Biphenyl‐ and phenylnaphthalenyl‐substituted 1H‐imidazole‐4,5‐dicarbonitrile catalysts for the coupling reaction of nucleoside methyl phosphonamidites

Crystal structures are reported for three substituted 1H‐imidazole‐4,5‐dicarbonitrile compounds used as catalysts for the coupling reaction of nucleoside methyl phosphonamidites, namely 2‐(3′,5′‐dimethylbiphenyl‐2‐yl)‐1H‐imidazole‐4,5‐dicarbonitrile, C₁₉H₁₄N₄, (I), 2‐(2′,4′,6′‐trimethylbiphenyl‐2‐yl)‐1H‐imidazole‐4,5‐dicarbonitrile, C₂₀H₁₆N₄, (II), and 2‐[8‐(3,5‐dimethylphenyl)naphthalen‐1‐yl]‐1H‐imidazole‐4,5‐dicarbonitrile, C₂₃H₁₆N₄, (III). The asymmetric unit of (I) contains two independent molecules with similar conformations. There is steric repulsion between the imidazole group and the terminal phenyl group in all three compounds, resulting in the nonplanarity of the molecules. The naphthalene group of (III) shows significant deviation from planarity. The C—N bond lengths in the imidazole rings range from 1.325 (2) to 1.377 (2) Å. The molecules are connected into zigzag chains by intermolecular N—H...N_imidazole [for (I)] or N—H...·N_cyano [for (II) and (III)] hydrogen bonds.     

Two 1-substituted 4-nitro­imidazoles

Crystalline 4-nitro-1-phenyl­imidazole, C₉H₇N₃O₂, (I), and 4′-­nitro-1-phenyl-4,1′-bii­imidazole, C₁₂H₉N₅O₂, (II), contain C—H⃛O and C—H⃛N hydrogen bonds, connecting the mol­ecules into infinite chains. The aromatic fragments in both compounds are nearly planar. The dihedral angles between the benzene and imidazole rings are 26.78 (5)° in (I) and 29.36 (8)° in (II).     

{μ‐N,N′‐Bis[3‐(dimethyl­amino)prop­yl]­oxamidato(2–)‐κ6N,N′,O′:N′′,N′′′,O}­bis­[(1H‐imidazole‐κN3)(methanol‐κO)copper(II)] bis­(perchlorate)

The structure of the title compound, [Cu₂(C₁₂H₂₄N₄O₂)(C₃H₄N₂)₂(CH₄O)₂](ClO₄)₂ or [Cu₂(dmoxpn)(HIm)₂(CH₃OH)₂](ClO₄)₂, where dmoxpn is the dianion of N,N′‐bis­[3‐(dimethyl­amino)prop­yl]oxamide and HIm is imidazole, consists of a centrosymmetric trans‐oxamidate‐bridged copper(II) binuclear cation, having an inversion centre at the mid‐point of the central C—C bond, and two perchlorate anions. The Cu^II atom has square‐pyramidal coordination geometry involving two N atoms and an O atom from the dmoxpn ligand, an N atom from an imidazole ring, and an O atom from a methanol mol­ecule. The crystal structure is stabilized by O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds and imidazole π–π stacking inter­actions to form a three‐dimensional supra­molecular array.     

mer‐Diaquabis(1H‐imidazole‐κN3)[orotato(2–)]cobalt(II)

In the title complex, mer‐diaqua[2,6‐dioxo‐1,2,3,6‐tetrahydropyrimidine‐4‐carboxylato(2−)]bis(1H‐imidazole‐κN³)cobalt(II), [Co(C₅H₂N₂O₄)(C₃H₄N₂)₂(H₂O)₂], the Co^II ion is coordinated by a deprotonated N atom and the carboxylate O atom of the orotate ligand, two imidazole N atoms and two aqua ligands in a distorted octahedral geometry. The title complex exists as discrete doubly hydrogen‐bonded dimers, and a three‐dimensional network of O—H...O and N—H...O hydrogen bonds and weak π–π interactions is responsible for crystal stabilization.     

