Crystal and molecular structures of quinazolines: A ring conformational study

The solid state structures of two dihydropyrimidines (DHPM) viz, 2-[(4-dimethylamino)phenyl]-1-phenethyl-2,3-dihydro-1H-quinazolin-4-one (compound 1) and 1-phenethyl-2p-tolyl-2,3-dihydro-1H-quinazolin-4-one (compound 2) are reported here. The compound 1 belongs to triclinic (P-1) space group with cell parameters a = 7.4314(12) Å, b = 9.9747(16) Å, c = 14.658(2) Å, = 104.142(3), = 102.584(3), = 98.188(3). The compound 2 also belongs to triclinic (P-1) space group with cell parameters a = 9.8707(11) Å, b = 9.9225(11) Å, c = 10.7425(13) Å, = 79.227(2), = 80.568(2), = 63.649(2). The structures show that the substituent at 2-position will play a key role in defining the pyrimidine ring conformation. The central dihydropyrimidine ring in both the structures are affected by conjugation. The sum of the valence angles around all the nitrogens is very close to 360, indicating that the state of hybridization of these atoms is sp². The DHP ring is puckered in such a manner that the atoms N1, C3, C4, C5, and N2 are coplanar and the sixth atom C2 is displaced 0.605 Å (0.18 Å for compound 2) above the least squares plane. The conformation of dihydropyrimidine ring can be described as a sofa with asymmetric parameters C_s[C2] = 6.09 (compound 1) and 4.73 (compound 2), respectively. The phenethyl group has a fully extended conformation with respect to the central pyrimidine ring (N2–C16–C17–C18 174.8(2) and 179.1(6) for compounds 1 and 2, respectively). The substituents on the DHPM ring, dimethylamino-phenyl/p-tolyl groups of compound 1/2 occupy equatorial/axial positions at C2. In the crystal packing, six membered rings form through dimerization using N–HO hydrogen bonding.     

Crystal structures of five policyclic compounds related to the natural product forskolin

(3(Z),4,6a,9a,9b)-(±)-3a,4,6a,7,8,9,9a,9b-octahydro-4,7,7, 9b-tetramethyl-3a-[3-(methoxymethyloxy)-3-methyl-1-butenyl]-5H-naphto[1,8-de]-1,3-dioxin-6-one (I), C₂₂H₃₆O₅,M _r=378.51, monoclinic,P2₁/n,a=6.330(1),b=14.576(2),c=22.837(2)Å,=93.04(1)°,V=2104.1(2)ų,Z=4,D _c=1.19 Mg/m³, (MoK)=0.71069Å,=0.8 cm^–1,F(000)=832,T=298 K,R=0.054 for 1971 observed reflections; (7a,10a,10b,12)-(±)-7a,9, 10,10a,10b,11,12,12a-octahydro-2,2,10,10,10b,12a-hexamethyl-2H,8H-1-benzopyrano[4a,5,6,-de][1,3,2]-benzodioxin-11-one (II), C₂₀H₂₉O₄,M _r=334.5, triclinic,P-1,a=10.595(2),b=12.152(1),c=8.073(1)Å,=106.53(1),=105.65(1), =66.29(1)°,V=897.9(2)ų,Z=2,D _c=1.24 Mg/m³, (MoK)=0.71069Å,=0.8 cm^–1,F(000)=362,T=298 K,R=0.046 for 2848 observed reflections; (7a,10a,10b,12, 12a)-(±)-7a,9,10,10a,10b,11,12,12a-octahydro-2,2,10,10,10b,12a-hexamethyl-2H,8H-1-benzopyrano[4a,5,6-de][1,3,2]-benzodioxin-11, 12-diol (III), C₂₀H₃₂O₅ (two molecules in the asymmetric unit),M _r=352.2, triclinic,P-1,a=12.948(3),b=13.615(3),c=12.197(4)Å,=101.16(2),=111.88(2), =69.48(2)°,V=1863.8(9)ų,Z=2,D _C=1.26 Mg/m³,(MoK)=0.71069 Å,=0.8 cm^–1,F(000)=768,T=298 K,R=0.060 for 4570 observed reflections; 4-acetoxy-4-[[(4a,5,8a)-(±)-hexahydro-4a,6,6-trimethyl-4H-1,3-benzodioxin-4-one]-5-yl]butan-2-one (IV), C₁₇H₂₆O₆,M _r=326.4, monoclinic,P2₁/c,a=10.495(2),b=12.050(2),c=14.216(2)Å,=108.51(1)°,V=1704.8(5)ų,Z=4,D _c=1.27 Mg/m³,(MoK)=0.71069 Å,=0.9 cm^–1,F(000)=704,T=298 K,R=0.049 for2455 observed reflections; (3a,4,5,6,6a,9a,9b)-(±)-4,5-epoxy-decahydro-3, 3a-dihydroxy-2-ethoxy-4,7,7,9b-tetramethyl-naphto-[1,8-bc]-pyran-6-ol-acetate (V), C₂₀H₃₂O₇,M _r=383.5, monoclinic,C2/c,a=10.353(2),b=17.975(3),c=21.188(3)Å,=91.29(1)°,V=3942(1)ų,Z=8,D _c=1.29 Mg/m³,(MoK)=0.71069 Å,=0.8 cm^–1,F(000)=1664,T=298 K,R=0.051 for 2120 observed reflections. We report here the complete structures of four decalin derivatives (compoundsI, II, III, V) and one related compound (compoundIV) synthetized in order to find an efficient synthetic approach for the natural productforskolin.     

