2,8,10,11-tetrachloro-12-oxahexacyclo-[7.2.1.02,8.03,7.04,11.06,10]dodeca-1,9-diol and disorder and mixed crystals in a system of tetracyclo-[6.3.0.04,11.05,9]undecanone and undecanol derivatives

2,8,10,11-Tetrachloro-12-oxahexacyclo[7,2.1.0^2.8.0^3.7.0^4.11.0^6.10]dodeca-1,9-diol is a strained cage molecule containing six five-membered rings and a four-membered ring. Twenty-five of the internal angles are less than 105° with 6 ranging from 89.5(3) to 97.4(3)°. The base promoted reaction of 3,6-dipyridyl-1,2,4,5-tetrazine with tetracyclo[6.3.0.0^4.11.0^5.9]undecane-3,6-dione yields the monoketone 6,7-[3,6-di(2-pyridyl)-4,5-pyridizino]tetracyclo[6.3.0.0^4.11.0^5.9]-undecan-2-one. This compound crystallizes in the centrosymmetric space group P2₁/n with enantiomers related by a center of symmetry. In the crystal investigated the molecules are disordered with each site containing about 80% of one isomer and 20% of the enantiomer. When the ketone is hydrogenated and the product isolated, two different crystals were found to have a ratio of alcohol to ketone of .71/.29 and .75/.25 or about 3/1. The alcohol and ketone occupy the same sites, but with opposite stereochemistries.     

Crystal and molecular structure ofN,N′-diphenylpiperazine N,N′-dioxide octahydrate

The title compound isN,N-DiphenylpiperazineN,N-dioxide octahydrate, C₁₆H₃₄N₂O₁₀:M _r=414.46, orthorhombic, space groupPnma (No. 62),a=12.327(2),b=9.804(1),c=17.443(4) Å,V _c=2108.1(5) ų,Z=4. The structure was solved by the direct method and refined toR=0.056 for 3032 observed MoK reflections. In theN,N-dioxide molecule, all atoms except those of the methylene groups lie on a crystallographic mirror plane. The piperazine ring takes the chair form, with two N-O bonds oriented axially in atrans configuration. The crystal structure is characterized by strong hydrogen bonding between the water molecules, as well as between theN-oxide groups and water molecules, giving rise to a three-dimensional network structure composed of edge-sharing four-membered, five-membered, six-membered, and fourteen-membered rings.     

Crystal structure of a bulky cyclic sulfite

The structure of the cyclic sulfite derived from the reaction of thionyl chloride withendo-8-hydroxy-exo-8-(endo-8-hydroxypentacyclo[5.4.0.0.^2,6.0^3,10.0^5,9]undec-exo-8-yl)pentacyclo-[5.4.0.0.^2,6.0^3,10.0^5,9]undecane is reported. All bond lengths and angles are consistent with the strained cage geometry. A static disorder of the terminal oxygen was found to be present.     

Ground state structures of molecules “prepared” for phototautomerization: 2,2′-bipyridyl-3,3′-diol and 2,2′-bipyridyl-3-ol

The crystal structures of two molecules undergoing fast intramolecular excited state proton transfer (2,2-bipyridyl-3,3-diol, BP(OH)₂, and 2,2-bipyridyl-3-ol, BP(OH)) are reported and compared with the results ofab initio and molecular mechanics calculations. Strong intramolecular hydrogen bonding is observed in both cases. The pyridyl rings are coplanar in BP(OH)₂, whereas in BP(OH) they form an angle of 3.7°.Dedicated to Prof. R. Zahradnik on the occasion of his birthday.     