Structural comparisons between methylated and unmethylated nitrophenyl lophines

The lophine derivative 2‐(2‐nitrophenyl)‐4,5‐diphenyl‐1H‐imidazole, C₂₁H₁₅N₃O₂, (I), crystallized from ethanol as a solvent‐free crystal and from acetonitrile as the monosolvate, C₂₁H₁₅N₃O₂·C₂H₃N, (II). Crystallization of 2‐(4‐nitrophenyl)‐4,5‐diphenyl‐1H‐imidazole from methanol yielded the methanol monosolvate, C₂₁H₁₅N₃O₂·CH₄O, (III). Three lophine derivatives of methylated imidazole, namely, 1‐methyl‐2‐(2‐nitrophenyl)‐4,5‐diphenyl‐1H‐imidazole methanol solvate, C₂₂H₁₇N₃O₂·CH₄O, (IV), 1‐methyl‐2‐(3‐nitrophenyl)‐4,5‐diphenyl‐1H‐imidazole, C₂₂H₁₇N₃O₂, (V), and 1‐methyl‐2‐(4‐nitrophenyl)‐4,5‐diphenyl‐1H‐imidazole, C₂₂H₁₇N₃O₂, (VI), were recrystallized from methanol, acetonitrile and ethanol, respectively, but only (IV) produced a solvate. Compounds (III) and (IV) each crystallize with two independent molecules in the asymmetric unit. Five imidazole molecules in the six crystals differ in their molecular conformations by rotation of the aromatic rings with respect to the central imidazole ring. In the absence of a methyl group on the imidazole [compounds (I)–(III)], the rotation angles are not strongly affected by the position of the nitro group [44.8 (2) and 45.5 (1)° in (I) and (II), respectively, and 15.7 (2) and 31.5 (1)° in the two molecules of (III)]. However, the rotation angle is strongly affected by the presence of a methyl group on the imidazole [compounds (IV)–(VI)], and the position of the nitro group (ortho, meta or para) on a neighbouring benzene ring; values of the rotation angle range from 26.0 (1) [in (VI)] to 85.2 (1)° [in (IV)]. This group repulsion also affects the outer N—C—N bond angle. The packing of the molecules in (I), (II) and (III) is determined by hydrogen bonding. In (I) and (II), molecules form extended chains through N—H...N hydrogen bonds [with an N...N distance of 2.944 (5) Å in (I) and 2.920 (3) Å in (II)], while in (III) the chain is formed with a methanol solvent molecule as the mediator between two imidazole rings, with O...N distances of 2.788 (4)–2.819 (4) Å. In the absence of the imidazole N—H H‐atom donor, the packing of molecules (IV)–(VI) is determined by weaker intermolecular interactions. The methanol solvent molecule in (IV) is hydrogen bonded to imidazole [O...N = 2.823 (4) Å] but has no effect on the packing of molecules in the unit cell.     

Effect of the Nature of the Substituent in N‐Alkylimidazole Ligands on the Outcome of Deprotonation: Ring Opening versus the Formation of N‐Heterocyclic Carbene Complexes

Complexes [Re(CO)₃(N‐RIm)₃]OTf (N‐RIm=N‐alkylimidazole, OTf=trifluoromethanesulfonate; 1 a – d ) have been straightforwardly synthesised from [Re(OTf)(CO)₅] and the appropriate N‐alkylimidazole. The reaction of compounds 1 a – d with the strong base KN(SiMe₃)₂ led to deprotonation of a central C? H group of an imidazole ligand, thus affording very highly reactive derivatives. The latter can evolve through two different pathways, depending on the nature of the substituents of the imidazole ligands. Compound 1 a contains three N‐MeIm ligands, and its product 2 a features a C‐bound imidazol‐2‐yl ligand. When 2 a is treated with HOTf or MeOTf, rhenium N‐heterocyclic carbenes (NHCs) 3 a or 4 a are afforded as a result of the protonation or methylation, respectively, of the non‐coordinated N atom. The reaction of 2 a with [AuCl(PPh₃)] led to the heterobimetallic compound 5 , in which the N‐heterocyclic ligand is once again N‐bound to the Re atom and C‐coordinated to the gold fragment. For compounds 1 b – d , with at least one N‐arylimidazole ligand, deprotonation led to an unprecedented reactivity pattern: the carbanion generated by the deprotonation of the C2? H group of an imidazole ligand attacks a central C? H group of a neighbouring N‐RIm ligand, thus affording the product of C? C coupling and ring‐opening of the imidazole moiety that has been attacked ( 2 c , d ). The new complexes featured an amido‐type N atom that can be protonated or methylated, thus obtaining compounds 3 c , d or 4 c , d , respectively. The latter reaction forces a change in the disposition of the olefinic unit generated by the ring‐opening of the N‐RIm ligand from a cisoid to a transoid geometry. Theoretical calculations help to rationalise the experimental observation of ring‐opening (when at least one of the substituents of the imidazole ligands is an aryl group) or tautomerisation of the N‐heterocyclic ligand to afford the imidazol‐2‐yl product.     

