Three-dimensional Diffractometer Data Research Articles

Hydrogen bonding of modified bases involving Watson-Crick sites: Crystal structure and conformation of Benzyl 6-aminopurine-7-carboxylate

Crystals of benzyl 6-aminopurine-7-carboxylate (C13H11N5O2) are monoclinic, space group C2/c, Z = 8, with a = 25.448 (9), b = 6.052 (1), c = 16.975 (6)A, β = 112.05 (5)°, M = 269.27, Dm= 1.49, Dx= 1.48 g/cm3. The structure was determined from three-dimensional diffractometric data by the multisolution technique and refined to a final reliability factor of 0.068. The molecule is planar with an intramolecular hydrogen bond from one of the amino hydrogens, Ha(N6) to the keto oxygen O(10) of the acyl group. The molecules are hydrogen bonded across the center of inversion by a pair of intermolecular hydrogen bonds using the Watson-Crick sites. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

The factors stabilizing square-planar geometries in σ-bonding amine adducts: crystal and molecular structure of bis( N-tosyl-β-alaninato)bis(piperidine)copper(II)

A violet, air-stable, crystalline compound of empirical formula [Cu(Ts-β-ala) 2(pipd) 2] (Ts=4- toluene sulfonyl group, hereafter abbreviated as tosyl group, Ts-β-ala= N-tosyl-β-alaninate ion, pipd = piperidine) was synthesized and characterized by means of structural and spectroscopic measurements. The crystal structure of the compound was determined from three-dimensional diffractometric data. The crystals are triclinic, space group P 1 , a = 9.305(1), b = 9.637(2), c = 12.727(2) Å, α = 61.50(2), β = 63.26(1), γ = 71.68(1)°, Z = 1. The structure was solved by the heavy atom method and refined through least-squares calculations to R = 0.032 for 2911 observed reflections. The copper atom lies on the symmetry center coordinating two piperidine and two carboxylic oxygens of N-tosyl-β-alanine in a square-planar arrangement. The second carboxylic oxygen is not involved in metal coordination. Electronic data are also discussed in comparison with those of other ternary Cu(II) carboxylate amine complexes.

Structural and spectroscopic study on imidazole-copper(II)-N-protected amino acid complexes. Crystal and molecular structure of tetrakis(imidazole)copper(II)bis(N-tosylvalinate)

A pink-red air-stable, crystalline compound of empirical formula [Cu(Im)4(N-tsval)2] (Im=imidazole; ts=4-toluenesulfonyl group, hereafter abbreviated as tosyl;N-tsval=N-tosylvalinate monoanion) was synthesized and characterized by means of structural and spectroscopic measurements. The crystal structure of the compound was determined from three-dimensional diffractometer data. The crystals are monoclinic, space groupC2/c, a=18.952 (5),b=12.372 (2),c=17.594 (3) A,β=93.77 (2)°,Z=4. The structure was solved by the heavy-atom method and refined through least-squares calculations toR=0.035 for 2284 observed reflections. The coordination about the copper atom is elongated octahedral, with four imidazole molecules as equatorial ligands and two sulfonic oxygens in axial positions.

Crystal and molecular structure ofS-methyl(pentafluorosulfanyl)thiocarbamate

The X-ray structure of S-methyl(pentafluorosulfanyl)thiocarbamate, SF5NHC(O)SCH3, has been determined from three-dimensional diffractometer data and refined by full-matrix least-squares techniques. The crystals are monoclinic:P21/m,a=5.008 (5),b=7.811 (2),c=9.348 (4) A, β=99.08 (7)°, andZ=2; finalR=0.046 for 517 observed reflections. The structure comprises hydrogen-bonded (NH⋯O) chains with the component monomers in thecis, cis-conformation, i.e., the arrangement of the nonhydrogen and nonfluorine atoms is nearly planar, the SF5 group and the O are in acis position with respect to the C-NH bond, and the O and the CH3 group are in acis position with respect to the C(O)-S bond. Theoretical methods including MNDO and molecular modeling were used to study the relative stabilities of the four possible conformations of SF5NHC(O)SCH3.

