Supramolecular structure of unnatural nucleobases: Revised structure of (2:1) 6-methylisocytosinium dihydrogen monophosphate adduct

Microwave-assisted synthesis and functionalization of 2-arylimidazo[1,2-a]pyrimidin-5(8H)-ones

Despite the limited applications and scarcity of commercial examples of imidazo[1,2-a]pyrimidines, their exceptional properties hold great potential, representing a significant challenge in discovering more critical applications. Herein, we present a microwave-assisted approach for preparing 2-arylimidazo[1,2-a]pyrimidin-5(8H)-ones and their alkylation and bromination products using easily accessible and inexpensive reagents, thus offering a promising avenue for further search. Notably, the photophysical properties of an N-alkyl derivative were investigated, and the results highlight the high potential of these compounds as modular fluorophores. All the products were obtained with high yields using highly efficient protocols, and the regioselectivity of the reactions was determined on the basis of NMR measurements and X-ray diffraction analysis.

Two tautomeric forms of 2-amino-5,6-dimethylpyrimidin-4-one

Derivatives of 4-hydroxypyrimidine are an important class of biomolecules. These compounds can undergo keto-enol tautomerization in solution, though a search of the Cambridge Structural Database shows a strong bias toward the 3H-keto tautomer in the solid state. Recrystallization of 2-amino-5,6-dimethyl-4-hydroxypyrimidine, C6H9N3O, from aqueous solution yielded triclinic crystals of the 1H-keto tautomer, denoted form (I). Though not apparent in the X-ray data, the IR spectrum suggests that small amounts of the 4-hydroxy tautomer are also present in the crystal. Monoclinic crystals of form (II), comprised of a 1:1 ratio of both the 1H-keto and the 3H-keto tautomers, were obtained from aqueous solutions containing uric acid. Forms (I) and (II) exhibit one-dimensional and three-dimensional hydrogen-bonding motifs, respectively.

6-Chloroisocytosine and 5-bromo-6-methylisocytosine: again, one or two tautomers present in the same crystal?

It is well known that pyrimidin-4-one derivatives are able to adopt either the 1H- or the 3H-tautomeric form in (co)crystals, depending on the coformer. As part of ongoing research to investigate the preferred hydrogen-bonding patterns of active pharmaceutical ingredients and their model systems, 2-amino-6-chloropyrimidin-4-one and 2-amino-5-bromo-6-methylpyrimidin-4-one have been cocrystallized with several coformers and with each other. Since Cl and Br atoms both have versatile possibilities to interact with the coformers, such as via hydrogen or halogen bonds, their behaviour within the crystal packing was also of interest. The experiments yielded five crystal structures, namely 2-aminopyridin-1-ium 2-amino-6-chloro-4-oxo-4H-pyrimidin-3-ide-2-amino-6-chloropyrimidin-4(3H)-one (1/3), C5H7N2(+)·C4H3ClN3O(-)·3C4H4ClN3O, (Ia), 2-aminopyridin-1-ium 2-amino-6-chloro-4-oxo-4H-pyrimidin-3-ide-2-amino-6-chloropyrimidin-4(3H)-one-2-aminopyridine (2/10/1), 2C5H7N2(+)·2C4H3ClN3O(-)·10C4H4ClN3O·C5H6N2, (Ib), the solvent-free cocrystal 2-amino-5-bromo-6-methylpyrimidin-4(3H)-one-2-amino-5-bromo-6-methylpyrimidin-4(1H)-one (1/1), C5H6BrN3O·C5H6BrN3O, (II), the solvate 2-amino-5-bromo-6-methylpyrimidin-4(3H)-one-2-amino-5-bromo-6-methylpyrimidin-4(1H)-one-N-methylpyrrolidin-2-one (1/1/1), C5H6BrN3O·C5H6BrN3O·C5H9NO, (III), and the partial cocrystal 2-amino-5-bromo-6-methylpyrimidin-4(3H)-one-2-amino-5-bromo-6-methylpyrimidin-4(1H)-one-2-amino-6-chloropyrimidin-4(3H)-one (0.635/1/0.365), C5H6BrN3O·C5H6BrN3O·C4H4ClN3O, (IV). All five structures show R2(2)(8) hydrogen-bond-based patterns, either by synthon 2 or by synthon 3, which are related to the Watson-Crick base pairs.

Cytosinium orotate dihydrate

The title compound, C₄H₆N₃O⁺·C₅H₃N₂O₄⁻·2H₂O or Cyt⁺·Or⁻·2H₂O, was synthesized by a reaction between cytosine (4-amino-2-hy­droxy­pyrimidine, Cyt) and orotic acid (2,4-dihy­droxy-6-carb­oxy­pyrimidine, Or) in aqueous solution. The two ions are joined by two N⁺—H⋯O⁻ (±)-(CAHB) hydrogen bonds, forming a dimer with graph-set motif R₂²(8). In the crystal, the ion pairs of the asymmetric unit are joined by four N—H⋯O inter­actions to adjacent dimers, forming hydrogen-bonded rings with R₂²(8) graph-set motif in a two-dimensional network. The formation of the three-dimensional array is facilitated by water mol­ecules, which act as bridges between structural sub-units linked in R₃²(8) and R₃²(7) hydrogen-bonded rings. The orotate anion is essentially planar, as the dihedral angle between the planes defined by the carboxylate group and the uracil fragment is 4.0 (4)°.

