scholarly journals Chlorido(pyridine-κN)(5,10,15,20-tetraphenylporphyrinato-κ4N)cobalt(III) chloroform hemisolvate

2012 ◽  
Vol 68 (8) ◽  
pp. m1104-m1105 ◽  
Author(s):  
Yassin Belghith ◽  
Jean-Claude Daran ◽  
Habib Nasri

In the title complex, [CoCl(C44H28N4)(C5H5N)]·0.5CHCl3or [CoIII(TPP)Cl(py)]·0.5CHCl3(where TPP is the dianion of tetraphenylporphyrin and py is pyridine), the average equatorial cobalt–pyrrole N atom bond length (Co—Np) is 1.958 (7) Å and the axial Co—Cl and Co—Npydistances are 2.2339 (6) and 1.9898 (17) Å, respectively. The tetraphenylporphyrinate dianion exhibits an important nonplanar conformation with major ruffling and saddling distortions. In the crystal, molecules are linkedviaweak C—H...π interactions. In the difference Fourier map, a region of highly disordered electron density was estimated using the SQUEEZE routine [PLATON; Spek (2009),Acta Cryst.D65, 148–155] to be equivalent to one half-molecule of CHCl3per molecule of the complex.

2012 ◽  
Vol 45 (6) ◽  
pp. 1287-1294 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori

The VLD (vive la difference) phasing algorithm combines the model electron density with the difference electron densityviareciprocal space relationships to obtain new phase values and drive them to the correct values. The process is iterative and has been applied to small and medium-size structures and to proteins. Hybrid Fourier syntheses show properties that are intermediate between those of the observed synthesis (whose peaks should correspond to the most probable atomic positions) and those of the difference synthesis (whose positive and negative peaks should correspond to missed atomic positions and to false atoms of the model, respectively). Thanks to these properties some hybrid syntheses can be used in the phase extension and refinement step, to reduce the model bias and more rapidly move to the target structure. They have been recently revisitedviathe method of joint probability distribution functions [Burla, Carrozzini, Cascarano, Giacovazzo & Polidori (2011).Acta. Cryst. A67, 447–455]. The results suggested that VLD could be usefully combined, forab initiophasing, with the hybrid rather than with the difference Fourier synthesis. This paper explores the feasibility of such a combination and shows that the original VLD algorithm is only one of several variants, all with relevant phasing capacity. The study explores the role of several parameters in order to design a standard procedure with optimized phasing power.


Author(s):  
Abdelhakim Laachir ◽  
Fouad Bentiss ◽  
Salaheddine Guesmi ◽  
Mohamed Saadi ◽  
Lahcen El Ammari

In the mononuclear title complex, [Co(N3)2(C12H8N4S)2], the cobalt(II) atom is located on an inversion centre and displays an axially weakly compressed octahedral coordination geometry. The equatorial positions are occupied by the N atoms of two 2,5-bis(pyridin-2-yl)-1,3,4-thiadiazole ligands, whereas the axial positions are occupied by N atoms of the azide anions. The thiadiazole and pyridine rings linked to the metal are almost coplanar, with a maximum deviation from the mean plane of 0.0273 (16) Å. The cohesion of the crystal is ensured by weak C—H...N hydrogen bonds and by π–π interactions between pyridine rings [intercentroid distance = 3.6356 (11) Å], forming a layered arrangement parallel to (001). The structure of the title compound is isotypic with that of the analogous nickel(II) complex [Laachiret al.(2013).Acta Cryst.E69, m351–m352].


2017 ◽  
Vol 73 (8) ◽  
pp. 1202-1207
Author(s):  
Agata Gapinska ◽  
Alan J. Lough ◽  
Ulrich Fekl