Structure of de-oxy corticosterone (4-pregnen-21-ol-3,20-dione)

Synthetic steroid de-oxy corticosterone (4-pregnen-21-ol-3,20-dione) crystallizes in the monoclinic space group P2₁, with a = 11.706(2); b = 11.171(3), c = 13.966(3) Å, and = 100.94(2)°, Z = 4. Ring A tends to acquire the conformation of a half-boat, rings B and C are in the chair configuration, and ring D is a 13, 14-half-chair. The ring junctions B/C and C/D are both trans, whereas the ring junction A/B is quasi-trans. The molecule as a whole is slightly convex toward the -side, with an angle of 16.01(0.36)° between the C10--C19 and C13--C18 vectors. Molecular packing and stacking interactions play the major role in structural association. Cohesion of the crystal is due to van der Waals interactions.     

Crystal structure of tetrahydrocortisol

The crystal structure of tetrahydrocortisol (3, 11, 17,21-tetrahydroxy-5-pregnan-20-one), C₂₁H₃₄O₅, has been determined by X-ray diffraction using CuK radiation. The crystals are orthorhombic, P2₁2₁2₁ witha=7.696(5),b=10.227(2),c=23.688(5) Å and Z=4. The structure was solved by direct methods and refined to a finalR-value of 0.053 with 1714 observed reflections. The rings A, B, C, D arecis, trans, andtrans fused, respectively. The rings, A, B, C, have almost perfect chair conformations and D has a distorted envelope conformation. The steroid skeleton as a whole is somewhat convex toward the -side. The molecules are held together by a three-dimensional network of hydrogen bonds. Despite the similar cell constants and common space group of the title compound with cortisone and 17-hydroxyprogesterone, they are not isostructural.     

Two acetylamino derivatives of 2,4-bis(trichloromethyl)-1,3-benzdioxin showing different types of hydrogen bonding: (a) (C13C)CH⋯O=C and (b) N-H⋯O=C

8-Acetylamino-6-methyl-2,4-bis(trichloromethyl)-1,3-benzdioxin, (I), is monoclinic,P2₁/c,a=15.174(4),b=11.977(7),c=9.911(3)Å,=99.72(2)°. 6-Acetylamino-2,4-bis(trichloromethyl)-1,3-benzdioxin, (II), is monoclinic,P2₁/_n,a=5.927(4),b=40.623(1),c =7.120(3)Å,=91.39(4)°. In compound (I) the imino hydrogen atom is locked in an intramolecular hydrogen bond to the proximate oxygen atom of the heterocyclic ring and is not available for intermolecular hydrogen bonding. Instead the weakly acidic hydrogen atom [Cl₃C-C(2)]H takes part in a hydrogen bond to the carbonyl oxygen atom in another molecule. In compound (II) a normal intermolecular hydrogen bond of the type N-HO=C occurs. The 6-acetylam-ino group is twisted about the (C_Ar-N) bond such that the angles NHO=C, C_ArH_ArO=C, NHOH_ArC_Ar, at the carbonyl oxygen group total 360° (where NH is in the related molecule). The packing in both compounds takes the form of infinite chains and in compound (II) partial overlap of the aromatic ring and the acetylamino group, with very little offset, also occurs.     

