X-ray diffraction investigation of trans-2,8-dihydroxy-2,8-diphenyl-4,4′,6,6′,10,10′, 12,12′-octamethylcyclohexasiloxane and trans-2,8-dihydroxy-2,4,4′,6,6′,8,10,10′, 12,12′-decamethyl-5-carbahexacyclosiloxane

The crystal structures of two organosilicon compounds are studied by X-ray diffraction. Crystals of trans-2,8-dihydroxy-2,8-diphenyl-4,4′,6,6′,10,10′,12,12′-octamethylcyclohexasiloxane, C₂₀H₃₆O₈Si₆, (I) are triclinic; at 110 K, a = 11.476(1) Å, b = 12.106(1) Å, c = 13.636(1) Å, α = 94.337(1)°, β = 112.669(1)°, γ = 112.216(1)°, space group $P\bar 1$ , Z = 2, and R = 0.057 for 5069 reflections with F > 4σ(F). Crystals of trans-2,8-dihydroxy-2,4,4′,6,6′,8,10,10′,12,12′-decamethyl-5-carbahexacyclosiloxane, C₁₁H₃₄O₇ Si₆, (II) are tetragonal; at 293 K, a = b = 15.487(3) Å, c = 11.364(3) Å, space group P4₂/n, Z = 4, and R = 0.055 for 955 reflections with F > 4σ (F). It is found that the structure of compound I, in which the substituents at the Si(1) atom differ in volume and inductive effect, contains two crystallographically independent molecules with different conformations of the hexasiloxane ring. In structure II, the oxygen atom and the methylene group are statistically disordered as a result of the location of the molecule at the center of symmetry. Although the SiCSi angle [122.1(1)°] differs noticeably from the tetrahedral angle, its value is characteristic of cyclohexasiloxanes and is not related to the disorder.     

X-ray diffraction study of 2,2′,4,4′,6,8,8′,10,10′,12-decamethylbicyclo[5.5.1]hexasiloxane and 2,2′,4,4′,6,8,8′,10,10′,12-decamethylbicyclo[5.5.1]-9-carbahexasiloxane

The crystal structures of two organosilicon compounds are studied by X-ray diffraction at 200 K. Crystals of 2,2′,4,4′,6,8,8′,10,10′,12-decamethylbicyclo[5.5.1]hexasiloxane (C₁₀H₃₀O₇Si₆) are monoclinic, a = 12.260(1) Å, b = 11.716(1) Å, c = 32.169(2) Å, β = 92.802(2)°, space group C2/c, Z = 8, wR2 = 0.132, and R1 = 0.053 for 3989 reflections with F > 4σ(F). Crystals of 2,2′,4,4′,6,8,8′,10,10′, 12-decamethylbicyclo[5.5.1]-9-carbahexasiloxane (C₁₁H₃₂O₆Si₆) are triclinic, a = 10.709(1) Å, b = 11.046(1) Å, c = 12.111(1) Å, α = 117.059(1)°, β = 95.566(1)°, γ = 108.088(1)°, space group $P\bar 1$ , Z = 2, wR2 = 0.115, and R1 = 0.048 for 3948 reflections with F > 4σ(F). It is found that the substitution of the methylene group for the oxygen atom is accompanied by a minor conformational change in the bicyclic fragment and the SiCSi angle changes from the tetrahedral angle to 121.0(1)°. The high variability of the SiOSi bond angles is confirmed.     

Synthesis and Structural Characterization of (2,4-Diamino-5-(3′,4′,5′-Trimethoxybenzyl)Pyrimidine Copper (II)) Complex