Meisenheimer complex from picric acid and diisopropylcarbodiimide

Reaction of picric acid with diisopropylcarbodiimide produces a pale yellow 1:1 adduct N-(2,4,6-trinitrophenyl)-N,N-di(isopropyl)urea (5) and a 1:2 adduct fluorescent red zwitterionic Meisenheimer complex (6) as approximately N,N,N-tri(isopropyl)-4-oxo-6-(isopropyliminio)-2-s-(2H)triazinespiro-1-2,4,6-trinitro cyclohexadienylide. Crystals of (5) are triclinic, P-1 (#2), with a = 10.444(13) Å, b = 15.47(2) Å, c = 17.74(2) Å, = 110.43(9)°, = 99.85(10)°, = 92.78(10)°, V = 2629(6) ų for Z = 6 (three molecules per asymmetric unit). Crystals of (6) are orthorhombic, Pna2₁ (#33), with a = 24.12(4), b = 9.011(19) Å, c = 10.87(2) Å, V = 2362(8) ų for Z = 4. Nitro groups in the Meisenheimer complex are twisted 2–8° from the mean formerly aryl ring plane; in (5), nitro groups are twisted out of the aryl plane by 11–62°. In the Meisenheimer complex, cationic charge is distributed over an iminium/guanidinium group; anion charge is distributed over the cyclohexadienide ring and attached nitro groups.     

Crystal and molecular structure of grayanotoxin VII

The crystal and molecular structure of a grayanotoxin VII is presented. The crystal is monoclinic, space group P2₁, with a = 7.647(1) Å, b = 11.7591(7) Å, c = 10.0873(6) Å, = 91.143(8)°, V = 906.9(1) ų, Z = 2. The structure was solved by direct methods and refined by full-matrix least-squares methods to a final R = 0.057 for 1494 independent reflections. The molecule has a tetracyclic structure consisting of two five-membered, one six-membered, and one seven-membered rings.     

Investigation of lignin models of the biphenyl type by X-ray crystallography and NMR spectroscopy

Lignin models of the biphenyl type have been synthesized and crystal structures of two of them have been determined. The tetraacetate of 5,5-bis(hydroxymethyl)-3,3-dimethoxy-2,2-biphenyldiol crystallizes in space group witha=11.319(2),b=12.232(6),c=9.242(3) Å, =101.66(3)°, =108.14(2)°, =79.08(2)° andZ=2.R=0.036 (2720 observed [I>3(I)] reflections). The acetate of 5,5-di-tert-butyl-2,3,3-trimethoxy-2-biphenylol crystallizes in space group witha=11.972(2),b=21.621(3),c=9.834(1) Å, =91.18(1)°, =113.13(1)°. =98.42(1)°, andZ=4.R=0.050 (8129 observed [I>3(I)] reflections).¹H NMR and¹³C NMR data for the above-mentioned compounds and a third model, the diacetate of 5,5-bis(1-hydroxyethyl)-2,2,3,3-tetramethoxybiphenyl, are reported. Observed signal positions are compared with those calculated on the basis of crystal structure data. The possibilities to obtain structural information about biphenyl structures in lignins from NMR spectra are discussed.     

Synthesis and X-ray structure of 5′-methoxy-2,4,6-trimethyl-2′-nitrosobiphenyl

The synthesis and X-ray crystal structure of 5-methoxy-2,4,6-trimethyl-2-nitrosobiphenyl is reported. The compound (C₁₆H₁₇NO₂) is monoclinic, with a = 11.080(4), b = 16.899(6), c = 15.410(5) Å, = 108.329(5)°, and space group P2₁/n. There are two independent molecules within the crystal. In each of these molecules the two phenyl rings are mutually orthogonal, with interplanar dihedral angles of 85.09 and 89.43° respectively. The nitroso substituents are essentially coplanar with the phenyl ring, with torsional angles of only 3.5 and 2.2°, respectively, while the methoxy groups make angles of 5.2 and 10.0°, respectively, with the phenyl ring.     

The chemistry of the “insoluble red woods.” Part 15. The crystal structures of 7-benzyloxy-6,2′,3′,4′-tetramethoxy- and 2,6,7,2′,3′,4′-hexamethoxy-isoflav-3-ene

