The synthesis and X-ray structural studies of 2-cholesteryl-2-thio-1,3,2-oxathiaphospholane and 2-cholesteryl-2-thio-1,3,2-dithiaphospholane

Two thiophospholane derivatives of cholesterol: 2-cholesteryl-2-thio-1,3,2-oxathiaphospholane (1) and 2-cholesteryl-2-thio-1,3,2-dithiaphospholane (2) were synthesized as new reagents for introducing a cholesteryl moiety at the 5-end of oligonucleotidesvia the phosphorothioate or phosphorodithioate bond. Compounds1 and2 were subjected to structural studies by X-ray methods. Both compounds crystallized in the orthorhombic system, space group P2₁2₁2₁,1 witha=6.283(1) Å,b=12.067(1) Å,c=38.983(3) Å,2 witha=6.371(1) Å,b=11.971(1) Å andc=39.502(3) Å. The five-membered heterocyclic rings of both compounds attain a half-chair conformation in the solid state. In structures of1 and2 a disorder of some atoms is observed. The absolute configuration at the phosphorus atom in1 of the components of diastereoisomeric mixture has been established.     

Crystal structure of (E)-5-hydroxypyrrolizidin-3-one and (Z)-5-thioketalpyrrolizidin-3-one

The crystal structures of (E)-5-hydroxypyrrolizidin-3-one (2) and (Z)-5-thioketalpyrrolizidin-3-one (3) have been determined by single-crystal x-ray diffraction techniques and refined by full-matrix least squares. Molecule2 crystallizes in the monoclinic space groupP2₁/a(No. 14) witha=7.887(3) Å,b=9.788(5) Å,c=9.316(4) Å,=100.6(1), andZ=4. Molecule 3 crystallizes in the monoclinic space groupP2₁/c witha=12.947(14) Å,b=10.553(14) Å,c=9.629(14) Å,=101.4(1), andZ=4. The calculated density for both molecules is 1.33 g cm^–1. FinalR-factors were 5.1% for2 and 8.59% for3. The x-ray results showed that a change in configuration occurred in the reaction going from2 to3.     

Crystal structure of rosmanol-9-ethylether

The title compound: 2H-10,4a-(epoxy-methano)-phenantren-12-one-1,3,4,9,10,10a-hexahydro-5,6-dihydroxy-9-etoxy-1,1-dirnethyl-7-(1-methylethyl), was isolated fromSalvia officinalis L. andHyssopus officinalis L. C₂₂H₃₀O₅, orthorhombic, P2₁2₁2₁, (No. 19)a=8.309(1),b=11.320(2),c=22.060(3) Å,V=2075.0(9) ų,Z=4,D _x=1.199 g·cm^–3, (CuK)=1.54184 Å,=6.43 cm^–1, F(000)=808,T=296(1) K. The structure was solved by direct methods and refined toR=0.047 for 1824 observed reflections collected on a CAD-4 diffractometer. In the course of structure refinement conformational disorder of the isopropyl moiety and the terminal methyl group pertaining to the ethoxy ligand was established. They result altogether in four different conformers.Alternatively it can be termed 9-ethoxyrosmanol.     

Structure of 2-hydroxymethyl-4-tert-butylphenol; comparison with 2-hydroxymethyl-4-isopropylphenol

2-hydroxymethyl-4-tert-butylphenol and 2-hydroxymethyl-4-isopropylphenol are isomorphous; they crystallize in the tetragonal system, space groupI4₁/a (No. 88); cell parameters area=b=25.205(4) Å, forc=6.705(2) Återt-butyl derivative anda=b=24.340(5) Å,c=6.471(1) Å for the isopropyl derivative. The structures were determined and refined usingShelx 76. The respectiveR values are 0.068 and 0.076. Thetert-butyl substituent is disordered with two possible orientations. Intramolecular interactions are due to H bonds around the 4 axis.     

NMR studies and X-ray crystallography of galdosol 5-methyl ether from Salvia officinalis L.

