High resolution crystal structure of ferricytochrome c′ from Rhodobacter sphaeroides

Cytochrome c isolated from Rhodobacter sphaeroides strain R26 (RSCP) crystallizes as a dimer of two identical 14-kDa subunits, in trigonal space group P3₁, with cell parameters a, b = 48.10 Å, c = 115.80 Å. The crystal structure of RSCP has been solved by molecular replacement using cytochrome c from Rhodobacter capsulatus (PDB ID: 1CPQ) as a search model. To ensure effective phase bias removal, the RSCP model was iteratively built into maps generated by a modified wARP procedure, Shake&wARP. The 1.8 Å model (PDB ID: 1GQA) has been refined to an R = 0.204 and freeR = 0.254. Each subunit consists of four antiparallel -helices, with the pentacoordinate heme covalently bound to a C–X–Y–C–H motif near the C-terminus. F14, located on helix A, blocks direct access to what would be the sixth distal ligand binding site of the heme. The dimer subunits form a flattened X shape, intermediate between the Type 1 and Type 2 cytochromes c. The presence of the aromatic F14 and a deep channel between helices B and C places RSCP into Group 1 cytochromes c. Clear electron density has revealed that the amino acid sequences for the cytochrome c from strains R26 and 2.4.1 are identical.     

Two acetylamino derivatives of 2,4-bis(trichloromethyl)-1,3-benzdioxin showing different types of hydrogen bonding: (a) (C13C)CH⋯O=C and (b) N-H⋯O=C

8-Acetylamino-6-methyl-2,4-bis(trichloromethyl)-1,3-benzdioxin, (I), is monoclinic,P2₁/c,a=15.174(4),b=11.977(7),c=9.911(3)Å,=99.72(2)°. 6-Acetylamino-2,4-bis(trichloromethyl)-1,3-benzdioxin, (II), is monoclinic,P2₁/_n,a=5.927(4),b=40.623(1),c =7.120(3)Å,=91.39(4)°. In compound (I) the imino hydrogen atom is locked in an intramolecular hydrogen bond to the proximate oxygen atom of the heterocyclic ring and is not available for intermolecular hydrogen bonding. Instead the weakly acidic hydrogen atom [Cl₃C-C(2)]H takes part in a hydrogen bond to the carbonyl oxygen atom in another molecule. In compound (II) a normal intermolecular hydrogen bond of the type N-HO=C occurs. The 6-acetylam-ino group is twisted about the (C_Ar-N) bond such that the angles NHO=C, C_ArH_ArO=C, NHOH_ArC_Ar, at the carbonyl oxygen group total 360° (where NH is in the related molecule). The packing in both compounds takes the form of infinite chains and in compound (II) partial overlap of the aromatic ring and the acetylamino group, with very little offset, also occurs.     

Crystal structure of an intermediate in the synthesis of artemisinin

C₁₄H₂₂O₃,M _r =238.33, P2₁2₁2₁,Z=4,a=6.892(2),b=11.453(1),c=17.159(5) Å. [1R–[1(R^*), 4, 4a, 8a]]–,4-Dimethyl-decahydro-7-oxo-1-naphtaleneacetic acid. The cyclohexane ring adopts a chair conformation and thecis-fused cyclohexanone ring is in a slightly distorted chair conformation. The molecular packing involves an hydrogen bond and C–H...O contacts.     

Helical chirality of pyrrolo[1,2-a][1,10]phenanthroline derivatives

The objective of the study was to confirm by X-ray analysis the phenomenon of helical chirality inferred from solution ¹H-NMR data for a series of derivatives based on the novel pyrrolo[1,2-a][1,10]phenanthroline system. The syntheses of the title compounds and their ¹H-NMR data are presented. Crystals of the representative compound ethyl, 1-(4-phenylbenzoyl)-pyrrolo[1,2-a][1,10]phenanthroline-3-carboxylate, with molecular formula C₃₁H₂₂N₂O₃, were found to crystallize in the triclinic system, space group P 1 with a = 7.8541(1), b = 11.2605(2), c = 13.4093(3) Å, = 92.244(1), = 90.292(1), = 106.475(1) and Z = 2. The X-ray analysis revealed the predicted helicity of the phenanthroline system as well as its origin, namely the proximity of the pyridine N atom and the carbonyl C atom of the phenylbenzoyl residue, with non-bonded distance N s C of only 2.465(2) Å. A secondary, but significant distortion, involving displacement of the carbonyl C atom by more than 0.5 Å from the pyrrole ring, was evident. The crystal structure is maintained by C–H s O hydrogen bonds and – interactions.     

