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 Nimino 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).

Experimental results and computational insight into sequential reactions of ß-(2-aminophenyl)-α,ß-ynones with aryl isocyanates/benzoyl isothiocyanate.

The investigation on tandem addition/cyclization reactions of ß-(2-aminophenyl)-α,ß-ynones with aryl isocyanates/benzoyl isothiocyanate is reported. Experimental results show the suitable conditions to selectively direct the reaction outcome towards the product of 6-exo-dig N-, O-, or S-annulation of the in situ generated alkynyl urea/thiourea intermediate. The reaction of a variety of ß-(2-aminophenyl)-α,ß-ynones with aryl isocyanates/benzoyl isothiocyanate led to the selective formation of quinazoline or benzoxazine/benzothiazine derivatives, respectively. Density functional theory calculations provide a plausible rationale for the reaction outcome.

Cytosinium orotate dihydrate.

The title compound, C4H6N3O(+)·C5H3N2O4(-)·2H2O or Cyt(+)·Or(-)·2H2O, was synthesized by a reaction between cytosine (4-amino-2-hy-droxy-pyrimidine, Cyt) and orotic acid (2,4-dihy-droxy-6-carb-oxy-pyrimidine, Or) in aqueous solution. The two ions are joined by two N(+)-H⋯O(-) (±)-(CAHB) hydrogen bonds, forming a dimer with graph-set motif R2(2)(8). In the crystal, the ion pairs of the asymmetric unit are joined by four N-H⋯O inter-actions to adjacent dimers, forming hydrogen-bonded rings with R2(2)(8) graph-set motif in a two-dimensional network. The formation of the three-dimensional array is facilitated by water mol-ecules, which act as bridges between structural sub-units linked in R3(2)(8) and R3(2)(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)°.

Benzamidinium 2-meth-oxy-benzoate.

The title mol-ecular salt, C7H9N2 (+.)C8H7O3 (-), was synthesized by reaction between benzamidine (benzene-carboximidamide) and 2-meth-oxy-benzoic 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 meth-oxy substituent forces the carboxyl-ate 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 R 2 (2)(8). These ionic dimers are then joined in ribbons running along the b-axis direction by another R 4 (2)(8) motif involving the remaining N(+)-H⋯O(-) hydrogen bonds. Remarkably, at variance with the well known carb-oxy-lic dimer R 2 (2)(8) motif, the carboxyl-ate-amidinium pair is not planar, the dihedral angle between the planes defined by the CN2 (+) and CO2 (-) atoms being 18.57 (12)°.

4-Meth-oxy-benzamidinium bromide.

The title salt, C8H11N2O(+)·Br(-), was synthesized by the reaction between 4-meth-oxy-benzamidine (4-amidino-anisole) and hydro-bromic 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 supra-molecular network featuring N-H(+)⋯Br(-) inter-actions.

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 2,6-dimeth-oxy-benzoate.

The title compound, C(8)H(11)N(2)O(+)·C(9)H(9)O(4) (-), was synthesized by the reaction of 4-meth-oxy-benzamidine (4-amidino-anisole) and 2,6-dimeth-oxy-benzoic acid. The structure consists of non-planar pairs of hydrogen-bonded 4-meth-oxy-benzamidinium cations and 2,6-dimeth-oxy-benzoate 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-meth-oxy substituents force the carb-oxy-ate 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 inter-molecular N-H⋯O hydrogen bonds.

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 nitrate.

The title salt, C8H11N2O(+)·NO3(-), was synthesized by a reaction between 4-meth-oxy-benzamidine (4-amidino-anisole) and nitric acid. The asymmetric unit comprises a non-planar 4-meth-oxy-benzamidinium 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 hydrogen oxalate monohydrate.

The title hydrated salt, C8H11N2O(+)·C2HO4(-)·H2O, was synthesized by a reaction of 4-meth-oxy-benzamidine (4-amidino-anisole) 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 mol-ecule 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 R(1)2(6) motif. These subunits are then joined through the remaining N-H⋯O hydrogen bonds to adjacent semi-oxalate anions into linear tetra-meric chains running approximately along the b axis. The structure is stabilized by N-H⋯O and O-H⋯O inter-molecular hydrogen bonds. The water mol-ecule 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.

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, C(8)H(11)N(2)O(+)·HSO(4) (-), has been synthesized by the reaction between 4-meth-oxy-benzamidine and sulfuric acid. The asymmetric unit comprises a nonplanar 4-meth-oxy-benzamidinium 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.

A new polymorph of 2,6-dimeth-oxy-benzoic acid.