The reaction of 7-benzyloxy-6,2,3,4-tetramethoxyisoflavylium perchlorate with 1-(2,4-dimethoxyphenyl)-3-(3,4-dimethoxyphenyl)-prop-l-ene and of 6,7,2,3,4-pentamethoxyisoflavylium perchlorate with the same propene yielded respectively 7-benzyloxy-6,2,3,4-tetramethoxyisoflav-3-ene (5) and 2,6,7,2,3,4-hexamethoxyisoflav-3-ene (7) whose structures have been established by X-ray crystallography. Crystals of (5) are monoclinic, space groupP2₁/a (No. 14) with four molecules in a unit cell of dimensionsa=8.528(2),b=13.294(3),c=19.629(4) Å,=99.92(2)°. Crystals of (7) are also monoclinic, space groupC2/c (No. 15) with eight molecules in a unit cell of dimensionsa=28.088(3),b=10.662(3),c=12.869(1) Å,=97.32(1)°. Both structures were solved by direct methods and refined by full-matrix least-squares calculations to finalR values of 0.053 and 0.041 for 1673 and 1424 observed data for (5) and (7) respectively. The molecular dimensions are in accord with accepted values.For Part 14 see Whalley, W. B., Ferguson, G., and Khan, M. A., (1980)J. Chem. Res. (M), 2219.     

Structure and molecular chirality of the acetonitrile adduct of the 2:1 salt of quinidine with biphenyl 5,5′-dinitro-2,2′-dicarboxylic acid (5,5′-dinitrodiphenic acid)

The molecule of the 21 salt consists of two quinidine cations and the 5,5-dinitrodiphenic anion. Both of the quinidine cations are protonated at the nitrogen atoms of the quinuclidine fragments. Owing to the interlocking hydrogen bonds between quinidine and the dinitrodiphenic ions, a rigid structure of the salt molecule has been formed. The alkaloid molecular conformation around the C(8)-C(9) bond is open. The conformational parameters of 5,5-dinitrodiphenic anion are considerably changed in comparison with the conformation of diphenic acid in the solid state. The absolute configuration of biphenyl 5,5-dinitro-2,2-dicarboxylic anion (R) is defined by the negative torsion angles around the line which connects the centers of both phenyl rings, and is the reverse of that observed in the diphenic acid-quinine salt. The present data confirm the observation that the chirality of the salt is controlled by the chirality of theCinchona alkaloid molecule.     

Synthesis ofcis-[Ru{4,4′-(t-Bu)2bpy}2(PPh3)Cl+][ClO 4 − ] and the crystal structure of its disordered hemiacetonitrile,hemitoluene solvate

The complexcis-[Ru{4,4-(t-Bu)₂bpy}₂(PPh₃)Cl⁺][ClO ₄ ^– ·0.5(toluene)·0.5(MeCN), where 4,4-(t-Bu)₂bpy=4,4-di(t-butyl)-2,2-bipyridyl crystallizes with an ordered racemic mixture of the chiral cations in the centrosymmetric triclinic space group (No. 2). The structure was refined toR=4.42% for those 6426 reflections with 20=5–50^o and |F _o|>6(F). Ruthenium ligand distances are Ru–Cl=2.423(2)Å, Ru–PPh₃=2.346(2)Å and Ru–N=2.056(4)–2.098(4)Å. Both the Ru(II)-containing cation and the perchlorate anion are ordered, but the toluene and acetonitrile exhibit an interesting type of scrambled disorder about the inversion center atx=1,y=1/2,z=0.     

Structure of 3,5-diamino-6-(2,3-dichlorophenyl)-1,2,4-triazine isethionate solvate (lamotrigine isethionate)

The crystal and molecular structure of lamotrigine isethionate, C₉H₈Cl₂N₅ ⁺ .HOC₂H₄SO₃ ^– has been determined by direct methods. The compound crystallizes in the tetragonal space group I4₁/a. The isethionate moiety forms multiple hydrogen bonds to the lamotrigine nucleus, three from one isethionate, two from a symmetry related isethionate and a further two from two different symmetry related molecules. Protonation of N(2) in the triazine ring, not observed in the native lamotrigine structure is presumably associated with the interaction of the isethionate moiety. Both rings in the lamotrigine moiety are essentially planar, with a dihedral angle of 66.08(7)° compared to 80.70° in native lamotrigine. The connecting bond length C(1)—C(6) = 1.493(3) Å also correlates well with values in related compounds (1.480(3) Å) in the native structures.     

