• Título: Efectos del Aluminio en Sistemas Biológicos: Una aproximación computacional
    Investigador Principal: LOPEZ PESTAÑA, Jose Javier
    Entidad Financiadora: UPV/EHU (Proyecto Estratégico/especial UPV/EHU)
    Duración: 2014-2018
    Financiación Total: 17.791,78 €
  • Título: Interacción del Aluminio (III) con bioligandos y efectos radicalarios en biomoléculas
    Investigador Principal:
    Jose Javier Lopez Pestaña
    Entidad Financiadora: Ministerio de Economía y Competitividad (MINECO)
    Duración: 2013-2015
    Financiación Total: 28.000,00 €
  • Título: Avances Química Cuántica
    Investigador Principal: Jesus M. Ugalde Uribe-Etxebarria
    Entidad Financiadora: Gobierno Vasco (Grupos Consolidados)
    Duración: 2013-2018
    Financiación Total: 401.598 €
  • Título: Nanopartículas de metales de transición
    Investigador Principal: Jesus M. Ugalde Uribe-Etxebarria
    Entidad Financiadora: Ministerio de Economía y Competitividad (MINECO)
    Duración: 2013-2015
    Financiación Total: 28.000,00 €
  • Título: EXPLOSIONES CULÓMBICAS INDUCIDAS POR PULSOR LASER ULTRAINTENSOS Y ULTRACORTOS
    Investigador Principal: Andreas HEIDENREICH
    Referencia: S-PC12UN002
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK)
    Duración: 2012-2013
    Financiación Total: 25110,59 €
  • Título: APLICACIONES DE LA TEORÍA DEL FUNCIONAL DE ORBITALES NATURALES A NANOPARTICULAS BIOLÓGICAS
    Investigador Principal: Mario PIRIS SILVERA
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK)
    Duración: 2012-2013
    Financiación Total: 25.110,59 €
  • Título: BASES MOLECULARES DE LA TOXICIDAD DEL ALUMINIO: AFINIDAD DEL ALUMINIO POR FOSFATOS DE INTERÉS BIOLÓGICO Y ACTIVACIÓN DE ESTRÉS OXIDATIVO
    Investigador Principal: LOPEZ PESTAÑA, Jose Javier
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK)
    Duración: 01/2013-06/2014
    Financiación Total: 7.746,70 €
  • Título: DESCRIPCIÓN DE INTERACCIONES NO-COVALENTES POR MEDIO DEL MÉTODO PNO5-PT2
    Investigador Principal: PIRIS SILVERA, Mario
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK)
    Duración: 01/2013-06/2014
    Financiación Total: 7.746,70 €
  • Título: DISEÑO DE NUEVOS MATERIALES NANOPOROSOS BASADOS EN EL AUTOENSAMBLADO DE NANOPARTÍCULAS SEMICONDUCTORAS
    Investigador Principal: MACHAIN BERAZA, Jon Mattin
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK)
    Duración: 01/2013-06/2014
    Financiación Total: 7.746,70 €
  • Título: ESTRATEGIAS COMPUTACIONALES PARA LA OPTIMIZACIÓN DE CELDAS SOLARES DE INYECCIÓN DIRECTA
    Investigador Principal: CASANOVA CASAS, David
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK)
    Duración: 01/2013-06/2014
    Financiación Total: 7.586,39 €
  • Título: LAS ESPECIES REACTIVAS DE OXIGENO (ROS) Y LA ENFERMEDAD DE ALZHEIMER
    Investigador Principal: Jon Mattin MATXAIN BERAZA
    Referencia: S-PC12UN006
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK
    Duración: 2012-2013
    Financiación Total: 25110,59 €
  • Título: DISEÑO DE NUEVOS NANOMATERIALES SEMICONDUCTORES PARA SU POSIBLE APLICACIÓN EN BIOLOGÍA
    Investigador Principal: UGALDE URIBE-ETXEBARRIA, Jesus M.
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK
    Duración: 2012-2013
    Financiación Total: 25110,59 €
  • Título: BASES MOLECULARES DE LA TOXICIDAD DEL ALUMINIO EN SISTEMAS BIOLÓGICOS Y DE SU ESPECIACIÓN EN VIVO
    Investigador Principal: LOPEZ PESTAÑA, Jose Javier
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK
    Duración: 2012-2013
    Financiación Total: 25110,59 €
  • Título: Interacciones no covalentes como pasos preliminares en reacciones químicas
    Investigador Principal: GRABOWSKI, Slawomir
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK
    Duración: 2012-2013
    Financiación Total: 25110,59 €
  • Título: AVANCES EN QUIMICA CUANTICA Y SU APLICACION A PROBLEMAS SELECCIONADOS DE NANOCIENCIA Y BIOQUIMICA
    Investigador Principal: Jesus M. UGALDE URIBE-ETXEBARRIA
    Entidad Financiadora: Ministerio de Ciencia e Innovación
    Duración: 2009-2011
    Financiación Total: 181.999,99 €
  • Investigador Principal:Jesus M. UGALDE URIBE-ETXEBARRIA
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK
    Duración: 2009-2010
    Financiación Total: 65.410,47 €
  • Título: AVANCES EN QUIMICA CUANTICA
    Investigador Principal: Jesus M. UGALDE URIBE-ETXEBARRIA
    Entidad Financiadora: Gobierno Vasco
    Duración: 2007 – 2012
    Financiación Total: 438.176,61 €
  • Título: NANOPARTÍCULAS SEMICONDUCTORAS EN ENTORNO BIOLÓGICO: APLICACIONES BIOMÉDICAS?
    Investigador Principal: Jose Javier LÓPEZ PESTAÑA
    Entidad Financiadora: Gobierno Vasco (Departamento de Industria, Programa SAIOTEK)
    Duración: 2010 – 2011
    Financiación Total: 54.188,03 €
  • Título: DISEÑO DE NANOPARTICULAS MAGNETICAS PARA SU APLICACION EN NANO-APARATOS
    Investigador Principal: Jesus M. UGALDE URIBE-ETXEBARRIA
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK
    Duración: 2011-2012
    Financiación Total: 25155,08 €
  • Título: APLICACIONES DE LA TEORIA DEL FUNCIONAL DE ORBITALES NATURALES A SISTEMAS BIOLOGICOS
    Investigador Principal: Mario PIRIS SILVERA
    Entidad Financiadora: Gobierno Vasco (Departamento Industria, Programa SAIOTEK
    Duración: 2011-2012
    Financiación Total: 25155,08 €
  • Título: AVANCES EN QUIMICA CUANTICA Y ALGUNAS APLICACIONES A PROBLEMAS SELECCIONADOS DE NANOCIENCIA Y BIOFISICA
    Investigador Principal: Jesus M. UGALDE URIBE-ETXEBARRIA
    Entidad Financiadora: Ministerio de Ciencia e Innovación
    Duración: 2012
    Financiación Total: 14.520,00 €

