TALP, un nou mètode de determinació d'estructures cristal·lines de fàrmacs i compostos moleculars per difracció de pols

La difracció de pols és una eina molt potent per a la determinació d'estructures cristal·lines de compostos tant iònics com moleculars quan no es disposa de monocristalls. Pel que fa als segons, les millores en els mètodes en l'espai directe dels darrers anys permeten tractar estructures cada cop més complexes malgrat les limitades resolucions espacials (dhkl) de les dades, sobretot per a molècules orgàniques. En aquest treball, es descriu i s'utilitza un nou mètode en l'espai directe, TALP, en el qual es combinen algoritmes de cerca (aleatòria o assistida amb la funció de rotació) amb afinaments per mínims quadrats ràpids de les coordenades atòmiques. Les intensitats del diagrama s'extreuen amb un procediment en tres passos i el model molecular es defineix a partir de les coordenades atòmiques, restriccions de distància i enllaços de lliure rotació. TALP ha resolt estructures amb tretze angles de torsió i amb més d'una molècula independent a la unitat asimètrica a partir de dades de difracció de pols de laboratori i utilitzant models teòrics. Com a exemple, s'explica la redeterminació pas a pas d'una estructura ja coneguda, la de l'(S)-ibuprofèn, amb TALP.Powder diffraction is a powerful tool for solving crystal structures of ionic and molecular compounds when no single crystals are available. The recent development of direct-space methods allows the resolution of complex structures of molecular compounds, despite the limited d-spacing resolution of the data for these materials and especially organic molecules. This paper describes the new direct-space multisolution method TALP and its application. It combines random or rotation function-assisted search algorithms with fast least square minimizations of atomic coordinates. Diffraction intensities are determined by a three-step procedure and the molecular model is defined in terms of atomic coordinates, distance restraints and free rotation bonds. TALP has solved structures containing thirteen torsion angles and more than one independent molecule in the asymmetric unit from laboratory powder diffraction data and calculated molecular models. By way of example, the step-by-step TALP redetermination of the known structure of (S)-ibuprofen is presented

Examining the adsorption of gases into solid crystalline molecular copper(II) 3,5-bis(trifluoromethyl)benzoate derivatives

Altres ajuts: acords transformatius de la UABTwo copper(II) complexes, both involving the anionic 3,5-bis(trifluoromethyl)benzoate ligand (TFMBz), have been prepared and their structure elucidated by single crystal-X ray diffraction. [Cu(TFMBz)2(ISNA)2] (1) is a mononuclear complex, in which the sphere of coordination of Cu(II) is completed by two neutral isonicotinamide (ISNA) auxiliary ligands. Hydrogen bonding formed between auxiliary ISNA ligands determines the formation of a 2D supramolecular network. [Cu2(TFMBz)4(DMSO)2] (2) is a binuclear complex, in which the four carboxylate ligands define the typical paddle wheel structure often found in copper complexes, containing also the ancillary dimethyl sulfoxide (DMSO) ligand in axial positions. The elucidated crystallographic data provide the static view of the crystal structures, which reveals only non-interconnected voids for both materials. Even that, compound 1shows an appreciable adsorption of CO2 at 273 K (ca. 1 CO2 molecule/Cu atom at 100 kPa), concomitant with a reduced adsorption of Ar or N2 under similar conditions, which implies a considerable degree of selectivity for CO2. Moreover, 1 does not adsorb N2 or Ar at 77 K and 100 kPa. This behavior suggests that the stablished intermolecular hydrogen bonds rest flexibility and dynamism to 1 at low temperature. Contrarily, increasing the temperature transient porosity is originated, which allows guest molecules to diffuse through the cavities. Compound 2 shows adsorption of N2 and Ar at 77 K, indicating that vibrations in the network and rotation of some CF3 groups, necessary to favor adsorbate diffusion, are still feasible at this low temperature

One-dimensional metal-organic frameworks built by coordinating 2,4,6-tris(4-pyridyl)-1,3,5-triazine linker with copper nodes : CO2 adsorption properties

Altres ajuts: acord transformatiu CRUE-CSICThe reaction between 2,4,6-tris(4-pyridyl)-1,3,5-triazine (4-tpt) and copper(II) hexafluoroacetylacetone (Cu(hfa)2) yields two different 1D metal-organic frameworks (MOFs), [(Cu(hfa)2)2(4-tpt)]n (1) and [Cu(hfa)2(4-tpt)]n (2). The Cu:4-tpt ratio in the new MOFs is determined by the reaction medium, particularly, the solvent used. The two compounds have been fully characterized, including crystal structure elucidation. [(Cu(hfa)2)2(4-tpt)]n (1), with a 2:1 Cu:4-tpt ratio, could be precipitated in either 1,1,2-trichloroethane or supercritical CO2. In (1), 4-tpt shows a tritopic coordination mode, but only half of the Cu(hfa)2 subunits act as a node, thus connecting two 4-tpt and giving a 1D network. The other half of Cu(hfa)2 subunits are connected only to one pyridine and thus protrude along the chains. The later Cu(hfa)2 fragments show a labile character and can be dissolved in diethyl ether to give the second MOF [Cu(hfa)2(4-tpt)]n (2), with a 1:1 Cu:4-tpt ratio. The compound (2) has also a 1D structure, with all the incorporated copper atoms acting as nodes. In this case, the packing of the chains defines accessible channels, which are perpendicular to the chain axis. After activation, N2 adsorption/desorption measurements at 77 K confirm the microporous character of (2) with an apparent surface area of 190 m2 g−1. Besides, at 273 K this material clearly shows a significant adsorption of CO2 prompted by noncoordinated nitrogen in the triazine linker