Synthesis and structure of the molecular complex between N-(N′, N′-dimethylaminopropyl)phenothiazine hydrochloride and 7,7,8,8-tetracyano-p-quinodimethane (DAPP-TCNQ)

Synthesis, spectroscopic, and X-ray structural analysis of the molecular complex between the N-(N, N-dimethylaminopropyl)phenothiazine hydrochloride, monohydrate, (DAPP) and 7,7,8,8-tetracyano-p-quinodimethane (TCNQ), has been carried out. Crystals of C₂₉H₂₇N₆OSCl are monoclinic, P2₁/c,a=12.190(2),b=7.695(2),c=28.928(3)Å, =91.68(1)°. The molecular complex consists of DAPP as donor binding to TCNQ as acceptor by the thiazine central ring and one of the aromatic rings stacking in parallel planes along thec-axis with an interplanar separation of 3.24Å and 3.16Å, respectively. The electronic and epr spectra of the complex are discussed.     

The structure of 20 oximo-5α-pregnano-16-eno[3,4-C]-1′,2′,5′-oxadiazole (HS976)

The crystal and the molecular structure of the steroidal oxadiazole 20-oximo-5-pregnano-16-eno[3,4-C]-1,2,5-oxadiazole (C₂₁H₂₈N₂O₃) has been determined by direct methods, and refined to a finalR of 0.086 for 3100 observed reflections. The compound crystallizes in space groupP2₁, with cell dimensionsa=18.284(6),b=13.992(4),c=7.370(3)Å,=96.97(3)°;V=1885 ų,Z=4,D _x =1.27 g cm^–3, =1.5418 Å, (CuK =5.95 cm^–1. The two independent molecules are related by a pseudo twofold axis. Both molecules exhibit similar overall topography, rings A, B, C, and D adopting distorted sofa, chair, chair, and distorted envelope conformations, respectively.     

Coordination complexes of 2,6-diarylpyrazines with copper(II) acetate

The coordination chemistry of a series of 2,6- and 2,3-diarylpyrazines with copper(II) acetate is reported. The 2:2 coordination complexes formed between two 2,6-diarylpyrazines and copper(II) acetate are characterized by X-ray crystallography. The structure (2,6-bis(3,5-dimethylphenyl)pyrazine)copper(II) acetate acetonitrile solvate, (C₄₈H₅₂Cu₂N₄O₈) (C₂H₃N) is triclinic, P 1, with a = 7.9685(10), b = 13.1893(16), c = 13.8267(17) Å, = 107.585(3)°, = 103.921(3)° and = 96.759(3)°. The structure of (2-(2,6-dimethylphenyl)-6-(3,5-dimethylphenyl)pyrazine)copper(II) acetate, C₄₈H₅₂Cu₂N₄O₈, is monoclinic, P2₁/c, with a = 8.2196(7), b = 12.5174(11), c = 21.7325(19) Å and = 96.201(2)°.     

The synthesis, characterization, and X-ray crystal structure of trans-bis(1,3-diamino-2-propanolato-N,N′,O)- cobalt(III) perchlorate trihydrate

The crystal structure of [Co(C₃H₉N₂O)₂]ClO₄3H₂O was established by single-crystal X-ray diffraction techniques. The compound crystallized in the monoclinic space group P2₁ with unit cell dimensions a = 6.715(2) Å, b = 12.097(3) Å, c = 9.904(3) Å, = 100.80(3), and z = 2. The final R value for 1359 reflections was 0.039. The 1,3-diamino-2-propanolato ligands are tridentately coordinated to cobalt atoms that have slightly distorted octahedral coordination. The five-membered chelate rings exhibit conformations between pure twist and pure envelope, while the six-membered ring adopts a boat confirmation.     

