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drug design

  • Ask ERCEA officers: a roundtable discussion on career development and ERC funding opportunities

    Speaker: Dr. Janka Mátrai
    Institute: European Research Council
    Country: Belgium
    Speaker Link: https://be.linkedin.com/in/janka-m%C3%A1trai-1685b920
    Speaker: Dr. Balázs Pinter
    Institute: European Research Council
    Country: Belgium
    Speaker Link: https://www.linkedin.com/in/balazs-pinter-b8611a92
    Time: 11:00 CET 30-Jan-24

    Dr Janka Mátrai and Dr Balázs Pinter

    Scientific Project Adviser at The Executive Agency of the European Research Council

    Janka Mátrai is a scientific project adviser at the ERCEA - The Executive Agency of the European Research Council (ERC), in the Life Sciences Unit. She is responsible for managing the whole life cycle
    of grant application, evaluation and follow-up processes in two panels, Integrative Biology: From Genes and Genomes to Systems, and Neuroscience and Disorders of the Nervous System,
    respectively. She is also involved in the widening participation campaign, which aims to close the gap between the Widening European Participation countries and the rest of the EU. Prior to this, she
    worked as a scientific project officer at the Joint Research Centre – Institute for Reference Materials and Measurements in the Standards for Innovation and Sustainable Development, Reference
    Materials for Biotechnology and Life Sciences Unit, where she was managing the production of certified DNA reference materials.
    After graduating from the Budapest University of Technology and Economics as a bioengineer, Janka obtained her PhD degree in Biochemistry and Bioinformatics at the Catholic University of Leuven
    (KUL), after which she continued with scientific research as a postdoctoral scientist in areas of Molecular Modelling and Drug Design, and Fundamental and Translational Medical Research, Gene
    Therapy and Regenerative Medicine at the Flanders Institute for Biotechnology (VIB) and the Free University of Brussels (VUB).
    In this session, Janka will discuss some important factors that shaped her career path. She will also share her experience with scholarships and grant applications, highlighting some dos and don’ts.

    Balazs Pinter recently joined the Physical Sciences and Engineering Unit of ERCEA – The Executive Agency of the European Research Council – as a scientific project adviser, where he is involved in all
    aspects of the implementation of ERC’s work programme, from the evaluation of proposal to the follow-up of projects in both chemistry panels of the agency: Physical and Analytical Chemical
    Sciences and Synthetic Chemistry and Materials. 
    Before joining ERCEA, Dr. Pinter was an assistant professor at The University of Texas at El Paso where he headed the Computational OrganoMetallic and Inorganic Chemistry (COMIC) research
    group with a research activity centred at the (photo)redox chemistry of transition metal complexes, and the rational engineering of their electrochemical properties via computational means, especially
    density functional theory (DFT) based methods, amongst others. Prior experiences include professorships in Chile and Belgium and various postdoc positions at Indiana University Bloomington,
    Duke University, Vrije Universiteit Brussel and research visits at University of Girona and Max-Planck Institute for Chemical Energy conversion. Dr. Pinter holds a PhD in Chemistry and an MSc in Chemical
    Engineering from Budapest University of Technology and Economics, Hungary. 
    In this session, Dr. Pinter will discuss the potential effect of omnipresent academic notions, such as ‘publish or perish’ and ‘red flags’ on the scientific career and in hiring processes, review the DORA
    principles and Open Science practices and present the funding schemes of ERC. 

    Keywords: molecular modelling, drug design, gene therapy, certified DNA reference materials, scientific project management, Density Functional Theory, photoredox catalysis, redox active ligands, DORA principles,
    Open Science

     

    References:

    European Society for Gene and Cell Therapy, Ask the Expert career session. 
    The European Research Council’s online classes. 
    Editorial, Nature 535, 465 (2016). Agencies must show that basic research is worth the investment
    Mátrai, J, et al. (2015), Certification report. DNA Certified Refence Material
    Mátrai J, et al. (2012). J Genet Syndr Gene Ther, S:1. Lentiviral Gene Therapy for Haemophilia A and B
    Mátrai J*, Cantore A*, Bartholomae C*, et al. (2011). Hepatology, 53 (5),1696-707. *Equal
    contribution. Hepatocyte-targeted expression by integrase-defective lentiviral vectors
    Mátés L, et al. (2009). Nat Genet. 41 (6), 753-61. Novel hyperactive Sleeping Beauty transposase
    enables robust stable gene transfer in vertebrates
    Mátrai J, et al. (2010). Curr Opin Hematol. 17 (5), 387-92. Preclinical and clinical progress in
    haemophilia
    Mátrai J, et al. A Guide to Human Gene Therapy, 2010. A Guide to Human Gene Therapy