Dinuclear complex of rhodium(III) with an amine-phenol ligand: synthesis and X-ray crystal structure

A new rhodium(III) complex of an amine-phenol ligand N,NN-bis-(2-hydroxybenzyl)1,3-diaminopropane was synthesized and characterized by X-ray diffraction studies. Diffraction data were collected by the-2 scan method using MoK. radiation. The structure was solved by conventional methods resulting in a final R factor of 0.037 for 1954 independent reflections (F _o >2(F _o )). The structure consists of a dinuclear complex with two -hydroxy bridges between the two Rh atoms. The overall charge of the molecule is neutral due to deprotonation of all phenolic groups. Crystal data: triclinic, space groupP¯1,a=7.308(3)Å;b=9.586(3)Å,c=12.686(5)Å, =87.51(2), =88.28(2), =71.70(3)°,V=866.6(6)ų;Z=2.     

Tetracyclo[6.3.0.04,11.05,9]undecane-2,7-dione

The compound crystallizes in the triclinic space group, , witha=6.7702(4),b=7.0180(4),c=9.1960(7) Å, =92.457(6), =96.150(6), =93.444(5)°, andZ=2. The structure contains a rather short intramolecular H...H contact of 2.26(4) Å.     

Crystal structure of diethoxynitrobenzene-p-tert-butylcalix [4]arene⋅2(CH3)2C=O: Evidence of intra- and intermolecular CH/π interactions forced by crystal packing

Diethoxynitrobenzene-p-tert-butylcalix[4]arene2(CH₃)₂C=O crystallized in the monoclinic system, space group P2₁/c, with cell dimensions a = 16.1437(2) Å, b = 21.0292(2) Å, c = 18.9685(3) Å and = 110.308(1)°. The asymmetric unit consists of a diethoxynitrobenzene-p-tert-butylcalix[4]arene molecule and two solvated acetone molecules. Besides the usual CH/ interaction between p-tert-butylcalix[4]arene cavity and a solvated acetone, this structure shows the intra- and intermolecular CH/ interactions among a nitrobenzene ring, ethylene bridge of the ethoxynitrobenzene side chain and a solvated acetone molecule.     

Crystal structure of 14, α-hydroxy,sandarocopimar-7, 15-diene-19-oic acid

C₂₀H₃₀O₃, M _r =318.46, Monoclinic,P2₁,a=12.232(2) ,b=11.491(2) ,c=14.160(3) , =115.2°(3),V=1800.3(7) ³,Z=4,D _x =1.18 Mg m^–3, (CuK)=1.5418 , =5.3 cm^–1,F(000)=696,T=298 K. FinalR=0.044 for 2645 reflections withI>2. The two crystallographically independent molecules in the unit cell adopt essentially similar conformations. The structure reveals atrans relationship between the hydrogen at C(9) and the methyl group at C(20). The stereochemistry at C(13) is S. Apart from van der Waals forces the structure is stabilized by hydrogen bonds.     

Templated assembly of 1,2-bis(chloromercurio) tetrafluorobenzene in the presence of THF

Slow evaporation of a THF solution containing the bidentate Lewis acid 1,2-bis(chloromercurio) tetrafluorobenzene (1) , yields colorless crystals of the complex 1₂-THF (2) as indicated by elemental analysis, thermal gravimetric analysis and ¹³C CPMAS solid-state NMR spectroscopy. As shown by X-ray analysis, the oxygen atom of the THF molecules bridges the two mercury center of the bidentate Lewis acid. Compound 2 forms an extended structure that features channels filled with THF molecules. In this structure, the individual molecules of the organomercurial are held together by - and Hg Cl interactions. Immersion of 2 in water results in THF loss to afford 1,2-bis(chloromercurio) tetrafluorobenzene in a pure form. Exposure to THF vapor results in a stoichiometric uptake and formation of a solid whose composition corresponds to that of 2.     