The title compound 2H-10,4a-(epoxy-methano)-phenantren-12-one-l,3,4,9,10,10a-hexahydro-6-hydroxy-5-methoxy-9-keto-1,1-dimethyl-7-(1-methylethyl) isolated fromSalvia officinalis L. have been investigated by nuclear magnetic resonance (NMR) spectroscopy and X-ray analysis. Investigation of¹H and¹³C NMR, homonuclear (COSY) (¹H-¹H) and heteronuclear (¹H-¹³C) spectra, permitted the unambiguous assignment of the¹H and¹³C spectra, what gave the possibility to resolve the signals of similar natural products. Crystal data are: C₂₁H₂₆O₅,M _r=358.43, orthorhombic,P2₁,2₁,2₁, (No. 19),a=10.671(2),b=11.976(3),c=14.601(5)Å,V=1865.9(9)ų,Z=4,D _x=1.276 mg^–3, (MoK)=0.7107 Å,=0.84 cm^–1, F(000)=768,T=293(1) K. The structure was solved by direct methods and refined toR=0.041 for 1832 observed reflections collected on CAD-4 diffractometer.     

Crystal structures of twoN-substituted 2-thioxo-1,3-dithiole-4-carboxamides

The two closely related compoundsN,N-dimethyl 5-(methylthio)-2-thioxo-1,3-dithiole-4-carboxamide1 andN-(p-methoxy-phenyl)-N-methyl 5-(methylthio)-2-thioxo-1,3-dithiole-4-carboxamide2 have been characterized by X-ray crystal structure determination. Crystal data for1: triclinic, ,a=6.767(1),b=12.594(2),c=6.648(1) Å, =101.38(1), =93.37(2), =79.62(1)°,V=546.2 ų,Z=2. Crystal data for2: monoclinic, Cc,a=19.836(4),b=6.057(1),c=15.860(3) Å, =127.61(3)°,V=1509.5ų,Z=4. The molecular structures of1 and2 show remarkable differences concerning the conformational behavior. These differences are related to the nature of the substituents at the nitrogen atom. The presence of an aromatic system in2 leads to an almost planar arrangement of the -oxoketene dithioacetal moiety. This effect is accompanied by a short intramolecular S...O contact of 2.648(2) Å. In the absence of an aromatic system, as is the case for compound1, neither a resonance effect along the -oxoketene dithioacetal fragment nor a short S...O distance is observed.     

Crystal structures of the new diphosphates,K2NiP2O7 and K6Sr2Ni5(P2O7)5

Crystalline K₂NiP₂O₇ (I): monoclinic, P2₁,a=9.230(2),b=17.540(8),c=8.319(9)Å, =91.44(2)°,Z=8,d _calc=3.067 g cm^–3, MoK =0.71069Å,R/R _w=6.5/9.4%, is characterized by the existence of face sharing NiO₆ octahedra with Ni–Ni separation of 2.827 Å (Ni–O; 1.93(2)–2.17(2)Å). K⁺ is seen in sites of seven, six, and fivefold coordination (K–O, averages; 2.83(2), 2.81(2), and 2.77(2)Å, respectively) P₂O₇ ^4– groups are observed in semieclipsed conformation. K₆Sr₂Ni₅(P₂O₇)₅ (II) crystallizes in monoclinic space group P2₁/c;a=11.038(7),b=9.533(13),c=7.438(2)Å, =100.13(4)°,D _calc=3.309 g cm^–3,Z=2,R/R _w=6.4/8.1%. Nickel atoms are distributed on planes parallel to the crystallographic (100) plane at =0 and =0.5. On the planes, =0, Ni²⁺ ions form successive linked trimers of edge sharing NiO₆ octahedra (Ni–Ni, 3.018(1), 3.008(1)Å; Ni–O, av 2.07(2)Å). The intermediate planes (=0.5) contain isolated and six coordinate Ni²⁺ ions (Ni–O av. 2.09(2)Å). Seven-coordinate potassium ions (K–O, av. 2.74(2)Å) are located on intermediate planes at =0.25 and 0.75. P₂O₇ ^4– groups are found in eclipsed conformation. Strontium atoms are located between nickel and potassium planes and are surrounded by seven oxygen atoms (Sr–O, av. 2.586(2)Å).     