5‐Methyl­sulfanyl‐3H‐1,2,3‐triazolo[4,5‐d]pyrimidin‐7(6H)‐one (2‐methyl­thio‐8‐aza­xanthine) monohydrate

The title compound, C₅H₅N₅OS·H₂O, crystallizes as the monohydrate. Disorder of the H atoms that participate in the hydrogen bonds implies that two different tautomers are present in the crystal structure, one of them with both acidic H atoms attached to the imidazole ring and the other with one acidic H atom on each ring.     

1,4‐Bis(2‐benzimidazolyl)­benzene

The title compound, C₂₀H₁₄N₄, lies about an inversion centre and the benz­imidazole moiety and the phenyl ring are twisted by 30.9 (1)°. The benz­imidazole moiety is completely planar, with a maximum deviation of 0.009 (2) Å. Intermolecular N—­H?N hydrogen bonds give rise to a layered structure, with the layers stacked by van der Waals interactions.     

Hexakis­(imidazole‐N3)­nickel(II) bis(4‐methoxy­benzoate)

In the title complex of [Ni(C₃H₄N₂)₆](C₈H₇O₃)₂, the Ni atom is in an octahedral environment formed by the tertiary N atom of the imidazole moieties. The methoxy­benzoate moieties act as a bridge connecting two hexakis­(imidazole)nickel(II) mol­ecules through N—H?O hydrogen bonds.     

4‐Phenyl‐1H‐imidazole (a low‐temperature redetermination), 1‐benzyl‐1H‐imidazole and 1‐mesityl‐1H‐imidazole

Low‐temperature studies of the simple variously substituted imidazole types 4‐phenyl‐1H‐imidazole, C₉H₈N₂, 1‐benzyl‐1H‐imidazole, C₁₀H₁₀N₂, and 1‐mesityl‐1H‐imidazole, C₁₂H₁₄N₂, extend comparisons between parent imidazole species and their derivatives, the pronounced double‐bond localization opposite the substituted N atom common to simple neutral species being redistributed aromatically on protonation.     

Reactivity studies of (η6-arene)ruthenium(II) dimers with arylazoimidazole ligands: molecular structure of [(η6-p-cymene)RuCl(Me-C6H4-Nequals;N-C3H2N2-1-CH3)]PF6

The complexes [{(η ⁶-arene)Ru(μ-Cl)Cl}₂] (arene?=?p-cymene (1), hexamethylbenzene reacts at low temperature with the arylazoimidazole (RaaiR′) ligands 2-(phenylazo)imidazole (Phai-H), 1-methyl-2-(phenylazo)imidazole (Phai-Me), 1-ethyl-2-(phenylazo)imidazole (Phai-Et), 2-(tolylazo)imidazole (Tai-H), 1-methyl-2-(tolylazo)imidazole (Tai-Me) and 1-ethyl-2-(tolylazo)imidazole (Tai-Et) to give complexes of the type [(η ⁶-arene)RuCl(RaaiR′)]⁺. The complexes were characterized by FTIR and ¹H NMR and ¹³C {¹H} NMR spectroscopy. The molecular structure of [(η ⁶-p-cymene)RuCl(Me-C₆H₄-N=N-C₃H₂N₂-1-CH₃)]PF₆ was established by single-crystal X-ray diffraction methods.     