A new crystalline form of 2,6-dimeth-oxy-benzoic acid, C(9)H(10)O(4), crystallizing in a tetra-gonal unit cell has been identified during screening for co-crystals. The asymmetric unit comprises a non-planar independent mol-ecule with a synplanar conformation of the carb-oxy group. The sterically bulky o-meth-oxy substituents force the carb-oxy group to be twisted away from the plane of the benzene ring by 65.72 (15)°. The carb-oxy group is disordered over two sites about the C-C bond [as indicated by the almost equal C-O distances of 1.254 (3) and 1.250 (3) Å], the occupancies of the disordered carboxym H atoms being 0.53 (5) and 0.47 (5). In the known ortho-rhom-bic form reported by Swaminathan et al. [Acta Cryst. (1976), B32, 1897-1900], due to the anti-planar conformation adopted by the OH group, the mol-ecular components are associated in the crystal in chains stabilized by linear O-H⋯O hydrogen bonds. However, in the new tetra-gonal polymorph, mol-ecules form dimeric units via pairs of O-H⋯O hydrogen bonds between the carb-oxy groups.

Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor.

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X-X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X-X···N with the chloride of N-chlorosuccinimide lead to Cl-X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔEint). The calculated ΔEint values for (imide)Br···N (-11.2 to -12.5 kcal/mol) are smaller than the values for (imide)I···N (-8.4 to -29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N-I covalent bond and I···N non-covalent bond of a (saccharin)N-I···N motif signify the covalent character for I···N halogen bonding.

A novel 1D-AF hybrid organic-inorganic chromium(II) methyl phosphonate dihydrate: synthesis, X-ray crystal and molecular structure, and magnetic properties.

Light-blue crystals of chromium(II) methyl phosphonate dihydrate, [Cr(CH(3)PO(3))(H(2)O)].H(2)O, were obtained in water by mixing filtered solutions of methylphosphonic acid and chromium(II) chloride in the presence of urea in an inert atmosphere. The compound was characterized by elemental analysis, TGA-DSC, X-ray crystallography, magnetic measurements, and UV-visible and FT-IR spectroscopies. The crystal and molecular structures (orthorhombic Pnma (no. 62): a = 4.4714(5) A, b = 6.8762(7) A, c = 19.180(2) A, Z = 4) have been solved using single-crystal X-ray diffraction. The chromium(II) ion is six-coordinated by oxygens (4 + 2) to form an elongated octahedron, with the four equatorial oxygen atoms belonging to [-PO(3)](2-) phosphonate groups. This stereochemistry of the Cr(II) ion (high-spin d(4) electronic configuration) is ascribed to the Jahn-Teller effect. The [CrO(6)] chromophore, the [CH(3)PO(3)](2-) anions, and the water molecules build a novel one-dimensional (1D) metal(II) oxide chain, anchored to each other within the ab plane by two oxygens of the phosphonate ligand. Within the chain, each Cr(2+) ion is connected through double oxygen bridges to its two neighbors, forming edge-sharing octahedra running along the b axis. The chains are further connected with the adjacent chains by phosphonate [-PO(3)](2-) groups of the ligand, forming an inorganic layer that alternates along the c axis of the unit cell with bilayers, consisting of methyl groups and water of crystallization. The thermal variation of the magnetic susceptibility follows the Curie-Weiss law, with a large negative Weiss constant, theta = -60 K, indicating the presence of antiferromagnetic AF exchange interactions between neighboring Cr(II) ions. The magnetic behavior and the magnetic dimensionality have been analyzed in terms of Fisher's classical limiting form of the Heisenberg chain theory, and a value of J = -9.3 cm(-1) was found. The negative value of the intra-chain exchange constant coupling J confirms the presence of an AF coupling. No sign of long-range magnetic ordering down to 2 K (the lowest measured temperature) is observed, in agreement with the predominant one-dimensional character of the exchange interactions.

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

Four organic salts, namely benzamidinidium orotate (2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate) hemihydrate, C(7)H(9)N(2)(+).C(5)H(3)N(2)O(4)(-).0.5H(2)O (BenzamH(+).Or(-)), (I), benzamidinium isoorotate (2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate) trihydrate, C(7)H(9)N(2)(+).C(5)H(3)N(2)O(4)(-).3H(2)O (BenzamH(+).Isor(-)), (II), benzamidinium diliturate (5-nitro-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate) dihydrate, C(7)H(9)N(2)(+).C(4)H(2)N(3)O(5)(-).2H(2)O (BenzamH(+).Dil(-)), (III), and benzamidinium 5-nitrouracilate (5-nitro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ide), C(7)H(9)N(2)(+).C(4)H(2)N(3)O(4)(-) (BenzamH(+).Nit(-)), (IV), have been synthesized by a reaction between benzamidine (benzenecarboximidamide or Benzam) and the appropriate carboxylic acid. Proton transfer occurs to the benzamidine imino N atom. In all four acid-base adducts, the asymmetric unit consists of one tautomeric aminooxo anion (Or(-), Isor(-), Dil(-) and Nit(-)) and one monoprotonated benzamidinium cation (BenzamH(+)), plus one-half (which lies across a twofold axis), three and two solvent water molecules in (I), (II) and (III), respectively. Due to the presence of protonated benzamidine, these acid-base complexes form supramolecular synthons characterized by N(+)-H...O(-) and N(+)-H...N(-) (+/-)-charge-assisted hydrogen bonds (CAHB).