The most accurate electronic structure methods based on N-particle wave functions are too expensive to be applied to large systems. It is clearer every day the need for treatments of electron correlation that scale favorably with the number of electrons. Among them, the Kohn-Sham formulation of the Density Functional Theory (DFT) has become very popular thanks to its relatively low computational cost. However, present-day functionals have several problems due mainly to the so-called “correlation kinetic energy”, but most importantly, currently available functionals are not N-representable. (more…)

Since the beginning of this century, the spin-flip (SF) method has emerged as a very attractive alternative to the MC approach in the electronic structure study of molecular species with a multi-reference character wave function. The SF methodology is based on the construction of electronic wave functions through promotions of α electrons into empty β spin-orbitals in combination with the use of a high spin single determinant as the reference configuration. The SF idea has been implemented and applied with a variety of electronic structure formalisms: equation of motion coupled cluster (EOM-SF-CC), configuration interaction (SF-CI), and density functional theory (SF-DFT). (more…)

The hydrogen bond (HB) is the subject of various studies since it is important in numerous chemical, physical and biological processes.i,ii,iii,iv One of first definitions of the hydrogen bond was given by Pauling v who stated that “under certain conditions an atom of hydrogen is attracted by rather strong forces to two atoms, instead of only one, so that it may be considered to be acting as a bond between them. This is called the hydrogen bond”. This interaction may be designated as X-H…Y, where X-H is the proton donating bond while Y is the proton acceptor. Pauling pointed out that X and Y atoms should be characterized by the high electronegativity, that the Y proton acceptor should posses at least one free electron pair and that the hydrogen bond is the electrostatic interaction. (more…)

In recent years the σ-hole concept was introduced and developed and it was applied to the halogen bond and to the other non-bonding interactions.i According to this concept the halogen bond is the electrostatic attraction between the positive potential of the halogen and the negative Lewis base center. This is because the half-filled p orbital of halogen participates in the covalent bond and there is an electron deficiency in the outer lobe of this p orbital; it is called the σ-hole. Hence the halogen atom electron deficient side may act as the Lewis acid. Such a situation may occur not only for halogen atoms and the σ-hole bond concept was introduced to discuss more extended class of non-bonding interactions. There are also the other examples of studies on non-bonding interactions; for example, the N…P attractive interaction was analyzed recently.ii (more…)

