An unusual syn conformation of 5‐formyluracil stabilized by supramolecular interactions

The asymmetric unit of the amino–oxo tautomer of 5‐formyluracil (systematic name: 2,4‐dioxo‐1,2,3,4‐tetrahydropyrimidine‐5‐carbaldehyde), C₅H₄N₂O₃, comprises one planar amino–oxo tautomer, as every atom in the structure lies on a crystallographic mirror plane. At variance with all the previously reported small‐molecule crystal structures containing the 5‐formyluracil residue, the formyl substituent in the title compound exhibits an unusual syn conformation. The molecules are linked into planar sheets parallel to the bc plane by a combination of six N—H...O and C—H...O hydrogen bonds. Four of the hydrogen bonds are utilized to stabilize the formyl group in the syn conformation.     

Molecular structure of ethynylbenzene from electron diffraction and ab initio molecular orbital calculations

The molecular structure and benzene ring distortions of ethynylbenzene have been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF/6-31G^* and 6-3G^** levels. Least-squares refinement of a model withC _2v, symmetry, with constraints from the MO calculations, yielded the following important bond distances and angles:r _g(C _i -C _o )=1.407±0.003 Å,r _g(C _o -C _m )=1.397±0.003 Å,r _g(C _m -C _p )=1.400±0.003 Å,r _g(Cr _i -CCH)=1.436 ±0.004 Å,r _g(C=C)=1.205±0.005 Å, C _o -C _i -C _o =119.8±0.4°. The deformation of the benzene ring of ethynylbenzene given by the MO calculations, including o-C_i-C_o=119.4°, is insensitive to the basis set used and agrees with that obtained by low-temperature X-ray crystallography for the phenylethynyl fragment, C₆H₅-CC-, in two different crystal environments. The partial substitution structure of ethynylbenzene from microwave spectroscopy is shown to be inaccurate in the ipso region of the benzene ring.     

The crystal structure of 3-methyluracil from X-ray powder diffraction data

The crystal structure of 3-methyluracil has been determined ab initio by conventional monochromatic X-ray powder diffraction data. The crystal data are: orthorombic, a=6.6294(1), b=13.1816(3), c=6.53938(9) (Å), V=571.45(3) (ų), space group Pbnm, Z=8. The structure was solved by direct methods and the final Rietveld refinement converged to R_p=0.0398, R_wp=0.0528, R_Bragg=0.0294. The crystal structure exhibits endless chains of planar molecules, connected via head-to-tail N-H?O hydrogen bonds.     

Layered hybrid organic-inorganic Co(II) alkylphosphonates. Synthesis, crystal structure and magnetism of the first two members of the series: Co[(CH3PO3)(H2O)] and Co[(C2H5PO3)(H2O)]

Co[(CH₃PO₃)(H₂O)] (1) and Co[(C₂H₅PO₃)(H₂O)] (2) were prepared by the hydrothermal method and isolated as blue-violet platelet crystals. They were characterized by X-ray diffraction, FT-IR, TGA-DSC techniques and their magnetic properties studied by a dc-SQUID magnetometer. Compound (1) shows an hybrid layered structure, made of alternating inorganic and organic layers along the a-direction of the unit cell. The inorganic layers contain Co(II) ions six-coordinated by five phosphonate oxygen atoms and one from the water molecule. These layers are separated by bi-layers of methyl groups and van der Waals contacts are established between them. In compound (2), the layered hybrid structure is rather similar to that described for compound (1), but the alternation of the inorganic and organic layers is along the b-direction of the unit cell. The magnetic behavior of (1) and (2) as function of temperature and magnetic field was studied. The compounds obey the Curie-Weiss law at temperatures above 100 K, the Curie C, and Weiss θ constants for the methyl derivative being and and for the ethyl derivative and , respectively. The observed magnetic moments for Co atom at room temperature (i.e. μ_eff=5.18 and 5.38 BM, respectively) are higher than those expected for a spin-only value for high spin Co(II) (S=3/2), revealing a substantial orbital contribution to the magnetic moment. The negative values of θ are an indication of the presence of antiferromagnetic exchange couplings between the near-neighbors Co(II) ions, within the layers. [Co(C_nH_2n+1PO₃)(H₂O)] (n=1,2) are 2D Ising antiferromagnets at low temperatures.     