Two coordination compounds containing tetra-n-butylammonium cations and bis-tfd-chelated molybdenum(IV) [tfd2− = S2C2(CF3)2 2−] and oxalate (ox2−, C2O4 2−) in complex anions are reported, namely bis(tetra-n-butylammonium) bis(1,1,1,4,4,4-hexafluorobut-2-ene-2,3-dithiolato)oxalatomolybdate(IV)–chloroform–oxalic acid (1/1/1), (C16H36N)2[Mo(C4F6S2)2(C2O4)]·CHCl3·C2H2O4 or (N n Bu4)2[Mo(tfd)2(ox)]·CHCl3·C2H2O4, and bis(tetra-n-butylammonium) μ-oxalato-bis[bis(1,1,1,4,4,4-hexafluorobut-2-ene-2,3-dithiolato)molybdate(IV)], (C16H36N)2[Mo2(C4F6S2)4(C2O4)] or (N n Bu4)2[(tfd)2Mo(μ-ox)Mo(tfd)2]. They contain a terminal oxalate ligand in the first compound and a bridging oxalate ligand in the second compound. Anion 1 2− is [Mo(tfd)2(ox)]2− and anion 2 2−, formally generated by adding a Mo(tfd)2 fragment onto 1 2−, is [(tfd)2Mo(μ-ox)Mo(tfd)2]2−. The crystalline material containing 1 2− is (N n Bu4)2-1·CHCl3·oxH2, while the material containing 2 2− is (N n Bu4)2-2. Anion 2 2− lies across an inversion centre. The complex anions afford a rare opportunity to compare terminal oxalate with bridging oxalate, coordinated to the same metal fragment, here (tfd)2MoIV. C—O bond-length alternation is observed for the terminal oxalate ligand in 1 2−: the difference between the C—O bond length involving the metal-coordinating O atom and the C—O bond length involving the uncoordinating O atom is 0.044 (12) Å. This bond-length alternation is significant but is smaller than the bond-length alternation observed for oxalic acid in the co-crystallized oxalic acid in (N n Bu4)2-1·CHCl3·oxH2, where a difference (for C=O versus C—OH) of 0.117 (14) Å was observed. In the bridging oxalate ligand in 2 2−, the C—O bond lengths are equalized, within the error margin of one bond-length determination (0.006 Å). It is concluded that oxalic acid contains a localized π-system in its carboxylic acid groups, that the bridging oxalate ligand in 2 2− contains a delocalized π-system and that the terminal oxalate ligand in 1 2− contains an only partially localized π-system. In (N n Bu4)2-1·CHCl3·oxH2, the F atoms of two of the –CF3 groups in 1 2− are disordered over two sets of sites, as are the N and eight of the C atoms of one of the N n Bu4 cations. In (N n Bu4)2-2, the whole of the unique N n Bu4 + cation is disordered over two sets of sites. Also, in (N n Bu4)2-2, a region of disordered electron density was treated with the SQUEEZE routine in PLATON [Spek (2015). Acta Cryst. C71, 9–18].


2008 ◽  
Vol 41 (3) ◽  
pp. 592-599 ◽  
Author(s):  
Angela Altomare ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Moliterni ◽  
Rosanna Rizzi

Fourier syntheses providing electron density maps are usually affected by truncation effects due to the limited data resolution. A recent theoretical approach [Altomare, Cuocci, Giacovazzo, Kamel, Moliterni & Rizzi (2008).Acta Cryst.A64, 326–336] suggests that the resolution bias may be reduced by correcting the current electron density maps in accordance with the physics of the diffraction experiment. We have implemented the approach inEXPO2004[Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004).J. Appl. Cryst.37, 1025–1028], a program devoted to the solution of crystal structures from powder data. The new algorithm was applied at the end of the direct methods modulus, to verify if the reduction of the resolution bias is able to improve the electron density maps and to provide additional power to direct methods. Application of this method to a large set of test structures indicates that resolution-bias correction often makes the difference between success and failure, and thus constitutes a new tool for reducing the dependence of modern crystallography on resolution effects. The chances of failure are expected to depend on the quality of the experimental data (e.g.the accuracy of the full-pattern decomposition procedure and the data resolution), on the size of the structure and on its chemical composition.


1996 ◽  
Vol 52 (3) ◽  
pp. 479-486 ◽  
Author(s):  
M. Helliwell ◽  
J. R. Helliwell ◽  
A. Cassetta ◽  
J. C. Hanson ◽  
T. Ericsson ◽  
...  

Data were collected close to the Ni K edge, using synchrotron radiation at the National Synchrotron Light Source, and using a Mo Kα rotating anode, from a crystal of a nickel-containing aluminophosphate, NiAl3P4O18C4H21N4 (NiAPO). These data sets, along with an existing Cu Kα rotating anode data set, allowed the calculation of several f′ difference-Fourier maps exploiting the difference in f′ for Ni between the various wavelengths. These differences are expected to be 7.8, 4.5 and 3.3 e for Mo Kα data to SR (synchrotron radiation), Cu Kα to SR and Mo Kα to Cu Kα, respectively. The phases were calculated either excluding the Ni atom or with Al at the Ni-atom site. The f′ difference-Fourier maps revealed peaks at the Ni-atom site, whose height and distance from the refined Ni-atom position depended on the f' difference and the phase set used. The largest peak was located at a distance of only 0.025 Å from the refined Ni-atom site and was obtained from the f′ difference map calculated with the coefficients |F Mo Kα − F SR| , using phases calculated with Al at the Ni-atom site. In all cases, it was found that these phases gave optimal results without introducing bias into the maps. The results confirm and expand upon earlier results [Helliwell, Gallois, Kariuki, Kaučič & Helliwell (1993), Acta Cryst. B49, 420–428]. The techniques described are generally applicable to other systems containing anomalous scatterers in chemical crystallography.