There are various non-bonding interactions which are important in numerous chemical processes and phenomena.i These interactions may be treated as counterparts or competitors of hydrogen bond. It was found that the common characteristic for them, including hydrogen bond, is the electron charge transfer from the Lewis base to the Lewis acid and that the amount of this transfer corresponds roughly to the strength of the interaction.ii The following non-bonding interactions may be mentioned; the dihydrogen bond, the halogen bond, the agnostic bond, the hydride bond and others. In recent years the σ-hole concept was introduced and developed and it was applied to non-bonding interactions.24f (more…)

Nanostructures of III-V (III: Ga, In; V: N, P, As) and II-VI (II: Zn, Cd; VI: S, Se, Te) semiconductor materials have attracted a great deal of interest due to their fascinating properties, which usually differ from their bulk counterparts. There are two main reasons responsibles for such a deviation. On the one hand, the confinement of electrons (and holes) in nanostructures gives rise to a size- and shape- dependent structure of electronic levels. On the one hand, the number of atoms forming the surface of a nanostructure is a significant fraction of the total. The unsaturated surface atoms tend to reorganize in order to minimize the surface energy, favouring certain crystalline phases and eventually leading to fancy atomic arrangements. Again, the stability of each polymorph depends on the size and the morphology of the nanostructure.

(more…)

Nanostructures are characterized by their high surface-to-volume ratio. Unsaturated surface atoms tend to rearrange their position in order to saturate the dangling bonds and minimize the surface energy. Such a reconstruction penetrates deep inside the nanostructure and determines, to a large extent, the morphology of the material. Solvent and surface attached ligands modify the surface energy and exert a strong influence on the atomic structure of the nanomaterial, which in turn, defines the electronic and optical structure of the material. Furthermore, surface attached ligands modify important properties of nanomaterials, including photophysics, charge transport, catalysis and magnetism. Tayloring nanostructures’ character by means of surface attached ligands has aroused the interest of chemists and physicists. Chemical functionalization has been proven to be very useful in designing materials with specific electrical and optical properties. Moreover, the application of nanomaterials in biology and medicine is based on the ability to make them water soluble and to cap them with specific surfactants in order to facilitate selective binding to target biomolecules or subcellular structures.

(more…)

SOFTWARE

In our group, we are working on the development of our own software in order to carry out several kind of theoretical calculations. Concretely:

PNOFID: Software to carry out calculations within the Natural Orbital Functional Theory, concretely, using different Piris Natural Orbital Functionals.

In addition, we use different software with Group license (Q-CHEM, ChemShell) , and mostly, with University license. To see the latter, click here.

HARDWARE

In order to perform our calculations, we make use of the Scientific Computing Service provided by the University of the Basque Country / Euskal Herriko Unibertsitatea.

The Scientific Computing Service  provides high performance  computing resources, specialized technical support and consulting to researchers at the UPV/EHU, other public organizations and companies.

The service  provides  its own computing resources with powerfull  hardware, upgrade policies and distributes the computational resources. The service analizes new tendencies in HPC (HighPerformance Computing) for its possible  implementation in the UPV / EHU. The IZO-SGI  is part of the General Research Servicees (SGIker) of the UPV / EHU, and therefore complies with the protocols established by thge SGIker.

All results published using the IZO-SGI  resources should acknowledgment its usage and send a copy of the publication. This publications will be used to evaluate the users when prioritizing the use of the Service herraminetas GeneralScientific Computing. The phrase we propose for the acknowledgments is:

Technical and human support provided by IZO-SGI, SGIker (UPV/EHU, MICINN, GV/EJ, ERDF and ESF) is gratefully acknowledged.

The contact people of this service are

Dr. Eduardo Ogando: edu.ogando, edu.ogando@ehu.es (tel. 946015022)

Dr. Jose M. Mercero: jm.mercero@ehu.es (tel. 943015312)

Aluminum is the third most abundant element in earth’s crust, but its chemical properties have prevented its presence in the biological cycle of living organisms. Nevertheless, the acidification of the environment due mainly to human intervention has facilitated its solubilitation, thus increasing its bioavailability. Toxic effects of aluminum in the human body have been reported, and this element has been related with neurodegerentative diseases such as Alzheimer Disease. Aluminum has also been claimed to exert an important pro-oxidant activity.

