1-(Ethoxymethyl)-6-(phenylselenyl)-5-ethyl uracil: a nucleoside analog

The compound, 1-(ethoxymethyl)-6-(phenylselenyl)-5-ethyl uracil, crystallizes in the monoclinic space group P2₁/n with unit cell parameters a = 5.304(1), b = 21.261(4), c = 13.996(4) Å, = 94.30(2)°, and Z = 4. The acyclic chain C1, O4, C4, C5 is in fully extended form and nearly perpendicular to the uracil base. The molecules are held together by van der Waal's forces.     

Synthesis,Characterization, and Crystal Structure of (2<Emphasis Type="Italic">E</Emphasis>)-3-(4-Fluorophenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one

The title chalcone, of formula C₁₅H₁₁F₁O_2, crystallized in the orthorhombic space group P2₁2₁2₁ (# 19) with crystal parameters a?=?6.9998(8) Å, b?=?12.6740(15) Å, c?=?12.8997(15) Å, V?=?1144.4(2) ų, Z?=?4, determined at 100 K with MoKα radiation. The solid-state structure displays an intramolecular S(6) hydrogen bond and the crystal architecture is maintained by intermolecular F?H, O?H, and C?C short contacts. A DFT geometry optimization is compared with the experimental structure. As ¹⁹F NMR spectroscopy can be used for metabolic tagging of biologically active compounds (including chalcones), the solution-state ¹⁹F chemical shift and ¹³C¹⁹F coupling constants (ⁿJ) are also reported.

Graphical Abstract

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Crystal Structure of 2-((<Emphasis Type="Italic">E</Emphasis>)-(5-Bromo-2- hydroxybenzylidene)hydrazono)-1,2-diphenylethanone

The molecular structure of the title compound, C₂₁H₁₅Br₁N₂O₂, was characterized by single crystal X-ray diffraction. The compound crystallizes in the triclinic sp. gr. \(P\bar 1\) with Z = 2. The molecule is not planar: the dihedral angle between the planes of two aromatic rings [C1/C6] and [C16/C21] is 84.9(2)°. The other dihedral angle between two aromatic rings [C9/C14] and [C16/C21] is 88.8(2)°. The title compound exists as a phenol-imine tautomer, in which a strong intramolecular O–H···N hydrogen bond is formed. This study verifies the preference of the phenol-imine tautomeric form in the solid state. A π–π stacking interactions are also observed, which may influence crystal stability: the distance between centroids is 3.702(2) Å.     

Two Crystal Forms of 4-{(2<Emphasis Type="Italic">E</Emphasis>)-2-[1-(4-Methoxyphenyl)ethylidene] hydrazinyl}-8-(trifluoromethyl)quinoline

Abstract  

The Schiff base, 4-{(2E)-2-[1-(4-methoxyphenyl)ethylidene] hydrazinyl}-8-(trifluoromethyl)quinoline, crystallizes in two polymorphic forms depending on the solvent. One of these forms is monoclinic (1M), space group P2₁/c with a = 10.2906(10) ?, b = 8.9211(7) ?, c = 18.4838(15), β = 97.271(8)°, and the other is orthorhombic (1O), space group Pbca, unit-cell parameters: a = 13.6485(12) ?, b = 9.0588(9) ?, c = 27.400(2) ?. The molecules in either crystalline form have similar bond lengths and angles, but one is nearly planar while the other has a significant twist. In monoclinic form the dihedral angle between terminal ring planes is 17.26(8)° while in the orthorhombic one it is 26.11(5)°, and in this latter case the central chain is almost coplanar with the quinoline ring system while in the former these two planes are significantly twisted. The crystal structures of both forms are determined by the interplay of van der Waals forces and weak directional interactions C–H···F, π···π stacking, and—in the case of 1M—short intermolecular C–F···N contact. The crystals of 1M decomposes slowly into the powder while the other form is stable. The powder diffraction pattern of the product of decomposition of 1M is similar to that calculated for 1O. This suggests that the decomposition is a consequence of the phase transition of the less stable monoclinic into more stable orthorhombic form.     

