V. Kasam, J. Salzemann, M. Botha, A. Dacosta, G. Degliesposti, R. Isea, D. Kim, A. Maass, C. Kenyon, G. Rastelli, M. Hofmann-Apitius and V. Breton (2009). "WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures." Malaria Journal, Vol. 8, 88.
Background:
Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the Plasmodium parasite, some are promising targets to carry out rational drug discovery. Motivation Recent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase.
Methods:
In silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate in silico docking and in information technology to design and operate large scale grid infrastructures.
Results:
On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, In vitro results are underway for all the targets against which screening is performed.
Conclusions:
The current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.
Andrés Pinzón, Emiliano Barreto, Adriana Bernal, Luke Achenie, Andrés González, Raúl Isea and Silvia Restrepo. (2009). "Computational models in plant-pathogen interactions: the case of Phytophthora infestans." Aceptado.
Raúl Isea, Juán L. Chaves, Esther Montes, Antonio J. Rubio-Montero, Rafael Mayo. (2009). "The evolution of Human Papillomavirus by means of a phylogenetic study." Studies in Health Technology and Informatics, vol. 147, pp. 245-250.
A. Acero, A. Alberto, F. Blanco, J. Blanco, F. Casteñon, JA. Fábregas, LA. Flores, M. Giménez, P. González, J. Guasp, R. Isea, P. Ladrón de Guevara, R. Mayo, E. Montes, A. Muñoz, M. Rodríguez, AJ. Rubio-Montero, E. Serradilla, and S. Troiani. (2009). "Grid and Supercomputing Activities at the ICT
Division of CIEMAT." In: 3rd Iberian Grid Infrastructure Conference, 2009, Valencia. IBERGRID Proceedings. Santa Cristina: NETBIBLO S.L., 2009. v.3. p.126-136. ISBN: 9788497454063.
Abstract:
In this paper we report about the Grid activities that are being
carried out at the Information and Communication Technologies Division
of CIEMAT. At the same time, a summary of the supercomputation ones is
also presented. Most of these activities have been developed in the framework
of the Sixth and Seventh Framework Programmes of the European
Commission, some of them mainly focused on the European communities,
but others on the Latin American ones too.
Raúl Isea, Esther Montes, Antonio J. Rubio-Montero, Rafael
Mayo. (2009). "Computational challenges on Grid Computing for workflows applied to Phylogeny." Lecture Notes in Computer Science, Vol. 5518, pp. 1130-1138.
LN. Ciuffo, L. Alves, AC Alves de Melo, G. Aparicio, P. Arce, I. Blanquer, DA Burbano, A. Carrión, V. Hernández, JM. Hurtado, R. Isea, JI. Lagares, J. López-Fenner, R. Mayo, E. Merino, E. Montes, R. Nogales-Cadenas, I. Oliveira, A. Pascual-Montano, MA. Pérez, R. Pezoa, JC. Roa, F. Romero, JA. Rubio-Montero, L. Salinas, F. Tirado, J. Verleyen, C. Vicente-Molina, ME Walter. (2009). "Biomedical applications in the EELA-2 Project." Proceeding NETTAB 2009, pp. 35-38. ISBN 978-88-7388-242-8.
Abstract:
The EELA-2 (E-science grid facility for Europe and Latin America) Project, co-funded by the European Commission, is providing a high capacity, production-quality Grid Facility for European and Latin American scientific collaborations. The project currently supports more than 50 applications, from which more than a half belong to Biomedicine. This paper briefly presents some of these applications, ranging from genes sequence alignment and analysis to medical imaging processing and phylogenetic calculations.
Raul Isea, Esther Montes, Antonio J. Rubio-Montero, y Rafael Mayo (2009). "Challenges and characterization of a Biological system on Grid by means of the PhyloGrid application." Proceedings of the First EELA-2 Conference, pp. 139-146. ISBN (978-84-7834-600-4).