2015 ◽  
Vol 71 (11) ◽  
pp. m207-m208 ◽  
Author(s):  
Souheyla Chetioui ◽  
Noudjoud Hamdouni ◽  
Djamil-Azzeddine Rouag ◽  
Salah Eddine Bouaoud ◽  
Hocine Merazig

The title complex, [Cu(C17H13N2O2)2], crystallizes with two independent molecules in the asymmetric unit. Each CuIIatom has a distorted ocahedral coordination environment defined by two N atoms and four O atoms from two tridentate 1-[(E)-(2-methoxyphenyl)diazenyl]naphthalen-2-olate ligands. In the crystal, the two molecules are linkedviaweak C—H...O hydrogen bonds which in turn stack parallel to [010]. A region of disordered electron density, most probably disordered methanol solvent molecules, was corrected for using the SQUEEZE routine inPLATON[Spek (2015).Acta Cryst.C71, 9–18]. Their formula mass and unit-cell characteristics were not taken into account during refinement.


2002 ◽  
Vol 58 (6) ◽  
pp. 1011-1017 ◽  
Author(s):  
Parthapratim Munshi ◽  
T. N. Guru Row

The charge-density distribution in 2H-chromene-2-thione (2-thiocoumarin), C9H6OS, has been determined from X-ray diffraction data measured at 90 K using a CCD detector, to a resolution of sinθ/λ < 1.08 Å−1. A multipolar-atom density model was fitted against 6908 reflections with I > 2σ(I) [R(F) = 0.021, wR(F) = 0.022, goodness of fit = 1.81] in order to generate the difference Fourier maps. The topological properties of the molecular electron density in terms of the bond critical points and the evaluation of the dipole moment show that the molecular dipole moment in the crystal is higher than the corresponding value derived from theoretical calculations.


IUCrData ◽  
2016 ◽  
Vol 1 (11) ◽  
Author(s):  
An-ran Wang ◽  
Cong Wang ◽  
Sheng-Li Li

The title compound, [Zn(NCS)2(C21H15N3)], crystallizes with three independent complex molecules in the asymmetric unit. In each complex molecule, the ZnIIatom is coordinated by three N atoms of a 4′-phenyl-2,2′:6′,2′′-terpyridine ligand, and by the N atoms of two NCS−anions. The ZnIIatoms are therefore five-coordinate, ZnN5, with distorted square-pyramidal geometries. In the crystal, the three independent molecules are linked by a series of offset π–π interactions [intercentroid distances vary between 3.680 (5) and 3.791 (5) Å], forming columns along thea-axis direction. The columns are linkedviaC—H...S interactions, forming a fence-like arrangement parallel to theabplane. A small region of disordered electron density was corrected for using the SQUEEZE routine inPLATON[Spek (2015).Acta Cryst.C71, 9–18], but the formula mass and unit-cell characteristics were not taken into account during the refinement.


Author(s):  
Wei Ding ◽  
Jianfeng Li

The title complex, [Fe(C44H28N4)(C5H8N2)2]·C4H8O, possesses inversion symmetry with the iron(II) atom located on a center of symmetry. The metal atom is coordinated in a symmetric octahedral geometry by four pyrrole N atoms of the porphyrin ligand in the equatorial plane and two N atoms of 1-ethylimidazole ligands in the axial sites; the complex crystallizes with a tetrahydrofuran solvent molecule. The average Fe—Np (Np is a porphyrin N atom) bond length is 1.995 (3) Å and the axial Fe—NIm (NIm is an imidazole N atom) bond length is 1.994 (2) Å. The two 1-ethylimidazole ligands are mutually parallel. The dihedral angle between the 1-ethylimidazole plane and the plane of the closest Fe—Np vector is 24.5°. In the crystal, the only significant intermolecular interactions present are C—H...π interactions.


2014 ◽  
Vol 70 (a1) ◽  
pp. C933-C933
Author(s):  
Edward Baker

A conversation with Dorothy Hodgkin on a long bus trip, just before I returned to New Zealand in 1970, left me full of determination and optimism. This presentation will recount my experience in starting a protein crystallography lab with only a sealed-source generator and a precession camera for equipment. Crystals had to be large (0.5 - 1.0 mm on edge) and X-ray data, collected at room temperature on a borrowed small-molecule diffractometer, accumulated very slowly. We corrected for absorption and decay and scaled data sets rather crudely. It was very much a do-it-yourself environment. With no CCP4, software had to be borrowed or adapted or written oneself; methods papers in Acta Cryst. were like gold as I pored through them trying to understand. Communications with friends, by airmail, were vital. An electron density map for the cysteine protease actinidin, at 2.8 Å, was immediately interpretable thanks to excellent data and phases from more derivatives than were really necessary. An R factor of 42% to 2.0 Å, for a model built in a Richards box, was really quite astonishing. Later FFT-based least squares refinement at the University of York in 1978 was even more astonishing as the R factor rocketed down [1]. No computer graphics, but the difference electron density told the story – in retrospect there was even evidence that the crystals (prepared from kiwifruit bought at the local shop) contained several genetic variants of the protein! It may not have been the most exciting protein in the world (except to me!) but what a way to learn protein crystallography and protein structure.


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