Abstract  The reaction of Cu(OOCCH₃)₂·H₂O with (2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl) pyrimidine (trimethoprim) in ethanolic solution at 80 °C affords the title complex which has been characterized by elemental, IR, and NMR (¹H and ¹³C).The crystal structure has been determined by single crystal X-ray diffraction. Compound 1 (C₃₆H₄₈Cu₂N₈O₁₄) is triclinic, space group P-1 with a = 7.2676(4) ?, b = 11.6721(7) ?, c = 12.8279(8) ?, α = 95.839(1)°, β = 93.456(1)°, γ = 105.541(1)°, Z = 1. Two copper atoms are coordinated directly to each other as well as are held together by four bridging aceto groups. Each copper atom is also bonded opposite the Cu–Cu vector to a trimethoprim molecule through the N(1) atom of the pyrimidine ring. Trimethoprim acts as a monodentate ligand through the pyrimidine nitrogen N(1) atom. The complex was screened for the activity against several bacteria, showing more activity against bacteria as compared to trimethoprim. Graphical Abstract  To enhance the activity of trimethoprim, its derivative was prepared and there bacterial activity against several bacteria was analyzed.      

Synthesis of (2,4-Diamino-5-(3′,4′,5′-trimethoxybenzyl) Pyrimidine) Copper (II) Complex at 20–25 °C and its Structural Characterization

Abstract  The title copper (II) complex with Trimethoprim was prepared at 20–25 °C and its crystal structure was determined by single crystal X-ray diffraction. Compound (C₃₆H₅₀Cu₃N₈O₁₆) is triclinic, space group P-1 with a = 6.4642(5) ?, b = 12.5495(9) ?, c = 13.4911(10) ?, α = 77.518(1)°, β = 85.326(1)°, γ = 84.413(2)°, Z = 1. In this compound, three copper atoms are bonded to each other, two terminal coppers are bonded to three oxygen atoms and N₁ of pyrimidine ring of Trimethoprim and central copper is bonded to four oxygen atoms. The amino nitrogen atoms are not involved in the coordination to the metal. Graphical Abstract  To enhance the activity of trimethoprim, its derivative was prepared and there bacterial activity against several bacteria was analyzed.      

Synthesis and structure of 5,5′,6,6′,7,7′,8,8′-octahydro-1,1′-di(methylthio)-3,3′-biisoquinoline

Title compound, C₂₀H₂₄N₂S₂, crystallizes in the orthorhombic system, space group Pbca, with cell constants a = 5.1968(5) Å, b = 15.6692(11) Å, c = 22.3881(11) Å , Z = 4, T = 293 K, D_cal = 1.299 g cm^–3. The structure was solved by direct methods and refined to R value of 0.0465 for 1566 reflections. Two methylthio-octahydroisoquinoline parts of molecule are related by the center of symmetry and possess the trans conformation. This conformation is more energetically stable than cis but the molecule can rotate about the C(6)–C(6) central bond at room temperature (molecular mechanics calculations). There is a short intramolecular contact C(5)–H(51) N(1) in the molecule. The molecules in the crystal form molecular layers parallel to (001) crystallographic plane and the molecular packing is determined by the van der Waals forces only.     

Crystal structures of 4,7-phenanthrolino-5,6:5′,6′-pyrazine tetrahydrate and 1,4,5,8,9,12-hexaazatriphenylene dihydrate

The crystal structures of 4,7-phenanthrolino-5,6:5,6-pyrazine tetrahydrate (I) and 1,4,5,8,9,12-hexaazatriphenylene dihydrate (II) have been determined from low temperature (173 K) x-ray single crystal diffraction data. I crystallizes in the triclinic system, space group P with a = 11.2687(6), b = 12.4766(6), c = 12.7068(7) Å, = 113.4740(10), = 91.605(2), = 114.587(2)°, V = 1449.33(13) ų, and Z = 4. II crystallizes in the orthorhombic system, space group Pca2₁ with a = 18.187(2), b = 9.2576(11), c = 6.9672(8) Å, V = 1173.0(2) ų, and Z = 4. In both structures the planar heterocyclic molecules stack with interplanar distances down to 3.3 Å, which is consistent with self--complexation. The crystal water molecules provide links between the columns of stacked molecules through hydrogen bonds. In each compound the N-C bond lengths fall into two distinct groups (mean values 1.330(3) vs 1.361(1) Å in I and 1.320(3) vs 1.357(5) Å in II), as do the C-C bonds of the central phenyl rings (1.411(4) vs 1.467(1) Å in I and 1.405(5) vs 1.458(4) Å in II).     