The structures of some iminium salts. Crystal structures and13C NMR studies of 3-aryl-2-propenylideniminium salts

The X-ray crystal structures ofE-N, N-dimethyl-3-phenyl-2-propenylideniminium perchlorate,1, andE-N, N-dimethyl-3-(p-methoxyphenyl)-2-propenylideniminium perchlorate,2, have been determined.E-N,N-dimethyl-3-phenyl-2-propenylideniminium perchlorate, (C₁₁H₁₄N⁺)(ClO₄ ^–),1, is orthorhombic:Pmcn (No. 62)a=6.595(1),b=18,288(4),c=10.216(2) Å,Z=4.E-N, N-dimethyl-3-(p-methoxyphenyl)-2-propenylideniminium perchlorate, (C₁₂H₁₆NO⁺)(ClO₄ ^–),2, is triclinic:P1 (No. 2) with cell dimensionsa=6.862(1),b=9.830(2),c=13.376(3) Å,=119.05(1),=114.99(2), =90.79(2)°, andZ=2. Data for both crystals were collected with the use of MoK radiation and a Syntex P2₁ diffractometer. The crystal structures were solved by standard methods and refined toR ₁=0.0688,R ₂=0.0772 for1 andR ₁=0.0790 andR ₂=0.0757 for 2 based on 869 and 1765 independent reflections, respectively. The bond distances are consistent with a highly localized structure with the positive charge situated principally in the iminium moiety. The¹³C NMR spectra of these salts were obtained on the crystalline solids by CPMAS methods. Since the^13C chemical shifts of the salts were very similar, in both solution and solid states, it was concluded that the structures of the salts were comparable in both phases and were analogous.     

Synthesis and characterization of a novel pentacyclic C16 diketone and derivatives

The syntheses and crystal structures of pentacyclo[9.4.1.0^5,14.0^7,13.0^12,15]hexadecane-3,9-dione (2), a novel C₁₆ diketone with potential inclusion ability, and the products of the reaction of2 withn-butyllithium andmeso-erythritol (i.e.,meso-1,2,3,4-butanetetrol) are described. Crystal data:2·H₂O, orthorhombic,Pmmn,a=10.7385(8),b=9.0188(6),c=6.8411(4)Å,V=662.55(7)ų, andR=0.039 (379 reflections);3 (product from reaction withn-butyllithium), triclinic,P¯1,a=8.7192(7),b=10.9351(8),c=12.1842(8)Å,=68.933(5),=75.850(6), =80.309(6)°,V=1047.0(1)ų, andR=0.081 (1811 reflections);4 (product from reaction with erythritol), triclinic,P¯1,a=7.7224(8),b=10.1976(8),c=10.7021(9)Å,=85.405(7),=85.766(8), =76.056(7)°,V=814.0(1)ų, andR=0.052 (1471 reflections).     

Crystal and molecular structure of 1-phenyl-3-(2-hydroxyphenylamino)-2-buten-1-one,C16H15NO2

Orange, yellow, and colorless crystals were obtained for the title compound. The orange crystals are triclinic, space groupP¯1,a=9.181(2),b=10.734(2),c=15.245(3) Å,=73.06(2),=79.21(2), =67.83(2)°,V=1325.9(5) ų,Z=4. Two different symmetry-independent molecules (moleculeA andB) were determined in the crystal unit. The conformation ofA is stabilized by an intramolecular H bond from the amino NH to the keto and phenolic O atoms [1.89(2) and 2.38(2) Å, respectively]. The conformation ofB is stabilized by only one intramolecular H bond, from the amino NH to the keto O atom [1.925(2) Å]. The colorless crystals (moleculeC) are monoclinic, space groupP2₁/n,a=11.883(3),b=11.004(3),c=10.053(3) Å,=95.93(3)°,V=1307.5(6) ų,Z=4. This conformation is stabilized by one intramolecular H bond, the same as in B, with N-HO, 1.84(3) Å. An intermolecular H bond is observed forA,B, and C, O-HO, 2.634(2), 2.640(2), and 2.697(2) Å, respectively. The yellow crystals are adducts with ethanol (¹H NMR, infrared and GC measurements).     