Crystal and molecular structure of putrescinium hydrogen phosphate dihydrate

The X-ray structure of putrescinium hydrogen phosphate dihydrate,\(H_3 \mathop N\limits^ + (CH_2 )_4 \mathop N\limits^ + H_3 \cdot HPO_4^{2 - } \cdot 2H_2 O\), has been determined from three-dimensional diffractometer data and refined by full-matrix least-squares techniques. The crystals are monoclinic,P21/c, a=6.5932(4),b=16.776(1),c=9.2375(7) A,β=95.772(6)°, andZ=4; finalR=0.036 for 1360 observed reflections. The putrescinium dication has the all-trans conformation. The structure contains a three-dimensional network of H bonds in which all available proton do nors are utilized. Each of the\( - \mathop N\limits^ + H_3\) groups interacts with three electron-rich atoms arranged in an equilateral triangle, but the character of the individual N-H⋯O bonds is different at opposite sides of the dication. The water molecules are involved in relatively strong H bonds but they do not interact with the cation.

Crystal and molecular structure of heptacain hydrochloride

The crystal and molecular structure of heptacain hydrochloride was determined from three-dimensional diffractometric data. The carbamate group was found to be rotated out of the benzene ring plane by 15.5°, whilst the piperidine ring is in a more stable chair conformation. The heptyloxy side chain is in a stable all-trans conformation. The structure was refined by the full matrix least-squares method to a final R value 0.1127 for the observed reflections.

Beiträge zur Chemie der Schwefelhalogenide, 9 [1]. Trifhiormethyldichlorsulfonium(IV)-hexafluoroarsenat(V) / Contributions to the Chemistry of Sulfur Halides, 9 [1] Trifluoromethyldichlorosulfonium(IV) Hexafluoroarsenate(V )

The synthesis of CF3SCl2 +AsF6 - is reported. The sulfonium salt is characterised by IR, Raman, 19F and 13C NMR spectroscopy. The vibrational assignment is based on a Cs model for the cation and assisted by a normal coordinate analysis. The crystal structure has been determined from three-dimensional diffractometer data at -133 K. The structural data for the cation are: C-F = 128.8(5) pm, C-S = 197,8(3) pm, S-Cl = 195,9(1) pm and F-C-F = 111,8(3)°, Cl-S-Cl = 104,22(5)°, C-S-Cl = 99,8(1)°.

X-ray diffraction and vibrational spectra of the guanidine:maleic acid (1:1) complex—two crystal forms

From an equimolar mixture of guanidine and maleic acid, two different crystal modifications of guanidinium hydrogen maleate, CH6N3+·C4H3O4−, were isolated and their crystal structures determined using three-dimensional diffractometer data. Crystals of both forms are orthorhombic:Pca21,a=19.012(8)b=3.758(1),c=11.119(5) A,Z=4 for form I;Fdd2,a=18.505(2),b=20.007(3),c=8.406(2) A,Z=16 for form II. The structures were solved by direct methods and refined by full-matrix least squares to conventionalR values of 0.064 for form I and 0.043 for form II, with 488 and 605 reflections respectively. The structures consist of planar guanidinium cations C(NH2)3+ and hydrogen-maleate residues C4H3O4−. There are no significant differences in distances and angles within the guanidinium and hydrogen-maleate units. However, a substantial difference appears in the length and geometry of the intramolecular hydrogen bond O⋯H⋯O. The packing of cations and anions is also completely different in the two forms. Infrared and Raman spectra of the title compound are presented, and salient differences between them and the spectrum of the symmetrically bonded potassium hydrogen maleate are discussed briefly.

The crystal structure of jaskolskiite, CuxPb2+x(Sb, Bi)2−xS5(x≈ 0.2), a member of the meneghinite homologous series

AbstractThe crystal structure of a new sulphosalt, jaskolskiite, CuxPb2+x(Sb, Bi)2−xS5(x≈ 0.2), has been determined. The space group isPbnm, witha= 11.312(2),b= 19.829(3),c= 4.088(1) Å,Z= 4 for the composition Cu0.19Pb2.22Sb1.17Bi0.62S5. The structure has been solved using its homologous relationship to meneghinite and refined from three-dimensional diffractometer data to anR-value of 0.072 for 472 observed reflections.The structure consists of slices (010) of SnS-like arrangement mutually related by then-glide planes and wavy interfaces. The metal positions M1 and M4 inside the slices represent Sb sites partly substituted by Bi and Pb. The M2 and M3 positions are on the surfaces of slices and represent Pb sites with some substitution by Bi in the case of M2. The tetrahedral sites in the slice interfaces are partially occupied by Cu. Jaskolskiite represents the 4th member of the meneghinite homologous series. The published chemical and structural data for the known homologues of meneghinite, withN= 1, 2, (3), 4 and 5, are systematized in the paper.

