Crystal Structure of Rabdoternin A

Abstract  

Rabdoternin A is a natural diterpenoid isolated from Rabdosia rubescen and its crystal structure was determined by X-ray single crystal diffraction. The compound compactly packs in an orthorhombic unit cell in the P2₁2₁2₁ space group with unit cell dimensions a = 7.9200(10) ?, b = 11.2411(14) ?, c = 20.474(2) ?, V = 1822.8(4) ?³ and Z = 4. Two intermolecular hydrogen bonds assemble the title compound into infinite two-dimensional networks along (001) plane.     

Crystal Structure of <Emphasis Type="Italic">N</Emphasis>-(2-Pyridylmethylene)benzene-1,4-diamine

Abstract  

The crystal structure of amino containing Schiff base, N-(2-pyridylmethylene)benzene-1,4-diamine, was determined via X-ray diffraction analysis. The title compound crystallizes in orthorhombic system, space group Pc2 ₁ n, with unit cell dimensions a = 5.8945(6), b = 11.9233 (10), c = 14.5356 (16) ?, V = 1021.59 (18) ?³, Z = 4. The molecules are linked by intermolecular N–H···N hydrogen bonds to form supramolecular sheets along with the bc crystallographic plane. The crystal structure is further stabilized by C–H···π stacking interactions.     

Synthesis and Molecular Structure Investigation by DFT and X-Ray Diffraction of ARNO

Abstract  

We report here the synthesis of (Z)-5-(4-nitrobenzyliden)-3-N(2-ethoxyphenyl)-2-thioxo-thiazolidin-4-one (ARNO) compound. The crystal structure has been determined by X-ray diffraction. The compound crystallizes in the triclinic system with space group P[`1] P\bar{1} and cell parameters: a = 9.1289(19), b = 9.3717(7), c = 12.136(3) ?, α = 102.133(11)°, β = 90.99(2)°, γ = 117.165(9)°, V = 895.4(3) ?³ and Z = 2. The structure has been refined to a final R = 0.05 for 2591 observed reflections. The refined structure was found to be significantly non planar. The molecule exhibits intermolecular hydrogen bond of type C–H⋯O and C–H⋯S. ab initio calculations were also were performed at Hartree–Fock and density functional theory levels. The full HF and DFT geometry optimization was carried out using LANL2DZ, 6-31G* and B3LYP/6-31+G** basis sets. The optimized geometry of the title compound was found to be consistent structure determined by X-ray diffraction. The minimum energy of geometrical structure is obtained by using level HF/LANL2DZ basis sets.     

Crystal and Molecular Structure Analysis of 2-Methylimidazole

Abstract  

The crystal structure of the title compound, C₄H₆N₂, has been determined using X-ray diffraction at 100 K. The crystal of 2-methylimidazole is in orthorhombic crystal system with space group P2₁2₁2₁ (Z = 4), lattice parameters: a = 5.9957(12) ?, b = 8.1574(16) ? and c = 9.7010(19) ?, V = 474.47(16) ?. The molecule of 2-methylimidazole is approximately planar. The maximum deviation from the least-squares imidazole plane, calculated for all non-H atoms is 0.006(2) ?. N–H···N hydrogen bonds link the molecules together, forming infinite chains of hydrogen bond pattern C(4) defined by the graph-set analysis. Two chains, which are almost antiparallel to each other, pass through each unit cell. The dihedral angle between the mean planes of molecules forming these intersecting chains is 76.90(4)°. No evidence was found for disorder of the hydrogen-bonding proton between the atoms N1 and N3. The significance of this study lies in the analysis of the interactions occurring via hydrogen bonds in this structure, as well as, in the comparison drawn between the molecular structure of 2-methylimidazole and those of several of other imidazole derivatives possessing a hydrogen atom in the N1 position.     

Crystal Structure and Characterization of Iridoid Related Compound Isoeucommiol

Abstract  

A single crystal of iridoid related compound isoeucommiol was obtained through NaBH₄ reduction of aucubigenin which was formed by enzymatic hydrolysis of aucubin. Its structure and stereochemistry were determined by X-ray diffraction. The crystal adopts an envelope conformation, presenting a triclinic system, space group P1 with Z = 1, unit cell dimensions a = 5.4158(13) ?, b = 6.5251(15) ?, and c = 7.1555(17) ?. Moreover, extensive network of intermolecular O–H···O hydrogen bonds in crystal lattices can be observed.     