Crystal structure and Hirshfeld surface analysis of a third polymorph of 2,6-di-meth-oxy-benzoic acid.

A third crystalline form of the title compound, C9H10O4, crystallizing in the centrosymmetric monoclinic space group P21/c, has been identified during screening for co-crystals. The asymmetric unit comprises a non-planar independent mol-ecule with a synplanar conformation of the OH group. The sterically bulky o-meth-oxy substituents force the carb-oxy group to be twisted away from the plane of the benzene ring by 74.10 (6)°. The carb-oxy group exhibits the acidic H atom disordered over two sites between two O atoms. A similar situation has been found for the second tetra-gonal polymorph reported [Portalone (2011 ▸). Acta Cryst. E67, o3394-o3395], in which mol-ecules with the OH group in a synplanar conformation form dimeric units via strong O-H⋯O hydrogen bonds. In contrast, in the first ortho-rhom-bic form reported [Swaminathan et al. (1976 ▸). Acta Cryst. B32, 1897-1900; Bryan & White (1982 ▸). Acta Cryst. B38, 1014-1016; Portalone (2009 ▸). Acta Cryst. E65, o327-o328], the mol-ecular components do not form conventional dimeric units, as an anti-planar conformation adopted by the OH group favors the association of mol-ecules in chains stabilized by linear O-H⋯O hydrogen bonds.

Redetermination of 2,6-dimethoxy-benzoic acid.

The crystal structure of the title compound, C(9)H(10)O(4), was first reported by Swaminathan, Vimala & Lotter [Acta Cryst. (1976), B32, 1897-1900]. It has been re-examined, improving the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar independent mol-ecule, as the meth-oxy substituents force the carb-oxy group to be twisted away from the plane of the aromatic ring by 56.12 (9)°. Due to the anti-planar conformation adopted by the OH group, the mol-ecular components do not form the conventional dimeric units, but are associated in the crystal in chains stabilized by linear O-H⋯O hydrogen bonds, involving the OH groups and the carbonyl O atoms, which form C(3) motifs.

A redetermination of 2-nitro-benzoic acid.

The crystal structure of the title compound, C(7)H(5)NO(4), was first reported by Kurahashi, Fukuyo & Shimada [(1967). Bull. Chem. Soc. Jpn, 40, 1296]. It has been re-examined, improving the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar independent mol-ecule, as the nitro and the carb-oxy substituents force each other to be twisted away from the plane of the aromatic ring by 54.9 (2) and 24.0 (2)°, respectively. The mol-ecules form a conventional dimeric unit via centrosymmetric inter-molecular hydrogen bonds.

Comparison of the structure and magnetic order in a series of layered Ni(II) organophosphonates, Ni[(RPO3)(H2O)] (R = C6H5, CH3, C18H37).

The reaction of nickel chloride with phenyl phosphonic acid under hydrothermal conditions resulted in the isolation of yellow-green single crystals of Ni[(C(6)H(5)PO(3))(H(2)O)]. The structure of the compound has been solved by X-ray single-crystal diffraction studies. Ni[(C(6)H(5)PO(3))(H(2)O)] crystallizes in the orthorhombic space group Pmn2(1) and is isostructural with the Mn(II), Fe(II), and Co(II) analogues. It presents the typical features of the hybrid 2D structures, consisting of alternating inorganic and organic layers. The former are formed by six-coordinated nickel(II) ions bridged by oxygen atoms into the layers. The inorganic layers are capped by the phenyl phosphonate groups, with phenyl groups of two adjacent ligands forming a hydrophobic bilayer region, and van der Waals contacts are established between them. The magnetic properties investigated by means of dc and ac susceptibility measurements point to an AF exchange coupling between nearest neighboring Ni(II) ions. Below 5 K, the compound orders magnetically showing the typical features of a canted antiferromagnet. The magnetic behavior and magnetic dimensionality of Ni[(C(6)H(5)PO(3))(H(2)O)] have been fully analyzed and compared to those of the Ni(II) parent compounds Ni[(RPO(3))(H(2)O)] (where R = CH(3), C(18)H(37)), which exhibit different symmetries of the inorganic layers and lengths of the R groups.