Crystal and molecular structure of 1,N6-ethenoadenosine hydrochloride

The X-ray structure of 1,N6-ethenoadenosine hydrochloride, C12H14N5O4Cl, has been determined from three-dimensional diffractometer data and refined by full-matrix least-squares techniques. The crystals are monoclinic:P21 No. 14,a=6.1540(5),b=18.511(1),c=6.7412(4) A,β=112.602(5)°,andZ=2; finalR=0.045 for 2662 observed reflections. The crystal and molecular structure of ∈ Ado·HC1 is very similar to that of Ado·HC1. On the other hand, the dimensions and conformation of the ∈ Ado·H+ cation are drastically different from those of Et ∈ Ado·H+. The ∈ adenosine·H+ moiety is not planar but has an S shape. The ribose is 2′-endo-3′-exo puckered, with ag+ side chain; the glycosidic torsion angle is in theanti region. The structure contains a three-dimensional network of H bonds in which also C-H⋯A interactions seem to play an important role. There is no base stacking in the structure.

Anisotropic scaling of three-dimensional intensity data

Three-dimensional diffractometer data collected from single crystals of large and anisotropic mosaic spread were shown to suffer from severe systematic errors. The application of anisotropic scaling of the structure factors in the refinement process proved to be very useful in correcting these errors, yielding more accurate parameters, comparable to those obtained from high- quality crystals.

Crystal structure of 1-(mesityl-2-sulphonyl)-3-nitro-1,2,4-triazole

The crystal structure of 1-(mesityl-2-sulphonyl)-3-nitro -1,2,4-triazole (1a) has been determined from three-dimensional diffractometer data. The triclinic unit cell, P, has dimensions a= 8.001(1), b= 8.140(2), c= 12.892(1)A, α= 98.22(1)°, β= 105.49(1)°, γ= 102.12(1)°, and Z= 2. The structure was solved by the heavy atom method and refined to R 0.0736 for 2 926 reflections (Fo > 3σFo). The crystal structure confirms that the product of reaction of 3-nitrotriazole and mesitylenesulphonyl chloride is 1-(mesityl-2-sulphonyl)-3-nitro-1,2,4-triazole.

Crystal and molecular structure of a 4,5-dimethyoxbilindione derived from etiobiliverdin-IVγ: a possible model compound for the phytochrome chromophore

The structure of a synthetic bile pigment, 3,8,12,17-tetraethyl-4,5-dimethoxy-2,7,13,18-tetramethyl-4,5-dihydrobilin-1,19(21H,24H)-dione, C33H44N4O4, has been determined using three-dimensional diffractometer data. It crystallizes in the triclinic space group P with a= 12,755 (2), b= 12.944(s), c= 12.615(2)A, α= 112.27°(2), β= 113.76°(2), γ= 75.45°(2), Z= 2. There is one-half of an n-hexane molecule of crystallization present per formula unit. The structure was solved by direct methods and refined by full-matrix least squares to yield a final R factor of 0.105. The compound, which could be considered as a model for the far-red form (Pfr) of the phytochrome chromphore, belongs to the class of bile pigments known trivially as bilipurpurins. Three of the four pyrrole rings form a conjugated system which is not strictly planar, but is quasi-helical in nature. The fourth ring which is joined to the others by an sp3 carbon atom, is considerably out of the plane of the other three. Bond lengths and angles show a large degree of bond fixation. There is intermolecular hydrogen bonding so that the molecules form hydrogen-bonded dimers.