4-Methoxybenzamidinium bromide

The title salt, C₈H₁₁N₂O⁺·Br⁻, was synthesized by the reaction between 4-meth­oxy­benzamidine (4-amidino­anisole) and hydro­bromic acid. In the cation, the amidinium group has two similar C—N bonds [1.304 (2) and 1.316 (2) Å], and its plane forms a dihedral angle of 31.08 (5)° with the benzene ring. The ions are associated in the crystal into a three-dimension hydrogen-bonded supra­molecular network featuring N—H⁺⋯Br⁻ inter­actions.

4-Methoxybenzamidinium nitrate

The title salt, C₈H₁₁N₂O⁺·NO₃⁻, was synthesized by a reaction between 4-meth­oxy­benzamidine (4-amidino­anisole) and nitric acid. The asymmetric unit comprises a non-planar 4-meth­oxy­benzamidinium cation and a nitrate anion. In the cation, the amidinium group has two similar C—N bond lengths [1.302 (3) and 1.313 (3) Å] and its plane forms a dihedral angle of 32.66 (5)° with the mean plane of the benzene ring. The nitrate–amidinium ion pair is not planar, as the dihedral angle between the planes defined by the CN₂⁺ and NO₃⁻ units is 19.28 (6)°. The ionic components are associated in the crystal via N—H⋯O hydrogen bonds, resulting in a three-dimensional network.

4-Meth-oxy-benzamidinium acetate

The title compound, C8H11N2O(+)·CH3CO2(-), was synthesized by a reaction between 4-meth-oxy-benzamidine (4-amidino-anisole) and acetic acid. In the cation, the amidinium group forms a dihedral angle of 11.65 (17)° with the mean plane of the benzene ring. The ionic components are associated in the crystal via N-H(+)⋯O(-) hydrogen bonds, resulting in a one-dimensional structure consisting of dimers and catemers and orientated approximately along the c axis.

4-Meth-oxy-benzamidinium hydrogen oxalate monohydrate

The title hydrated salt, C₈H₁₁N₂O⁺·C₂HO₄⁻·H₂O, was synthesized by a reaction of 4-meth­oxy­benzamidine (4-amidino­anisole) and oxalic acid in water solution. In the cation, the amidinium group forms a dihedral angle of 15.60 (6)° with the mean plane of the benzene ring. In the crystal, each amidinium unit is bound to three acetate anions and one water mol­ecule by six distinct N—H⋯O hydrogen bonds. The ion pairs of the asymmetric unit are joined by two N—H⋯O hydrogen bonds into ionic dimers in which the carbonyl O atom of the semi-oxalate anion acts as a bifurcated acceptor, thus generating an R¹₂(6) motif. These subunits are then joined through the remaining N—H⋯O hydrogen bonds to adjacent semi-oxalate anions into linear tetra­meric chains running approximately along the b axis. The structure is stabilized by N—H⋯O and O—H⋯O inter­molecular hydrogen bonds. The water mol­ecule plays an important role in the cohesion and the stability of the crystal structure being involved in three hydrogen bonds connecting two semi-oxalate anions as donor and a benzamidinium cation as acceptor.

Solid-phase molecular recognition of cytosine based on proton-transfer reaction. Part II. supramolecular architecture in the cocrystals of cytosine and its 5-Fluoroderivative with 5-Nitrouracil

BACKGROUND

Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular heterosynthons of molecular salts fabricated through proton-transfer reactions, might be used to investigate the theoretical sites of cytosine-specific DNA-binding proteins and the design for molecular imprint.

RESULTS

Reaction of cytosine (Cyt) and 5-fluorocytosine (5Fcyt) with 5-nitrouracil (Nit) in aqueous solution yielded two new products, which have been characterized by single-crystal X-ray diffraction. The products include a dihydrated molecular salt (CytNit) having both ionic and neutral hydrogen-bonded species, and a dihydrated cocrystal of neutral species (5FcytNit). In CytNit a protonated and an unprotonated cytosine form a triply hydrogen-bonded aggregate in a self-recognition ion-pair complex, and this dimer is then hydrogen bonded to one neutral and one anionic 5-nitrouracil molecule. In 5FcytNit the two neutral nucleobase derivatives are hydrogen bonded in pairs. In both structures conventional N-H...O, O-H...O, N-H+...N and N-H...N- intermolecular interactions are most significant in the structural assembly.

CONCLUSION

The supramolecular structure of the molecular adducts formed by cytosine and 5-fluorocytosine with 5-nitrouracil, CytNit and 5FcytNit, respectively, have been investigated in detail. CytNit and 5FcytNit exhibit widely differing hydrogen-bonding patterns, though both possess layered structures. The crystal structures of CytNit (Dpka = -0.7, molecular salt) and 5FcytNit (Dpka = -2.0, cocrystal) confirm that, at the present level of knowledge about the nature of proton-transfer process, there is not a strict correlation between the Dpka values and the proton transfer, in that the acid/base pka strength is not a definite guide to predict the location of H atoms in the solid state. Eventually, the absence in 5FcytNit of hydrogen bonds involving fluorine is in agreement with findings that covalently bound fluorine hardly ever acts as acceptor for available Brønsted acidic sites in the presence of competing heteroatom acceptors.