of novel cyano substituted benzimidazole derivative

Novel cyano-substituted benzimidazole derivatives 3 and 4 were synthesized from 4-N,N-dimethylamino-benzaldehyde and 2-cyanomethyl-benzimidazole. 2-(1H-benzimidazol-2-yl)-3-(4-N,N-dimethylamino-phenyl)-acrylonitrile hydrochloride monohydrate 4 has been studied by ¹H and ¹³C NMR, IR, MS, UV/Vis and fluorescence spectroscopy and confirmed by X-ray crystal structure analysis. The interaction of 4 with ct-DNA has also been investigated by fluorescence spectroscopy and melting temperature determination experiment. According to the emission spectra recorded in the absence and presence of ct-DNA at different ratios r ([compound]/[polynucleotide]), 4 showed marked decrease in the fluorescence intensity and very strong hypochromic effect. Melting temperature experiment showed weak stabilization of double helix. To determine binding mode of 4, other additional experiments are necessary. The molecules of 4 are almost planar with the dihedral angle between benzimidazole and phenyl rings of 6.99(6)°. The protonation of nitrogen atom of benzimidazole ring is followed by π-electrons delocalization in the region resulting in C–N bond distances equality [1.341(2) and 1.337(2) Å]. Both NH groups of benzimidazole ring form intermolecular hydrogen bonds, one with the oxygen atom of water molecule [N···O 2.689(2) Å] and the other with Cl^? ion (N···Cl^? 3.051(1) Å). Except proton acceptor, water molecule acts as double proton donor in the formation of intermolecular hydrogen bonds with Cl^? ion [O···Cl^? 3.126(2) and 3.169(2) Å]. In that way, infinite chains along [110] direction are formed.     

Synthesis and characterization of bidentate NHC-Pd complexes and their role in amination reactions

The new well-defined and air-stable ortho-xylyl-linked N-heterocyclic carbene (NHC) Pd complexes (2a-d) have been synthesized and characterized by elemental analysis, ¹H NMR, ¹³C NMR, IR spectroscopy, and single crystal X-ray diffraction studies. The palladium atom in the complex 2a lies on a crystallographic mirror plane and can be described as having a square-planar coordination environment with the carbene atoms of the benzimidazole rings of the ligand occupying two coordination sites in cis positions. Two further coordination sites are occupied by chloride ligands. The benzimidazole rings are connected to each other by an ortho-xylyl bridge. The catalytic activity of these palladium complexes has been tested in the coupling reactions of various N-containing substrates with bromobenzene. A preliminary catalytic study shows that the bis(NHC)-Pd complexes are highly active in the Buchwald-Hartwig amination reaction.     

Polarity and structure of 2-(1-methylbenzimidazol-2-yl)-1-phenyl- and -1,2-diphenyl-1-nitroethenes

Polarity of 2-(1-methylbenzimidazol-2-yl)-1-phenyl- and -1,2-diphenyl-1-nitroethenes was determined and their structure was studied using electronic and ¹H, ¹³C NMR spectroscopy, dipole moments measuring, XRD analysis, and quantum-chemical calculations. It was shown that the 2-(1-methylbenzimidazol-2-yl)-1-nitro-1-phenylethene has Z-configuration both in crystal and solution. The nitro group and benzimidazole substituent in its molecule are removed from the plane of the double bond. For 1,2-diphenyl-1-nitroethene E-structure is typical.     

A novel entry to 2′-O-aminopropyl modified nucleosides amenable for further modifications

2′-O-aminopropyl modified 4,6-difluoro-substituted benzimidazole nucleosides were synthesized in a two-step synthesis via Michael reaction and a Raney-nickel catalyzed reduction in high yields. These building blocks were used as a starting point for the conjugation of different carboxylic acids to enhance the lipophilicity or cationic character of oligonucleotides when used in biological assays or medical applications.