Resumen:
In this work we present a new application that is being developed. PhyloGrid is able to perform large-scale phylogenetic calculations as those that have been made for estimating the phylogeny of all the sequences already stored in the public NCBI database. The further analysis has been focused on checking the origin of the HIV-1 disease by means of a huge number of sequences that sum up to 2900 taxa. Such a study has been able to be done by the implementation of a workflow in Taverna.
- G. Aparicio, F. Blanco, I. Blanquer, C. Bonavides, J.L. Chaves, M. Embid, A. Hernández, V. Hernández, R. Isea, J.I. Lagares, D. López, R. Mayo, E. Montes, HR. Mora. (2009). "Developing Biomedical Applications in the framework of EELA". Handbook of Research on Grid Technologies and Utility Computing: Concepts for Managing Large-Scale Applications. Edited By Emmanuel Udoh and Frank Zhigang Wang;
Capítulo XX; pp. 206-218. Editorial IGI Global; ISBN: 978-1-60566-184-1.
Introduction:
EELA (E-Infrastructure shared between Europe and Latin America, see http://www.eu-eela.org) is a Project funded by the European Commission that began in January 2006. Its objective is building a digital bridge between the existing e-Infrastructure initiatives in Europe and those that were emerging in Latin America, through the creation of a collaborative network that shares an interoperable Grid infrastructure to support the development and test of advanced applications.
One of the areas of work is the identification and support of Grid enhanced applications. This scientific research covers several fields, but due to the high social impact in the Latin American society, one of the pillars of the Project is Biomedicine and, consequently, the applications that can be run on the Grid.
Some of them, falling in three typical categories of bioinformatics applications, computational biochemical processes and biomedical models, were selected and started to be deployed on the infrastructure for both production and dissemination purposes.
This document describes these biomedical applications running in the Project and the advances and scientific results that have been achieved, among others, in the field of cancer diseases, the drug discovery in Malaria, the determination of sequences in parasite diseases and in the HIV origin.
Will Sandoval, Raul Isea, Evelyn Rodriguez, and José L. Ramírez (2008). "A biochemical and genetic study of Leishmania donovani pyruvate kinase". Gene. Vol. 424, pp. 25-32
Abstract:
Here we present a biochemical and molecular biology study of the enzyme pyruvate kinase (PYK) from the parasitic protozoa Leishmania donovani. The PYK gene was cloned, mutagenised and over expressed and its kinetic parameters determined. Like in other kinetoplastids, L. donovani PYK is allosterically stimulated by the effector fructose 2,6 biphosphate and not by fructose 1,6 biphosphate. When the putative effector binding site of L. donovani PYK was mutagenised, we obtained two mutants with extreme kinetic behavior: Lys453Leu, which retained a sigmoidal kinetics and was little affected by the effector; and His480Gln, which deployed a hyperbolic kinetics that was not changed by the addition of the effector. Molecular Dynamics (MD) studies revealed that the mutations not only altered the effector binding site of L. donovani PYK but also changed the folding of its domain C.
- Esther Montes, Raul Isea and Rafael Mayo (2008). "Phylogrid: a development for a workflow in phylogeny." Iberian Grid Infrastructure Conf. Proc. Vol. 2, pp. 378-387. ISBN: 978-84-9745-288-5.
Abstract:
In this application we work on the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check the accuracy of the results in the intermediate stages as well as do a multiple alignment of the sequences previously to the final result. To do this, no knowledge from his/her side about the computational procedure is required.
- G. Rivera, F. González-Nilo, T. Perez-Acle, Raul Isea, and D.S. Holmes (2007) "The Virtual Institute for Integrative Biology (VIIB"). Proceedings of the Third Conference of the EELA Project. R. Gavela, B. Marechal, R. Barbera et al. (Eds.) pp. 111-120. ISBN 978-84-7834-565-6.
