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.      

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.     

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.     

Bis(2,6-(2′,6′-diisoproylanil)diformyl-4-chloro-phenolate) nickel(II)

Bis(2,6-(2,6-diisoproylanil)diformyl-4-chloro-phenolate) nickel(II) was prepared by the reaction of 2,6-(2,6-diisoproylanil)diformyl-4-chloro-phenol with nickel chloride. The title complex crystallized in P2₁/c, with cell dimensions a = 9.962(2) Å, b = 12.087(3) Å, c = 24.445(6) Å, and = 97.032(5), giving a volume of 2921.4(13) ų. The bis(2,6-(2,6-diisoproylanil)diformyl-4-chloro-phenolate) nickel(II) adapts an ideal parallelogram, in which the Ni atom is coordinated with two phenolic oxygen atoms [O(1), O(1A)] and two imino nitrogen atoms [N(1), N(1A)].     

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.     

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.      

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 tris-(2,2′,2″)-triaminoethylamino-salicylidene iron(III) complex

Tris-(2,2,2)-triaminoethylamino-salicylidene iron(III) crystallizes in the monoclinic crystal system witha=7.766(2),b=25.423(5),c=13.318(5) Å, =118.04(3)°, space group P2₁/c,V=2320.8(6) ų,Z=4, andD _x=1.464 g cm^–3. The center of the axially distorted octahedron is occupied by the Fe atom which is coordinated by six donor nitrogen and oxygen atoms infac positions. The planes of coordinated atoms (N and O) with the Fe(III) atom are almost planar and the maximum elevated atom from these planes is O(1) (–0.1065 Å).     

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.     

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.     

5-(thien-2-yl) uracil analogs: 5-(5-methylthien-2-yl)-2′-deoxyuridine, 5-(5-thien-2-yl)-2′-deoxyuridine,and 5-(5-bromothien-2-yl)-2′-deoxyuridine

Crystal structures of 5-(5-methylthien-2-yl)-2-deoxyuridine (I), 5-(5-thien-2-yl)-2-deoxyuridine (II) and 5-(5-bromothien-2-yl)-2-deoxyuridine (III) have been obtained from data collected on a four-circle Enraf-Nonius diffractometer (CAD-4 system). Space group, unit/cell parameters and finalR indices are:I, monoclinic,P2₁,a=9.105(2),b=20.819(2),c=7.932(2) Å, =98.79(2)°,R=5.7%;II, monoclinic,P2₁,a=8.720(4),b=20.793(4),c=7.884(4) Å, =95.06(2)°,R=5.8%;III, monoclinic,P2₁,a=9.260(2),b=41.655(7),c=7.926(2) Å, =97.996(13)°,R=9.4%. Structural properties of the title compounds are compared with those of 5-(5-chlorothien-2-yl)-2-deoxyuridine (IV) previously reported in order to explain their affinity for HSV-1 thymidine kinase and their eventual interaction with viral DNA polymerase. The main structural features observed are the coplanarity of the uracil and thienyl cycles stabilized by a S–O intramolecular interaction and the formation of dimeric intermolecular H bonds between two uracil moieties.     

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.     

Crystal structure of the methanol solvate of (η5-cyclopentadienyl)[1,2-bis(diphenylphosphino)ethane] nitroruthunium(II) Ru(η5-C5H5)dppe)(NO2)·CH3OH

The title complex crystallizes in the centrosymmetric monoclinic space group C2/c (No. 15) withZ=8. The structure was refined toR=4.49% for those 2745 independent reflections with 2=5–50^o and |F |>6(F). Ruthenium-ligand distances are as follows: Ru-P=2.284(2) and 2.286(2) Å, Ru-NO₂=2.049(6) Å and Ru-C(Cp)=2.210(10)-2.246(9) Å. Bond lengths within the nitro ligand are N(1)-O(1)=1.226(10) Å and N(1)-O(2)=1.244(10) Å. The methanol of solvation is ordered but is subject to large thermal vibrational motions.     

Crystal structures of (η5-C5H4COMe)M(CO)3Me (M=Mo,W)

The crystal structures of ( ⁵-C₅H₄COMe)M(CO)₃Me (M=Mo,W) have been determined. They are not isostructural. M=Mo isP2₁/c,a=10.205(6),b=14.192(8),c=8.135(6) Å,=93.43(4)° andD(calc)=1.71 g cm^–3 forZ=4. M=WisP2₁/c,a=12.580(7),b=6.830(5),c=13.750(7) Å,=93.72(4)° andD(calc)=2.20 g cm^–3 forZ=4. Both have a four-legged piano stool geometry with the substituted carbon making the closest M-C( ⁵) approach. The methyl group in the M=W derivative is disordered between twotrans-ligand positions. The average bonding parameters for the more accurately determined Mo analog are: Mo-C()⁵)=2.34(3) Å, Mo-CO=1.98(2) Å, Mo-Me=2.304(4) Å.     