Crystal and molecular structures of three modifications of the androgen dehydroepiandrosterone (DHEA)

The crystal and molecular structures of three forms of the androgen DHEA (dehydroepiandrosterone) have been determined by single crystal X-ray diffraction. They are: Form I, a polymorph crystallizing in space group P2₁ withZ=4; Form S1, a hydrate with composition DHEA. (1/4)H₂O, space group C2,Z=8; and Form S4, a methanol half-solvate, DHEA. (1/2)CH₃OH, space group C222₁,Z=8. The A, B, and C steroid ring conformations adopted in the five crystallographically independent DHEA molecules are invariably: chair, 8, 9-half-chair, and chair, respectively, while the D ring conformation ranges from a 14-envelope to a 13, 14-half-chair. In Forms I and S1, intermolecular hydrogen bonding is of the head-to-tail type with water molecules participating as donors in Form S1. In Form S4, DHEA molecules pack in head-to-head fashion, their hydroxyl groups being linked by hydrogen bonding to the solvent hydroxyl group. The hydroxyl H atoms of both DHEA and the included methanol are disordered, giving rise to an unusual linearly-propagating flip-flop hydrogen bonding scheme.     

Thermodynamic vs. kinetic control in the Diels-Alder cycloaddition of cyclopentadiene to 2,3-dicyano-p-benzoquinone

Diels-Alder cycloaddition of cyclopentadiene (1a) to 2,3-dicyano-p-benzoquinone (2a), when performed in methanol solvent at ambient temperature, proceeds with kinetic control to afford 1,4,4a,8a-tetrahydro-5,8-dioxo-1,4-methanonaphthalene-4a,8a-dicarbonitrile (7, 77% yield). However, when this cycloaddition is performed by refluxing an equimolar solution of1a and2a in benzene for 3 h, the product of thermodynamic control, i.e., 1,4,4a,8a-tetrahydro-5,8-dioxo-1,4-methanonaphthalene-6,7-dicarbonitrile (3a) is obtained in 64% yield. The structure of3a was confirmed by an analysis of the reduced intramolecular photocyclization product,9.     

Molecular structure of 1-phenyl-1-dimethylamino-4,4-bis(trimethylsilyl)-2-aza-3λ3-phosphabutadiene-1,3

The crystal and molecular structure of 1-phenyl-1-dimethylamino-4,4-bis(trimethylsilyl)-2-aza-3³-phosphabutadiene-1,3, Me₂N(Ph)C=N—P=C(SiMe₃)₂ (1), has been determined. Crystal data: triclinic, P1¯, a = 8.975(4), b = 10.001(5), c = 12.440(6) Å, = 79.04(4), = 77.98(4), = 73.07(4)°, V = 1034.7 ų, Z = 2, and D _c = 1.08 g cm^–3. The main geometrical parameters of 1 as well as ab initio (HF/6-31+G**) calculations of the model systems show no clear evidence of high efficiency of the (C=N)— (P=C) conjugation.     