Abstract:
The Virtual Institute for Integrative Biology (VIIB) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, metagenomics, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomics, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services
and protein simulations for biotechnological and medical applications. Human resource development has been promoted through co-sponsored students and shared teaching and seminars via video conferencing. E-Science challenges include: interoperability and connectivity concerns, high performance computing limitations, and the development of customized computational frameworks and flexible workflows to efficiently exploit shared resources without causing impediments to the user. Outreach programs include training workshops and classes for high school teachers and students and the new Adopt-a-Gene initiative. The VIIB has proved an effective way for small teams to transcend the critical mass problem, to overcome geographic limitations, to harness the power of large scale, collaborative science and improve the visibility of Latin American science It may provide a useful paradigm for developing further e-Science initiatives in Latin America and other emerging regions.
- V. Hernández, I. Blanquer, G. Aparicio, Raúl Isea, J. L. Chaves, A. Hernández, H. R. Mora, D. López, M. Fernández, F. Blanco and R. Mayo (2007). "Biohealth in EELA". Proceedings of the NETTAB Conference. Vol. 7, pp. 145-156
- V. Hernández, I. Blanquer, G. Aparicio, Raul Isea, J.L. Chaves, A. Hern�ndez, H.R. Mora, M. Fernández, A. Acero, E. Montes and R. Mayo. (2007). "Advances in the biomedical applications of the EELA Project". ." Studies in Health Technology and Informatics. Vol. 126, pp. 31 - 36.
Abstract:
In the last years an increasing demand for Grid Infrastructures has result ed in several international collaborations. This is the case of the EELA Project, which has brought together collaborating groups of Latin America and Europe. One year ago we presented this e-infrastructure used, among others, by the biomedical groups for the studies of oncological analysis, neglected diseases, sequence alignments and computational phylogenetics. After this period, the achieved advances are summarised in this paper.
- J.L. Chaves, G. Díaz, V. Hamar, Raúl Isea, F. Rojas, N. Ruiz, R. Torrens, M. Uzcategui, J. Florez-Lopez, H. Hoeger, C. Mendoza, L.A. Nun~ez (2007) "e-Science initiatives in Venezuela". Proceedings of the Spanish Conference on e-Science Grid Computing , ISBN 978-84-7834-544-1, pp. 45-52.
Abstract:
Within the context of the nascent e-Science infrastructure in Venezuela, we describe several web-based scientific applications developed at the Centro Nacional de Calculo Cientifico Universidad de Los Andes (CeCalCULA), Merida, and at the Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas. The different strategies that have been followed for implementing quantum chemistry and atomic physics applications are presented. We also briefly discuss a damage portal based on dynamic, nonlinear, finite elements of lumped damage mechanics and a biomedical portal developed within the framework of the \textit{E-Infrastructure shared between Europe and Latin America} (EELA) initiative for searching common sequences and inferring their functions in parasitic diseases such as leishmaniasis, chagas and malaria.
- R. Abarca, A. Acero, G. Andronico, G. Aparicio, C. Baeza, R. Barbera, I. Blanquer, M. Carrillo, D. Carvalho, J. Casado, J.L. Chaves, C. Cherubino, A. Cofío, J. Cruz, M. Diniz, M.T. Dova, I. Dutra, F. Echeverría, L. Enriquez, F. Fernández-Lima, F. Fernández-Nodarse, M. Fernández, V. Fernández, J.M. Gutiérrez, A. Hernández, V. Hernández, Raul Isea, D. López, G. Lucet, B. Marechal, R. Mayo, R. Miguel, E. Montes, H.R. Mora, L. Nellen, L.N. Ciuffo, R. Pezoa, A. Porto, P. Rausch, A.J. Rubio-Montero, L. Salinas, E. Silva (2007) "Building a Network in Latin America: e-Infrastructure and Applications". Proceedings of the Spanish Conference on e-Science Grid Computing ISBN 978-84-7834-544-1, pp. 83-96.
Abstract:
Several international Projects andCollaborations have emerged in the last years due to the increasing demand for Grid resources in many places around the world. One importantaspect of these initiatives deals with thegridification of computing intensive scientificapplications otherwise difficult to run efficiently. The EELA Project (E-Infrastructure shared between Europe and Latin America) is a collaboration of Latin America and Europe Institutions which has developed a performant e-Infrastructure for e-Science applications. Nowadays many groups have already ported their applications on the EELA Grid and are obtaining first results thanks to the Network that has been created. This paper describes theconsolidated e-Infrastructure and the progressachieved so far as well as the new challenges that the Project is addressing.