Crystal structure of bis(η5-methylcyclopentadienyl)-bis(4-methylbenzenesulfonato-O)-molybdenum(IV)

The compound bis(⁵-methylcyclopentadienyl)-bis(4-methylbenzenesulfonato-O)-molybdenum (IV) crystallizes in space-group P2₁/c, a = 8.2956(5), b = 26.896(3), c = 11.4196(11) Å, = 96.101(7)°, Z = 4. The sulfonate ligands are monodentate and the molybdenum atom has pseudotetrahedral coordination geometry, with angles O–Mo–O 72.0(1)° and Cp–Mo–Cp 134.9(1)° (Cp = ring centroid).     

The structure of Wallach's compound. Single-crystal X-ray structure determination oftrans-2,5-bis(trichloromethyl)-N-(1′-hydroxy-2′,2′,2′-trichloroethyl)-4-imino-1,3-dioxolane

The structure of Wallach's compound, C₇H₄O₃NCl₉, prepared in 1874 from concentrated aqueous solutions of potassium cyanide and chloral hydrate, has long been undecided. By single crystal X-ray crystallography it has now been established astrans-2,5-bis(trichloromethyl)-N-(1-hydroxy-2,2,2-trichloroethyl)-4-imino-1,3-dioxolane, confirming the tentative assignment by¹H and¹³C NMR spectrography. The title compound is monoclinic,P2₁/c;a=8.445 (1),b=10.948(1),c=17.923(4) Å;=94.36(1)°;Z=4. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least squares to a finalR value of 0.041 using 2101 reflections.     

Structure of N,N′,N″-tris(carboxymethyl)-1,3,5-benzenetricarboxamide trihydrate

The title compound, C₁₅H₁₅N₃O₉·3H₂O, crystallizes in the centrosymmetric space group R with a = 13.642(5), b = 13.642(5), c = 18.692(5) Å, D _calc = 1.440 g cm³, and z = 6. An extensive three-dimensional hydrogen bonded network is observed. The network arises from 15 hydrogen bonds per asymmetric unit. Six identical N—H···O hydrogen bonds are formed between two triacid molecules, which results in the face-to-face dimerization of the two triacid molecules. The dimers form extended sheets through hydrogen bond interaction with water molecules. The sheets are held together by hydrogen bonds via the water molecules. The planes of the benzenoid ring are parallel to each other.     

The crystal structure of triiodo (η5-methoxycarbonyl-cyclopentadienyl)-dicarbonylmolybdenum(IV)

Crystals of (C₅H₄COOMe)Mo(CO)₂I₃ are monoclinic, space-group P2₁/c, with a = 9.402(2), b = 10.675(3), c = 15.314(2) Å, = 106.79(1)°, and Z = 4. The coordination geometry is distorted octahedral with the ring centroid at one vertex and the iodide ligands defining a face.     

The crystal structure and IR spectra of μ-(bipyrimidine-N1,N1′,N5,N5′)-bis[(azido-N1)(methanol)(bipyrimidine-N1,N1′)copper(II)] bis(triflate) bis(methanol)

The structure of the title compound [Cu₂(bipym)₃(N₃)₂(CH₃OH)₂](CF₃SO₃)₂(CH₃OH)₂ has been determined by X-ray diffraction. The crystals are triclinic, space group P1, with a = 8.1844(5), b = 11.0253(6), c = 12.9089(7) Å, = 80.249(4), , = 74.933(5), = 74.001(4)°, and Z = 1. The structure consists of a dinuclear Cu(II) unit formed of two didentate bipym ligands, one bis-didentate bipym ligand, two azido anions, and two coordinating methanol molecules. The Cu(II) atom is elongated tetragonally surrounded by two nitrogens of the didentate bipym ligand, one nitrogen of the bis-didentate ligand, and one nitrogen of the azido anion forming the equatorial plane with one nitrogen of the bis-didentate ligand and an oxygen atom of the methanol molecule as the axial atoms. A noncoordinating triflate anion and an additional methanol molecule are also in the crystal lattice and have a hydrogen bond distance of 2.801(3) Å with an angle of 157(4)°. The cations link by O – H ··· N bonds into infinite chains running in the c-direction.     

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.