Crystal structure of a synthetic anabolic agent: stanazolol ethanol solvate, 17β-hydroxy-17α methylandrostano[3,2-c]pyrazole ethanoate

The crystal and molecular structure of 17-hydroxy-17 methylandrostano[3,2-c]pyrazole ethanoate (stanazolol ethanol solvate), C₂H₃₀N₂OC₂H₅OH, has been determined by direct methods and refined by full-matrix least squares to a final R of 0.0577 for 4021 observed reflections and 245 parameters using Cu K radiation, = 1.54178 Å. The compound crystallizes in space group P2₁2₁2₁ with Z = 4 molecules per unit cell. In the steroid skeleton the ring A adopts a half-chair conformation, being considerably strained, as a consequence of the fused planar pyrazole ring E. Rings B and C however are chairs and ring D has a 13,14 half-chair conformation. All rings of the steroid skeleton are trans-connected. The OH group of the solvated ethanol molecule is hydrogen bonded to the -oriented carbonyl substituent O(20) of ring D. The molecules are further held together in the crystal structure by head–tail hydrogen bonding between N(1)H in the pyrazole ring and O(20), which consequently is an acceptor for the two H-bonds. Overall the molecule lacks any significant curvature with no interplanar dihedral angle greater than 7°. Possible binding modes of stanazolol with the human androgen receptor are discussed.     

The bibliographic search in the Cambridge Structural Database: problems arising with Asiatic names

A bibliographic search for a Chinese author in the Cambridge Structural Database using the option SURNAME or AUTHOR does not result in all entries published by this author. This can be due to the order in which surname and first name were written in the original publication and/or writing the first name with or without a hyphen. The most efficient way to retrieve all entries consists of the translation of the Chinese characters of the author's name into two or three parts and then use the TEXT option. Attention is paid to the fact that this problem can also occur in other (scientific) databases and with authors from other nationalities.     

Guayulin B

The sesquiterpene guayulin B, C₂₃H₃₀O₃, 1, crystallizes with two independent molecules in monoclinic space group P2₁ with a = 18.099 (1), b = 6.0649(6), c = 19.126(1) Å, = 100.82(1)°, V = 2062.1(5) ų, and Z = 4. The double bonds of the cyclodecadiene ring are E, both methyl groups on the 10-membered ring are -oriented. The cyclopropane ring at C6 and C7 also has the orientation, while the anisoyloxy group is oriented . The 10-membered rings of the two independent molecules have the same conformation as that of guayulin A.     

Synthesis and characterization of ternary L-histidine complexes. Crystal structure of (2,2′-dipyridyl)-(L-histidinato-N,N′,O)copper(II) perchlorate 1.5 hydrate

A series of ternary complexes of copper(II), cobalt(II) and zinc(II) with L-histidine, 1,10-phenanthroline, 2,2-dipyridyl or imidazole having perchlorate or acetate as counterions were synthesized and characterized by conventional methods and for [Cu(bipy)(L-hist)]ClO₄·1.5H₂O and X-ray crystal structure was determined. The crystals belong to the monoclinic space groupC2 witha=18.843(3),b=10.582(2),c=11.020(2), =115.20(10)°,Z=4,R=0.0535. The structure is consistent of [Cu(bipy)(L-hist)]⁺ cations, perchlorate ions and water molecules. The geometry around copper is trigonal bipyramidal with one N,N,O tridentate L-histidine molecule and one 2,2-dipyridyl ligand, the apical sites are occupied by the -amino nitrogen [Cu–N(71) 1.995(8)] and by N(11) of 2,2-dipyridyl [Cu–N(11) 1.983(7)], the equatorial plane is formed by the N(3) imidazole -nitrogen [Cu–N(3) 2.140(6)], O(82) carboxylic oxygen [Cu–O(82) 2.009(5)] and N(22) [Cu–N(22) 2.010(7)].     

“Trimethyl lock” facilitated spirocyclizations: A structural analysis

A trimethyl lock was shown earlier to significantly facilitate certain cyclization reactions. Our renewed interests in such facile cyclization systems stemmed from their potential applications in the preparation of redox-, esterase-, and phosphatase-sensitive prodrugs. Furthermore, such systems have also been used for the development of redox-sensitive protecting groups for amines and alcohols. However, there is an undesirable spirocyclization reaction associated with certain trimethyl lock facilitated cyclization systems. In an effort to probe factors important for the controlling of the undesirable spirocyclization reaction, we undertook the X-ray crystallographic studies of the such trimethyl lock facilitated spirocyclization systems. The spirocyclization product was crystallized from ethyl acetate/hexane mixture (space group: P2₁/c,a=13.467(1),b=13.297(2),c=13.626(8) Å, =92.120(6)°. It was found that spirocyclization results in release of steric congestion caused by the trimethyl lock to a larger degree than the desired lactonization. However, this release of steric congestion itself is not enough to bring about the cyclization. A kinetically reactive nucleophile is also essential for the initiation of the spirocyclization reaction. This is consistent with the fact that such spirocyclization reactions require specific base catalysis.     

