Metal–nucleobase interactions in magnesium(II) and manganese(II) complexes with adenine: Influence of the anion on the non-covalent stabilization of 7H-adenine tautomer

Buffer-Dependent Photophysics of 2-Aminopurine: Insights into Fluorescence Quenching and Excited-State Interactions

2-Aminopurine (2AP) is the most widely used fluorescent nucleobase analogue in DNA and RNA research. Its unique photophysical properties and sensitivity to environmental changes make it a useful tool for understanding nucleic acid dynamics and DNA-protein interactions. We studied the effect of ions present in commonly used buffer solutions on the excited-state photophysical properties of 2AP. Fluorescence quenching was negligible for tris(hydroxymethyl)aminomethane (TRIS), but significant for phosphate, carbonate, 3-(N-morpholino) propanesulfonic acid (MOPS), and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffers. Results indicate that the two tautomers of 2AP (7H, 9H) are quenched by phosphate ions to different extents. Quenching by the H2PO4- ion is more pronounced for the 7H tautomer, while the opposite is true for the HPO42- ion. For phosphate ions, the results of the time-resolved fluorescence study cannot be explained using a simple collisional quenching mechanism. Instead, results are consistent with transient interactions between 2AP and the phosphate ions. We postulate that excited-state interactions between the 2AP tautomers and an H-bond acceptor (phosphate and carbonate) result in significant quenching of the singlet-excited state of 2AP. Such interactions manifest in biexponential fluorescence intensity decays with pre-exponential factors that vary with quencher concentration, and downward curvatures of the Stern-Volmer plots.

Coordination capacity of cytosine, adenine and derivatives towards open-paddlewheel diruthenium compounds

[Ru₂Cl₂(DPhF)₃] (DPhF = diphenylformamidinate) links preferentially to the junctions of RNA (ribonucleic acid) structures, although the bonding mode is not known. In order to clarify this question the reactions between [Ru₂Cl₂(DPhF)₃] and cytosine (Hcyto), cytidine (Hcyti), cytidine 2',3'-cyclic monophosphate sodium salt (NacCMP), adenine (Hade), adenosine (Haden) and adenosine 3',5'-cyclic monophosphate (HcAMP) have been carried out. In the resultant complexes, cyto (cytosinate), cyti (cytidinate), cCMP (cytidine 2',3'-cyclic monophosphate monoanion), ade (adeninate), aden (adenosinate) and cAMP (deprotonated adenosine 3',5'-cyclic monophosphate) are bonded to the diruthenium unit as N,N'-bridging ligands, as confirmed by the solution of the crystal structures of [RuCl(DPhF)₃(cyto)] and [RuCl(DPhF)₃(ade)] by X-ray diffraction. The axial positions of the diruthenium species are still available for additional interactions with other residues that could explain its preference towards RNA junctions.

Crystal structures of N6-modified-aminoacid/peptide nucleobase analogs: hybrid adenine–glycine and adenine–glycylglycine molecules

Anion–π interactions in crystal structures of N⁶-modified-aminoacid and dipeptide adenine analogs are investigated using X-ray crystallography and DFT calculations.

Spectroscopic investigation on cocrystal formation between adenine and fumaric acid based on infrared and Raman techniques

As an important component of double-stranded DNA, adenine has powerful hydrogen-bond capability, due to rich hydrogen bond donors and acceptors existing within its molecular structure. Therefore, it is easy to form cocrystal between adenine and other small molecules with intermolecular hydrogen-bond effect. In this work, cocrystal of adenine and fumaric acid has been characterized as model system by FT-IR and FT-Raman spectral techniques. The experimental results show that the cocrystal formed between adenine and fumaric acid possesses unique spectroscopical characteristic compared with that of starting materials. Density functional theory (DFT) calculation has been performed to optimize the molecular structures and simulate vibrational modes of adenine, fumaric acid and the corresponding cocrystal. Combining the theoretical and experimental vibrational results, the characteristic bands corresponding to bending and stretching vibrations of amino and carbonyl groups within cocrystal are shifted into lower frequencies upon cocrystal formation, and the corresponding bond lengths show some increase due to the effect of intermolecular hydrogen bonding. Different vibrational modes shown in the experimental spectra have been assigned based on the simulation DFT results. The study could provide experimental and theoretical benchmarks to characterize cocrystal formed between active ingredients and cocrystal formers and also the intermolecular hydrogen-bond effect within cocrystal formation process by vibrational spectroscopic techniques.

Concentration dependent tautomerism in green [Cu(HL¹)(L²)] and brown [Cu(L¹)(HL²)] with H₂L¹ = (E)-N'-(2-hydroxy-3-methoxybenzylidene)benzoylhydrazone and HL² = pyridine-4-carboxylic (isonicotinic) acid

The in situ formed hydrazone Schiff base ligand (E)-N'-(2-hydroxy-3-methoxybenzylidene)benzoylhydrazone (H₂L¹) reacts with copper(II) acetate in ethanol in the presence of pyridine-4-carboxylic acid (isonicotinic acid, HL²) to green-[Cu(HL¹)(L²)]·H₂O·C₂H₅OH (1) and brown-[Cu(L¹)(HL²)] (2) complexes which crystallize as concomitant tautomers where either the mono-anion (HL¹)⁻ or di-anion (L¹)²⁻ of the Schiff base and simultaneously the pyridine-carboxylate (L²)⁻ or the acid (HL²) (both through the pyridine nitrogen atom) function as ligands. The square-planar molecular copper(II) complexes differ in only a localized proton position either on the amide nitrogen of the hydrazone Schiff base in 1 or on the carboxyl group of the isonicotin ligand in 2. The proportion of the tautomeric forms in the crystalline solid-state can be controlled over a wide range from 1:2 = 95 : 5 to ∼2 : 98 by increasing the solution concentration. UV/Vis spectral studies show both tautomers to be kinetically stable (inert), that is, with no apparent tautomerization, in acetonitrile solution. The UB3LYP/6-31+G* level optimized structures of the two complexes are in close agreement with experimental findings. The solid-state structures feature 1D hydrogen-bonded chain from charge-assisted O((-))H-N and O-H((-))N hydrogen bonding in 1 and 2, respectively. In 1 pyridine-4-carboxylate also assumes a metal-bridging action by coordinating a weakly bound carboxylate group as a fifth ligand to a Cu axial site. Neighboring chains in 1 and 2 are connected by strong π-stacking interactions involving also the five- and six-membered, presumably metalloaromatic Cu-chelate rings.