Crystallization and structural studies of n‐benzyloxycarbonyl‐L‐tyrosine‐L‐glycine‐ethyl ester (Z‐Tyr‐Gly‐OEt)

It is axiomatic that efficient crystal production reflects upon the quality of structure. An empirical relation for mass proportions of two solvents in crystallization of Z‐Tyr‐Gly‐OEt shows a linear relationship. The dipeptide crystallizes in orthorhombic space group P2₁2₁2_1, with cell parameters a = 5.0680(1) Å, b = 13.8650(1) Å and c = 28.2630(1) Å, Z = 4, D_calc= 1.339Mg/m³, μ=0.820mm^‐1, F₀₀₀=848, CuKα = 1.5418 Å. The structure was solved by direct methods and final R1 and wR2 are 0.444 and 0.1276, respectively. The structure analysis reveals the trans conformation of the peptide unit with ω = ‐178.2(5)°, implying only a slight deviation from planarity. The torsion angles at glycine [ϕ, ψ = ‐84.4(7)°, 179.9(5)°] are characteristic of left‐handed poly glycine II helices. A number of N‐H…O, O‐H…O and C‐H…O hydrogen bondings play a role in stabilizing the molecules within unit cell. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Presence of pseudo‐peptide bond in the crystal structure of n‐(t‐butoxycarbonyl)‐ε‐n′‐benzyloxycarbony‐l‐lysyl‐l‐isoleucine (boc‐lys(obzl)‐ile)

The dipeptide Boc‐Lys(OBzl)‐Ile crystallizes in monoclinic space group P2₁ with cell parameters a = 5.003(1), b = 19.199(3), c = 15.270(2)Å, β =93.42(1)°, V = 1464.1(3)ų, Z = 2, D_cal = 1.117 Mg/m³ at T = 293 K. The structure was solved by direct methods and refined by full‐matrix least‐squares procedure to a final R = 0.096 and wR = 0.101 using 1379 reflections. The peptide unit is in trans conformation and the molecule takes up an extended conformation. In the lysine side chain, delocalization of electrons and pseudo peptide bond formation is observed at the interaction site of benzyloxycarbonyl group. Both N‐H…O and main chain C‐H…O hydrogen bonds stabilize the molecules in the unit cell in a parallel β‐sheet fashion. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Crystal structures of N1, N5‐dibenzoyltetrahydro‐4‐methyl‐1, 5‐benzodiazepin‐2‐one (DBTBO) and tetrahydro‐4‐methyl‐1, 5‐benzodiazepin‐2‐one (TBO)

Adducing structural analogies between the two fused systems, N1, N5‐Dibenzoyltetrahydro‐4‐methyl‐1,5‐benzodiazepin‐2‐one, C₂₄H₂₀N₂O₃ (DBTBO CCDC 200341) and Tetrahydro‐4‐methyl‐1,5‐benzodiazepin‐2‐one, C₁₀H₁₂ N₂O (TBO CCDC 200342) helps to find the pharmacological differences from the view point of variant hetero atom substitutions in the hetero cycle. Both the diazepines crystallized in identical monoclinic space group P2₁/n with a = 14.1134(1) Å, b = 9.2444(1) Å, c = 16.3812(1) Å; β = 107.11(1)º, V = 2042.7(3) ų for DBTBO and a = 9.3363(7) Å, b = 10.4895(8) Å, c = 9.9852(7) Å, β = 91.314(1)º, V = 977.62(1) ų for TBO, respectively. The two structures were solved by direct methods and refined by full‐matrix least‐squares procedure to final R‐values of R1 = 0.0575(DBTBO) and R1 = 0.0984(TBO). Structural differences include non‐identical boat conformations of these seven‐membered rings and the different non‐bonding interactions in the benzodiazepine pair.     