Crystal structure of a nucleoside analog: 2′,3′-dideoxy-3′-fluoro-5-bromocytidine

The title compound crystallizes in the orthorhombic space groupP2₁2₁2₁ witha=5.084(1),b=14.322(3),c=16.065(2)Å,Z=4. The structure was solved by the heavy atom method and refined by full-matrix least-squares calculations to a finalR value of 0.033 for 1106 unique observed reflections. The N-glycosidic torsion anglex has a value of –153.7(4)°, in the anti-range. The sugar pucker is²T₃ withP=175(1)° and=30(1)°. The C4-C5 conformation is + sc with =46.7(7)°. The structure is stabilized by N-HN, N-HO and O-HO hydrogen bonds and C-HO close contacts.     

Crystal and molecular structure of 3-methoxy-6-nor-6,7-secooestra-1,3,5(10),9(11), 14-penten-17-one-8β-ethyl carboxylate

C₂₀H₂₂O₄,M _r =326.39, triclinic,P¯1,a=10.365(2),b=11.383(2),c=8.461(1) Å, =103.60(1),=104.44(1), =105.23(1)°,Z=2, (CuK)=1.54178 Å;R=0.0633 for 1940 reflections. The results of the X-ray analysis have shown that the ethyl carboxylate substituent is oriented. The geometry of the main skeleton of the molecule has not revealed any significant differences in the present compound and in the case of the epimeric molecule.     

Syntheses and structures of dihydrocalix[4]arenes bearing O-benzonitrile and O-acetonyl substituents

Three 25,27-dihydrocalix[4]arene derivatives, bearing benzonitrile and acetone groups on the oxygens, were prepared and structurally characterized. All three structures crystallize in , with cell dimensions: bis(benzonitrile)calix[4]arene·toluene, a = 11.530(2) Å, b = 12.013(2) Å, c = 14.089(4) Å, = 103.555(18)°, = 94.341(18)°, = 104.704(16)°, and V = 1815.9(7) ų; anti-bis-acetone-calix[4]arene, a = 7.5847(8) Å, b = 12.0948(17) Å, c = 15.3375(16) Å, = 78.982(10)°, = 76.932(9)°, = 73.129(10)°, and V = 1299.6(3) ų; syn-bis-acetone-calix[4]arene, a = 9.080(3) Å, b = 10.391(3) Å, c = 14.816(3) Å, = 96.998(19)°, = 100.02(2)°, = 103.93(3)°, and V = 1299.6(3) ų.     

Polymorphs of nitrofurantoin. 2. Preparation and X-ray crystal structures of two anhydrous forms of nitrofurantoin

The preparation and X-ray crystal structures of two polymorphs of the antibacterial drug nitrofurantoin are reported. The -polymorph is triclinic, space groupP¯1 witha=6.774(1),b=7.795(1),c=9.803(2)Å, =106.68(1),=104.09(2), =92.29(1)°,Z=2. The-polymorph is monoclinic, space groupP2₁/n witha=7.840(5),b=6.486(1),c=18.911(6)Å,=93.17(3)°,Z=4. The nitrofurantoin molecules adopt the same, planar conformation in both polymorphs. Both crystal structures are built up from layers held together by van der Waals forces. In each polymorph, intralayer cohesion is effected by N-HO and C-HO hydrogen bonds, but their arrangements differ in the two crystals. The significance of the C-HO hydrogen bond, now known to occur in four modifications of nitrofurantoin, is discussed.     