Synthesis,characterization and crystal structure of oxovanadium(IV) complex with tridentate o-van-gly and bidentate phenanthroline

A novel oxovanadium(IV) complex with tridentate schiff base and bidentate phenanthroline ligands, VO(o-van)(phen) 2H₂O[o-van-gly: o-vanillin-glycine; phen: phenanthroline], was synthesized and characterized by elemental analysis, IR and UV-vis spectra. The crystal structure was determined by X-ray single crystal diffraction analysis. The crystal of title complex (C₂₂H₂₁N₃O₇V, M_w = 490.36) belongs to triclinic, space group P-1 with the following crystallographic parameters: a = 9.247(3) Å, b = 10.125(4) Å, c = 13.100(5) Å, = 106.343(6), = 96.042(7), = 101.726(7), V = 1135.0(7) ų, Z = 2, D_c = 1.435 Mg m^–3, (MoK = 0.485 mm^–1, F(000) = 506, and final R₁ = 0.0779, wR₂ = 0.1598 for observed reflections 1606 (I > 2(I)). V(IV) is six-coordinate with three oxygen atoms and three nitrogen atoms in a distorted octahedral geometry. The complex forms a 3-D network via – stacking and hydrogen bonds.     

Crystallographic and spectroscopic studies on ethylenediaminetetraacetic acid (edta) III. Crystal and molecular structure of α-edta and infrared studies on α- and β-edta

-Edta is monoclinic:C2/c,a= 11.812,b = 9.647,c = 12.970 Å, = 113.23 ° andZ = 4. The structure has been determined by direct methods with CuK diffractometer data, and refined by full-matrix least squares toR = 7.2% for 737 observed reflexions. The molecule exists as a zwitter ion in acis conformation, and possesses crystallographic two-fold symmetry. The nitrogen atom is protonated and takes part in hydrogen bonding. -Edta is hydrated, in this specimen, refinement indicated a value of 0.39 H₂O per molecule of edta. A short (2.47 Å) hydrogen bond links oxygen atoms in adjacent molecules. Infrared spectra are reported for both -edta and -edta; the results are discussed in terms of the crystal structures. The formulation of -edta with 0.39 mole H₂O is explained.     

Crystal structure of di(N-benzyl piperidinium) pentachloroantimonate(III) dihydrate

The salt di(N-benzyl piperidinium) pentachloroantimonate(III) dihydrate crystallizes in the orthorhombic system with space group Cmc2₁, the unit cell dimensions are: a = 29.383(1), b = 10.509(2), c = 9.941(1) Å, with Z = 8. The structure shows a layer arrangement perpendicular to the a axis: planes of SbCl₆ octahedra alternate with planes of [C₁₂H₁₇N]⁺ cations. The SbCl₆ octahedra are connected through a O(W)–HCl hydrogen bonds and a chlorine bridge, so that infinite unidimensional chains of composition [SbCl₅(H₂O)₂]^2n– _n are formed in the structure along the c direction. These chains are connected to [C₁₂H₁₇N]⁺ entities by N–HCl and N–HO(W) hydrogen bonds, forming a three-dimensional network. It was found that lengths of Sb–Cl bonds may differ from each other. The differences shown as a distortion of the SbCl₆ octahedra were attributed to the Sb(III) lone electron pair stereoactivity.     

Synthesis and crystal structure of N-<Emphasis Type="Italic">tert-</Emphasis>butyl-N′-thio [O-(1-methylthioethylimino)-N″-methylcarbamic acid]-N,N′-dibenzoylhydrazine

The novel compound N-tert-butyl-N-thio[O-(1-methylthioethylimino)-N-methyl carbamic acid]- N,N-dibenzoylhydrazine has been synthesized by the reaction of N-tert-butyl-N,N-dibenzoylhydrazine with N-sulfenyl chloride of O-(1-methylthio ethylimino) -N-methylcarbamic acid. Its structure was determined by X-ray single crystal diffraction. The crystal belongs to monoclinic, space group P2₍₁₎/n with the following crystallographic parameters: a = 7.569(3) Å, b = 20.585(7) Å, c = 16.347(5) Å, = 90, = 92.606(6), = 90, V = 2544.4(14) ų, z = 4, Dx = 1.276 mg/m³, F(000) = 1032, T = 293(2) K, 2.34 25.01, the final R factor: R₁ = 0.0475, wR₂ = 0.0907. The N–N bond adopts a gauche conformation with a dihedral angle() of 98.8 for C(17)=N(1)=N(2)=C(7), whereas its parent compound N-tert-butyl-N,N-dibenzoyl hydrazine has the dihedral angle of –71.8.     

