1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling

Probing Peripheral H-Bonding Functionalities in BN-Doped Polycyclic Aromatic Hydrocarbons

The replacement of carbon atoms at the zigzag periphery of a benzo[fg]tetracenyl derivative with an NBN atomic triad allows the formation of heteroatom-doped polycyclic aromatic hydrocarbon (PAH) isosteres, which expose BN mimics of the amidic NH functions. Their ability to form H-bonded complexes has never been touched so far. Herein, we report the first solution recognition studies of peripherally NBN-doped PAHs to form H-bonded DD·AA- and ADDA·DAAD-type complexes with suitable complementary H-bonding acceptor partners. The first determination of K_a in solution showed that the 1:1 association strength is around 27 ± 1 M^-1 for the DD·AA complexes in C₆D₆, whereas it rises to 1820 ± 130 M^-1 for the ADDA·DAAD array in CDCl₃. Given the interest of BN-doped polyaromatic hydrocarbons in supramolecular and materials chemistry, it is expected that these findings will open new possibilities to design novel materials, where the H-bonding properties of peripheral NH hydrogens could serve as anchors to tailor the organizational properties of PAHs.

Spectroscopic investigations on DNA binding profile of two new naphthyridine carboxamides and their application as turn-on fluorescent DNA staining probes

Two new 10-methoxydibenzo[b,h][1,6]naphthyridine-2-carboxamide derivatives (R1 and R2) have been synthesized and characterized using different spectral techniques. The binding of these probes with DNA was investigated using spectral (Electronic, fluorescence, ¹H NMR and circular dichroism) and molecular docking studies. These probes exhibited a strong fluorescence around 440 nm upon excitation around 380 nm. Electronic and competitive fluorescence titration studies, in HEPES [(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)] buffer/dimethyl sulfoxide (pH 7.4) medium, suggest that these probes bind strongly to DNA, which is substantiated by ¹H NMR study. The binding constants are calculated to be 5.3 × 10⁷ and 6.8 × 10⁶ M^-1 for R1 and R2, respectively. From the results of spectral studies, it is proposed that the mechanism of binding of these probes with DNA is through minor groove binding mode, which is further confirmed by circular dichroism and molecular docking studies. Initial cell viability screening using MTT (3-[4,5-methylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) assay shows that normal Vero cells are viable towards these probes at nano molar concentration, which is the concentration range employed in the present study for DNA staining (IC₅₀ in the order of 0.023 mM). The enhancement in fluorescence intensity of these probes upon binding with DNA enables the staining of DNA in agarose gel in gel electrophoresis experiment. The sensitivity of these probes is comparable with that of ethidium bromide and DNA amounts as low as 4 nano gram are detectable.Communicated by Ramaswamy H. Sarma.

Crystal structures of the dioxane hemisolvates of N-(7-bromo-methyl-1,8-naphthyridin-2-yl)acetamide and bis-[N-(7-di-bromo-methyl-1,8-naphthyridin-2-yl)acetamide]

The syntheses and crystal structures of N-(7-bromo-methyl-1,8-naphthyridin-2-yl)acetamide dioxane hemisolvate, C11H10BrN3O·0.5C4H8O2, (I), and bis-[N-(7-di-bromo-methyl-1,8-naphthyridin-2-yl)acetamide] dioxane hemisolvate, 2C11H9Br2N3O·0.5C4H8O2, (II), are described. The mol-ecules adopt a conformation with the N-H hydrogen pointing towards the lone electron pair of the adjacent naphthyridine N atom. The crystals of (I) are stabilized by a three-dimensional supra-molecular network comprising N-H⋯N, C-H⋯N and C-H⋯O hydrogen bonds, as well as C-Br⋯π halogen bonds. The crystals of compound (II) are stabilized by a three-dimensional supra-molecular network comprising N-H⋯N, C-H⋯N and C-H⋯O hydrogen bonds, as well as C-H⋯π contacts and C-Br⋯π halogen bonds. The structure of the substituent attached in the 7-position of the naphthyridine skeleton has a fundamental influence on the pattern of inter-molecular noncovalent bonding. While the Br atom of (I) participates in weak C-Br⋯Oguest and C-Br⋯π contacts, the Br atoms of compound (II) are involved in host-host inter-actions via C-Br⋯O=C, C-Br⋯N and C-Br⋯π bonding.

Crystal structure of N-(7-di-bromo-methyl-5-methyl-1,8-naphthyridin-2-yl)benzamide-pyrrolidine-2,5-dione (1/1)

The title compound, C17H13Br2N3O·C4H5NO2, is a co-crystal of N-(7-di-bromo-methyl-5-methyl-1,8-naphthyridin-2-yl)benzamide and pyrrolidine-2,5-dione (succinimide). The benzamide mol-ecule exhibits pseudo-mirror symmetry, with an r.m.s. deviation of the non-H atoms of 0.09 Å (except for the two Br atoms). The angle between the least-squares planes of the two mol-ecules is 26.2 (2)°. In the crystal, the two mol-ecules are mutually linked by N-H⋯O and N-H⋯N hydrogen bonds. The packing is consolidated by C-H⋯(O,N) hydrogen bonds and π-π stacking inter-actions.

Crystal structure of 9-(dibromomethyl)-1,1-difluoro-3,7-dimethyl-1H-[1,3,5,2]oxadiazaborinino[3,4-a][1,8]naphthyridin-11-ium-1-uide

The mol­ecule in the title compound, C₁₂H₁₀BBr₂F₂N₃O, exhibits point group symmetry m.

The mol­ecule of the title 1,8-naphthyridine-BF₂ derivative, C₁₂H₁₀BBr₂F₂N₃O, is located on a mirror plane running parallel to the entire ring system and the attached methyl C atoms. Individual mol­ecules are stacked along the b-axis direction. The cohesion in the crystal structure is accomplished by C—H⋯F hydrogen bonds and additional off-set π–π inter­actions [centroid-to-centroid distance = 3.6392 (9) Å, slippage 0.472 Å], leading to the formation of a three-dimensional supra­molecular network.

Iodine-catalyzed synthesis of dibenzo[b,h][1,6]naphthyridine-11-carboxamides via a domino reaction involving double elimination of hydrogen bromide

An iodine-catalyzed reaction of 2-aminobenzamides and mucobromic acid was described and utilized to synthesize a variety of 6-oxo-5,6-dihydrodibenzo[b,h][1,6]naphthyridine-11-carboxamide derivatives in refluxing THF. As the two bromine atoms in mucobromic acid were found missing in the dibenzonaphthyridine products, a domino-type reaction mechanism involving a double elimination of hydrogen bromide was proposed.