Crystal structure and conformational analyses of a synthetic tetrapeptide t‐Boc‐L‐Val‐Aib‐Gly‐L‐Leu‐OMe

Crystal structure of a terminally blocked synthetic peptide, t‐Boc‐L‐Val‐Aib‐Gly‐L‐Leu‐OMe has been investigated. Two different conformers of peptide with one co‐crystallized water molecule, coexist in the crystal structure, in C2 space group. Both the conformers are stabilized by two intramolecular 1← 4 hydrogen bonds, between (Boc) C=O … HN (Gly) and (Val) C=O … HN (Leu), forming consecutive type II‐I' β‐turns. In the crystal, water interlinks peptide molecules, making a triangular bridge of pyramidal type. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Crystal Structure of 2‐methyl cinnamanilide and 2‐methoxy cinnamanilide

The crystal structures of two cinnamanilide derivatives 2‐methyl cinnamanilide (C₁₆ H₁₅ N O – compound I) and 2‐methoxy cinnamanilide (C₁₆ H₁₅ N O₂ – compound II) are reported. In both crystal structures, the cinnamamide group is almost planar. The inter‐planar angle between the two phenyl rings are 71.6(1)° for compound I and 7.5(1)° for compound II. The N‐H…O and C‐H…O type of hydrogen bond interactions between the amide group and the carbonyl group stabilizes the molecular packing as chains in the crystal lattice.     

Crystal Structure of 5,6‐Dinitrobenzimidazole.monohydrate

The title compound (C₇H₆N₄O₅) crystallizes in the monoclinic space group P2₁/c with a=8.566(1) Å, b=14.493(3) Å, c=7.583(1) Å, β=87.75(1)°, V=940.7(3) ų, Z=4, D_x=1.597 g.cm^‐3. The structure was solved by direct methods and refined by full‐matrix least‐squares method (R=0.0696). The title compound consists of an imidazole ring with the two NO₂ groups and one water molecule. The short inter‐ molecular N‐H^…N [2.03(5) Å] and O_water‐H^…O [1.98(5) Å] hydrogen bonds are highly effective in holding the molecule in a stable state as a whole.     

Crystal Structure of Diethyl 2‐[2,2,2‐ trifluoro‐1‐(indole‐3‐yl)‐ethyl]‐2‐acetamidomalonate

The title compound (C₁₉H₂₁F₃N₂O₅) has been determined from three dimensional X‐ray diffraction data. The crystals are monoclinic, a = 7.626(4)Å, b = 17.515(4)Å, c = 15.066(3)Å, β = 101.02(3)°, V = 1975(1)ų, Z = 4, D_calc = 1.393g cm^‐3, space group P2₁/c. The structure was solved by direct methods and refined by full‐matrix least‐squares method (R = 0.039).     

Crystal structure of bis(2-butyl-4-chloro-imidazole)5-iminoethane

The title compound (C₁₈H₂₆N₆Cl₂) crystallizes in monoclinic space group P2₁/c with a = 14.867(4) Å}, b = 7.758(2) Å}, c = 9.671(3) Å}, = 108.78(1), V = 1056.0(5) Å}³, Z = 2, D_cal = 1.250 Mg/m³ at T = 293 K. The structure was solved by direct methods and refined by full-matrix least-squares procedures to final R = 0.0650 and wR = 0.1719 using 2493 reflections. The imidazole ring is planar and the n-butyl chain adopts an extended conformation. The molecules in the crystal are stabilized by N–H s N type of intermolecular hydrogen bondings in addition to van der Waals forces.     

