Miguel Quirós

Crystallography Open Database - an open-access collection of crystal structures

The Crystallography Open Database (COD) is an ongoing initiative by crystallographers to gather all published inorganic, metal–organic and small organic molecule structures in one database, providing a straightforward search and retrieval interface. The COD adopts an open-access model for its >80 000 structure files.

Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration

Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

Metal complexes of [1,2,4]triazolo-[1,5-a]pyrimidine derivatives

Abstract This article covers all the research work published until September 1998 about the coordination chemistry of 1,2,4-triazolo-[1,5-a]pyrimidine derivatives. The revision is mainly focused in the structural features of the compounds, obtained from single crystal X-ray diffraction. The references are classified according to the present metal atoms. These kind of ligands display a broad versatility when binding metal ions, monodentate binding through the endocyclic nitrogen atom at position 3 being however their main coordinating behaviour. Dimeric and polymeric structures are observed when a bidentate binding through N3–N4 or N3–N1, respectively, takes place. N1–O7 chelating binding mode has also been observed in a few cases. In some cases, dimers or polymers are also generated when the present auxiliary ligands are the ones that bridge the metal centres.

Crystal structure of ciprofloxacin hexahydrate and its characterization

Ciprofloxacin hexahydrate has been prepared and its crystal structure has been determined by X-ray crystallography. The molecule is in the zwitterionic form in solid state, the carboxylic proton being present at terminal piperazine nitrogen atom (N(74)) which is in contrast to the previously reported structures of quinolones. Water molecules are involved in a very complicated hydrogen bonding network. Different other techniques (IR, Raman spectroscopy, thermal and elemental analysis) were used to characterize the title compound and to compare its properties with similar compounds.

Synthesis, Spectroscopic and X-ray Structural Study of cis-diazidobis- (ethylenediamine)Cobalt(III) Thiocyanate

Reaction of cis-diazidobis(ethylenediamine)cobalt(III)nitrate with ammonium thiocyanate in a 1 : 2 molar ratio in aqueous medium gave the title cobalt(III) compound, cis-[Co(en)2(N3)2]SCN, as reddish brown crystals in almost quantitative yield. The complex salt was characterized by elemental analysis, IR, electronic, 1H and 13C NMR spectroscopic studies. An X-ray structure determination revealed an ionic structure with the monoclinic space group P21/c, having cell dimensions a = 12.1950(6), b = 9.0317(5), c = 12.6017(7) Å; β = 113.419(1)°, V = 1273.63(12) Å3 and Z = 4. The structure was refined by a full-matrix least-square procedures to R 1 = 0.0297 and wR 2 = 0.0697.

X-ray diffraction structures of two N-salicylidene tryptophananato diaquocopper(II) complexes: erythro and threo isomers

Abstract X-ray crystal structures are reported for two novel N-salicylidene tryptophanato diaquocopper(II) isomers, [Cu(Sal-Trp)(h2O)2, erythro (1) and hreo (2). The coordination geometry about the copper in both complexes is approximately square-pyramidal with the tridentate Sal-Trp Schiff base ligand and the oxygen atom O(W1) of one water molecule occupying the corners of a square. The coordination sphere about the copper is completed by an axial OW(2) water molecule. In 1, O(W2) [CuO(W2) distance 2.25(1) A] is at the same side of the indole ring (syn disposition—“erythro” isomer), whereas in 2 the O(W2) and the α-amino acid chain are disposed anti (“threo” isomer), with a longer CuO(W2) distance, 2.485 A. IR, ESR, electronic spectral data and magnetic properties are discussed and related to the copper binding mode derived from the crystal structure determination.

PD(II) AND PT(II) D-PENICILLAMINE COMPLEXES. CRYSTAL STRUCTURE OF A TRIDENTATE D-PENICILLAMINE CLUSTER OF PD(II)

Abstract Complexes of formula [M2(D-Pen-)2Cl2], where M=Pd or Pt and d -Pen-= d -penicillaminate were synthesized and characterized by the usual spectroscopic methods. Red crystals suitable for X-ray study were obtained, after several days, from the mixture of K2PdCl4\D-Penicillamine solutions. The crystals were identified as [Pd3(Pen2-)3].7\8KCl.19\8H2O. The structure shows four chemically but not crystallographically equivalent trinuclear clusters in the cell. Three d -penicillamine molecules act as divalent anions in tridentate fashion between three palladium atoms forming neutral units. Each S atom bridges two palladium atoms inside the molecular units. Potassium and chloride ions are curiously distributed along the crystallographic units contributing, together with the water molecules, to the stability of the crystal. The capacity of the penicillamine to act as tridentate ligand can be related to the capacity to capture toxic metals.