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 structure of a nucleoside analogue, 2′,3′-dideoxy-3′-fluoro-5-chlorocytidine

The title compound, 1-(2,3-dideoxy-3-fluoro--d-erythro pentofuranos-1-yl)-5-chlorocytosine, crystallises in the orthorhombic space groupP2₁2₁2₁ witha=5.142(1),b=14.177(2),c=15.721(2) Å,Z=4. The crystal structure was solved by the heavy atom method and refined by full-matrix least-squares method to a finalR value of 0.031 for 1629 unique observed reflections. The N-glycosidic torsion angle is –156.1(2)° and the sugar moiety is anti to the cytosine base. The sugar pucker is ₂ ³ T withP=178.2(1)° and=31(1)°. The atom 05 is in a +sc conformation with respect to the furanose ring. The molecular packing in the crystal is stabilized by N-HN, N-HO, O-HO hydrogen bonds and C-HO close contacts.     

Crystal structure of a nucleoside analog, 2′,3′-dideoxy-3′-azido-5-chlorocytidine

The title compound, l-(2,3-dideoxy-3-azido--D-erythro pentofuranos-1-yl)-5-chlorocytosine, crystallizes in the orthorhombic space groupP2₁2₁2₁ witha=5.840(1),b=13.780(1),c=15.396(2)Å,Z=4. The structure was solved by direct methods and refined by full-matrix least-squares calculations to a finalR value of 0.033 for 1688 unique observed reflections. The N-glycosidic torsion angle has a value of –160.8(1)°, in the and range. The sugar pucker is ₂ ³ T withP=180(1)° and=34(1)°. The C4–C5 conformation is +sc with =50.8(2)°. The azido group is nonlinear and oriented trans to the C3–C4 bond. The molecular packing in the crystalline space is stabilized by N-HN, N-HO, O-HO hydrogen bonds and C-HO close contacts.     

Hydrogen bonds and π–π stacking interaction in 4′, 7-dimethoxylisoflavone and 4′,7-diacetyl-O-isoflavone

4′,7-dimethoxylisoflavone, C₁₇H₁₄O₄, (I), is linked into a supramolecular structure by a variety of weak but direction-specific intermolecular forces, the molecules are linked into chains through C–H⋅sO hydrogen bonds, these chains are further linked by face-to-face (F-tape) π–π stacking into a one-dimensional bi-chain, another type π–π stacking, edge-to-face (T-tape), assemble the bi-chain into framework together with C–H⋅sO hydrogen bonds. 4′,7-diacetyl-O-isoflavone, C₁₉H₁₅O₆, (II), shows some discrepancies with I and the molecules are assembled into framework all by C–H⋅sO hydrogen bonds. The molecules are linked into centrosymmetric dimers built from classic R₂² (8) rings by pairs of C–H⋅sO hydrogen bonds, the dimers are linked into (011) sheets by combination of the R₂² (8) ring and C–H⋅sO hydrogen bonds, another C–H⋅sO hydrogen bond assemble the sheets into three-dimensional network.     

Anticancer agent development: X-ray crystal structure and keto-enol tautomerism of dimethyl 1-hydroxy-6,7-methylenedioxy-4-(3′,4′,5′-trimethoxyphenyl-trans-3,4-dihydronaphthalene-2,3-dicarboxylate

Structural and conformational information obtained from the crystal structure and solution¹H nmr investigations of the title compound are compared. The 4-aryltetralone, C₂₄H₂₄O₁₀, crystallizes as a chloroform solvate in the monoclinic space group, P2₁/n, witha=12.519(4),b=17.938(6),c=12.534(9)Å,=111.90(5)°, and D_calc=1.51 g cm^–3 forZ=4. The data for this compound were collected at –150°C. Least-squares refinement of 2796 observed [F _o5(F _o)] reflections led to the final agreement index ofR=0.062. A threefold static disorder was observed for one of the carboxyl groups. The second carboxyl group participates in an intramolecular hydrogen bond and is thus ordered. The¹H nmr spectrum revealed the title compound to exist as a keto-enol tautomeric mixture in solution. Vicinal hydrogen coupling constant analysis proved reliable in ascertaining B-ring stereochemistry of 2,3-disubstituted-4-aryltetralones.     