Crystal structure of (3,3′,4,4′-tetramethyl-1,1′-diphosphaferrocen-2-yl) carboxylic acid and its bis-[W(CO)5] complex·0.5C5H12: Conformation of 1,1′-diphosphaferrocenes

The structures of (3,3,4,4-tetramethyl-1,1-diphosphaferrocen-2-yl)carboxylic acid (1) and its bis-[W(CO)₅] pentane solvate complex (2) have been determined by X-ray analysis. The compound 1 crystallizes in the monoclinic P2₁ /n space group with Z = 4; a = 7.8404(9), b = 14.9441(16), c = 11.7730(14) Å, = 92.773(10)°, V = 1377.8(3) ų, and D_calc = 1.553 g cm^–3. The compound 2 crystallizes in the triclinic space group with two complex molecules and one pentane molecule in the unit cell. Cell parameters: a = 10.7070(2), b = 12.577(2), c = 13.239(3) Å, = 84.00(2), = 77.58(1), = 66.06(1)°, V = 1591.0(5) ų, and D_calc = 2.100 g cm^–3 .The fully eclipsed conformation of the phospholyl rings with P···P secondary bonding of 3.353(1) Å is observed in 1 and a partially eclipsed conformation is found in 2. The 10 possible conformations of 1,1-diphosphaferrocenes were described as the function of conformational parameter and observed geometry of the phospholyl rings.⁷ We suppose that the earlier conclusions concerning the destabilizing nature of 1,1-diphosphaferrocene conformations with < 100° cannot be considered as general. The mode of W – P coordination, the structural changes of 1 by W(CO)₅ coordination, the structural effect of phospholyl rings substitution by the –COOH group, and hydrogen bonds are analyzed.     

Structure of 2,2′-anhydro-3′-O-acetyl-2′thio-1-β-D-arabinofuranosylcytosine hydrochloride1

2,2-Anhydro-3-O-acetyl-2-thio-1--D-arabinofuranosylcytosine hydrochloride crystallizes in space group P2₁2₁2₁ witha=10.373(1),b=14.517(2),c=9.496(1) Å. Reflections were measured on a diffractometer and the structure was solved by direct methods. Least-squares refinement converged atR=0.056 andR _w =0.063. The study of this crystal structure showed that the alterations in the geometry of 2,2-anhydro-1--D-arabinofuranosylcytosine when the bridge oxygen is replaced by sulfur are localized in the region of the fused ring. The angle at the bridge atom decreases to nearly 90°, with concomitant enlargements of about 5°–7° in the angles opposite to the bridge atom. Angle C(1)-N(1)-C(6) decreases by 4°. Also, the amount of double bond character in the bond formed by C(2) and the bridge atom decreases. A survey of the conformational features of S,2-cyclonucleosides and comparison with O,2-cyclonucleosidcs showed that their preferred conformations are the same. However, S,2-cyclonucleosides exhibit a wider range of P and values. This correlates with a greater ease of the sulfur containing five-membered ring to pucker as compared to the oxygen-cyclo ring.This paper is part of the authors' dissertation (Vitali, 1986).     

9[1-(2-Hydroxy ethoxy)-3-hydroxy propyl] guanine: a nucleoside analog

The compound 9[1-(2-hydroxy ethoxy)-3-hydroxy propyl] guanine crystalizes in the tetragonal system, space group P4₁2₁2 with a = 11.106 (1), c = 20.558 (2) Å, and Z = 8. The acyclic chain C1¯O1¯C4¯C5¯O5 is in the extended configuration and the glycosidic torsion angle (C4¯N9¯C1¯O1) is 125.1 (8)°. The molecules are held together by Van der Waal's forces.     

Crystal and molecular structure of a new diterpenyl glycoside from Pteris cretica L.

The crystal and molecular structure of a new diterpenyl glycoside, Ptr-1, is presented. The crystal is triclinic, space group P1, with a = 8.2414(8) Å, b = 13.0826(9) Å, c = 6.1427(8) Å, = 95.345(9)°, = 111.589(8)°, = 96.726(7)°, V = 604.9(1) ų, Z = 1. The structure was solved by direct methods and refined by full-matrix least-squares methods to a final R = 0.049 (Rw = 0.099) for 1872 independent reflections. The molecular structure is based on a glycopyranosyl group and a tetracyclic group. The glycopyranosyl group is -D-allopyranosyl group. The tetracyclic group consists of 1 five-membered and 3 six-membered rings.