Crystal structures of two azo compounds, 2-methyl-2-(4-bromphenylazo)-1,3-indandione and 2-methyl-2-(4-ethoxyphenylazo)-1,3-indandione

In the two title compounds, the 2-methyl-1,3-dioxoindan-2-yl and 4-(brom; ethoxy) phenyl groups aretrans with respect to one another. The phenyl ring and the azo group are not coplanar in the two molecules. The five-membered rings of the two compounds adopt an envelope conformation. The crystallographic parameters are as follows: 2-Methyl-2-(4-bromphenylazo)-1,3-indandione (I): monoclinic, P2₁/a witha=8.098(2),b=14.442(2),c=12.554(1)Å, =100.55(2)^o, andD _calc=1.58 g cm^–3 forZ=4; 2-methyl-2-(4-ethoxyphenylazo)-1, 3-indandione (II): monoclinic, P2₁/a witha=8.258(2),b=14.449(1),c=13.559(2)Å, =101.19(1)^o, andD _calc=1.29 g cm^–3 forZ=4.     

Crystal and molecular structures of 5,7-dimethyl-1,8-naphthyridine-2-ol (=LH) and of its mercury (II) complex HgL2 and synthesis of some lanthanide/HgL2 heterometallic complexes

The crystal structures of the title compounds have been determined by single crystal diffraction methods. Crystals of 5,7-dimethyl-1,8-naphthyridine-2-ol (1) are monoclinic, space groupP2₁/n witha=7.336(2),b=8.989(2),c=13.125(3)Å,=95.72(3)°,V=861.2(4)ų,Z=4,D _c =1.34 g cm^–3, finalR=0.052. The molecules are linked in pairs by two N-HO hydrogen bonds, and these dimers are stacked in a discontinuous, stepped fashion. Crystals of HgL₂ (2) are monoclinic space groupP2₁,/c witha=4.044(2),b=12.147(2),c=18.093(5)Å,=93.32(2)°,V=887.3(4)ų,Z=2,D _c =2.05 g cm^–3, finalR=0.051. In2 the mercury binds to N(1) to form a linear N-Hg-N coordination geometry, and the HgL₂ molecules form a continuous stacked structure. The syntheses of the compounds ML₄(NO₃)₃·H₂O (M=Nd, Gd, and Er), PrHg₂L₄(NO₃)₃, andM ₂Hg₃L₆(NO₃)₆ (M=Gd, Er) are also reported.     

Synthesis and X-ray structures of [H3O+·18-crown-6] n [MCl 4 n− ]; (M=Fe,n=1;M=Co,n=2); compounds which form liquid clathrates with aromatic solutions

The title compounds, [H₃O⁺·18-crown-6][FeCl ₄ ^– ] (1), and [H₃O⁺·18-crown-6]₂[CoCl ₄ ^2– ] (2), were prepared by air oxidation of Fe(CO)₅ for1, and Co₂(CO)₈ for2, in the presence of 18-crown-6, H₂O and HCl(g) in toluene. Liquid clathrates formed immediately for both species:1·4.3 C₇H₈ and2·3.7 C₇H₈.1 crystallizes in the orthorhombic space group P2₁ma witha=10.357(1),b=11.824(1),c=8.961(1) Å, andD _c=1.46 g cm^–3 forZ=2. Refinement based on 935 observed reflections led to a finalR value of 0.089.2 crystallizes in the monoclinic space group C2/c witha=16.225(1),b=11.522(1),c=20.136(1)Å, =97.75(2)^o, andD _c=1.37 g cm^–3 forZ=4. Refinement based on 1322 observed reflections led to a finalR value of 0.11.     

Crystal structures of N-(2-aminoethyl)-1-naphthaleneneacetamide nitrate and hydrogen tartrate dihydrate

Nitrate (1): C₁₄H₁₇N₂O⁺·NO ₃ ^– , orthorhombic, Pbca,Z=8,a=9.6924(4),b=27.664(2) andc=10.8589(6)Å.Hydrogen tartrate dihydrate (2): C₁₄H₁₇N₂O⁺·C₄H₅O ₆ ^– ·2H₂O, orthorhombic, P2₁2₁2₁,Z=4,a=7.6703(5),b=7.9368(4) andc=31.953(2)Å. In the solid state, cation conformation differ due to molecular flexibility, very different anionic environments, and resultant hydrogen bonding patterns. Despite these differences, the two structures maintain the same separations (about 7.35 Å) of the two most distant potential pharmacophoric groups, i.e., the aromatic ring and the protonated amine group.     