Synthesis and structural evidence for new diimidazo-[1,5-a:1′,5′-d] pyrazinediones

The synthesis of derivatives of 5H, 10H-diimidazo [1,5-a:l,5-d] pyrazine-5,10-dione is described. The mechanism of the reaction is discussed and the chemical, spectral and X-ray data giving the evidence of the structure of these compounds are presented. X-ray studies were carried out on compound6c (C₂₄H₂₂N₆O₂) witha=9.250(3),b=11.879(3),c=10.250(3),Z=2 and space groupP2₁/a. The structure was solved using direct methods and refined by weighted full-matrix least squares. The refinement, based on 990 reflections withI2.5(I), converged to a finalR of 0.041 andR _w=0.036.     

Crystal structure of 2,2,3-trimethyl-3-(2′,4′,5′-tricyanophenyl) cyclopentyl-1-acetic acid, methyl ester, C20H21N3O2

The title compound crystallizes in space group P2₁/n, with a = 14.600(2), b = 7.091(2), c = 18.211(5) Å, and = 103.67(2)°. Owing to the centric space group, both C(1) and C(3) chiral centers are either R or S. The acetate group is equatorial, the H(1) and the methyl group at C(3) are axial and reciprocally trans.     

A novel class of naturally occurring halogenated pyrroles, 1,1′-dimethyl-3,3′,4,4′,5,5′-hexabromo-2,2′-bipyrrole, 5,5′-dichloro-1,1′-dimethyl-3,3′,4,4′-tetrabromo-2,2′-bipyrrole, and 1,1′-dimethyl-3,3′,4,4′,5,5′-hexachloro-2,2′-bipyrrole

Crystal structure determinations of the three title hexahalogenated bipyrroles, (I) C₁₀H₆Br₆N₂, (II) C₁₀H₆Br₄Cl₂N₂, and (III) C₁₀H₆Cl₆N₂, reveal essentially planar pyrrole rings having dihedral angles of 64.7, 65.1, and 64.2° between the least-squares planes, favoring in each case a closer methyl–halogen conformation. All three complexes crystallize in the orthorhombic space group Pbcn with the following cell dimensions: (I) a = 12.654(3) Å, b = 8.853(2) Å, c = 13.753(3) Å, = = = 90°, Z = 4; (II) a = 12.438(6) Å, b = 8.753(6) Å, c = 13.696(3) Å, = = = 90°, Z = 4; (III) a = 12.088(6) Å, b = 8.566(4) Å, c = 13.486(8) Å, = = = 90°, Z = 4.     

Crystal and molecular structure of 2′,4′-dimethoxyflavone

C₁₇H₁₄O₄,M _r =282.3, triclinic,P-1,a=8.469(3),b=8.516(2),c=20.425(8)Å,=84.95(3),=81.98(3), =70.47(2)°,V=1373(13)ų,Z=4,D _x =1.365 g cm^–3, (MoK )=0.71069 Å,=0.91 cm^–1,F(000)=592,T=294K,R=0.038 for 3577 observed reflections (F>3 (F)). The asymmetric unit is composed of two molecules. These two molecules, which are in planar conformations, differ in 4-methoxyl group orientation. Short intramolecular contacts are found between the -benzopyran portion and the dimethoxyphenyl ring.     

X-ray structure of 3′,4-dimethylthio-3,4′-diquinolinyl sulfide

The title compound (C₂₀H₁₆N₂S₃) is monoclinic, witha=31.550(9),b=8.504(3),c=14.745(3) Å,=114.14(3)°,Z=8 and space groupC2/c. The structure was solved by direct methods and refined toR=0.038 for 3012 reflections. The molecule exists in an uncommon conformation. Two quinoline moieties are nearly perpendicular to each other (80.9(3)°). Both methylthio groups have different orientation (the 4-SCH₃ group is nearly perpendicular and the 3-SCH₃ is nearly coplanar to the quinoline moieties). Two pairs of sulfur atoms in ortho-positions remain in very close contact. The conformation of the molecule explains an unusual¹H NMR spectrum.Part XVI in the series of Azinyl Sulfides.     