Synthesis and the Crystal Structure of (<Emphasis Type="Italic">E</Emphasis>)-2-(7-(3-(Thiophen-2-yl)acrylamido)-2,3-dihydro-5-oxobenzo[e][1,4]oxazepin-1(5H)-yl)ethyl acetate

Abstract  

Details of the synthesis and crystal structure determination of (E)-2-(7-(3-(thiophen-2-yl)acrylamido)-2,3-dihydro-5-oxobenzo[e][1,4]oxazepin-1(5H)-yl)ethyl acetate are presented. The compound crystallizes in the triclinic P−1 space group (a = 8.3377(17), b = 9.792(2), c = 12.469(3) ?, α = 96.39(3)°, β = 108.50(3)°, γ = 97.68(3)°, V = 943.9(3) ?³, Z = 2). Interesting features of the structure include intermolecular hydrogen bonding between the amide proton on one molecule and the carbonyl oxygen of the dihydrooxazepinone ring on an adjacent molecule, the boat conformation of the dihydrooxazepinone ring, and π-π stacking between thiophene and phenyl rings on adjacent molecules with a distance between centroids of 3.79(2) ?.     

4-(<Emphasis Type="Italic">E</Emphasis>)-2-[3-(3-[(<Emphasis Type="Italic">E</Emphasis>)-2-(4-cyanophenyl)-1-diazenyl]hexahydro-1-pyrimidinylmethyl)hexahydro-1-pyrimidinyl]-1diazenylbenzonitrile: X-ray crystal structure

4-(E)-2-[3-(3-[(E)-2-(4-cyanophenyl)-1-diazenyl]hexahydro-1-pyrimidinylmethyl)hexahydro-1-pyrimidinyl]-1-diazenylbenzonitrile (1) has been synthesized by reaction of p-cyanobenzene diazonium chloride with a mixture of formaldehyde and 1,3-propanediamine. The crystal structure has been determined by single crystal X-ray diffraction analysis. The bis-triazene (1) adopts a folded conformation, similar to previously studied ethylenediamine analogues, and there is evidence of -stacking in the crystal packing. The two planar phenyltriazenyl groups are almost parallel, forming an angle of 6.6(1), and display weak intermolecular s interactions between molecules. This result establishes the structure of the product of this diazonium coupling reaction as the 1-(1-hexahydropyimidinylmethyl)hexahydropyrimidine derivative and not the alternate tetraazabicyclo[5.5.1]tridecane derivative. Crystal data: 1C₂₃H₂₆N₁₀, monoclinic, space group P2₁/c, a = 10.717(1) Å, b = 7.749(1) Å, c = 28.252(2) Å, = 97.223(2), V = 2327.5(5) ų, for Z = 4.     

Crystal structure of a salt complex between (<Emphasis Type="Italic">S</Emphasis>)-2-(2′-methylbenzyl)succinic acid and (<Emphasis Type="Italic">R</Emphasis>)-1-phenylethylamine

The optically pure 2-(2′-methylbenzyl)succinic acid were obtained by the optical resolution of the racemates with the chiral host 1-phenylethylamine. The structure of the salt complex between (S)-2-(2′-methylbenzyl)succinic acid and (R)-1-phenylethylamine was first elucidated by X-ray analysis: Monoclinic, Space group P2₁ with a=6.0781(12) ?, b=8.8224(18) ?, c=17.675(4) ?, β=97.64(3)°, V=939.4(3) ?³, Z=2, the absolute structure parameter is 0 (9). The crystal structure indicates that the hydrogen bonds are formed between the acetate anions and the protonated amino group. The intermolecular hydrogen bond links the salt complex into a quasi-two-dimentional netlike structure.     