- L. M. Cardenas, V. Hernández, R. Mayo, I. Blanquer, J. Perez-Griffo, Raúl Isea, L. Nun~ez, H.R. Mora, M. Fernández (2006). "Biomedical applications in EELA". Stud Health Technol Inform. Vol. 120, 397-400.
Abstract:
The current demand for Grid Infrastructures to bring collabarating groups between Latina America and Europe has created the EELA proyect. This e-infrastructure is used by Biomedical groups in Latina America and Europe for the studies of ocnological analisis, neglected diseases, sequence alignments and computation plygonetics.
- Raul Isea, C. Aponte, and R. Cipriani(2004). "Can the RNA of the Cowpea Chlorotic Mottle Virus be released through a channel by means of free diffusion? A Test in silico". Biophysical Chemistry.vol. 107 (1-2): 101-106.
Abstract:
Cowpea chlorotic mottle virus (CCMV), a plant virus which is member of the Bromoviridae family, is used as a model for the diffusion of a random, short, single stranded RNA, [5'-R(PGpGpApCpUpUpCpGpGpUpCpC)-3')], through achannel on the pseudo-three-fold axis using molecular dynamic simulations. This proposition is based the fact that CCMV undergoes a dynamic structural transition as a response to changes of pH, temperature and ionic strength. Results indicate that the RNA looses its secondary structure and moves into the capside channel by free diffusion. These results are congruent with the hypothesis suggesting that the CCMV capside does not have to dissolve in order to release the RNA into the host.
- L. Kedzierski, A.A. Escalante, Raúl Isea, C.G. Black, J.W. Barnwell and R.L. Coppel (2002). "Phylogenetic analysis of the genus Plasmodium based on the gene encoding adenylosuccinate lyase". Infect Genet Evol. Vol. 1: 297-301.
Abstract:
Phylogenetic studies of the genus Plasmodium have been performed using sequences of the nuclear, mitochondrial and plastid genes. Here we have analyzed the adenylosuccinate lyase (ASL) gene, which encodes an enzyme involved in the salvage of host purines needed by malaria parasites for DNA synthesis. The ASL gene is present in several eukaryotic as well as prokaryotic organisms and does not have repeat regions, which facilitates the accuracy of the alignment. Furthermore, it has been shown that ASL is not subject to positive natural selection. We have sequenced the ASL gene of several different Plasmodium species infecting humans, rodents, monkeys and birds and used the obtained sequences along with the previously known P. falciparum ASL sequence, for structural and phylogenetic analysis of the genus Plasmodium. The genetic divergence of ASL is comparable with that observed in other nuclear genes such as cysteine proteinase, although ASL cannot be considered conserved when compared to aldolase or superoxide dismutase, which exhibit a slower rate of evolution. Nevertheless, a protein like ASL has a rate of evolution that provides enough information for elucidating evolutionary relationships. We modeled 3D structures of the ASL protein based on sequences used in the phylogenetic analysis and obtained a consistent structure for four different species despite the divergence observed. Such models would facilitate alignment in further studies with a greater number of plasmodial species or other Apicomplexa.
- M. Pilar Gamasa, J. Gimeno, B.M. Martín-Vaca, Raul Isea, and A. Vegas (2002). "Synthesis and Characterization of 2-Oxacycloalkylideneruthenium(II) Complexes: X-ray Crystal Structure of the 2-Oxacycloheptylidene complex". Journal
of Organometallic Chemistry. Vol. 651: 22-33.