Rapid Eco-Friendly Synthesis and Structure of 3-Hydroxy-3-nitromethyl-1,3-dihydro-indol-2-one

Abstract  

3-Hydroxy-3-nitromethyl-1,3-dihydro-indol-2-one was synthesized from isatin by Henry reaction using an eco-friendly method and characterized by NMR and MS. The crystal structure was determined from single-crystal X-ray diffraction data. It crystallizes in the orthorhombic space group, Pbca, with unit cell dimensions a = 10.515 (2) Å, b = 7.3736 (14) Å, and c = 23.261 (4) Å. The two rings are coplanar and the angle between hydroxyl group and nitromethyl group is 109.07(9)°. In the crystal structure, intermolecular N–H···O and O–H···O hydrogen bonds are responsible for the formation of a 3-dimensional network. No intramolecular hydrogen bond exists.     

Crystal Structure of 2-(2,2-Dibromovinyl)-1-methyl-1<Emphasis Type="Italic">H</Emphasis>-imidazole-4,5-dicarbonitrile

Abstract  

The crystal structure of 2-(2,2-dibromovinyl)-1-methyl-1H-imidazole-4,5-dicarbonitrile (C₈H₄Br₂N₄, Mr = 315.92) has been determined by single crystal X-ray diffraction analysis. The compound crystallizes in the monoclinic crystal system with space group P2₁/c and unit cell parameters: a = 15.144(2), b = 16.382(3), c = 8.267(1) ?, β = 95.76(2)^o and Z = 8. The final reliability index is 0.0297 for 2505 observed reflections. The two molecules of 2-(2,2-dibromovinyl)-4,5-dicyano-1-methylimidazole are localized in independent part of unit cell. The crystal packing is stabilized by C–H···N hydrogen bonds and Br···N intermolecular interactions.     

A Low Temperature Structure of Nonane-1,9-Diaminium Chloride Chloroacetate: Hydroxyacetic Acid (1:1)

Abstract  

The crystal structure of nonane-1,9-diaminium chloride chloroacetate–hydroxyacetic acid (1:1) was determined by X-ray diffraction at 100(1)K. The asymmetric unit is composed of diaminium dication, chloroacetate and chloride anions, and neutral hydroxyacetic acid molecule. The aliphatic chain of 1,9-diamine is fully extended and it deviates only slightly from the perfect all-trans conformation. The two acidic residues are also nearly planar. The layer structure is obtained as a consequence of hydrogen bond interactions of a different lengths, with N–H and O–H groups playing the role of donors and oxygen atoms and chloride cations as acceptors. The pattern of H bonding is investigated by graph-set analysis. Crystal data: crystal system: monoclinic, a = 4.6418 (2) ?, b = 25.5128 (11) ?, c = 15.9943 (9) ?, β = 99.784 (5)°, Z = 4, space group: P21/c, V = 1866.6(1) ?³.     

One Dimensional Hydrogen Bonded Arrangement in New Schiff-Base Compound (<Emphasis Type="Italic">E</Emphasis>)-2-(2,5-dimethoxybenzylideneamino)phenol (1): Synthesis,Characterization, Crystal Structure and Conformational Studies

Abstract  

New Schiff-base compound (E)-2-(2,5-dimethoxybenzylideneamino)phenol (1) was synthesized and characterized by elemental analyses, FT-IR and ¹H-NMR spectroscopy and single crystal X-ray diffraction. Molecular orbital calculation has been carried out for 1 by using HF method at 6-31G basis set. The title compound 1 crystallizes in monoclinic system, space group C2/c, with a = 19.4581(13) ?, b = 9.5805(5) Ǻ, c = 13.8431(7) Ǻ, β = 93.471(2)°, V = 2575.9(3) Ǻ³ and Z = 8. In the crystal structure two molecules are stabilized by a pair of intermolecular O1–H1···N1ⁱ hydrogen bonds. The dimeric units are further linked via C6–H6···O3ⁱⁱ hydrogen bond.     

Crystal and Molecular Structure of Rhaponticin from Rheum hotaoense

Abstract  

Rhaponticin was isolated from the rhizome and root of Rheum hotaoense C.Y. Cheng et C.T. Kao and its crystal structure was determined by single crystal X-ray diffraction. The compound compactly packs in a triclinic unit cell in the P1 space group with unit cell dimensions a = 5.1240(12) ?, b = 7.0453(17) ?, c = 14.535(4) ?, α = 83.182(3)°, β = 89.212(3)°, γ = 68.956(3)°, V = 1486.0(2) ?³, Z = 1, D _calcd = 1.436 Mg m⁻³ and F(000) = 222. The atoms of the stilbene moiety are nearly coplanar, and the dihedral angle between ring (C2–C7) and ring (C10–C15) is 9.0°. The O–H⋯O hydrogen bonding interactions link the molecules into a complicated 3D framework.     

