Supramolecular association in proton-transfer adducts containing benzamidinium cations. I. Four molecular salts with uracil derivatives

A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine

Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the N_imino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C-Br^…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).

6-Methyluracil: a redetermination of polymorph (II)

6-Methyluracil, C5H6N2O2, exists in two crystalline phases: form (I), monoclinic, space group P21/c [Reck et al. (1988). Acta Cryst. A44, 417–421] and form (II), monoclinic, space group C2/c [Leonidov et al. (1993). Russ. J. Phys. Chem. 67, 2220–2223]. The structure of polymorph (II) has been redetermined providing a significant increase in the precision of the derived geometric parameters. In the crystal, molecules form ribbons approximately running parallel to the c-axis direction through N—H...O hydrogen bonds. The radical differences observed between the crystal packing of the two polymorphs may be responsible in form (II) for an increase in the contribution of the polar canonical forms C—(O−)=N—H+ relative to the neutral canonical form C(=O)—N—H induced by hydrogen-bonding interactions.

Supramolecular association in proton-transfer adducts containing benzamidinium cations. III. Three molecular salts of 3-methoxy-, 4-methoxy- and 3,4,5-trimethoxybenzoates with benzamidine

Three molecular salts, benzamidinium 3-methoxybenzoate, C7H9N2(+)·C8H7O3(-), (I), benzamidinium 4-methoxybenzoate, C7H9N2(+)·C8H7O3(-), (II), and benzamidinium 3,4,5-trimethoxybenzoate monohydrate, C7H9N2(+)·C10H11O5(-)·H2O, (III), were formed from the proton-transfer reactions of 3-methoxy, 4-methoxy- and 3,4,5-trimethoxybenzoic acids with benzamidine (benzenecarboximidamide, benzam). Monoclinic salts (I) and (II) have a 1:1 ratio of cation to anion. In monoclinic salt (III), two cation-anion pairs and two water molecules constitute the asymmetric unit. In all three molecular salts, the amidinium fragments and the carboxylate groups are completely delocalized, and the delocalization favours the aggregation of the molecular components into nonplanar dimers with an R(2)(2)(8) graph-set motif by N(+)-H···O(-) (±) charge-assisted hydrogen bonding (CAHB). Of the three molecular salts, (I) and (II) show similar conformations of the anionic components and exhibit bidimensional isostructurality, which consists of alternating R(2)(2)(8) and R(6)(4)(16) rings resulting in a corrugated sheet propagated parallel to the crystallographic ab plane. In molecular salt (III), the R(2)(2)(8) synthon is retained but the supramolecular structure is different, due to the presence of three bulky methoxy substituents and a water molecule. The structures reported here further demonstrate the robustness of R(2)(2)(8) hydrogen-bonded synthons having the benzamidinium cation as a building block, whereas N(+)-H···O(-) hydrogen bonds external to the salt bridge contribute to the overall structure organization.

Benzamidinium 2-meth-oxy-benzoate

The title mol­ecular salt, C₇H₉N₂^+.C₈H₇O₃⁻, was synthesized by reaction between benzamidine (benzene­carboximidamide) and 2-meth­oxy­benzoic acid. In the cation, the amidinium group has two similar C—N bonds [1.3070 (17) and 1.3145 (16) Å] and is almost coplanar with the benzene ring, making a dihedral angle of 5.34 (12)°. In the anion, the meth­oxy substituent forces the carboxyl­ate group to be twisted by 69.45 (6)° with respect to the plane of the aromatic fragment. In the crystal, the components are connected by two N⁺—H⋯O⁻ (±)CAHB (charge-assisted hydrogen bonds), forming centrosymmetric ionic dimers with graph-set motif R₂²(8). These ionic dimers are then joined in ribbons running along the b-axis direction by another R₄²(8) motif involving the remaining N⁺—H⋯O⁻ hydrogen bonds. Remarkably, at variance with the well known carb­oxy­lic dimer R₂²(8) motif, the carboxyl­ate–amidinium pair is not planar, the dihedral angle between the planes defined by the CN₂⁺ and CO₂⁻ atoms being 18.57 (12)°.

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.

