WHAT ARE WE OFFERING: (Super)Computer assisted design and optimization of products in the following subject areas:

  1. Computer assisted design of luminescent molecules for monitorization of metals in biological environments.
  2. Chelation, isolation and segregation of actinide and lanthanide species. Luminescent and magnetic properties of actinide atoms embedded into nano-structured matrices.
  3. Simulation of cluster behavior under ultraintense laser irradiation.
  4. Optimization of passivant ligands for nanoscale materials. Assessment of their stability and properties in various solvents and in biological environments.
  5. Optimization of antioxidant molecules toward Reactive Oxygen Species (ROS) and Reactive Nitrogen Species (RNS).
  • Advantages: (1) Those derived from the design and optimization of processes by computer assisted modelling. (2) Those derived from the set up of a technology observatory

WHAT WILL THE PRODUCT OR SERVICE BE USED FOR ? (1) Detection and monitorization of potentially toxic metals in biological enviornments. (2) Controlling the size and properties of nano-structures materials. (3) Contrast agent design for the spectral/magnetic imaging in medicine. (4) Antioxidant seeding compounds.

TYPE OF PARTNER SOUGHT: High-tech company. Industry oriented research laboratory. Product optimization company/laboratory.

SECTORS: Fine Chemistry, Medicinal Chemistry, Nanotechnology, Pharmaceutical, Energy.

CONTACT: jesus.ugalde@ehu.es (+34 943 018190)

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.

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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.

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 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.

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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.

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In progress

26. Mikel Irigoien Urtasun (POLYMAT) “Theoretical Modeling of Self-Healing Materials”. Directors: Fernando Ruipérez (POLYMAT), Jon M. Matxain

25. Xabier Telleria Allika “Statically screened potentials, Hookean systems and Quantum Dots”, Directors: Xabier Lopez, Jon M. Matxain

24. Irene Casademont “Estudio Computacional de Moléculas Fotosensibilizadoras a partir de Descriptores del Enlace Químico y la Teoría del Funcional de la Densidad”, Directors: Eduard Matito, Eloy Ramos-Córdoba, Jesus M. Ugalde Uribe-Etxebarria.

23. Sebastian Sitkiewicz “Development of Density Functionals for the Calculation of Nonlinear Optical Properties”, Directors: Eduard Matito, Josep M. Luis, Jesus M. Ugalde Uribe-Etxebarria.

22. Mireia Via Nadal “To be announced”, Director: Eduard Matito.

21. Olatz Uranga Barandiaran “Computational studies on photophysical properties of molecular aggregates” Directors: David Casanova, Fréderic Castet, Xabier Lopez

20. Ion Mitxelena Etxeberria “Development and applications of NOFT”, Director: Mario Piris.

19. Gabriele dala Torre  “Computational Studies of New Aluminum Chelating Agents” Director: Xabier Lopez Pestaña.

Defended

18. Jon Uranga Barandiaran “Protein Oxidation by the Attack of OH Radicals / OH Erradikalen Erasoen bidezko Proteinen Oxidazioa” (2017) Directors: Jon M. Matxain Beraza, Jesus M. Ugalde Uribe-Etxebarria

17. Elisa Jimenez IzalStructure and Electronic Properties of Endohedrally Doped II-VI Hollow Nanoclusters” (2014). Directors: Jon M. Matxain Beraza, Jesus M. Ugalde Uribe-Etxebarria

16Jon Mikel Azpiroz Apezetxea “Computational Modeling of Semiconductor Nanoclusters” (2014) Director: Jesus M. Ugalde Uribe-Etxebarria

15. Oier Lakuntza IrigoienMetanoaren aktibazioa hamargarren taldeko hidrido hidroxido/sulfhidrido katioien bitartez katalizatua” (2012) Director: Jesus M. Ugalde Uribe-Etxebarria.

14. Elena Formoso EstensoroTheoretical characterization of pentacovalent oxyphosporane intermediate structures of the hydrolysis of RNA catalyzed by RNase A” (2010) Director: Jose J. Lopez Pestaña.

13. Julen Larrucea CorcheroAluminio katioiaren aminoazido aromatikoen gaineko eraginaren azterketa konputazionala / Computational study of the effect of aluminum cation on aromatic aminoacids” (2009) Director: Jesus M. Ugalde Uribe-Etxebarria

12. Elixabete Rezabal Astigarraga “Binding and specificity of aluminum in proteins” (2007). Director: Jesus M. Ugalde Uribe-Etxebarria

11. Eider San SebastianStudy of protein-protein interactions involved in cancer metastases and autoimmune diseases. Design of new antimetastatic molecules” (2007) Directors: Jose J. Lopez Pestaña y Fernando P. Cossío.

10. Jon I. Mujika GorostidiTwisted amides: characterization of their electronic structure and analysis of their accelerated hydrolysis(2006) Director: José J. López Pestaña

9. Iñaki Silanes CristóbalEthylene polymerization by Group IV transition metal metallocenes” (2006) Director: Jesus M. Ugalde Uribe-Etxebarria.

8. Jon M. Matxain BerazaSmall clusters of II-VI materials” (2002). Director: Jesus M. Ugalde Uribe-Etxebarria. Doctorado Europeo. Premio Extraordinario de Doctorado 2003.ISBN: 84-8373-461-3. Publisher: Editorial Service of the University of the Basque Country.

7. Jose M. Mercero LarrazaAluminum(III) interactions with aminoacid chains” (2001) Director: Jesus M. Ugalde Uribe-Etxebarria. Doctorado Europeo. Premio Extraordinario de Doctorado 2001.

6. Arantxa Irigoras Balda, ”Water Dehydrogenation by First-Row Tansition Metals Cations: A Paradigm for Two-State Reactivity” (1999). Director: Jesus M. Ugalde Uribe-Etxebarria. Doctorado Europeo. ISBN: 84-8373-197-5. Publisher: Editorial Service of the University of the Basque Country.

5. Guillermo Roa ZubiaEstudio teorico de la estructura y reactividad de cetenas e isocianatos” (1999). Directors: Jesus M. Ugalde Uribe-Etxebarria, Fernando P. Cossío.

4. América Graciela García, ”Aplicaciones de la Teoría del Funcional de la Densidad a Enlaces (2e,3c) y Complejos de Transferencia de Carga” Premio Extraordinario de Doctorado (1997). Director: Jesus M. Ugalde Uribe-Etxebarria.

3. Elso Manuel Cruz, ”La Química del Catión P+. Reacciones en Condiciones Interestelares” (1997) Director: Jesus M. Ugalde Uribe-Etxebarria.

2. Xabier Lopez Pestaña, ”On The Gas-Phase Chemistry of P+: Ionic Clusters, Dioxides And Interstellar Chemistry” (1995) Director: J. M. Ugalde Uribe-Etxebarria. Doctorado Europeo. Premio Extraordinario de Doctorado (1995).

1. Maria Lourdes DomínguezDensidades y Distribuciones Bielectrónicas Atómicas y Moleculares a partir de Funciones de Onda Construidas con GTO’s”. Director: Jesus M. Ugalde Uribe-Etxebarria.