    Mátrai J, et al. (2008). Eur Biophys J. 38 (1), 13-23. The activation pathway of Δα-Chymotrypsin
    Le Roy K, et al. (2013). Plant Physiol. 161 (4), 1670-81. Defective Invertases in Plants: Tobacco Nin88
    Fails to Degrade Sucrose
    Mátrai J, et al. (2001). J. Org. Chem. 66 (17), 5671-5678. Mechanism of the Ring−Chain
    Rearrangement in Phosphiranes
    Veszprémi T, et al. (2001). THEOCHEM. 538 (1-3): 189-195. Lithium azaphospholide complexes
    A Science Club in Brussels. Belgian Club of Hungarian Scientists

    Sandoval-Pauker, C.; Pinter, B. “Electronic Structure Analysis of Copper Photoredox Catalysts
    Using the Quasi-Restricted Orbital Approach”, J. Chem. Phys., 2022, 157, 074306.
    Sandoval-Pauker, C.; Molina-Aguirre, G.; Pinter, B. “Status report on copper (I) complexes in
    photoredox catalysis; photophysical and electrochemical properties and future prospects.”
    Polyhedron, 2021, 199, 115105.
    Medina, E.; Pinter, B. “An electron density difference analysis on the oxidative- and reductive
    quenching cycles of classical iridium and ruthenium photoredox catalysts”, J. Phys. Chem. A, 2020,
    124, 4223–4234.
    Pinter, B.; Al-Saadon, R.; Chen, Z., Yang, W. “Spin-state energetics of iron(II) porphyrin from the
    particle-particle random phase approximation” Eur. Phys. J.B., 2018, 91, 270.
    Gazvoda, M.; Virant, M.; Pinter, B.; Košmrlj, J., “Mechanism of copper-free Sonogashira reaction
    operates through palladium-palladium transmetallation” Nat. Commun. 2018, 9, 4814.

    Recording:

    Video is available only for registered users.

  • Modeling environment effects in quantum chemistry

    Speaker: Professor Benedetta Mennucci
    Institute: University of Pisa
    Country: Italy
    Speaker Link: https://molecolab.dcci.unipi.it/

    Benedetta Mennucci

    Department of Chemistry, University of Pisa,
    via G. Moruzzi 13, 56124 Pisa (ITALY)

    Web: molecolab.dcci.unipi.it


    Video Recording

    Video is available only for registered users.

    Abstract

    The environment plays a fundamental role in determining properties and processes of molecular systems. Its modeling however represents a real challenge and approximate methods have to be introduced. A very effective strategy is to partition the whole system in two subsystems (the one where the property and/or the process of interest is localized at and the rest) and describe the two parts with different but coupled approaches. In the most successful formulation of this strategy, the subsystem of interest is treated at an accurate quantum chemical level while the rest is modeled through a classical model. In this lecture, an overview of the resulting hybrid methods (both in their continuum and atomistic formulations) will be presented and discussed in terms of their applicability and limitations.

  • Molecular dynamics of aqueous [uo2]2+ diffusion in clays

    Speaker: Sergio Perez-Conesa
    Institute: University of Seville
    Country: Spain
    Speaker Link: https://scholar.google.com/citations?hl=en&user=U3LpfWkAAAAJ&view_op=list_works&sortby=pubdate

    S. Perez-Conesa, J. M. Martínez and E. Sánchez Marcos

    Department of Physical Chemistry
    University of Seville
    41012 Seville, Spain


    Video Recording

    Video is available only for registered users.

    Abstract

    Knowledge of actinide aqueous solution confined in smectite clay interlayers are crucial when designing permanent geological high level radioactive waste facilities. The actinide ions are sealed using montmorillonite containing clays to prevent radionuclide scape1. A computational study of [UO2]2+ (aq) hydration structure and diffusion inside montmorillonite clay was accomplished. The first actinide-clay ab initio interaction potential has been created based on the Hydrated Ion concept2,3. Additionally it is the first application of the hydrated ion model to a confined medium chemical problem. The developed potential was used to carry out NPT classical molecular dynamics simulations for Montmorillonite clay containg [UO2]2+ with two possible interlayer water contents. The z-density profiles reflect the formation of stable pentaaquo uranyl outer-shell complexes in agreement with EXAFS studies3 without any external imposed constraint. The complex interacts with the clay by the formation of 1.4 hydrogen bonds between its first hydration shell and the surface. Groups of three Mg substitutions were identified as strong interaction sites of the pentahydrate. The constrictivity factor ,δint, calculated from the self-diffusion coefficients agrees semiquantitatively with experiment. Diffusion is enhanced by an increase of concentration of uranyl in the clay interlayer.

    References

    [1] Birkholzer, J. et al. Ann. Rev. Environ. Resources 2012, 37, 79–106.
    [2]Pappalardo, R. R. et al. J. Phys. Chem. 1993, 97, 4500–4504.
    [3]Martínez J.M. et al. J. Am. Chem. Soc. 1999, 121, 3175–3184.
    [4]Catalano, J. G. et al. Geochimica et Cosmochimica Acta 2005, 69, 2995 –3005