Carbon-13?proton coupling constants in N-substituted imidazoles. A 13C NMR study and MO calculations

The ¹³C NMR data of imidazole, and N-methyl-, N-acetyl-, N-trifluoroacetyl-, N-heptafluorobutyryl- and 2-methyl-imidazoles, were obtained from proton-noise decoupled and single frequency NOE ¹³C NMR spectra. The considerable changes in the directly-bonded (C, H) coupling constants upon N-acetylation of the imidazole ring, which are comparable to those noted when going from the neutral to the cationic form of imidazole, are primarily due to the large π-electron transfer ability of the N-acetyl- and N-trifluoroacetyl-substituents. The differences in magnitude of the three-bond (C, H) coupling constants along different paths in the imidazole ring may be attributed to the larger π-contributions across a pyridine-like nitrogen than along a pyrrole-like nitrogen.     

Exploring the potential energy hypersurface of histamine monocation: Tautomerism in gas phase

The potential energy hypersurface of the histamine monocation is determined by ab initio methods at the STO -4G level using analytical gradient techniques. Three transition states and two minima have been found for the N_τ? H tautomer. One of the transition states connects the trans conformational region with a minimum gauche structure, where the proton of the ammonium group is approximately halfway between the N_π of the imidazole group and the N of the ammonium group, but nearer to the N_π. This minimum connects the potential energy surface of the N_τ? H tautomer with the imidazolium one. In the latter region, three transition states and two minima have been found. Critical points are discussed in relation with experimental data and histamine H₂ receptor models.     

2‐[6‐(1H‐Benzimidazol‐2‐yl)‐2‐pyridyl]‐1H‐benzimidazol‐3‐ium perchlorate monohydrate

The title compound, C₁₉H₁₄N₅⁺·ClO₄^?·H₂O, contains planar C₁₉H₁₄N₅⁺ cations, perchlorate anions and water mol­ecules. The two closest parallel cations (plane‐to‐plane distance of 3.41 Å), together with two neighbouring perchlorate anions and two water mol­ecules, form an electrically neutral quasi‐dimeric unit. Two acidic H atoms of the cation, both H atoms of the water mol­ecule, the N atoms of the imidazole rings and three of the four O atoms of the perchlorate anion are involved in the hydrogen‐bonding network within the dimeric unit. The remaining third acidic H atom of the imidazole rings and the water mol­ecules complete a two‐dimensional network of hydrogen bonds, thus forming puckered layers of dimers. The angle between the planes of two neighbouring dimeric units in the same layer is 33.25 (3)°.     

Two isomorphous imidazole (Him) complexes: [MCl2(Him)2(H2O)2] (M = Co and Ni)

The structures of aqua­di­chloro­bis(1H‐imidazole)­cobalt(II), [CoCl₂(Him)₂(H₂O)₂] (Him is 1H‐imidazole, C₃H₄N₂), (I), and aqua­di­chloro­bis(1H‐imidazole)­nickel(II), [NiCl₂(Him)₂(H₂O)₂], (II), are isomorphous and consist of monomers with inversion symmetry. The three monodentate ligands (imidazole, chlorine and aqua), together with their symmetry equivalents, define almost perfect octahedra. Hydro­gen‐bonding interactions via the imidazole and aqua H atoms lead to a three‐dimensional network.     

mer‐Di­aqua­bis(1H‐imidazole‐κN3)(orotato‐κ2N3,O4)­nickel(II)

The title mononuclear complex, [Ni(C₅H₂N₂O₄)(C₃H₄N₂)₂(H₂O)₂] or [Ni(HOr)(im)₂(H₂O)₂] (im is imidazole and H₃Or is orotic acid, or 2,6‐dioxo‐1,2,3,6‐tetra­hydro­pyrimidine‐4‐carboxylic acid), has been synthesized and the crystal structure determination is reported. The Ni^II ion in the complex has a distorted octahedral coordination geometry comprised of one deprotonated pyrimidine N atom and the adjacent carboxyl­ate O atom of the orotate ligand, two tertiary imidazole N atoms and two aqua ligands. An extensive three‐dimensional network of OW—H⋯O and N—H⋯O hydrogen bonds, and π–π and π–ring interactions are responsible for crystal stabilization.     

