José Daniel Martín-Ramos

Three new modes of adenine-copper(II) coordination: interligand interactions controlling the selective N3-, N7- and bridging μ-N3,N7metal-bonding of adenine to different N-substituted iminodiacetato-copper(II) chelates

Abstract The reaction of Cu2CO3(OH)2, various N-substituted-iminodiacetic acids [RN(CH2CO2H)2)] and adenine (AdeH) in water yields crystalline samples of mixed-ligand copper(II) complexes of formulas [Cu(A)(N7AdeH)(H2O)]·H2O (A=N-methyl- or N-ethyl-iminodiacetato(2−); compounds 1 and 2, respectively), [Cu(B)(N3AdeH)(H2O)]·H2O (B=N-benzyl- or N-(p-methylbenzyl)-iminodiacetato(2−); compounds 3 and 4, respectively) as well as [Cu4(pheida)4(μ-N3,N7AdeH)2(H2O)4]·2H2O (pheida=N-phenethyl-iminodiacetato(2−)). Crystal structures of the acid H2pheida and compounds 1–5 are reported. H2pheida acid exhibits a typical zwitterionic structure. Copper(II) compounds were also studied by TG analysis (with FT-IR study of the evolved gasses), IR, electronic and ESR spectra and magnetic susceptibility data. The N-alkyl- or N-benzyl-like-iminodiacetato(2−) ligands (A or B) give complexes with Cu(II)/(A or B)/AdeH equimolar ratio, whereas pheida yields an unexpected tetranuclear compound with a 2:2:1 Cu(II)/pheida/AdeH molar ratio. In 1 and 2 AdeH binds to the metal by N7, whereas in 3 and 4 the N3 atom is used. An unexpected bridging μ-N3,N7AdeHdicopper(II) binding mode is found in the tetra-nuclear compound 5 (without interligand π,π-stacking interactions). These AdeHCu(II) binding modes have not been referred in the literature before. The difference in AdeHCu(II) binding modes in compounds 1 or 2 and 3 or 4 is rationalised on the basis of the absence or presence of a flexible N-benzyl-like substituent in the iminodiacetato(2−) ligand skeleton, which prevents or permits the interligand π,π-stacking interactions.

Synthesis, XRD structures and properties of diaqua(iminodiacetato)copper(II), [Cu(IDA)(H2O)2], and aqua(benzimidazole)(iminodiacetato)copper(II), [Cu(IDA)(HBzIm)(H2O)]

Abstract The stoichiometric reaction of copper(II) hydroxycarbonate with iminodiacetic acid (H2IDA) in water under reduced pressure yields good crystalline samples of [Cu(IDA)(H2O)2] (compound I). Using equimolar amounts of benzimidazole (HBzIm) the above reaction produces crystals of [Cu(IDA)(HBzIm)(H2O)] (compound II). Both compounds were characterised by TG analysis (with IR study of the evolved gasses in the pyrolysis), spectral and/or magnetic properties (IR, electronic, ESR spectrum, magnetic susceptibility in the 1.8–300 K range) and single crystal X-ray diffraction. The structure of I was re-determined (final R1=0.022) and it confirms the earlier reported distorted octahedral Cu(II) coordination (type 4+1+1), the fac-terdentate chelating and bridging roles for IDA ligand, as well as the ‘polymeric’ chain structure, but with a rather different hydrogen bonding network. In compound II (final R1=0.035) the Cu(II) exhibits a square base pyramidal coordination (type 4+1) and the IDA exhibits the mer-terdentate chelating configuration observed earlier for complexes having equimolar Cu(II)/IDA/HIm or HIm-like ratio, but now with a large dihedral angle (31.3°) between basal Cu(II) coordination and HBzIm mean planes.

