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

Patterns of CT lung injury and toxicity after stereotactic radiotherapy delivered with helical tomotherapy in early stage medically inoperable NSCLC

To evaluate toxicity and patterns of radiologic lung injury on CT images after hypofractionated image-guided stereotactic body radiotherapy (SBRT) delivered with helical tomotherapy (HT) in medically early stage inoperable non-small-cell lung cancer (NSCLC)

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

Self-assembling of calcium salt of the new DNA base 5-carboxylcytosine

Supramolecular architectures involving DNA bases can have a strong impact in several fields such as nanomedicine and nanodevice manufacturing. To date, in addition to the four canonical nucleobases (adenine, thymine, guanine and cytosine), four other forms of cytosine modified at the 5 position have been identified in DNA. Among these four new cytosine derivatives, 5-carboxylcytosine has been recently discovered in mammalian stem cell DNA, and proposed as the final product of the oxidative epigenetic demethylation pathway on the 5 position of cytosine. In this work, a calcium salt of 5-carboxylcytosine has been synthesized and deposited on graphite surface, where it forms self-assembled features as long range monolayers and up to one micron long filaments. These structures have been analyzed in details combining different theoretical and experimental approaches: X-ray single-crystal diffraction data were used to simulate the molecule-graphite interaction, first using molecular dynamics and then refining the results using density functional theory (DFT); finally, data obtained with DFT were used to rationalize atomic force microscopy (AFM) results

The experimental gas-phase structures of 1,3,5-trisilylbenzene and hexasilylbenzene and the theoretical structures of all benzenes with three or more silyl substituents

The structures of 1,3,5-trisilylbenzene and hexasilylbenzene in the gas phase have been determined by electron diffraction, and that of 1,3,5-trisilylbenzene by X-ray crystallography. The structures of three trisilylbenzene isomers, three tetrasilylbenzenes, pentasilylbenzene and hexasilylbenzene have been computed, ab initio and using Density Functional Theory, at levels up to MP2/6-31G*. The primary effect of silyl substituents is to narrow the ring angle at the substituted carbon atoms. Steric interactions between silyl groups on neighbouring carbon atoms lead first to displacement of these groups away from one another, and then to displacement out of the ring plane, with alternate groups moving to opposite sides of the ring. In the extreme example, hexasilylbenzene, the SiCCSi dihedral angle is 17.8(8)°

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

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

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