Synthesis and Crystal Structure of 5-[2-(6-bromonaphthalenyloxymethyl)]-3-(4-morpholinomethyl)-1,3,4-oxadiazole-2(3<Emphasis Type="Italic">H</Emphasis>)-thione

Abstract  The title compound, C₁₈H₁₈BrN₃O₃S, a derivative of 1,3,4-oxadiazole, crystallizes in the triclinic space group P-1 with unit cell parameters a = 6.8731(3), b = 8.9994(4), c = 15.7099(6) ?, α = 92.779(3)°, β = 130.575(3)°, γ = 107.868(4)°, Z = 2. The dihedral angle between the mean planes of the planar naphthyl and morpholine (chair) rings with the planar oxadiazol ring is 50.1(8) and 76.8(6)°, respectively. The planar naphthyl ring is twisted 52.2(5)° with the mean plane of the morpholine ring. A group of four intermolecular close contacts are observed between a bromine atom and hydrogen atoms from the closely packed naphthyl, morpholine and oxy–methyl groups in the unit cell. These molecular interactions in concert with an additional series of π–π stacking interactions that occur between the center of gravity of the two 6-membered rings of the naphthalene group influence the twist angles of each of these three groups. A MOPAC AM1 calculation of the conformation energy of the crystal structure [226.0128(9) kcal] compared to that of the minimum energy structure after geometry optimization [29.9744(1) kcal] reveals a significantly reduced value. The twist angles of the three groups above also change after the AM1 calculation giving support to the influence of both intermolecular C–H···Br short-range interactions and Cg π–π stacking interactions on these angles which therefore play a role in stabilizing crystal packing. Graphical Abstract  Crystal structure of 5-{[(6-bromonaphthalen-2-yl)oxy]methyl}-3-(morpholin-4-ylmethyl)-1,3,4-oxadiazole-2(3H)-thione, C₁₈H₁₈BrN₃O₃S, is reported and its geometric and packing parameters described and compared to a MOPAC computational calculation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Synthesis and Crystal Structure of (<Emphasis Type="Italic">S</Emphasis>)-2-((<Emphasis Type="Italic">S</Emphasis>)-2-(<Emphasis Type="Italic">N</Emphasis>-Ts-Amino)-3-methylbutanoyl)-3-(1H-indol-3-yl)-6-phenyl-3,4-dihydro-1,2,4-triazin-5(2H)-one

Abstract  

The diastereoselective synthesis, NMR and X-ray structure of (S)-2-((S)-2-(N-Ts-amino)-3-methylbutanoyl)-3-(1H-indol-3-yl)-6-phenyl-3,4-dihydro-1,2,4-triazin-5(2H)-one—a potential antivirus agent are reported. The compound crystallizes in the triclinic space group P1 with unit cell parameters: a = 5.9259(6) ?, b = 9.6370(12) ?, c = 12.9541(9) ?, α = 109.210(9)°, β = 90.804(7)°, γ = 105.074(10)° and Z = 1.     

Crystal structure of (Z)-1-(sec-butyl)-3-(4-dimethylaminophenyl)-2-(1H-1,2,4-triazol-1-yl)propen-2-one

The crystal structure of the title compound is determined by X-ray diffraction studies. The structure is solved by the direct method. The experimental data are obtained on a DAR-UMB diffractometer by the θ-θ/2θ scan technique using MoK _α radiation. The crystal is monoclinic, a = 17.913(3) Å, b = 17.239(3) Å, c = 5.501(5) Å, γ = 74.4(3)°, space group P2₁/a, Z = 4 for C₁₇H₂₂N₄O, and ρ_calcd = 1.211 g/cm³. The molecule consists of the phenyl and triazole rings and the dimethylamino, carbonyl, and isopropyl groups attached to the rings. The dihedral angle between the rings is 67.4°. The carbonyl oxygen atom and the triazole ring are in the trans position relative to each other. The N-C-C-O torsion angle is 172.8°. The molecule is in the Z isomeric form.     

Synthesis and crystal structure of [ReOCl<Subscript>2</Subscript>(L)] (HL = 2-(1-ethanolaminomethyl)-1-methylimidazole)

The title compound was prepared from the reaction of (n-Bu₄N)[ReOCl₄] with the ligand HL in acetonitrile. The chelate L is coordinated as a terdentate uninegative N, N,O^–-donor ligand in a distorted octahedral coordination geometry around the rhenium(V) ion. The structure has a triclinic space group P-1 with a = 6.9796(3), b = 7.1530(3), c = 12.0416(6) Å, = 73.742(2), = 86.458(2), = 73.928(3), V = 554.50(4) ų, and Z = 2.     