Coordination complexes of 2,6-diarylpyrazines with copper(II) acetate

The coordination chemistry of a series of 2,6- and 2,3-diarylpyrazines with copper(II) acetate is reported. The 2:2 coordination complexes formed between two 2,6-diarylpyrazines and copper(II) acetate are characterized by X-ray crystallography. The structure (2,6-bis(3,5-dimethylphenyl)pyrazine)copper(II) acetate acetonitrile solvate, (C₄₈H₅₂Cu₂N₄O₈) (C₂H₃N) is triclinic, P 1, with a = 7.9685(10), b = 13.1893(16), c = 13.8267(17) Å, = 107.585(3)°, = 103.921(3)° and = 96.759(3)°. The structure of (2-(2,6-dimethylphenyl)-6-(3,5-dimethylphenyl)pyrazine)copper(II) acetate, C₄₈H₅₂Cu₂N₄O₈, is monoclinic, P2₁/c, with a = 8.2196(7), b = 12.5174(11), c = 21.7325(19) Å and = 96.201(2)°.     

Bis(triphenylphosphoranylidene)ammonium tetraethylborate, (Ph3P)32N+BEt34-: preparation and structure

The compound (Ph₃P)₃2N,⁺BEt₄ ^- is readily prepared from (Ph₃P)₂N⁺Cl^– and LiBHEt₃. The NMR spectrum (¹H, ¹³C. ¹¹B, ³³P) are reported. C₄₄H₅₀NBP₂ M = 665.64, Triclinic, P (#2), a = 11.530(4), b = 15.397(9), c = 11.497(9) Å, = 102.94(6), = 102.87(4), = 89.34(4)°, V = 1938(4) ų, and Z= 2.     

A new monoclinic crystal phase of [Bu4N][Ni(dmit)2]

The crystal structure of the title compound, tetrabutylammonium bis(2-thioxo-1,3-dithiole-4,5-dithiolato)nickelate(III), [N(C₄H₉)₄][Ni(C₃S₅)₂], is the fourth known phase of this polymorphous compound. It is monoclinic space group P2₁/c, with a = 20.040(2) Å, b = 13.1151(17) Å, c = 12.1093(15) Å, = 105.456(15)°, and V = 3067.5(6) ų with Z = 4, for D _calc = 1.503 g cm^–3. The [Ni(dmit)₂] anion packing arrangement consists of arrays of side-on touching anions and these arrays are connected via head-to-tail close S S contacts.     

X-ray and NMR studies on the rotational isomerism about the C(5)-C(6) bond of 6-substituted methyl 2,3,4,-tri-O-acetyl-6-X-α-D-glucopyranoside derivatives

The rotamers about the C(5)–C(6) bond of a series of 2,3,4-tri-O-acetyl-6-X--D-glucopyranozide derivatives resulting by substitution at C(6) or O(6) have been studies with¹H-NMR spectroscopy (400 MHz) and X-ray structure analysis. The methyl 2,3,4-tri-O-acetyl-6-O-triphenylmethyl--D-glucopyranoside and the N-(I-O-methyl-2,3,4-tri-O-acetyl--D-glucopyranose-6-yl)-pyridinium nitrate crystallize in the P2₁ space group with =14.940(1),b=11.232(1),c=9.0773(7), and =94.480(7) anda=7.670(1),b=15.384(3),c=9.624(1) and =104.90(1), respectively; the methyl 2,3,4-tri-O-acetyl-6-O-nitro--D-glucopyranoside and methyl 2,3,4-tri-O-acetyl-6-O-deoxy-6-iodo--D-glucopyrano-side crystallize in the P2₁2₁2₁ space group witha=5.630(1),b=14.360(1) andc=22.388(3), anda=5.556(1),b=14.303(6) andc=21.963(6), respectively.     