Reaction of triflyl-imidazole with aldoximes: facile synthesis of nitriles and formation of novel aldoxime-bis(N-triflyl)-imidazole adducts

The synthetic utility of N-triflylimidazole as an in situ reagent for facile, high yielding, synthesis of various aliphatic, aromatic, and heteroaromatic nitriles from the corresponding aldoximes has been demonstrated. With benzaldoximes, in the presence of certain substitutents (2-F; 2-OMe; 3-CF₃; 2-Me-5-F) a different course of reaction was observed, leading instead to novel 1:1 aldoxime-bis(N-triflyl)imidazole covalent adducts, in which the aldoxime oxygen atom is bonded to the imidazole C-2 ring carbon. For these aldoximes, conversion to nitrile could be effected by reaction with Tf₂O in the absence of imidazole. The molecular structure of the adduct formed from 2-methyl-5-fluoro-benzaldoxime was confirmed by X-ray analysis. Plausible mechanisms for the formation of 1:1 covalent adducts have been considered. Various attempts to isolate such adducts via the reaction of an authentic sample of bis(N-triflyl)imidazolium trifate with aldoxime were unsuccessful. Remarkably, whereas isolated benzaldoxime adducts undergo deprotonation/methylation with NaH/MeI, an authentic sample of bis(N-triflyl)imidazolium triflate did not undergo H/Me exchange under these conditions. These transformations are discussed.     

Intermolecular interactions in two (ferrocenylmethyl)benzimidazoles incorporating the 4-MeOC6H4 and 3,4-(MeO)2C6H3 groups: analysis of MeO—C—C distortions from ideal 120° geometry

The title compounds, 1-ferrocenyl­methyl-2-(4-methoxy­phenyl)-1H-benz­imidazole, [Fe(C₅H₅)(C₂₀H₁₇N₂O)], (I), and 2-(3,4-di­methoxy­phenyl)-1-ferrocenyl­methyl-1H-benz­imid­az­ole, [Fe(C₅H₅)(C₂₁H₁₉N₂O₂)], (II), are model electroactive compounds for anion sensor and antimalarial applications. Distortions from the ideal 120° angle about the MeO—C—C groups are evident, with angles of 115.1 (2) and 125.0 (2)° in (I), and 115.9 (2) and 124.6 (2)°, and 115.7 (2) and 125.1 (2)° in (II). The main intermolecular hydrogen bonds in (I) comprise C—H⋯N and C—H⋯π(C₅H₅) interactions, while in (II), only weak C—H⋯π(imidazole) and C—H⋯π(arene) interactions are present.     

15N NMR shifts for imidazole and 1-methyl imidazole in CH2Cl2 relative to aqueous solution

The ¹⁵N NMR frequencies for imidazole nitrogens undergo significant shifts when imidazole or 1-methyl imidazole is taken from aqueous to CH₂Cl₂ solution. This shift is probably primarily due to strong hydrogen-bonding between ¹⁵N₃ of imidazole and H₂O protons in aqueous solution.     

Specific ion-molecule interactions of imidazole and 1-methylimidazole in nitrobenzene

We have studied, by conductivity measurements, the formation of hydrogenbonded complexes between imidazoles and ions in the three systems triethylammonium picrate (Et₃NHPic)+imidazole (Im), triethylammonium bromide (Et₃NHBr)+Im, and Et₃NHPic+1-methylimidazole (1-MeIm) in nitrobenzene in order to specify the importance of the two functions of the imidazole molecule, the tertiary nitrogen N₃, and the imino group N₁-H. While 1-MelIm forms only a single complex with the cationic species Et₃NH⁺, imidazole enters into specific interactions as well with the cations through its basic site N₃ and with the anions through its imino group. The complexing of the anions by imidazole, always weaker than the complexing of the cations, is more effective for Br^– than for Pic^–. Moreover, if imidazole is used as ligand, a 1:2 complex is formed between the cation and the imidazole, in which the second molecule of imidazole is bonded to the N-H group of the first by a hydrogen bond at the tertiary N atom. We did not observe a correlation between the equilibrium constants K ₁ ⁺ for the complexing of the cation Et₃NH⁺ by imidazole and pyridines (k ₁ ⁺ for pyridine, 3–4 dimethylpyridine, and imidazole are 8, 24, and 165, respectively) and the pK _a values of these ligands due to the fundamental difference in the structure of the imidazole and pyridine molecules, although both are considered as aromatic nitrogen bases.