Supramolecular association in proton-transfer adducts containing benzamidinium cations. II. Concomitant polymorphs of the molecular salt of 2,6-dimethoxybenzoic acid with benzamidine

Two concomitant polymorphs of the molecular salt formed by 2,6-dimethoxybenzoic acid, C(9)H(10)O(4) (Dmb), with benzamidine, C(7)H(8)N(2) (benzenecarboximidamide, Benzam) from water solution have been identified. Benzamidinidium 2,6-dimethoxybenzoate, C(7)H(9)N(2)(+)·C(9)H(9)O(4)(-) (BenzamH(+)·Dmb(-)), was obtained through protonation at the imino N atom of Benzam as a result of proton transfer from the acidic hydroxy group of Dmb. In the monoclinic polymorph, (I) (space group P2(1)/n), the asymmetric unit consists of two Dmb(-) anions and two monoprotonated BenzamH(+) cations. In the orthorhombic polymorph, (II) (space group P2(1)2(1)2(1)), one Dmb(-) anion and one BenzamH(+) cation constitute the asymmetric unit. In both polymorphic salts, the amidinium fragments and carboxylate groups are completely delocalized. This delocalization favours the aggregation of the molecular components of these acid-base complexes into nonplanar dimers with an R(2)(2)(8) graph-set motif via N(+)-H···O(-) charge-assisted hydrogen bonding. Both the monoclinic and orthorhombic forms exhibit one-dimensional isostructurality, as the crystal structures feature identical hydrogen-bonding motifs consisting of dimers and catemers.

4-Meth-oxy-benzamidinium chloride monohydrate

In the cation of the title compound, C(8)H(11)N(2)O(+)·Cl(-)·H(2)O, the C-N bonds of the amidinium group are identical within experiemental error [1.305 (2) and 1.304 (2) Å], and its plane forms a dihedral angle of 25.83 (8)° with the phenyl ring. The ionic components are associated in the crystal into polymeric hydrogen-bonded supra-molecular tapes stabilized by N-H(+)⋯Cl(-) and N-H(+)⋯Ow inter-molecular hydrogen bonds, and by Ow-H⋯Cl(-) inter-actions.

4-Meth-oxy-benzamidinium hydrogen sulfate

The title salt, C₈H₁₁N₂O⁺·HSO₄⁻, has been synthesized by the reaction between 4-meth­oxy­benzamidine and sulfuric acid. The asymmetric unit comprises a nonplanar 4-meth­oxy­benzamidinium cation and one hydrogen sulfate anion. In the cation, the amidinium group has two identical C—N bonds [1.306 (2) and 1.308 (2) Å], and its plane forms a dihedral angle of 6.49 (8)° with the mean plane of the benzene ring. The ionic components are associated in the crystal via N—H⁺⋯O⁻, resulting in chains running approximately along the b-axis direction whicg are interconnected by O—H⋯O⁻ hydrogen bonds.

4-Meth-oxy-benzamidinium 2,6-dimeth-oxy-benzoate

The title compound, C₈H₁₁N₂O⁺·C₉H₉O₄⁻, was synthesized by the reaction of 4-meth­oxy­benzamidine (4-amidino­anisole) and 2,6-dimeth­oxy­benzoic acid. The structure consists of non-planar pairs of hydrogen-bonded 4-meth­oxy­benzamidinium cations and 2,6-dimeth­oxy­benzoate anions. In the cation, the amidinium group is tilted by 27.94 (10)° with respect to the benzene ring. In the anion, the sterically bulky ortho-meth­oxy substituents force the carb­oxy­ate group to be twisted away from the plane of the benzene ring by 73.24 (6)°. The ions are further associated in the crystal into chains along the b-axis direction by inter­molecular N—H⋯O hydrogen bonds.

Conformational studies of hydantoin-5-acetic acid and orotic acid

Hydantoin-5-acetic acid [2-(2,5-dioxoimidazolidin-4-yl)acetic acid] and orotic acid (2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid) each contain one rigid acceptor–donor–acceptor hydrogen-bonding site and a flexible side chain, which can adopt different conformations. Since both compounds may be used as coformers for supramolecular complexes, they have been crystallized in order to examine their conformational preferences, giving solvent-free hydantoin-5-acetic acid, C5H6N2O4, (I), and three crystals containing orotic acid, namely, orotic acid dimethyl sulfoxide monosolvate, C5H4N2O4·C2H6OS, (IIa), dimethylammonium orotate–orotic acid (1/1), C2H8N+·C5H3N2O4−·C5H4N2O4, (IIb), and dimethylammonium orotate–orotic acid (3/1), 3C2H8N+·3C5H3N2O4−·C5H4N2O4, (IIc). The crystal structure of (I) shows a three-dimensional network, with the acid function located perpendicular to the ring. Interestingly, the hydroxy O atom acts as an acceptor, even though the carbonyl O atom is not involved in any hydrogen bonds. However, in (IIa), (IIb) and (IIc), the acid functions are only slightly twisted out of the ring planes. All H atoms of the acidic functions are directed away from the rings and, with respect to the carbonyl O atoms, they show an antiperiplanar conformation in (I) and synperiplanar conformations in (IIa), (IIb) and (IIc). Furthermore, in (IIa), (IIb) and (IIc), different conformations of the acid O=C—C—N torsion angle are observed, leading to different hydrogen-bonding arrangements depending on their conformation and composition.

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.