Abstract:
The oxacyclocarbene complexes [Ru{-COCH2(CH2)nCH2}(η5-C9H7)LL'][PF6].(L = L' = PPh3, n = 1 (2a), 2 (3a), 3 (5a); L = L' = PMe2Ph, n = 1 (2b), 2 (3b), 3 (5b): LL' = dppm, n = 1 (2c), 2 (3c), 3 (5c); L = PPh3. L'= PMe3, n = 1 (2d), 2 (3d), 3 (5d)) have been prepared by reaction of [RuCl(η5-C9H7)LL'] with 3-butyn-1-ol. 4-pentyn-1-ol and 5-hexyn-1-ol in refluxing ethanol and in the presence of NaPF6. The process involves alkyne to vinylidene tautomerization to give hydroxyalkylvinylidene intermediate complexes. The vinylidene complexes [Ru{-C=C(H)(CH2)3CH2OH}(η5-C9H7)LL'][PF6] (L = L' = PPh3 (4a), L = L' = PMe2Ph (4b). L = PPh3. L' = PMe3 (4d)) have been isolated from the reaction of [RuC](η5-C9H7)LL'] with 5-hexyn-1-ol. The first structure for a 2-oxacycloheptylidene complex, 5a, has been determined by X-ray diffraction methods. The molecular structure shows the typical pseudooctahedral three-legged piano-stool geometry around the ruthenium atom, which is linked to the phosphorus atoms of the triphenylphosphine ligands and to the Cα of the oxacyclic carbene ligand; the coordination around the ruthenium atom is completed by a η5-bonded indenyl ligand with the benzo ring orientated nearly trans to the carbene group (CA = 16.6(6)�). The Ru-C1 distance, 1.89(1) �, is somewhat shorter than that found for other oxacyclic carbene ruthenium(II) complexes. The oxacycloheptylidene ring adopts a 'pseudochair' conformation for the seven member ring and shows an appreciable deviation from vertical orientation (DA = 29.7(5)�).
- A.A. Escalante, H.M. Grebert, Raul Isea, I.F. Goldman, L. Basco, M. Magris, S. Biswas, S. Kariuki and Altaf A. Lal (2002). "A study of genetic diversity in the gene encoding the circumsporozoite protein (CSP) of Plasmodium falciparum from different transmission areas XVI. Asembo Bay Cohort Project". Mol Biochem Parasitol. Vol. 125: 83-90.
Abstract:
We have investigated the genetic diversity of the gene encoding the CS protein. A total of 75 complete and 96 partial sequences are studied. We find high levels of genetic polymorphisms as evidenced by 50 and 24 alleles at the Th2R and Th3R epitopes, respectively. Overall, we find that African isolates are more polymorphic as compared with parasites from other geographic regions. We conclude that the uneven geographic polymorphism may have an adverse impact on the effectiveness of vaccines based on this antigen alone. We find extensive polymorphism in the repeat allotypes, or RATs. In order to explore how the protein structure may impose restrictions in the number of repeats, we have simulated the stability of the structure of the tandem repeat region. Our analysis suggests that the protein structure may play an important role in the observed polymorphism in the number of CS repeats in Plasmodium falciparum. We explored the linkage and recombination events among the polymorphic sites. We found that putative recombination events overlap with linked sites. We discuss how this pattern is explained by the action of positive natural selection, where the recombination events detected are convergent mutations. We conclude that it is inappropriate to use linkage-recombination patterns on genes under positive selection for assessing the structure of parasite populations.
- Raul Isea (2001). "What is the maximum
stretching for C-C single bond?" J. of Molecular Structure
(Theochem). Vol. 540: 131-138.
Abstract:
The objective of this work is to determine the maximum stretch of the C-C bond before it misses the character of single bond, employing both the Atoms in Molecules (AIM) and Electron Localization Function (ELF) methods. It was concluded that C-C distances up to 2.0 A could be considered single bonds.
- J. Murgich, O. Leon, E. Rogel, and Raul Isea (2001). "A Molecular Mechanics - Density Functional Study of the Adsorption of Fragments of Asphaltenes and Resins on the (001) Surface of Fe2O3" Petroleum Science and Technology. Vol. 10: 1081-1091.
