Site selectivity of halogen oxygen bonding in 5- and 6-haloderivatives of uracil

Seven 5-and 6-halogenated derivatives of uracil or 1-methyluracil (halogen = Cl, Br, I) were studied by single crystal X-ray diffraction. In contrast with pure 5-halouracils, where the presence of N-H…O and C-H…O hydrogen bonds prevents the formation of other intermolecular interactions, the general ability of pyrimidine nucleobases to provide electron donating groups to halogen bonding was confirmed in three crystals and cocrystals containing uracil with the halogen atom at the C6 position. In the latter compounds, among the two nucleophilic oxygen atoms in the C=O moiety, only the urea carbonyl oxygen O1 can act as halogen bond acceptor, being not saturated by conventional hydrogen bonds. The halogen bonds in pure 6-halouracils are all rather weak, as supported by Hirshfeld surface analysis. The strongest interaction was found in the structure of 6- iodouracil, which displayed the largest (13%) reduction of the sum of van der Waals (vdW) radii for the contact atoms. Despite this, halogen bonding plays a rol

Acetoguanamine N,N-dimethyl­formamide solvate

The structure of acetoguanamine (or 2,4-diamino-6-methyl-1,3,5-triazine) has been determined as the N,N-dimethyl­formamide solvate, C4H7N5·C3H7NO. The mol­ecular components are associated in the crystal structure to form ribbons stabilized by three N—H⋯N and one N—H⋯O hydrogen bonds which involve NH groups as donors and the N atoms of the heterocyclic ring and the carbonyl O atom of the solvent as acceptors

Redetermination of 5-iodo­uracil

The title compound (systematic name: 2,4-dihydr­oxy-5-iodo­pyrimidine), C4H3IN2O2, which was first reported by Sternglanz, Freeman & Bugg [Acta Cryst. (1975 ▶), B31, 1393–1395], has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar mol­ecule in a slightly distorted B25 boat conformation. The mol­ecules are associated in the crystal structure to form ribbons stabilized by N—H⋯O hydrogen bonds which involve NH groups and two carbonyl O atoms

Biguanidinium dichloride

The asymmetric unit of the title compound, C2H9N5 2+·2Cl−, is composed of one diprotonated biguanidinium cation and two chloride anions. The diprotonated cation consists of two planar halves twisted by 36.42 (6)°. The ions are associated in the crystal structure by extensive hydrogen bonding into a three-dimensional network; the diprotonated biguanidinium cation is hydrogen bonded to the chloride anions

2-(1H-Benzotriazol-1-yl)acetohydrazide

The title compound, C8H9N5O, was synthesized by the reaction of ethyl 2-(benzotriazol-1-yl)acetate with hydrazine hydrate in ethanol. In the amide group, the C—N bond is relatively short [1.3283 (16) Å], suggesting some degree of electronic delocalization in the mol­ecule. In the crystal structure, mol­ecules are linked into infinite chains along the a axis by inter­molecular O—H⋯N hydrogen bonding

Redetermination of orotic acid monohydrate

The crystal structure of the title compound, which is also known as vitamin B13 (systematic name: 2,6-dioxo-1,2,3,6-tetra­hydro­pyrimidine-4-carboxylic acid monohydrate), C5H4N2O4·H2O, was reported for the first time by Takusagawa & Shimada [Bull. Chem. Soc. Jpn (1973 ▶), 46, 2011–2019]. The present redetermination provides more precise values of the mol­ecular geometry. The asymmetric unit comprises a planar diketo tautomer and a solvent water mol­ecule. In the crystal structure, mol­ecules are connected by O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds involving NH groups, two carbonyl O atoms and the solvent water mol­ecule

Nicotinohydrazide

In the title compound (alternative name: pyridine-3-carbo­hydrazide, C6H7N3O), the asymmetric unit contains a single mol­ecule. In contrast with nicotinic acid and nicotinamide, the C=O bond is found to be oriented cis with respect to the Cipso C N fragment in the pyridine ring. The pyridine ring and the hydrazide group make a dihedral angle of 34.0 (2)°. In the crystal structure, mol­ecules are associated into a three-dimensional framework by a combination of N—H⋯N and three-centre N—H⋯O hydrogen bonds

5-fluorocytosine/isocytosine monohydrate. The first example of isomorphic and isostructural co-crystal of pyrimidine nucleobases

To date, despite the crucial role played by cytosine, uracil, and thymine in the DNA/RNA replication process, no examples showing isomorphic and isostructural behavior among binary co-crystals of natural or modified pyrimidine nucleobases have been so far reported in the literature. In view of the relevance of biochemical and pharmaceutical compounds such as pyrimidine nucleobases and their 5-fluoroderivatives, co-crystals of the molecular complex formed by 5-fluorocytosine and isocytosine monohydrate, C4H4FN3O·C4H5N3O·H2O, have been synthesized by a reaction between 5-fluorocytosine and isocytosine. They represent the first example of isomorphic and isostructural binary co-crystals of pyrimidine nucleobases, as X-ray diffraction analysis shows structural similarities in the solid-state organization of molecules with that of the (1:1) 5-fluorocytosine/5-fluoroisocytosine monohydrate molecular complex, which differs solely in the H/F substitution at the C5 position of isocytosine. Molecules of 5-fluorocytosine and isocytosine are present in the crystal as 1H and 3H-ketoamino tautomers, respectively. They form almost coplanar WC base pairs through nucleobase-to-nucleobase DAA/ADD hydrogen bonding interactions, demonstrating that complementary binding enables the crystallization of specific tautomers. Additional peripheral hydrogen bonds involving all available H atom donor and acceptor sites of the water molecule give a three-dimensional polymeric structure. In the absence of H· · · F hydrogen-bonding interactions, the robustness of the supramolecular architectures based on three-point recognition synthons is responsible for the existence of isostructurality between the two molecular complexes. © 2020 by the author. Licensee MDPI, Basel, Switzerland

Crystal structure and Hirshfeld surface analysis of a third polymorph of 2,6-dimethoxybenzoic 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 mol­ecule with a synplanar conformation of the OH group. The sterically bulky o-meth­oxy substituents force the carb­oxy group to be twisted away from the plane of the benzene ring by 74.10 (6)°. The carb­oxy group exhibits the acidic H atom disordered over two sites between two O atoms. A similar situation has been found for the second tetra­gonal polymorph reported [Portalone (2011). Acta Cryst. E67, o3394–o3395], in which mol­ecules with the OH group in a synplanar conformation form dimeric units via strong O—H...O hydrogen bonds. In contrast, in the first ortho­rhom­bic 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 mol­ecular components do not form conventional dimeric units, as an anti­planar conformation adopted by the OH group favors the association of mol­ecules in chains stabilized by linear O—H...O hydrogen bonds

Redetermination of 3-deaza­uracil

The crystal structure of the title compound, 4-hydr­oxy-2-pyridone, C5H5NO2, which has been the subject of several determinations using X-rays and neutron diffraction, was first reported by Low & Wilson [Acta Cryst. (1983). C39, 1688–1690]. It has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a planar 4-enol tautomer having some degree of delocalization of π-electron density through the mol­ecule. In the crystal structure, the mol­ecules are connected into chains by two strong O—H⋯O and N—H⋯O hydrogen bonds between the OH and NH groups and the carbonyl O atom