Supramolecular Isomerism in Cobalt(II) Coordination Polymers Built from 3,5-Bis(trifluoromethyl)benzoate and 4,4'-Bipyridine

Acord transformatiu CRUE-CSICThe reaction of [Co2(H2O)(TFMBz)4(py)4] (1) (TFMBz: 3,5-bis(trifluoromethyl)benzoate; py: pyridine) with 4,4'-bipyridine (bpy) in different solvents yields four coordination polymers with unlikely structures but with the same stoichiometry. Three of them contain similar ladder chains consisting of binuclear nodes "Co2(TFMBz)4", in which two of the TFMBz ligands show bidentate bridge coordination, double linked to each adjacent node by bpy but packed in different fashions. The different packing affects the compound porosity; thus, [Co2(TFMBz)4(bpy)2]n (2), precipitated using low-polarity solvents such as supercritical CO2 (scCO2), n-butyl acetate, or heptane and also in acetonitrile, is microporous, with a surface area of 330 m2 g-1, showing the N2 adsorption/desorption isotherm at 77 K with a gate-opening effect at low relative pressures (P/P0 = 0.05). The isomer [Co2(TFMBz)4(bpy)2]n (3), synthesized in ethoxyethanol, presents a surface area of 230 m2 g-1. A third chain packing isomer, [Co2(TFMBz)4(bpy)2]n (4), is obtained in acetone and has only non-interconnected voids. Finally, precursor 1 is combined with bpy in a highly polar solvent such as water to give [Co(TFMBz)2(bpy)]n (5). In this isomer, all the carboxylate units act as bidentate bridging ligands, generating chains that are interlinked by bpy, leading to a 2D network, which after packing yields a non-porous structure. The resolution of structures 2-5 is only possible with the recently developed 3D electron diffraction method based on the collection of diffraction patterns on sub-micron-sized single crystals. The variation of magnetic susceptibility as a function of temperature is also measured. Overall, our work provides insightful information on the complex landscape of metal-organic framework solids that are formed by crystallization using different solvent media

Application of synchrotron through-the-substrate microdiffraction to crystals in polished thin sections

The synchrotron through-the-substrate X-ray microdiffraction technique is applied to the structural study of microvolumes of randomly oriented crystals embedded in polished thin sections. The whole procedure is discussed in detail with the help of examples from petrology, and possible future developments are envisaged. The synchrotron through-the-substrate X-ray microdiffraction technique (tts-μXRD) is extended to the structural study of microvolumes of crystals embedded in polished thin sections of compact materials [Rius, Labrador, Crespi, Frontera, Vallcorba & Melgarejo (2011). J.Synchrotron Rad. 18, 891-898]. The resulting tts-μXRD procedure includes some basic steps: (i) collection of a limited number of consecutive two-dimensional patterns (frames) for each randomly oriented crystal microvolume; (ii) refinement of the metric from the one-dimensional diffraction pattern which results from circularly averaging the sum of collected frames; (iii) determination of the reciprocal lattice orientation of each randomly oriented crystal microvolume which allows assigning the hkl indices to the spots and, consequently, merging the intensities of the different frames into a single-crystal data set (frame merging); and (iv) merging of the individual crystal data sets (multicrystal merging) to produce an extended data set suitable for structure refinement/solution. Its viability for crystal structure solution by Patterson function direct methods (δ recycling) and for accurate single-crystal least-squares refinements is demonstrated with some representative examples from petrology in which different glass substrate thicknesses have been employed. The section of the crystal microvolume must be at least of the same order of magnitude as the focus of the beam (15 × 15 µm in the provided examples). Thanks to its versatility and experimental simplicity, this method­ology should be useful for disciplines as disparate as petrology, materials science and cultural heritage

Facile, fast and green synthesis of a highly porous calcium-syringate bioMOF with intriguing triple bioactivity

A facile, fast and green strategy based on ethanol is utilized to prepare a new bioMOF, namely, CaSyr-1, with particular characteristics of full biocompatibility given by using just calcium and syringic acid, the latter being a phenolic natural product found in fruits and vegetables, permanent porosity with an outstanding surface area >1000 m2 g−1, and a micropore diameter of 1.4 nm close to mesopore values. Collectively, these data establish CaSyr-1 as one of the most porous bioMOFs reported to date, with high molecular adsorption capacity. The CaSyr-1 adsorptive behavior is revised here through the reversible adsorption of CO2 and the encapsulation of bioactive ingredients in the structure. Remarkably, CaSyr-1 enables the development of triple therapeutic entities, involving bioactive Ca2+, syringic acid and an impregnated drug