Abstract:
A combination of Molecular Mechanics and Density Functional Theory allowed the calculation of the charge distribution and the adsorption energy on the (001) surface of hematite (α-Fe2O3) of a set of twelve molecules that represent fragments of resins and asphaltenes. The results showed that no covalent bond was formed with the inorganic surface upon adsorption, which indicates that physisorption instead of chemisorption takes place. In aromatic hydrocarbons, the adsorption energy was found to be proportional to the molecular surface, which indicates the main role, played for the van der Waals forces in the adsorption of these molecules. For 2-substituted naphthalenes, the energy decreased with the increase in the length of the alkyl chain. This decrease was related to the gain in deformation energy of the alkyl chain that was required by the adsorption process. The aromaticity and the H/C ratios were found to be good indicators of the ability of the molecules to be adsorbed on the hematite surface. In particular, molecules with high aromaticity and low H/C ratio show high adsorption energy. This result can explain the experimental finding of a high content of high aromatic and low hydrogen content molecules found in asphaltenic deposits extracted from wells. Substitution of the central -CH2- group by N-H, O or S at the five-member ring in fluorene produced complex changes in the adsorption energies. In some these molecules, the atoms protruding from the molecular plane produced reduced adsorption energies.
- Raul Isea, C. Rivas and A. Vegas (2000). "Tridimensional Structure of the Zinc Cyanide Ion [Zn27(CN)55]- determined by Quantum Mechanical Calculations (QMC) as a Complementary Method to Force Field (FF)." Journal of Molecular Structure (Theochem). Vol. 507: 193-196.
Abstract:
The aim of this work was to determine the lowest energy conformation of the [Zn27(CN)55]− ion using ab initio SCF techniques. The theory on atoms in molecules was used to characterize both the normal bonds and the intermolecular interactions responsible for the helical structure type.
- Raul Isea, M. Capparelli, D. Gomez, and H. Gil (2000). "Crystal Structure of 5-phenylhydantoic acid, C6H5NHCONHCH2COOH." Zeitschrift fur Kristallographie, New Crystal Structures. Vol. 215: 167-169.
- A. J. Arce,*. Ruben Machado, Ysaura De Sanctis, Raul Isea, Reinaldo Atencio, A.J. Deeming (1999). "Synthesis and molecular structure of cisoid and transoid isomers of [Re2(CO)6(1,1'-bis(indenylidene)] derived from the reaction of [Re2(CO)8(MeCN)2] and diazoindene" J. Organometally Chemistry. Vol. 580: 339-343.
Abstract:
The compound [Re2(CO)8(MeCN)2] reacts with diazoindene (C9H6N2) while refluxing in THF to afford three dirhenium products in which C9H6N2 is cleaved with loss of N2 and with incorporation of the residual indenylidene group into the products. Two indenylidene groups are coupled in two diastereomers of [Re2(CO)6(μ,η5:η5-1,1′-C18H12)] where C18H12=bis(indenylidene). X-ray structures show that these isomers are related as RR/SS and RS isomers. These have the two Re(CO)3 groups coordinated transoid and cisoid, respectively to a trans bis(indenylidene) bridge. The third product is the μ-indenylidene complex [Re2(CO)8(μ,η1:η5-C9H6)], which was also structurally characterised by X-ray diffraction.
Más Otras Publicaciones con mi MENTOR y MAESTRO: Dr. Angel VEGAS
- Raul Isea, A. Vegas and A. Ramos-Gallardo (1998). "Distribution of the M-M Distances in the Oxides of the Group 13 Elements and their Spinels and Delafossites" Acta. Cryst. Vol B . Vol. B54: 35-40.
Abstract:
An analysis of the distribution of the M-M distances (M = Al, Ga, In, Tl) in all their binary, ternary and quaternary oxides, contained in the Inorganic Crystal Structure Database (ICSD95), shows that the M-M distances are not distributed uniformly, but present maxima at values which are near the corresponding distances in pure metals. As for boron, this feature reflects the tendency of these elements to form aggregates in their compounds. These metal aggregates maintain distances and, in many instances, also the topology of the elemental structures, as is illustrated here with two families of structures, i.e. spinels and delafossites. In spinels, the group 13 cations form a 3D (three-dimensional) network of truncated tetrahedra, which are also found in the Zintl phases of these elements. In MgAl2O4 the Al subnet is identical, in topology and dimensions, to that of CaAl2 and both reproduce exactly half of the f.c.c. (face-centred cubic) net of Al metal.