Three‐Dimensional Structure Constructed via Hydrogen Bonds and π‐π Stacking Interaction. Crystal Structure of [Cu(AFO)2(H2O)2](ClO4)2.2(AFO).2H2O (AFO = 4,5‐Diazafluoren‐9‐one)

The structure of the title complexes [Cu(AFO)₂(H₂O)₂](ClO₄)₂.2(AFO).2H₂O (AFO = 4,5‐Diazafluoren‐9‐one)has been established by single‐crystal X‐ray diffraction. The complex crystallizes in the triclinic space group P‐1 with cell constants a = 7.659(3) Å, b = 11.066(3) Å, c = 14.203(5) Å, alpha = 75.16(3)°, β = 79.87(3)°, gamma = 85.71(3)°, Z = 1. The structure was solved by direct methods and refined to R₁ = 0.0595 (wR₂ = 0.1164). The X‐ray analysis reveals that a pair of AFO ligands chelate to a Cu(II) atom in an asymmetric fashion with one Cu‐N bond being much longer than the other, the Cu(II) atom is further coordinated by a pair of aqua ligands to form an elongated octahedral geometry. In the crystal of the complex, the mononuclear complex cations [Cu(AFO)₂(H₂O)₂]²⁺, uncoordinated AFO molecules, lattice water molecules and perchlorate anions are assembled into 3‐D structure via hydrogen bonds and π‐π stacking interaction.     

Synthesis and crystallographic characterization of a chiral complex of (R)‐2‐(pyridin‐2‐ylmethylene)amino‐2′‐hydroxy‐1,1′‐binaphthyl(L) with hydrated nickel(II) acetate

A chiral complex of (R)‐2‐((pyridin‐2‐ylmethylene)amino)‐2′‐hydroxy‐1,1′‐binaphthyl ( L ) with hydrated nickel (II) acetate has been synthesized and spectroscopically characterized. The crystal structure of [NiL₂(CH₃OH)(CH₃COO)]CH₃COO·CH₃OH has been determined by single‐crystal X‐ray diffraction. The complex crystallizes in the orthorhombic space group P 2(1) 2(1) 2(1) with cell constants a = 15.1035 (19), b = 17.836 (2), c = 18.730 (2)Å, α = β = γ = 90.00°, Z = 4. The structure was solved by direct methods and refined to R = 0.0346 (wR₂ = 0.0863). The analytical result of the crystal structure indicates that a pair of L ligands chelate to a Ni (II) atom in an asymmetric fashion with one Ni‐N bond being longer than the other, the Ni (II) atom is further coordinated by one methanol molecule and one acetate anion to form a distorted octahedral geometry. In the crystal of the complex, the coordination cation [NiL₂(CH₃OH)(CH₃COO)]⁺, the uncoordinated methanol molecule and uncoordinated acetate anion are further assembled into one‐dimensional chain structure via intermolecular hydrogen bonds along the a‐axis. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Crystal structure of N‐(2‐methoxyphenyl)‐3,6‐diphenyl‐1,4‐dihydro‐1,2,4,5‐tetrazine‐1‐carbonamide

The title compound, C₂₂H₁₉N₅O₂, was prepared and its structure was determined by X‐ray diffraction [CCDC 216074]. The compound crystallizes from ethanol in the orthorhombic system, space group P2₁2₁2₁, with unit cell parameters: a =10.048(1) Å, b = 13.935 (2) Å, c =14.607(2) Å, Z =4, and V=2045.3(5) ų. The crystal structure was solved by direct methods and refined by full‐matrix least‐squares to a final R‐value of 0.0516 with 3621 unique reflections. The central six‐membered ring of the compound has a boat conformation and is not homoaromatic, in which adjacent atoms N1 and N4 deviate from the plane of the ring by 0.4546(33) Å and 0.3786(33) Å, respectively. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Crystal and Molecular Structure of (9R)‐10,11‐dihydro‐6′‐methoxy‐cinchonan‐9‐ol‐4‐chlorobenzoate hydrochloride

The crystal structure of the title compound has been determined by single crystal X‐ray diffraction methods. C₂₇H₂₉N₂O₃Cl.HCl is one of the cinchona alkaloids. It crystallizes in the space group P2₁2₁2₁ with a = 11.745(3), b = 12.353(6), c = 17.253(6) Å and Z = 4. The structure was refined to a final R value of 0.062 for 2155 observed reflections. The C—N distances are unequal in the quinoline ring system. In quinulidine ring, the bonds around N are more tetrahedral. The spatial arrangement and torsion angles show the open conformation of the molecule. The molecular packing is stabilized by hydrogen bonding.     