Amorphous Ca-phosphate precursors for Ca-carbonate biominerals mediated by Chromohalobacter marismortui

Although diverse microbial metabolisms are known to induce the precipitation of carbonate minerals, the mechanisms involved in the bacterial mediation, in particular nucleation, are still debated. The study of aragonite precipitation by Chromohalobacter marismortui during the early stages (3–7 days) of culture experiments, and its relation to bacterial metabolic pathways, shows that: (1) carbonate nucleation occurs after precipitation of an amorphous Ca phosphate precursor phase on bacterial cell surfaces and/or embedded in bacterial films; (2) precipitation of this precursor phase results from local high concentrations of PO43− and Ca2+ binding around bacterial cell envelopes; and (3) crystalline nanoparticles, a few hundred nanometres in diametre, form after dissolution of precursor phosphate globules, and later aggregate, allowing the accretion of aragonite bioliths.

Ring–ring or nitro-ring π,π-interactions in N-(p-nitrobenzyl)iminodiacetic acid (H2NBIDA) and mixed-ligand copper(II) complexes of NBIDA and imidazole (Him), 2,2′-bipyridine (bipy) or 1,10-phenanthroline (phen). Crystal structures of H2NBIDA, [Cu(NBIDA)(Him)(H2O)], [Cu(NBIDA)(bipy)]·3H2O and [Cu(NBIDA)(phen)]·2H2O

Abstract N-(p-nitrobenzyl)iminodiacetic acid (H2NBIDA) and the mixed-ligand copper(II) complexes with NBIDA and imidazole (Him), 2,2′-bipyridine (bipy) or 1,10-phenanthroline (phen) were prepared and characterised by thermal, spectral, magnetic and X-ray diffraction methods. Our aim is to study various possibilities of the N-(p-nitrobenzyl) arm in the iminodiacetate(2−) ion (IDA) skeleton to be involved in π,π-interactions which contribute to molecular recognition processes and crystal building. Analysis of the shortest aromatic ring–ring interactions were carried out with platon program and let us conclude that in free H2NBIDA acid (1) and [Cu(NBIDA)(Him)(H2O)] (2) only inter-molecular benzyl–benzyl π,π-stacks occur, whereas in [Cu(NBIDA)(bipy)]·3H2O (3) and [Cu(NBIDA)(phen)]·2H2O (4) there are both inter-molecular nitro-benzyl π,π-interactions (instead of benzyl–benzyl π,π-stacks) and α,α′-diimine-α,α′-diimine ring–ring π,π-interactions. In compound 2 NBIDA ligand has a typical mer-NO2 tridentate conformation, whereas in 3 or 4 it exhibits an unusual fac-O2+N(apical) conformation. The molecular recognition pathway in 3 and 4 is discussed on a structural basis, considering a variety of interligand interactions involved in molecular recognition processes to build these and closely related crystals. We conclude that both the presence of a non-coordinating N-substituent in the IDA-like ligand and the chelation of Cu(II) by an aromatic α,α′-diimine (bipy or phen) display active roles for promote a fac-O2+N(apical) conformation and various modes of interligand π,π-stacking interactions.

The coordination chemistry of (2-thiazolin-2-yl)hydrazine hydrochloride (TzHyHCl)—II. Study of its interaction with zinc(II) and cadmium(II)

Abstract The complexation equilibria of (2-thiazolin-2-yl)hydrazine hydrochloride (TzHyHCl) with zinc(II) and cadmium(II) have been studied in aqueous solution at 298 K and 0.1 M ionic strength in NaClO 4 . The formation constants were determined and are discussed in terms of the characteristics of the ligand. The compounds [ZnCl(TzHy) 2 ]Cl and [Cd(TzHy)( μ -Cl) 2 ] n · n H 2 O have been isolated and their crystal structures determined. In the Zn II compound, the geometry around the central atom is a distorted trigonal-bipyramid composed of four nitrogen atoms from two TzHy ligands and one chlorine. The Ca II complex is polymeric, with octahedrally coordinated cadmium linked into infinite chains by double (μ-chloro) bridges. The coordination sphere around each cadmium center is completed by two nitrogen atoms from a TzHy ligand. In both cases, the crystal structure is stabilized by an extensive hydrogen-bond network.