Synthesis of 7,4′-Bis-(hydroxyl)-8,3′,5′-tris-(hydroxymethyl)isoflavone and Crystal Structure of its Ester

Abstract 7,4′-bis-(hydroxyl)-8,3′,5′-tris-(hydroxymethyl)isoflavone (I) and its ester were synthesized and examined by IR, element analysis and ¹H NMR. The crystal of 7,4′-bis-(acetyl oxide)-8,3′,5′-tris-(acetoxymethyl)isoflavone (II) was studied by X-ray diffraction. (II) crystallizes in the monoclinic with space group P2 ₁ /c. a = 17.987(3) ?, b = 17.972(3) ?, c = 8.4087(11) ?, β = 97.703(3)°, V = 2693.7(6) ?³ and Z = 4. The molecular structure of the ester consists of a benzopyranone moiety, a phenyl moiety, two acetyl oxides and three acetoxymethyl groups. Hydrogen bonds and aromatic stacking interactions link the ester into a two-dimensional structure. Index Abstract 7,4′-bis-(hydroxyl)-8,3′,5′-tris-(hydroxymethyl)isoflavone and its ester were synthesized and examined by IR, element analysis and ¹H NMR. The result of the ester’s crystal structure showed that hydrogen bonding and aromatic π–π stacking assemble the ester into a two-dimensional networking structure.      

Synthesis and crystal structure of 1-(1′,3′-dimethyl-5′-chloropyrazol-4′-carbonyl′-3-(2′-chlorophenyl)-5-amino-4-cyanopyrazole

The title compound 1-(1,3-dimethyl-5-chloropyrazol-4-carbonyl)-3-(2-chlorophenyl)-5-amino-4-cyanopyrazole (C₁₆H₁₂Cl₂N₆O) has been synthesized and characterized by X-ray diffraction: Triclinic, space group P1, with a = 8.6712(8) Å, b = 9.5091(10) Å, c = 11.2170(11) Å = 71.531(2)°, = 84.683(2)°, = 74.099(2)° Z = 2; V = 843.7(14) ų. C(10), O(1), C(11), and N(2) atoms are coplanar with the average deviation of 0.0071 Å, which form 11.03° and 43.93° dihedral angles with pyrazole planes (I) and (II), respectively.     

7-Hydroxy-2-(2,3,4-trimethoxyphenyl)-4H-1-benzopyran-4-one: (7-hydroxy-2′,3′,4′-trimethoxyflavone)

7-Hydroxy-2,3,4-trimethoxyflavone, (C₁₈H₁₆O₆),M _r =328.32 crystallizes in the orthorhombic system, space groupPbna, with the following crystal data:a=8.853(2),b=12.870(2),c=26.293(3)Å,V=2996(1)ų,Z=8, MoK, =0.67 cm^–1,D _c =1.454 g·cm^–3,F(000)=1376,T=294K. The structure was solved by direct-methods and has been refined by full-matrix least-squares methods to a finalR value (F>(F)) of 0.0496. The molecule is not planar, the dihedral angle between the phenyl ring and the fused ring system is 27.3°. There are no intramolecular hydrogen bonds, but intermolecular short hydrogen contacts exist between hydroxyl hydrogen and carbonyl oxygen atoms.     

Crystal structure of 9,12-ethano-12a-methoxycarbonyl-5, 8a,9,12,12a,12b-hexahydro-6H-[1,2]dioxino[4′,5′:4,5] isoxazolo[3,2-a]isoquinoline, C17H19NO5

The title compound crystallizes in the space group P2₁/n, with a = 18.423(3), b = 9.628(3), c = 19.243(2) Å, = 116.208(8)°, with two independent molecules in the asymmetric unit, which are not enantiomers. The chiral centers C8a, C9, C12, C12a, C12b are either S,R,S,R,R or R,S,R,S,S, respectively, because of the centric space group.