BCN­Routing : càlcul web de rutes amb pgRouting, OpenStreetMap i OpenLayers

En aquest projecte s'ha desenvolupat una interfície web per calcular rutes a la ciutat de Barcelona. Les rutes calculades són a peu, entre un punt d'origen qualsevol i un punt d'interès turístic de la ciutat com a destí. Per això s'han extret les dades dels carrers de Barcelona d'OpenStreetMap i s'han insertat a una base de dades postgreSQL/postGIS, juntament amb una capa vectorial de punts d'interès turístic que s'ha creat amb el SIG d'escriptori qGIS. El càlcul de les rutes amb les dades de la base de dades s'ha realitzat amb l'extensió pgRouting, i la interfície web per seleccionar els punts d'origen i destí, mostrar els mapes, i mostrar les rutes resultat, s'ha desenvolupat utilitzant la llibreria OpenLayers.The use of Geographic Information Systems (GIS) to solve spatial problems and get information about land­related aspects is becoming a common practice in institutions and companies. Therefore, taking advantage of already created open source geospatial tools is vital for the creation of high quality free GIS. Routing applications are gaining relevance every day thanks to the popularization of GPS and future Galileo. A previous data preparation and a correct spatial database structure is required to successfully apply complex algorithms to it. In the past few years, the development of pgRouting as an open source library that provides routing functionality to PostgreSQL/PostGIS has opened new possibilities for shortest path search in these databases. In this contribution, we have developed a GIS system for shortest path search between a given point and an interesting place in the city of Barcelona. The street information has been extracted from OpenStreetMap, a layer of tourist attraction points has been created, and everything has been stored in a PostGIS database. After a data structure preparation for routing capabilities, we will apply the Disjktra algorithm implementation provided in pgRouting to search for the shortest path between two nodes. Result presentation in a web­mapping application will be build using OpenLayers library. Routing tools supplied in the pgRouting extension for PostGIS databases, as well as additional tools to work with OpenStreetMap data, simplify the process of data structure creation and facilitate the resolution of shortest path search routing problems.En este proyecto se ha desarrollado una interfaz web para calcular rutas en la ciudad de Barcelona. Las rutas se calculan a pie, entre un punto de origen cualquiera y un punto de interés turístico de la ciudad como destino. Para ello se han extraído los datos de las calles de Barcelona de OpenStreetMap y se han insertado en una base de datos postgreSQL/postGIS, junto con una capa vectorial de puntos de interés turístico que se ha creado con el SIG de escritorio qGIS. El cálculo de las rutas con los datos de la base de datos se ha realizado con la extensión pgRouting, y la interfaz web para seleccionar los puntos de origen y destino, mostrar los mapas, y mostrar las rutas resultado, se ha desarrollado utilizando la librería OpenLayers

Síntesi d’àcids cianocarboxílics: hidrocarboxilació i deuteriocarboxilació catalítica selectiva. Desenvolupament de fosfines i complexos de pal∙ladi i platí

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Solvent Influence in the Synthesis of Lead(II) Complexes Containing Benzoate Derivatives

A series of lead(II) complexes incorporating benzoate derivative ligands was prepared: [Pb(2MeOBz)] (1), [Pb(2MeOBz)(HO)] (2), [Pb(1,4Bzdiox)(DMSO)] (3), [Pb(1,4Bzdiox)(HO)] (4), [Pb(Pip)(HO)] (5), and [Pb(Ac)(Pip)(MeOH)] (6) (2MeOBz: 2-methoxybenzoate; 1,4Bzdiox: 1,4-benzodioxan-5-carboxylate; DMSO: dimethylsulfoxide; Ac: acetate; Pip: piperonylate; MeOH: methanol). All compounds were characterized via elemental analysis, ATR-FTIR spectroscopy, and powder XRD. In addition, the crystal structures of some compounds were elucidated. Compounds 1 and 2, involving 2-methoxybenzoate, were closely related, only differing in the presence of one extra aqua ligand found for the latter. However, this implies key changes in the studied properties, e.g., 2 shows solid-state luminescence that displays a different color as a function of the crystal orientation, while 1 does not. The crystal structure of 2 revealed a 1D coordination polymer. A similar relationship was found between compounds 3 and 4, incorporating 1,4-benzodioxan-5-carboxylate. In this pair, only 4, with aqua ligands, displayed a greenish-yellow-color solid-state luminescence. Furthermore, two new lead(II) piperonylate complexes, 5 and 6, were obtained from the reaction between lead(II) acetate and piperonylic acid. In water, all acetate ligands in the metal precursor were displaced and [Pb(Pip)(HO)] (5) was isolated, while in methanol, a mixed acetate-piperonylate complex, [Pb(Ac)(Pip)(MeOH)] (6), was precipitated. Considering only conventional Pb-O bonds, the crystal structure of 6 was described as a 1D coordination polymer, although, additionally, the chains were associated via tetrel bonds, defining an extended 2D architecture

Síntesi d'àcids cianocarboxílics : hidrocarboxilació i deuteriocarboxilació catalítica selectiva. Desenvolupament de fosfines i complexos de pal·ladi i platí /

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