Copper(II) and nickel(II) chelates with dihydrogen Trans-1,2-diaminocyclohexane-N,N,N′,N′-tetraacetate(2−) ion (H2CDTA2−). Synthesis, XRD structure and properties of [Cu(H2CDTA)]·H2O and [Ni(H2CDTA)(H2O)·4H2O

Abstract Stoichiometric reactions of metal hydroxycarbonates with the acid trans -1,2-cyclohexanediaminotetraacetic acid (H 4 CDTA) in water under reduced pressure yielded [Cu(H 2 CDTA)]·H 2 O ( I ) and [Ni(H 2 CDTA) (H 2 O)]·4H 2 O ( II ). Both compounds were characterized by TG-DTA analysis, spectral properties (IR, reflectance and RSE) and X-ray diffraction. In I the copper(II) atom exhibits a distorted square-base coordination (type 4+1) by chelation of one H 2 CDTA 2− ligand through two N and two O (carboxylate) at the square base and one O (carboxylic) at the apex of the coordination polyhedron; a second carboxymethyl group of H 2 CDTA 2− remains free. In II the H 2 CDTA 2− chelating ligand also plays a quinquedentate role, but one water molecule achieves the slightly distorted octahedral coordination of the nickel(II) atom. Appropriate comparisons with the structure of [M(H 2 EDTA)(H 2 O)] (M = Ni, Cu complexes suggest that the steric constraints in the H 2 CDTA ligand promotes the distorted five-coordination of the Cu II chelate in I as well as the hydration of the nearly octahedral Ni II derivative ( II ). The double protonation of the ligand H 2 CDTA 2− is carried out over different kinds of chelate rings, G and R, for Cu II and Ni II M(CDTA) derivatives, respectively (where G and R, indicate metal-glycinate rings nearly coplanar or perpendicular to the plane MNN, respectively).

The influence of Salt Concentration on the Precipitation of Magnesium Calcite and Calcium Dolomite by Halomonas Anticariensis

The influence of Salt Concentration on the Precipitation of Magnesium Calcite and Calcium Dolomite by Halomonas Anticariensis This research focuses on the formation of Ca-Mg carbonates by Halomonas anticariensis in solid media at different salt concentration and incubation time, and discusses the possible role of metabolic activity, bacteria surfaces and carbonic anhydrase in precipitation. Mineral saturation indexes of the solutions indicate that inorganic precipitation of different carbonates is possible in all media used but their precipitation did not occur in sterile control experiments. On the other hand H. anticariensis produced different Ca-Mg carbonates depending on salt concentration and Mg+2/Ca+2 ratios, in spite of its weak carbonic anhydrase activity. Incubation time does not influence the nature of the precipitates. At low salinity H. anticariensis precipitates magnesium calcite. A Ca-Mg carbonate phase with very small particle size, high lattice distortion (strain) and lattice parameters similar to those of disordered kutnohorite is presented and this phase is here referred to as non-stoichiometric calcium- rich dolomite, formed at high salinity. These Calcium-rich dolomites are rarely present in most natural habitats because this phase is thermo dynamically 32 metastable and it is subsequently transformed into calcite and dolomite.

Conformational analysis on cyclohexane, oxane, and thiane derivatives bearing two geminal electron-withdrawing groups and acetoxy substituents at the β and β' carbons

Abstract A qualitative conformational analysis on cyclohexane, oxane, and thiane structures bearing two geminal electron-withdrawing groups and having two acetoxy substituents at the β and β′ positions has been performed. The predominant conformation in thiane structures is determined by a preponderant hockey-stick effect. In the other structures, the predominant conformation is determinated by the competition between stabilizing gauche and destabilizing steric effects depending on the R1 and R2 bulks. Molecular mechanics procedure reproduces the conformational behaviour in compounds 25–32. Crystals of 29 are triclinic, P-1, a= 9.607(6), b= 13.437(8), c= 14.838(8)A , α= 106.50(7) β= 98.61(6), β= 91.17°, V= 1836(2) A3, Z=4, Dx= 1.246 Mg·m−3, λ (Mo Kα) = 0.71069 A, μ= 0.094 mm−1, F(000)= 736, T= 293 °K, R= 0.046 and wR= 0.063, S= 0.88, for 2277 unique observed reflections with F2o 8σ(F2o). The bond lengths and angles are normal and do not reflect delocalization.