A structural profile of the bis(2,2′-bipyridyl)monochlorocopper(II) cation. Crystal structures of bis(2,2′-bipyridyl)monochlorocopper(II) perchlorate and the nitrate trihydrate

The crystal structures of the title compounds [Cu(bipy)2Cl][ClO4], (1), and [Cu(bipy)2Cl][NO3]·3H2O, (2), have been determined by X-ray diffraction methods using three-dimensional diffractometer data; the structures were solved by heavy-atom techniques and successive Fourier synthesis. Compound (1) crystallises in the monoclinic space group P21/c with a= 10.761(5), b= 12.253(5), c= 16.990(5)A, β= 112.18(5)°, Z= 4, and (2) crystallises in the monoclinic space group P21/a with a= 14.305(5), b= 21.213(5), c= 8.234(5)A, β= 114.90(4)°, Z= 4. The [Cu(bipy)2Cl]+ cation in both (1) and (2) involves a square-pyramidal distorted trigonal-bipyramidal CuN4Cl chromophore with the distortion in (1) greater than in (2). From a correlation of the bond-length and bond-angle distortion of the structures of five[Cu(bipy)2Cl]+ cation distortion isomers a structural profile has been constructed between a near regular trigonal-bipyramidal CuN4Cl chromophore of C2 symmetry, and a square-pyramidal chromophore. The electronic reflectance spectra have been established as an ‘electronic criteria of stereochemistry’ for the CuN4Cl chromophore, which involves a single peak at 12 500 cm–1 for the trigonalbipyramidal geometry and twin peaks at 13 240 and 10 470 cm–1 for the square-pyramidal distorted structure.

Non-stoichiometric, hydrothermally synthesized cliffordite

The structure of hydrothermally synthesized cliffordite, approximate formula UTe3O9, space groupPa3-T 6 ,a=11.335(5) A was refined toR=0.053 with 501 independent three-dimensional diffractometer data. A full matrix least squares refinement yielded for one of the two U-positions a site occupancy factor of 0.82. A quantitative electronprobe microanalysis confirmed the corresponding U:Te ratio. A discussion of the charge balance is given. From reflectivity measurements the refractive indexn of cliffordite was determined to be 2.25(2) for λ=5890 A.

Préparation et structure cristalline d'un nouvel oxychlorure d'uranium: Le dioxypentachlorodiuranium, U 2O 2Cl 5

The preparation of a new uranium oxychloride, U2O2Cl5, is described. The compound is orthorhombic, Cmmm, with a=8.431(3) , b=13.663(3) , c=4.106(2) , Z=2, Dm=4.76 g cm−3, Dx=4.81. The structure was solved from three-dimensional diffractometer data with Patterson and Fourier syntheses and full-matrix least-squares refinement. The final R value is 0.072 after absorption correction. The structure consists of (UCl4/2Cl1/2O2/2)∞2 layers parallel to the (010) plane and linked in the b direction by bridging Cl atoms. The uranium atoms show noninteger formal valence while they are structurally equivalent; their coordination polyhedra are regular pentagonal bipyramids. Structural relationships among PaCl5, β-U3O8, U2O2Cl5, and RbIn2F7 are discussed in terms of MX7 entities.

Spectroscopic study and x-ray structure of bis(N-methylimidazole)bis(2,4,6, trichlorophenolato)cobalt(II)

The preparation, spectroscopic study and X-ray structure of the mixed-valence compound Pt(NMIz) 4− PtCl 6 are described; NMIz stands for N-methyl-imidazole. The crystal and molecular structure has been determined by a single crystal X-ray analysis using three-dimensional diffractometer data. The compound crystallizes in the triclinic system, with four formula units in the unit cell, space group F 1 and lattice parameters a = 15.228(11), b = 17.855(12), c = 11.177(8) Å, α = 91.98(6), β = 106.94(6), γ = 115.76(7)°. The structure was solved and refined using the heavy-atom method and subsequent least-squares techniques. Refinements using 2335 observed reflections (Mo-Kα radiation) led to final values for R and R w of 0.077 and 0.075 respectively. The Pt(II) ions are surrounded in a square-planar geometry by four NMIz ligands (Pt−N = 1.986−2.012(14) Å and N−Pt−N = 92.6(6)°). Pt(IV) is octahedrally coordinated by the six Cl − ions (Pt−Cl = 2.313−2.323(6) and Cl−Pt−Cl = 88.3−89.9(2)°). In addition there is an interaction between the Pt(NMIz) 2+ 4 ions and the PtCl 2− 6 ions (with Pt⋯Cl = 3.538(5) Å and Pt(II)⋯Cl-Pt(IV) = 144.1°) and Pt(II). Pt(IV) = 5.588 Å), resulting in chain-type behaviour along the c-axis. Optical, infrared and far-infrared spectra agree with this structure. No clear intervalence charge-transfer absorption could be detected which might be related to the relatively long Pt(II)⋯Pt(IV) distance in this compound.