Synthesis and Crystal Structure of a New Mestranol Acetate

Abstract  

A new mestranol acetate, 17α-ethinyl-17-hydroxy-3-methoxyestra-1,3,5(10)-triene-6-one-17-acetate, was synthesized by an efficient three-step sequence starting from norethindrone. The structure of the new steroid was characterized by ¹H NMR, ¹³C NMR, MS, IR spectrum and X-ray single crystal diffraction. It crystallizes in the triclinic system, space group P1. The molecules are arranged in a head-to-tail fashion without intra- and intermolecular hydrogen bonding.     

The Structure of the Antioxidant 2,3,4-Trihydroxybenzoic Acid Dihydrate

Abstract  

The structure of 2,3,4-trihydroxybenzoic acid dihydrate has been determined at 120 K from a twinned crystal. The compound crystallizes in the centrosymmetric space group \textP[`1] \text{P}\bar{1} with Z = 2 and unit cell parameters a = 6.6165(14), b = 7.2341(14), c = 9.716(2) Å, α = 75.632(16), β = 76.818(17), γ = 77.520(16)°. There is extensive hydrogen bonding within the structure and evidence for intermolecular π–π interactions between parallel aromatic rings. The compound does not display the familiar carboxylic acid hydrogen-bonded dimer found in many similar compounds. The 2,3,4-trihydroxybenzoic acid molecules are however arranged in a head-to-tail chain and linked through two water molecules in an unusual intermolecular hydrogen bonding motif.     

Hydrogen Bonded Triple Helical Structure of 3-Hydroxyquinoxaline-2-carboxalidine-4-aminoantipyrine

Abstract  

The title compound, C₂₀H₁₇N₅O₂·2H₂O, was synthesized by the condensation of 3-hydroxyquinoxaline-2-carboxaldehyde with 4-aminoantipyrine. The crystal structure was determined at 100 K. The molecule crystallizes in the amide tautomeric form with two molecules of lattice water in the trigonal space group P [`3] \overline{3} with a = 19.651(2) ?, c = 8.831(2) ?, Z = 6, V = 2953.3(9) ?³. Molecules assemble into a triple helix by intermolecular hydrogen bonds. The pitch distance of the helix is 26.493 ?. DFT calculations on gas phase models reveal that the iminol form of the compound is relatively stable by 3.1 kJ mol⁻¹.     

Low Temperature X-Ray Crystallographic Structure of the Antiplasmodial Compound 5-N-Hydroxyethanequindoline Hydrochloride 0.5CH3OH

Abstract  

The structure of 5-N-hydroxyethanequindoline hydrochloride methanolate, C₁₇H₁₅ON₂ Cl·?CH₃OH, M _r = 314.78, has been determined from X-ray diffraction data. The crystals are monoclinic, space group C2/c, with Z = 8 molecules per unit cell and a = 18.179(11), b = 7.317(5), c = 24.125(15) ?, β = 110.155(10)°, V _c = 3012(3) ?³, crystal density D _c = 1.388 Mg m⁻³. The structure was solved by direct methods, and the asymmetric unit comprises the 5-N-hydroxyethanequindoline hydrochloride and ?CH₃OH moiety. The methanol is unusually disordered over a twofold axis with the C atom slightly removed from the twofold axis. Restraints were applied to the bond lengths of the two components of the disordered CH₃OH, and to the anisotropic thermal displacement parameters of the disordered CH₃OH carbon atom. The heterocyclic quindoline ring system and the first C atom of the hydroxyethane side chain are planar within 0.02 ?, with the terminal C–OH atoms of the side chain significantly out of the plane. The crystal structure is maintained via three hydrogen bonds all involving the chlorine atom an oxygen in the hydroxyethane side chain, a nitrogen in the quindoline moiety and the methanol oxygen.     

Crystal and Molecular Structure of (S)-N-(2-Hydroxyphenyl)pyrrolidine-2-carboxamide

Abstract  

(S)-N-(2-Hydroxyphenyl)pyrrolidine-2-carboxamide was synthesized from Cbz-l-proline through two steps and characterized by NMR and MS. The crystal structure was determined from single-crystal X-ray diffraction data. It crystallizes in the monoclinic space group, P2₁, with unit cell dimensions a = 7.284(6) ?, b = 10.262(9) ?, and c = 7.975(7) ?, α = 90.00°, β = 114.451(14)°, γ = 90.00° and Z = 2. The absolute configuration of the chiral center is determined as S. In the crystal structure, intermolecular and intramolecular hydrogen bonds are responsible for the formation of a 1-dimensional network.     