Crystal structures of (I) 2-(9,9-dipropylfluorene-2-yl)-9,9- dipropylfluorene and (II) 2-(1,1-dimethylpropyl)-7- {4-[(1,1-dimethylpropyl)-9,9-diethylfluoren-2-yl]phenyl}-9,9-diethylfluorene and (III) 2-(4-ethylphenyl) -7-[7-(ethylphenyl)-9,9-dipropylfluoren-2-yl]-9,9-dipropylfluorene

The crystal structures of the three fluorene related molecules, (I) 2-(9,9-dipropylfluorene-2-yl)-9,9-dipropylfluorene, [Exalite 384, C₃₈H₄₂], (II) 2-(1,1-dimethylpropyl)-7-{4-[(1,1-dimethylpropyl)-9,9-diethylfluoren-2-yl] phenyl}-9,9-diethylfluorene, [Exalite 404, C₅₀ H₅₈], and (III) 2-(4-ethylphenyl)-7-[7-(ethylphenyl)-9,9-dipropylfluoren-2-yl]-9,9-dipropylfluorene, [Exalite 416, C₅₄H₅₈], have been determined. Structural details reveal a novel new bonding arrangement at the C2 atoms of symmetry-related fluorene moieties in all three molecules producing a linear type array with an inversion center connecting adjacent asymmetric units within each molecule. Exalite 384 is monoclinic, space group P2₁/c with a = 9.002(2) Å, b = 16.275(4) Å, c = 10.525(1) Å, = 103.05(1), and V = 1502.1(5) ų with Z = 4, for d _calc = 1.103 g/cm³. Exalite 404 is triclinic, space group P1 with a = 10.383(1) Å, b = 13.404(2) Å, c = 7.7007(9) Å, = 105.296(9), = 104.23(1), = 73.707(9), and V = 974.9(2) ų with Z = 2, for d _calc = 1.141. Exalite 416 is monoclinic, space group P2₁/c with a = 15.99(10) Å, b = 11.178(8) Å, c = 23.766(4) Å, = 104.21(4), and V = 4117(4) ų with Z = 4, for d _calc = 1.141 g/cm³.     

Synthesis and crystal structure of 3-chloro-<Emphasis Type="Italic">N</Emphasis>-(2-chloro-5-(1,3-dioxo-4,5,6,7-tetrahydro-1H-isoindol-2(3H)-yl)-4-fluorophenyl)-2,2-dimethylpropanamide

The title compound 3-chloro-N-(2-chloro-5-(1,3-dioxo-4,5,6,7-tetrahydro-1H-isoindol-2(3H)-yl)-4-fluorophenyl)-2,2-dimethylpropanamide was synthesized by the reaction of 2-(5-amino-4-chloro-2-fluorophenyl)-4,5,6,7-tetrahydro-2H-isoindole-1,3-dione with 3-chloro-2,2-dimethylpropanoyl chloride. Its structure was determined by X-ray single crystal diffraction. The crystal belongs to triclinic, space group P-1 with the following crystallographic parameters: a = 9.595(3) Å, b = 12.093(4) Å, c = 18.433(6) Å, α = 83.961(5)^∘, β = 84.819(5)^∘, γ = 67.920(5)^∘, μ = 0.361 mm⁻¹, V = 1967.9(10) ų, Z = 4, Dx = 1.395 mg/m³, F(000) = 856, T = 293(2) K, 1.11^∘ ≤ θ ≤ 25.01^∘. The X-ray results demonstrated that the reaction of 2-(5-amino-4-chloro-2-fluorophenyl)-4,5,6,7-tetrahydro-2H-isoindole-1,3-dione with 3-chloro-2,2-dimethylpropanoyl chloride in tetrahydrofuran at room temperature yielded 3-chloro-N-(2-chloro-5-(1,3-dioxo-4,5,6,7-tetrahydro-1H-isoindol-2(3H)-yl)-4-fluorophenyl)-,2-dimethylpropanamide.     