The Crystal and Molecular Structure of 11,12‐dibromo‐ 7,8—benzo‐1,5‐di(p—tolylsulphonyl)‐1,5‐diazacyclononan

The crystal structure of the title compound, C₂₅H₂₆Br₂N₂O₄S₂ was determined by single crystal X‐ray diffraction technique. The crystals are monoclinic, space group C 2/c, with a=20.7142(2) Å b=11.7910(2) Å, c= 10.6735(3) Å, β=98.549(2)°, V=2577.94(9) ų, Z=4. The structure was solved by direct methods and refined by least‐squares methods to a final R=0.046 for 1866 observed reflections with I>2sigma(I). The title compound, displays disordered geometry around the C1 atom located almost on twofold axis. The nine‐membered heterocylic ring is close to the half‐chair conformation. The dihedral angle between phenyl rings is 34.2(1)°.     

Structure and conformation of a nickel complex: {2‐Hydroxo‐3‐piperidine‐1‐yl‐methyl‐N,N′(bis‐5‐bromobenzylpropylenediimine)nickel(II)perchlorate}

The title compound, a nickel complex [C₂₃H₂₆N₃O₂Br₂Ni.(ClO₄)] (CCDC 199520) crystallizes in triclinic space group P with the cell parameters a = 10.2560(4), b = 10.8231(4), c = 12.0888(5)Å, α = 99.404(1), β = 99.780(1), γ = 92.252(1)° and V = 1301.49(9)ų. The structure was solved by Patterson method and refined by full‐matrix least‐squares procedures to a final R = 0.0497 using 6287 observed reflections. In the complex, the piperidine ring takes chair conformation and the geometry around the Ni ion is slightly distorted square planar. The dihedral angle between the planes [N‐Ni‐N and O‐Ni‐O] is 9.4(1)°. The chelate ring containing both the nitrogen atoms adopts twisted boat conformation. The molecules in the crystal are stabilized by N‐H…O and C‐H…O types of hydrogen bonds in addition to a C‐H…π interaction. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Crystal Structure Analysis of {[μ‐N,N′‐Bis(salicylidene)‐2,2′‐dimethyl‐1,3‐propanediaminato](dimethylformamide) zinc(II)}diiodomercury(II)

The title compound, a hetero‐dinuclear complex with Zn^II and Hg^II ions, forms crystals which belong to the monoclinic system, space group P2₁/n, with unit cell dimensions a = 11.2217(12), b = 17.7493(11), c = 13.9293(13) Å, β = 94.830(3)°, V = 2764.5(4) ų. The cell contains four molecules. The Zn…Hg distance is 3.5362(15) Å.     

Crystal Structure of N,N'‐Bis(3‐(o‐dimethylaminoimino‐ethyl) ‐2‐hydroxy‐5‐methyl)‐benzylpiperazine

The structure of the synthesized title compound, C₃₀H₄₆N₆O₂ , was solved by using X‐ray diffraction techniques. The compound crystallized in monoclinic space group P2₁/n with cell dimensions a = 14.0629(7), b = 6.5696(3), c = 17.7948(8)Å, β = 111.35(2)°, V = 1531.2(1)ų, Z = 2, D_cal = 1.134 Mgm^‐3 and T = 293(2)K. The molecule possesses a center of symmetry, and hence, there is half a molecule in the asymmetric unit. The piperazine ring adopts chair conformation with the substituents at the equatorial position, subtending a dihedral angle of 88.87(1)° with the phenyl ring. The phenyloxy hydrogen is involved in an intramolecular O‐H...N type of hydrogen bond.