Structure of bis(2-pyridine-N-oxide) diselenide and its formation from tetraphenylantimony(V)selenopyridine-N-oxide

The structure of bis(2-pyridine-N-oxide) diselenide was determined by single crystal X-ray diffraction. The compound crystallized in the triclinic system and the structure was solved in the space group . The lattice constants were determined to bea=7.174(2),b=7.176(2),c=11.070(2) , =87.67(2)°, =73.68(2)°, and =89.57(2)°;Z=2,D _x=1.906 Mg m^–3. The final least squares refinement based on 1942 independent observed reflections yieldedR=0.033,wR=0.044. The Se–Se bond length is 2.326(1) and each Se is coordinated to the O atom of the corresponding N-oxide moiety at a distance of about 2.6 .     

Molecular structure of N-(2-phenylethyl)amide of α-(1,1-ethylenedioxy)-ethyl γ-hydroxybutyric acid (I) and1H NMR spectra of (I) and N-(p-methoxybenzyl)derivative (III)

The spectroscopic and X-ray investigation of the N-(2-phenylethyl) amide of -(1,1-ethylenedioxy)-ethyl--hydroxybutyric acid are reported. The¹H NMR spectra for the title structure and for the N-(p-methoxybenzyl) amide of -(1,1-ethylenedioxy)-ethyl--hydroxybutyric acid are given. The N-(2-phenylethyl)amide of -(1,1-ethylenedioxy)-ethyl--hydroxybutyric acid, C₁₆H₂₃O₄N, crustallizes in the monoclinic space groupP2 ₁/c witha=21.547(5),b=6.333(2),c=11.822(3) Å and =101.01(2)°. The dioxolane ring has a half-chair conformation with C₂(O3)=2.4° and ||_av=18.2°. The inconsiderable deviations from planarity of the six atoms of the amide group are caused mainly by twist around the C4–N1 bond and out-of-plane bending at the N1 atom ((C4–N1)=4°, X_N =7°, X_c =0.4° ). The amide group plane is nearly coplanar with the phenyl ring. The molecules are connected by two intermolecular hydrogen bonds.     

Synthesis and crystal structure of bis(2,2′-bipyridyl)mononitritozinc(II) perchlorate. An example of a six-coordinate cis-octahedral ZnN4O2 chromophore

The crystal structure of bis(2,2-bipyridyl)mononitritozinc(II) perchlorate, [Zn(bipy)₂ (ONO)][ClO₄] (1) has been determined. The complex is monoclinic, with a = 10.9195(4) Å, b = 12.2320(5) Å, c = 16.5477(8) Å, = 105.6150(10), P2₁/n space group, with final R1 = 0.0657 and wR2 = 0.1630. The complex involves a [Zn(bipy)₂ (ONO)]⁺ cation and a [ClO₄]^– anion. The ZnN₄O₂ chromophore is six-coordinate, with a cis-distortion of the two oxygens of the nitrite, O(1) and O(2), at distances 2.216(5) and 2.197(5) Å from the zinc (Zn– O _mean = 2.206(5) Å, O = 0.019(5) Å) and two out of plane Zn–N bonds, Zn–N(2) and Zn–N(3), at 2.129(4) and 2.135(4) Å (Zn–n _mean/out = 2.132(4) Å, n _2,3 = 0.006(4) Å). The two inplane nitrogens, N(1) and N(4), at distances Zn–N(1) = 2.090(4) and Zn–N(4) = 2.085(4) Å (Zn–n _mean/in = 2.087(4) Å, n _1,4 = 0.005(4) Å) are greater than 2.0 Å, but slightly shorter than the axial bonds. The inplane angles ₁, ₂, and ₃ in 1 have values 150.33(18), 108.98(17), and 99.73(18) respectively. The stereochemistry is cis-distorted octahedral, with an ₃ = 99.37(18), which is lower than ₃ = 103.4(1) observed in [Zn(bipy)₂(ONO)][NO₃] (5). Comparison with the corresponding [Cu(bipy)₂(ONO)][Y] complexes suggested that the cis-distortion of the CuN₄O₂ chromophore in the copper(II) series does not originate in the Jahn–Teller or pseudo-Jahn–Teller effect.