X-ray single-crystal structure and magnetic properties of Fe[CH(3)PO(3))] x H(2)O: a layered weak ferromagnet

The crystal and molecular structure of the layered weak-ferromagnet Fe[CH(3)PO(3)] x H(2)O has been solved by X-ray single-crystal diffraction techniques. Crystal data for Fe[CH(3)PO(3)] x H(2)O are the following: orthorhombic space group Pna2(1); a =17.538(2), b = 4.814(1), c = 5.719(1) A. The structure is lamellar, and it consists of alternating organic and inorganic layers along the a direction of the unit cell. The inorganic layers are made of Fe(II) ions octahedrally coordinated by five phosphonate oxygen atoms and one from oxygen of the water molecule. Each phosphonate group coordinates four metal ions, through chelation and bridging, making in this way a cross-linked Fe-O network. The resultant layers are then separated by bilayers of the methyl groups, with van der Waals contacts between them. The compound is air stable, and it dehydrates under inert atmosphere at temperatures above 120 degrees C. The oxidation state of the metal ion is +2, and the electronic configuration is d(6)( )()high spin (S = 2), as determined from dc magnetic susceptibility measurements from 150 K to ambient temperature. Below 100 K, the magnetic moment of Fe[CH(3)PO(3)] x H(2)O rises rapidly to a maximum at T(max) approximately equal to 24 K, and then it decreases again. The onset of peak at T = 25 K is associated with the 3D antiferromagnetic long-range ordering, T(N). The observed critical temperature, T(N), is like all the other previously reported Fe(II) phosphonates, and it appears to be nearly independent of the interlayer spacing in this family of hybrid organic-inorganic layered compounds. Below T(N), the compound behaves as a "weak ferromagnet", and represents the third kind of magnetic materials with a spontaneous magnetization below a finite critical temperature, ferromagnets and ferrimagnets being the other two types.     

Molecular structure of aniline in the gaseous phase: A concerted study by electron diffraction and ab initio molecular orbital calculations

The molecular structure of free aniline has been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF and MP2 levels of theory, using the 6-31G^*(6D) basis set. Least-squares refinement of a model withC _s symmetry, with constraints from MP2 calculations, has led to an accurate determination of the C-C-C angle at theipso position of the benzene ring, =119.0±0.2 (where the uncertainty represents total error). This parameter provides information on the extent of the interaction between the nitrogen lone pair and the system of the benzene ring, and could not be determined accurately by microwave spectroscopy. The angles at theortho, meta, andpara positions of the ring are 120.3±0.1, 120.7±0.1, and 119.0±0.3, respectively. Important bond distances are r _g(C-C)=1.398±0.003 å andr _g(C-N) =1.407±0.003 å. The effective dihedral angle between the H-N-H plane and the ring plane, averaged over the large-amplitude inversion motion of the amino group, is ¦¦=44±4. The equilibrium dihedral angle is calculated to be 41.8 at the HF level and 43.6 at the MP2 level, in agreement with far-infrared spectroscopic information. The MO calculations predict that the differencer(C_ortho-C_meta) -r(C_ipso-C_ortho) is 0.008–0.009 å. They also indicate that the nitrogen atom is displaced from the ring plane, on the side opposite to the amino hydrogens. The displacement is 0.049 å at the HF level and 0.072 å at the MP2 level. The two calculations, however, yield very different patterns for the minute deviations from planarity of the ring carbons.     

1,3‐Bridged p‐methyloctahomotetraoxacalix[4]arene–bis‐crown‐3

The title compound, 13,21,35,43‐tetra­methyl‐3,6,9,17,25,28,31,39,46,49‐decaoxahepta­cyclo­[21.21.3.3^11,33.0^2,41.0^10,15.0^19,24.0^32,37]pentaconta‐1,10,12,14,19,21,23,32,34,36,41,43‐dodecaene, C₄₄H₅₂O₁₀, differs from previously reported 1,3‐bridged calix­[4]­arene–bis‐crown compounds in having an enlarged calixarene ring and shorter polyoxy­ethyl­ene bridges. The cavity is partly filled by the bridges.     

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).     

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, C₇H₉N₂⁺·C₅H₃N₂O₄⁻·0.5H₂O (BenzamH⁺·Or⁻), (I), benzamidinium isoorotate (2,4‐dioxo‐1,2,3,4‐tetrahydropyrimidine‐5‐carboxylate) trihydrate, C₇H₉N₂⁺·C₅H₃N₂O₄⁻·3H₂O (BenzamH⁺·Isor⁻), (II), benzamidinium diliturate (5‐nitro‐2,6‐dioxo‐1,2,3,6‐tetrahydropyrimidin‐4‐olate) dihydrate, C₇H₉N₂⁺·C₄H₂N₃O₅⁻·2H₂O (BenzamH⁺·Dil⁻), (III), and benzamidinium 5‐nitrouracilate (5‐nitro‐2,4‐dioxo‐1,2,3,4‐tetrahydropyrimidin‐1‐ide), C₇H₉N₂⁺·C₄H₂N₃O₄⁻ (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).