Synthesis and Crystal Structure of the Heteronuclear Decavanadates Complex: [Fe(phen)<Subscript>3</Subscript>]<Subscript>2</Subscript>·[V<Subscript>10</Subscript>O<Subscript>28</Subscript>]·15H<Subscript>2</Subscript>O

Abstract  

A new decavanadate metal complex [Fe(phen)₃]₂·[V₁₀O₂₈]·15H₂O (phen = 1,10-phenanthroline) has been synthesized from a hydrothermal reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. The crystal structure analysis reveals that the polyoxoanions are decorated with the [Fe(phen)₃]³⁺ cations, and that the water molecules play the bridge role on the packing modes. They are further contacted to form supramolecular networks through extensive hydrogen bonding.     

Synthesis and Crystal Structure of 5-Chloro-3-Methyl-1-Phenyl-1H-Pyrazole-4-Carbaldehyde

Abstract  

The title compound, 5-chloro-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde 2, was prepared in a series of syntheses to produce new pyrazole derivatives, and its crystal structure was determined by X-ray diffraction method. The crystal belongs to monoclinic, space group P2₁/c with unit cell parameters a = 6.7637(4) ?, b = 6.8712(3) ?, c = 22.4188(10) ?, β = 93.8458(14)o, V = 1039.56(9) ?³ and Z = 4. X-Ray reveals that the aldehydic fragment is almost coplanar with the adjacent pyrazole ring, but the two ring planes are inclined at 72.8(1)o. The molecule is linked to its neighbor by two directionally specific C–H···O interactions.     

Synthesis, Characterization and Crystal Structure of N,N′-Bis(2,3-Dimethoxybenzylidene)-1,2-Diaminoethane

Abstract  

Synthesis and characterization of single crystals of a new organic Schiff-base derivative, N,N′-bis(2,3-dimethoxybenzylidene)-1,2-diaminoethane is reported. Good quality single crystals with size 10 mm × 1 mm × 1 mm were grown by slow evaporation technique from a methanol solution at room temperature. The grown crystals have been characterized by elemental analyses and functional groups were identified using FT-IR and ¹H-NMR spectroscopy. Crystal structure of the title compound has been determined by single crystal X-ray diffraction. The title compound has a monoclinic symmetry, space group P2₁/c, lattice parameters are a = 4.4159(3) ?, b = 14.2333(9) ?, c = 15.0601(10) ?, β = 97.755(5)°, Z = 2, V = 937.91(11) ?³.     

Structure of <Emphasis Type="Italic">O</Emphasis>-Methyl-trinitrophloroglucinol Derivatives

Abstract  

The structures of mono, di, and tri-O-methyl derivatives of 2,4,6-trinitrophloroglucinol were determined by single crystal X-ray diffraction. As the number of methoxy groups increased from one to three the unit cell volume increased at a rate greater than the formula weight of the asymmetric unit such that crystal density decreased from 1.823 to 1.619 Mg/m³. The structural data reveal that the decreased density is related to increased angles between the plane of the phenyl ring and the planes defined by the nitro and methoxy groups, as well as fewer inter molecular interactions.     

Crystallographic and Computational Analysis of the Supramolecular Structure of 2,5-Dimethylpyrazolo[1,5-a]pyrimidin-7(4H)-one

Abstract  

The structure of 5-dimethylpyrazolo[1,5-a]pyrimidin-7(4H)-one 1 has been determined by X-ray crystallography. The compound 1 crystallizes in the space group P−1 with two molecules in the asymmetric unit solvated with one molecule of the acetic acid The unit cell parameters are a = 8.796(1) ?, b = 10.531(1) ?, c = 10.680(1) ?, α = 96.901(2)o, β = 98.135(2)o, γ = 107.248(2)o. In the crystal molecules A and B are linked into R ₂²(9) hydrogen bonded rings and these rings form chains parallel to [101] Overall, the supramolecular structure 1 consists of two hydrogen bonded and two π–π stacking dimers. An energetic interplay between these dimers has been studied using B3LYP DFT calculations. In addition π–π interactions are analyzed using the Bader’s atoms in molecules’ (AIM) theory.