On the optical resolution of bicyclic enones through host-guest complex formation: The crystallographic result

The structures of two molecular inclusion complexes have been elucidated by X-ray crystallography from single crystal diffraction data. Compound (1): (–)-(R,R)-trans-4,5-bis(hydroxy-diphenylmethyl)-2,2-dimethyl-1,3-dioxacyclopentane·(–)-R-6-methylbicyclo[4.4.0] dec-1-ene-3-one, C₃₁H₃₀O₄·C₁₁H₁₆O, is orthorhombicP2₁2₁2₁,a=9.606(2),b=9.708(1),c=36.628(3) Å,V=3415.8(8) ų. Compound (2): (–)-(R,R)-trans-4,5-bis(hydroxy-diphenylmethyl)-2,2-dimethyl-1,3-dioxacyclopentane. (–)-R-6-methylbicyclo[4.4.0]dec-1-ene-3,7-dione, C₃₁H₃₀O₄·C₁₁H₁₄O₂, is orthorhombicP2₁2₁2₁,a=9.671(1),b=9.691(2),c=36.526(4) Å,V=3423.3(9) Å₃. Each structure was solved by direct methods and refined to final R values of 0.051. In each structure there is host-host and host-guest hydrogen bonding: despite the existence of a second H-bond acceptor in the guest of (2), the structures of (1) and (2) are isomorphous; the thermal properties of (1) and (2) have been characterized by DTA and TGA thermograms.     

Phenylmercury(II) dithiophosphates. Crystal structure of (O,O′-diethyldithiophosphate) phenylmercury(II)

The phenylmercury(II) derivatives PhHgS₂P(OR)₂ (R=C₂H₅, C₆H₁₁ and C₆H₅) have been synthesized. (O,O-diethyldithiophosphate) phenylmercury(II), C₁₀H₁₅HgO₂PS₂, crystallizes in the monoclinic space groupP2₁/c (n° 14) witha=7.330(5),b=18.085(2),c=11.552(4)Å,=105.96(5)°,V=1472.3(6)ų,Z=4,D=2.088 g.cm^–3. The mercury atom is coordinated to the phenyl carbon atom and to a ligand sulphur atom in an almost linear arrangement (C-Hg-S angle, 176.0(2)°. The ligand is almost monodentate, its second sulphur atom only being involved in a weak secondary intermolecular bond.IR and Raman studies of the other two compounds suggest the same coordination scheme. Positive ion FAB and¹³C,³¹P and¹⁹⁹Hg NMR spectra are also discussed.     

Crystal structures of three 1-arylpropane-1,2-diol 2-aryl ether derivatives and the acetate of 2,6-dimethoxy-4-(1-(E)-propenyl)phenol

The crystal structures ofthreo-2-[2,6-dimethoxy-4-(1-(Z)-propenyl)phenoxy]-1-(4-hydroxy-3,5-dimethoxyphenyl)-1-propanol (7b),threo-2-(2,6-dimethoxy-4-propylphenoxy)-1-(3,4-5-trimethoxyphenyl)-1-propanol (7c), the diacetate oferythro-2-[2,6-dimethoxy-4-(1-(Z)-propenyl)phenoxy]-1-(4-hydroxy-3,5-dimethoxyphenyl)-1-propanol (8d) and the acetate of 2,6-dimethoxy-4-(1-(E)-propenyl)phenol (9) have been determined by single-crystal X-ray diffraction methods;7b,7c, and8d are structurally closely related to a class of optically-active neolignans of 1-arylpropane-1,2-diol 2-aryl ether type occurring in plant extracts. The reflection intensities were recorded at room temperature for7b and8d, at -140°C for7c and at -120°C for9. Compound7b crystallized as needles in the orthorhombic space groupPna2₁ witha=27.055(3),b=11.850(8),c=6.717(4)Å andZ=4.R became 0.041 for 1792 observed [I>3(I)] reflections used in the refinement of the structure. Compound7c crystallized as prisms in the monoclinic space groupP2₁/a witha=12.565(4),b=13.96(1),c=12.846(7)Å,=93.86(3)° andZ=4. The refinement gaveR=0.051 for 2101 observed [I>3(I)], unique reflections. Compound8d crystallized as prisms in the monoclinic space groupP2₁/n witha=13.182(4),b=8.518(5),c=23.322(5)Å,=106.12(2)° andZ=4. The finalR-valuebecame 0.042 for 2131 observed [I>3(I)], unique reflections. Compound9 crystallized as prisms in the orthorhombic space groupPca2₁ witha=18.216(4),b=9.483(3),c=7.416(2)Å andZ=4. TheR-value became 0.038 for 1502 observed [I>3(I)], unique reflections. The crystals of7b are stabilized by moderately strong hydrogen bonds. All the 1-arylpropane-1,2-diol 2-aryl ethers examined adopted conformations in which the aromatic groups tend to be as remote as possible. Observed double bond lengths in the propenyl groups of the compounds examined (1.30 Å) deviate significantly from the expected value (1.34 Å). The cause of this discrepancy is discussed.     