Molecular structure of N-(2-phenylethyl)amide of α-(1,1-ethylenedioxy)-ethyl γ-hydroxybutyric acid (I) and1H NMR spectra of (I) and N-(p-methoxybenzyl)derivative (III)

The spectroscopic and X-ray investigation of the N-(2-phenylethyl) amide of -(1,1-ethylenedioxy)-ethyl--hydroxybutyric acid are reported. The¹H NMR spectra for the title structure and for the N-(p-methoxybenzyl) amide of -(1,1-ethylenedioxy)-ethyl--hydroxybutyric acid are given. The N-(2-phenylethyl)amide of -(1,1-ethylenedioxy)-ethyl--hydroxybutyric acid, C₁₆H₂₃O₄N, crustallizes in the monoclinic space groupP2 ₁/c witha=21.547(5),b=6.333(2),c=11.822(3) Å and =101.01(2)°. The dioxolane ring has a half-chair conformation with C₂(O3)=2.4° and ||_av=18.2°. The inconsiderable deviations from planarity of the six atoms of the amide group are caused mainly by twist around the C4–N1 bond and out-of-plane bending at the N1 atom ((C4–N1)=4°, X_N =7°, X_c =0.4° ). The amide group plane is nearly coplanar with the phenyl ring. The molecules are connected by two intermolecular hydrogen bonds.     

Crystal and molecular structure of glutaconic acid

Crystals of Glutaconic acid, C₅O₄H₆, are triclinic, space group P , with the cell dimensions (294 K), a = 4.843(1) Å, b = 10.188(1) Å, c = 12.609(1) Å, = 83.46(1)°, = 80.02(1)°, = 78.71(1)°, V = 598.8(3) ų with D _m = 1.47, D _x = 1.443 gcm ^–3. There are two independent molecules in the asymmetric unit. The crystal structure was solved by multi solution techniques with three-dimensional data collected (to the limit of 2_max of 154° for Cu K) on a CAD-4 diffractometer. The crystal structure was refined by full matrix least squares method to a final R value of 0.058 for 1894 reflections (I 2). The two independent molecules are conformationally similar. In both the molecules, the carboxyl ends are trans to each other with respect to the central C=C double bond in the structure. The molecules are self-paired through dimeric type of hydrogen bonding involving the terminal carboxyl groups, characteristic of many dicarboxylic acid structures. The crystal structure is stabilized by a series of O–HO hydrogen bonds of the glutaconic acid dimeric units. Free radicals have been shown to be involved in a number of chemical and biological processes and lipid peroxidation is one such process. Glutaconic acid was chosen as a simple unsaturated model of a fatty acid. When irradiated with X-rays, it was found to form a stable free radical structure. ESR (electron spin resonance) and ENDOR (electron nuclear double resonance) studies were used to characterize the free radical structure and correlate with the X-ray structure. The free radical was found to be HOOC–CH=CH–CH–COOH with the glutaconic acid in the trans conformation. The damage occurs at the -carbon atom (the first carbon of the double bond). The damage consists of a loss of an hydrogen atom. This results in an unpaired electron in the p-orbital delocalized over the three central carbon atoms. The two -proton couplings were resolved in the ENDOR spectrum. ESR spectra show that the two molecules are magnetically similar that is in agreement with the crystal structure that reveals that the two independent molecules are conformationally similar. This is the characteristic type of damage that occurs in lipids when they form free radicals that in turn reacts with oxygen and other compounds and ultimately results in cellular damage.     

Synthesis and crystal structure of macrocyclic nickel(II) complex bridged by chromate

A novel compound catena-(-CrO₄-O,O)[Ni(L¹)Ni(L²)] 3H₂O (1) (L¹ = 3,5,10,12-tetramethyl-1,4,8,11-tetraazacyclotetradecane and L² = 2,5,9,12-tetramethyl-1,4,8,11-tetraazacyclotetradecane) has been synthesized for the first time and structurally characterized. 1 crystallizes in the triclinic space group P with a = 9.623(1), b = 10.084(1), c = 12.723 (3) Å, = 66.74(2), = 75.20(1), = 72.02(1)°, V = 1066.2(3) ų, and Z = 2. The coordination environment around the Ni(II) ions is an axially elongated octahedron with the secondary amines of the isomeric ligands and two oxygen atoms of [CrO₄]^2–.