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

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

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

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

Exploring the role of neutral/ionized TPI hydrogen bonds and OPI halogen bonds for multifacial recognition in 5-halouracils/aminoazine cocrystals

Ten new heterodimers were synthesized in different stoichiometry to explore the role exerted by potential proton-transfer reactions in the supramolecular structures of A-B cocrystals formed by 5-haloderivatives of uracil (halogen = F, Cl, Br, I; coformer A) coupled with aminoazines as 2-aminoadenine simulants (melamine, 2,4,6-triaminopyrimidine, 2,6-diaminopyridine; coformer B) for pyrimidine nucleobase recognition. The crystallographic analysis showed that in all binary cocrystals the expected three-point hydrogen bonds (TPI), charged or uncharged depending on the acid/base properties of the components, were used for WC interfacial recognition. Moreover, the general ability of pyrimidine nucleobases to provide electron donating groups to halogen bonding has been confirmed in six of eight cocrystals containing the 5-bromo or 5-Iododerivatives coupled with 2,4,6-triaminopyrimidine or 2,6-diaminopyridine. “Lateral” one-point halogen bonds cooperate with hydrogen bonds in directing the overall crystal structures. Considerations of the relative acidities of coformers A and of the relative basicities of coformers B allowed us to design and characterize by single-crystal X-ray diffraction the first ternary pyrimidine nucleobase-containing cocrystal based on the JANUS-WEDGE concept [1]: the (1:1:1) triad showing a 2,4,6-triaminopyrimidine molecule wedged via neutral and ionized TPI between the 5-fluorouracil/1-methyluracil pair in reverse WC fashion (Fig. 1)

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

A new polymorph of 2,6-dimeth­oxy­benzoic acid

A new crystalline form of 2,6-dimeth­oxy­benzoic acid, C9H10O4, crystallizing in a tetra­gonal unit cell has been identified during screening for co-crystals. The asymmetric unit comprises a non-planar independent mol­ecule with a synplanar conformation of the carb­oxy group. The sterically bulky o-meth­oxy substituents force the carb­oxy group to be twisted away from the plane of the benzene ring by 65.72 (15)°. The carb­oxy 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 ortho­rhom­bic form reported by Swaminathan et al. [Acta Cryst. (1976), B32, 1897–1900], due to the anti­planar conformation adopted by the OH group, the mol­ecular components are associated in the crystal in chains stabilized by linear O—H⋯O hydrogen bonds. However, in the new tetra­gonal polymorph, mol­ecules form dimeric units via pairs of O—H⋯O hydrogen bonds between the carb­oxy groups

(3R,5S)-5(3)-Carb­oxy-3,4,5,6-tetra­hydro-2H-1,4-thia­zin-4-ium-3(5)-carboxyl­ate

The molecule of the zwitterionic title compound, C6H9NO4S, which lies on a mirror plane, shows a puckered chair conformation of the six-membered ring with the S and N atoms out of the mean plane of the other four C atoms by 0.929 (2) and 0.647 (2) Å, respectively. The ionized carboxyl group is equatorially oriented. The hydrogen-bonding network includes very short O—H⋯O [2.470 (2) Å] and N—H⋯S [3.471 (2) and 3.416 (2) Å] inter­molecular contacts