Crystal structure analyses of bis(triphenyl- phosphoranyliden)ammonium bis(pentafluoroethyl) argentate, [Ph3P=N=PPh3][Ag(C2F5)2] and bis[bis(triphenylphosphoranyliden)ammonium] tetrachloro-diargentate, [Ph3P=N=PPh3]2[ClAg(μ-Cl)2AgCl]

Bis(triphenylphosphoranyliden)ammonium bis(pentafluoroethyl)argentate, [Ph₃P=N= PPh₃][Ag(C₂F₅)₂] (1) and bis[bis(triphenylphosphoranyliden)ammonium]tetrachloro-diargentate, [Ph₃P=N=PPh₃]₂[ClAg(μ-Cl)₂AgCl] (2) were crystallized from the reaction mixture of pentafluoroethylsilver(I) and bis(triphenylphosphoranyliden)ammonium chlo-ride. Crystallization of 1 occurs in the centrosymmetric monoclinic space group P2₁/c (No. 14) with a = 17.083(2) Å, b = 11.600(2) Å, c = 19.833(2) Å, β = 109.66(1)°, V = 3700.8(7) ų, Z = 4. 2 crystallizes in the centrosymmetric orthorhombic space group Pbca (No. 61) with a = 19.540(1) Å, b = 15.926(1) Å, c = 20.160(1) Å, V = 6273.6(3) ų, Z = 8.     

Conformations of 2-C:1-N-carbonyl-2-deoxy-d-glycopyranosylamines

Geometry and molecular conformation of theN-toluenesulfonyl1 andN-acetyl-2 derivatives of peracetylated 2-C:1-N-carbonyl-2-deoxy--d-glucopyranosylamine were investigated with the use of X-ray diffraction methods. Compound1 (C₂₀H₂₃NSO₁₀) crystallizes in the monoclinic P2₁ space group, withZ=2 anda=8.238(1),b=7.988(1),c=16.928(2)Å, =99.12(1)°. Compound2 (C₁₅H₁₉NO₉) crystallizes in orthorhombic P2₁2₁2₁ space group withZ=4 anda=8.385(1),b=8.550(1),c=24.000(2) Å. Analysis of differences in bond lengths and angles between compounds1 and2 and other compounds of this class showed that the electronwithdawing effect by the residue located at the nitrogen atom can be manifested by lengthening of the -lactam C-N bonds, with simultaneous shortening of the distance between two carbon atoms at the ring fusion. Semi-empirical calculations suggested that the title compounds displayed two positively charged centers, susceptible for attack of nucleophiles, one at the carbonyl group of -lactam and the second at the anomeric carbon atom. Atomic charges, however, calculated for compounds1 and2 did not explain their different reaction directions during alcoholysis.Part 3. For part 1 and 2, see Refs. 5 and 6.     

The crystal and molecular structures of 2-hydroxy-1-naphthalenecarboxaldehyde and 3-hydroxy-2-naphthalenecarboxaldehyde

The crystal and molecular structures of 2-Hydroxy-1-naphthalenecarboxaldehyde (I) and 3-Hydroxy-2-naphthalenecarboxaldehyde (II) were determined. Compound (I) crystallizes in the space groupP2 ₁/n witha+5.589(2),b+9.352(2), andc+15.490(3) Å, =98.14(3)°, andZ+4. Compound (II) crystallizes inP2 ₁/n witha+16.831(11),b+5.936(3), andc+8.295(3) Å =97.24(5)°. andZ+4. The structures were solved by direct methods, and refined by fullmatrix least squares toR+0.071 andR _w+0.083 forI, andR+0.047 andR _w+0.061 forII.