- A. Vegas and R. Isea (1998). "Distribution of the M-M Distances in the Rare Earth Oxides" Acta. Cryst. Vol B . Vol. B54: 732-740.
Abstract:
A systematic study of the distribution of the M-M distances in all the binary, ternary and quaternary oxides of the rare earth elements (RE = Sc, Y, La-Lu), contained in the Inorganic Crystal Structure Database (ICSD) has been carried out. The results indicate that the RE-RE distances are not distributed uniformly, but present maxima which are close to the corresponding distances in the pure metals. In some of the histograms (Y, Ce, Pr, Sm, Tb, Dy, Ho, Lu) two maxima appear which correspond to the nearest-neighbor (b.c.c., h.c.p.) and second-nearest neighbor (b.c.c.) distances of the elemental phases. As examples of this behavior, the cation arrays of the binary oxides, hydroxides and ternary oxides of both the delafossite and α-NaFeO2 type are analyzed. In all of them the cations form aggregates whose topologies and distances can be related to the structure of the parent metals. The size of the metal aggregates seems to decrease with increasing oxygen content.
- A. Vegas and R. Isea (1997). "The Cation Array of the Oxihydroxydes of Trivalent Metals" J. Solid State Chem. Vol. 131: 358 - 362.
Abstract:
The structures of the oxyhydroxides of trivalent metals,MOOH, are analyzed in terms of their cation arrays. ForM=Al, Ga, In, Sc, Mn, Y, andLn, the cations form aggregates which can be derived from the structures of their parent metal. However, the compounds of the 3dtransition metals, V, Cr, and Fe, showM�Mdistances which are expanded with respect to those of their metallic nets. These distances are on the order of 3.00 � and coincide with theM�Mdistance of the nextpelement, in this case Ga. This could be interpreted in terms of the charge transfer from thedorbitals to the metalporbitals via the O atoms. In the case of Yb, a tetragonal YbOOH phase is stabilized whose cation array is a distortion of fcc Yb in which the O2−and the OH−anions are inserted into the metallic net without any volume increase.
- C. Navarro-Ranninger, F. Zamora, L. A. Martínez-Cruz, Raul Isea and J. R. Masaguer (1996). "Synthesis and NMR structural analysis of several orthopalladated complexes of substituted benzoimidazole, -oxazole and �thiazole and study of two polymorphic crystals" J. of Organometallic Chemistry. Vol. 131: 358 � 362. Vol. 518: 29-36.
Abstract:
The full assignation of 1H and 13C NMR parameters using both homo- and hetero-nuclear two dimensional spectroscopy techniques (COSY, HMQC and HMBC) allows the determination of electronic properties in cyclopalladated complexes obtained by reaction of N-methyl-2-phenylbenzimidazole (a), 2-phenylbenzothiazole (b) and 2-phenylbenzoxazole (c) with palladium salts.
The attempts to separate the anti and syn isomers (detected by NMR) led to the formation of two different kinds of crystal for the 2-phenylbenzoxazole palladium complex, 1c (yellow and orange). The X-ray diffraction study of these crystals indicates the formation of two polymorphic phases both in anti disposition.
- Raul Isea and A. Vegas (1995). "Distribution des distances Me-Me (Me=Mg, Ca, Sr) dans leurs composéds." C. R. Acad. Sci. S�érie IIb. Vol. 320: 397-402.
Abstract:
Les distances Me-Me (jusqu'a 7 �) dans tous les composés d'un métal donné (Me = Mg, Ca, Sr) ne sont pas distribuées d'une facon aléatoire. Par contre, elles sont concentrées autour des valeurs co�ncidant avec celles des phases du métal pur. La densité superficielle de distances (Nd/4 π r2) en fonction de r (�) est équivalente a une fonction de distribution radiale G (r) des matériaux amorphes. A partir de G (r) on peut obtenir la courbe de diffusion S (q), correspondant a la moyenne structurale de toutes les phases de l'élément