Crystal structure and electronic properties of ammine[tris(2-aminoethyl)amine]copper(II) diperchlorate and potassium penta-amminecopper(II) tris(hexafluorophosphate)

The crystal structure of the title compounds [Cu(tren)(NH3)][ClO4]2(1) and K[Cu(NH3)5][PF6]3(2) have been determined by X-ray diffraction methods using three-dimensional diffractometer data; the structures were solved by heavy-atom techniques and successive Fourier synthesis. Compound (1) crystallises in a cubic unit cell, space group P213, with dimensions a= 11.626(3)A and Z= 4, and (2) crystallises in the orthorhombic unit cell, space group Imma with dimensions, a= 14.90(1), b= 11.79(1), c= 10.57(1)A, and Z= 4. The cation in (1) has a trigonal-bipyramidal molecular structure with strict C3 symmetry while that in (2) has a square-based pyramidal molecular structure with strict C2v symmetry. The polycrystalline and single-crystal electronic properties for these two σ-bonding CuN5 chromophores are reported and related to the one-electron energy levels for the two stereochemistries, using extended-Huckel molecular-orbital calculations, and correlated with earlier data on high-symmetry five-co-ordinate CuN5 chromophores.

Syn- and anti-Conformation in oxodipyrromethenes: crystal and molecular structure of 3,4-dimethyl-2,2′-pyrromethen-5(1H)-one and its N-methyl derivative

The structure of two oxodipyrromethenes have been determined from three-dimensional diffractometer data. One is 3,4-dimethyl-2,2′-pyrromethen-5(1H)-one, C11H12N2O (I), which crystallizes in the monoclinic space group P21/n with a= 13.597(1), b= 5.809(1), c= 12.558(1)Å, β= 101.29(1)°, Z= 4. The second is a derivative of this compound in which one of the pyrrole nitrogen atoms is methylated. This is 1′,3,4-trimethyl-2,2′-pyrromethen-5(1H)-one, C12H14N2O, (II). It also crystallizes in P21/n with a= 7.122(1), b= 22.873(1), c= 7.012(1)Å, β= 104.64(2)°, Z= 4. Both structures were solved by direct methods and refined by full-matrix least squares. The isomers obtained both had the Z-configuration, but in (I), the nitrogen atoms are syn, while in (II), they are anti. Both compounds show relatively small deviation from planarity, but (II) shows larger deviations than (I). Both form hydrogen-bonded dimers between the lactam oxygen atom and pyrrole nitrogen atoms. A comparison of the structures in the solid state and in solution indicates the difference in energy between a planar and twisted conformation is small.

Conformational studies. Part 7. Crystal and molecular structure of 17β-bromoacetoxy-19-nor-5α-androstan-3-one and 17β-bromoacetoxy-5α-androstan-3-one

The crystal and molecular structures of the title compounds have been determined by X-ray crystallography. Whereas the 19-nor-derivative (1) C20H29BrO3, crystallises in the orthorhombic system, space group P212121 with Z= 4 in a unit cell of dimensions a= 6.134(1), b= 12.580(2), and c= 25.297(3)A, the other (2) C21H31BrO3, crystallises in the monoclinic space group P21 with Z= 2 in a unit cell a= 12.972(2), b= 7.321(1), c= 10.580(2)A, β= 99.71(1)°. Both structures were solved by the heavy-atom method and refined by full-matrix least-squares calculations from three-dimensional diffractometer data, to R 0.961 for 1 057 reflections (1), and R 0.042 for 1 075 reflections (2). The conformation of ring A in both molecules is affected by intramolecular packing effects. Ring A in (1) is abnormally flattened whereas in (2) it is more puckered than expected. Bond lengths and angles are normal.