Crystal Structure and Hirshfeld Surface Analysis of (E)-1-(4-Bromophenyl)-2-(2,2-Dichloro-1-(4-Fluorophenyl)vinyl)diazene

Crystallography Reports - The CuCl-catalyzed olefination with CCl4 in the presence of tetramethylethylenediamine in DMSO leads to the formation of...     

Synthesis,X-Ray Crystal Structure and Spectroscopic Properties of 1,2,3,4-Tetrahydro-2-(thenyl)-3-(<Emphasis Type="Italic">N</Emphasis>-thenylidine)-4-oxoquinazoline

Abstract  

The Schiff base formed between anthraniloyl hydrazide and thiophen-2-aldehyde is synthesized. Reaction of this Schiff base with VOSO₄ in methanol at room temperature does not yield the expected vanadium complex; instead, the Schiff base is transformed to 1,2,3,4-tetrahydro-2-(thenyl)-3-(N-thenylidine)-4-oxoquinazoline, which has been characterized by elemental analyses and by LC–MS, i.r., n.m.r. and electronic spectroscopies. The X-ray crystal structure of the quinazoline product is reported. The compound crystallizes with monoclinic (P2₁/n) space group, and the cell parameters are: a = 5.9442(7) ?, b = 13.6357(15) ?, c = 19.455(2) ?, β = 90.499(2)°. The oxo-quinazoline product is found to be luminescent when excited at its lowest energy transition.     

Synthesis,Spectroscopic Studies and X-ray Analysis of (<Emphasis Type="Italic">E</Emphasis>)-2-(2-Fluorophenyl)-3-(6-Nitrobenzo[d][1,3]dioxol-5-yl) Acrylic Acid

Abstract  

In the solid-state structure of the title compound, C₁₆H₁₀FNO₆, the configuration about the C=C double bond is E. The compound crystallized in the triclinic system, having space group P-1 with unit cell dimensions a = 5.829(10) ?, b = 8.801(16) ?, c = 13.543(3) ?, α = 87.753(15)°, β = 81.945(15)°, γ = 86.342(14)°. The structure of the molecule is V-shaped and in the crystal the molecules are linked to form inversion dimers connected by pairs of C–H···O hydrogen bonds.     

An X-ray Crystallographic Study of the Related Triazenes, 1,4-Di[(<Emphasis Type="Italic">E</Emphasis>)-2-(2-nitrophenyl)-1-diazenyl]piperazine and Methyl 4-{(E)-2-(4-methylpiperazino)-1-diazenyl}benzoate

Abstract The crystal structures of methyl 4-{(E)-2-(4-methylpiperazino)-1-diazenyl}benzoate (2a) and 1,4-di[(E)-2-(2-nitrophenyl)-1-diazenyl]piperazine (3a) have been determined by single crystal X-ray diffraction analysis. The bis-triazene (3a) adopts an unusual pseudo-boat conformation in the piperazine ring, with a dihedral angle of 52.20(0.06)° between the two planes defined within the piperazine ring. The crystal structures of 2a and 3a are compared with the structure of the triazene (4) and the closely related bis-triazene (5). The piperazine ring of 2a adopts a typical chair conformation, whereas the piperazine ring of 3a adopts an unusual boat conformation. Crystal data: 2a C₁₃H₁₈N₄O₂, monoclinic, space group P2₁ /n, a = 13.849(3) ?, b = 6.577(1) ?, c = 14.904(3) ?, α = 90°, β = 96.098(3)°, γ = 90° and V = 1,349.8(4) ?³, for Z = 4. 3a C₁₆H₁₆N₈O₄, triclinic, space group P-1, a = 7.6066(6) ?, b = 8.3741(7) ?, c = 14.507(1) ?, α = 78.673(1)°, β = 81.877(1)°, γ = 73.445(1)° and V = 865.0(1) ?³, for Z = 2. Index abstract The crystal structures of methyl 4-{(E)-2-(4-methylpiperazino)-1-diazenyl}benzoate (2a) and 1,4-di[(E)-2-(2-nitrophenyl)-1-diazenyl]piperazine (3a) have been determined by single crystal X-ray diffraction analysis.