(more…)

 

The rapid progress in electronic structure theory and computer technology during the last two decades has made possible the determination of accurate wave functions for small and medium size molecules. However, this is only the first step in solving problems of chemical interest as most application of quantum mechanics in chemistry deal with the computation of expectation values or density functions in terms of which the properties of sought are rationalized. This requirement is closely related with one of the major challenges of quantum chemistry: the development of practical procedures for the extraction of chemically interesting information from N-electron wavefunctions. (more…)

Finding the energies of bound states of screened Coulomb potentials has raised considerable interest for many years. There are many problems for which the reduction of the long-range Coulomb interactions due to the screening can drastically affect the results emerging from the consideration of bare Coulomb potentials. Thus, the calculation of thermodynamic properties of many-body systems in partially ionized gases, i.e., plasmas, has seen a rebirth since the inclusion of screening effects. The screened Coulomb potential can be represented by different models, the most famous of which is the analytic exponentially decaying potential of Yukawa type. (more…)

Designing new chemical compounds is one of the most ambitious goals of every chemist. Nonetheless, efforts made for the understanding of the chemistry of new chemical compounds often yield new paradigms which open unexpected research areas. All-metal aromatic molecules, recently synthesized by Li et al, constitute one such an example. Indeed, rationalizing the unexpected large resonance energy of Al4(2-) has yield the concept of multiple-fold aromaticity, as that present in molecules that posses more than one independent delocalized bonding system, either σ-type or π-type, each of them satisfying the 4n+2 electron counting rule of aromaticity.

(more…)

 The interest in free-radical processes in living systems has increased exponentially during the last decade. The huge complexity of the evolved processes makes necessary the analysis of the problem from a fundamental point of view. Radicals are ubiquitous intermediates in a variety of ordinary biochemical reactions. Some of the radicals that are most abundantly produced in natural biochemical reactions are Reactive Oxygen Species (ROS) such as hydroxyl, hydroperoxyl and superoxide anion, and Reactive Nitrogen Species (RNS), such as nitrogen monoxide and peroxynitrite.

(more…)

The study of small nanoclusters may serve as a bridge between bulk materials and atomic structures. In these nanoclusters, the coexistence of different type of metals may give rise to interesting electronic, structural, chemical or catalytical properties. The study of the chemical bond in small clusters is a crucial issue to understand and predict the behaviour of nanomaterials of more realistic sizes.

In the last years has been highlighted the relevance of transition metals as catalysts in oxidative damage processes involving biological macromolecules. Recent studies have shown that transition metals like Fe, Cu, Cd, Cr, Pb, Hg, Ni and V possess the ability to generate reactive oxygen and nitrogen species, ROS and RNS, that is, radicals concerned in biological reactions which may cause severe damage in a wide range of molecules, producing, among other effects, lipid peroxidation, DNA damage, dramatic sulfhydryl decrease, protein alteration, etc., symptomatic of different diseases such as cancer, vascular affections, neurological disorders (Alzheimer’s and Parkinson’s disease), etc.

(more…)

 

  • Prof. Isidore Last, School of Chemistry, Tel Aviv University, Israel.

The amide bond is the essential structural motif of the protein backbone. The hydrolysis reaction of amides, often used as a model for the cleavage of peptide bonds, is thus of primary concern for living systems. The hydrolysis of non-activated amides is very slow and in most cases undetectable. An amide bond’s stability is ascribed to its partial double bond character, caused by the delocalization between the nitrogen lone pair and the π* orbital of CO bond. As a consequence, amides show a characteristic short C-N bond length and a rigid planar conformation. This stability also has important chemical consequences, a low reactivity toward nucleophilic attacks on the carbon and important basicity shifts of the nitrogen with respect to amines. (more…)

Many proteins are synthesized in biologically inactive forms, and are activated in post-translational processes such as proteolytic cleavage. This process is usually catalyzed by external proteins, but some proteins are able to self-catalyze the reactions without the need for any other protein or cofactor. We are interested in one of this post-translational process, known as protein splicing. In protein splicing, a segment of an inactive protein, the intein (internal protein), is excised from the rest of the protein, and the two flanking domains, the C- and N-exteins, join each other, forming a biologically active protein (see Figure).

(more…)

Hookean systems and Quantum DotsExact solutions of the Schrodinger equation for multiparticle systems with interparticle Coulombic interactions are unknown. One can try to find such exact solutions by modeling the interparticle interaction potential. Within this context, a much studied model is the Hookean two-electron atom, a system possessing a nucleus with charge +2 interacting through a harmonic potential with the electrons which, in turn, repel each other through the usual Coulomb interaction. (more…)