Influence of pseudohalide ligands on the structural versatility and properties of novel ternary metal complexes with 1,2,4-triazolo(1,5-a)pyrimidine†

Eight new multidimensional metal(II) complexes [Zn(tp)2(NCS)2] (1), [Ni(tp)2(H2O)2(µ-tp)2Ni(NCS)4]n (2), [Co(tp)2(H2O)2(µ-tp)2Co(NCS)4]n (3), [Cd(tp)2(NCS)2]n (4), [Mn(tp)2(NCS)2(H2O)2] (5), [Zn(tp)2(NCO)2] (6), [Cd(tp)(NCO)2]n (7) and [Cd(tp)(N3)2]n (8) have been synthesized by conventional reactions of the 1,2,4-triazolo[1,5-a]pyrimidine with metallic(II) salts in the presence of thiocyanate, cyanate and azide as auxiliary ligands. X-Ray diffraction studies on these compounds show that species 1, 5 and 6 are mononuclear units in which zinc and manganese have tetrahedral and octahedral coordination geometry, respectively. Complexes 2 and 3 are isostructural and consist of neutral chains with triazolopyrimidine bridging ligands through N1, N3 nitrogen atoms. Compound 4 exhibits a 2D rectangular-grid-like structure and complexes 7 and 8 are cyanate-bridged chains formed by defective cubanes. Magnetic and luminescent properties of these materials have also been studied.

Synthesis and study of trinuclear Pd(II) and Pt(II) complexes with 2-mercaptonicotinic acid: Crystal and molecular structure of [Pd3(mercaptonicotinic acid)3Cl3]

Pd(II) and Pt(II) complexes of 2-mercaptonicotinic acid of formulae (M (mercaptonicotinic acid) Cl ) were synthesized and 33 3 characterized by the usual spectroscopic techniques including mass spectrometry. The crystal structure was obtained for the palladium complex. The molecule has a ternary symmetry, and mercaptonicotinic acid coordinates in a bidentate (N,S) mode to each palladium ion. The sulfur atom acts as a bridge between two palladium atoms. The fourth coordination site in the plane square geometry of the Pd(II) is occupied by a chloride ion. Identical molecular structure is proposed for the platinum compound in agreement with the spectroscopic and theoretical results.

Structural and ab initio studies of AgAg bonding in the silver(I) dimer bis-μ-(5,7-dimethyl[1,2,4]triazolo[1,5-a]pyrimidine)dinitrato disilver(I)

Abstract This work is an attempt to address the issue of metal-metal bonding in d10 systems. The compound [Ag(dmtp)(NO3)]2, where dmtp represents the ligand 5,7-dimethyl[1,2,4]triazolo[1,5-a]pyrimidine, has been prepared, characterized by thermal analysis and IR spectroscopy and its structure has been solved by X-ray diffraction. The compound is triclinic, space group P 1 , a = 5.1295(4), b = 9.6009(7), c = 10.332(2) A , α = 103.73(1), β = 99.14(1), γ = 97.67(1)°, Z = 2, Dcal = 2.200 g cm−3, R = 0.029 for 4144 observed reflections. The compound exhibits a [Ag2(dmtp)2]2+ core structure with two silver atoms bridged by the dmtp ligands via N3 and N4 to give eight-membered Ag2N4C2 rings. The nitrato groups are coordinated in a semibridging and semichelating way (distances AgO, 2.816(2) A for non-bridging and 2.653(2) and 2.749(2) A for bridging oxygens). The AgAg separation is 3.058(1) A, only 0.17 A greater than in metallic silver. In order to make checking of the possible AgAg bonding, a theoretical analysis has been performed, based on the properties of the charge density distribution derived from ab initio MO calculations using STO-3G∗ and 3-21G(∗) wavefunctions, a significant direction interaction between the two metal centres having been found. Similar conclusions have been obtained for the model compound [Ag(NHCHNH)]2 after performing a geometry optimization and using improved LANL2DZ wavefunctions that take into account relativistic effect.