NLeSC grants for Lucas Visscher and Chris de Graaf
Professor Visscher and Dr. Chris de Graaf from the Divisions Theoretical Chemistry and Medicinal Chemistry have both been awarded NLeSC grants by the Netherlands Organization for Scientific Research (NWO) of €500.000
12/22/2014 | 10:06 AM
Theoretical Chemists work with Netherlands eScience Center on automating quantum chemical simulations
Prof. dr. Lucas Visscher from the division of Theoretical Chemistry has been awarded an NLeSC grant by the Netherlands Organization for Scientific Research (NWO) of €500.000. The grant enables him to work on the software necessary to study thousands of molecules with sophisticated quantum chemical methods.
Prediction of the properties and stability of new molecules by quantum mechanical calculations is an important tool for chemists and is used extensively to select and tune molecules or reaction conditions. Due to complexity of these simulations much effort is spent in setting up the calculations and converting data formats so that calculations are typically done for one molecule at a time. By automating manual procedures researchers can become more productive and able to study thousands of molecules at once using parallel computers. This yields a wealth of detailed data (molecular structures, transition states, charge distributions, electronic excitation energies) to rationally design solar cells, reduce solvent losses in organic synthesis, tune catalysts, or develop better LEDs, to name just a few applications.
Starting point of the project is software originally developed in the theoretical chemistry department by Christoph Jacob (now professor in Braunschweig) and Visscher to automate density functional theory calculations. This PyADF software will be combined with software used in distributed computing (controlling parallel computers) and bioinformatics (data management and workflow construction), using the combined expertise of the theoretical chemists and the eScience engineers. Associate partner SCM is contributing both personell and software to the project and forms the link to a large community of academic and industrial chemists worldwide that already employ quantum chemical methods developed in Amsterdam.
While the software can be used for many purposes, the consortium will focus on two science cases that illustrate its potential. The first is related to the research of Ivan Infante on improving the properties of so-called quantum dots, nanocrystals that can be tuned to absorb light of virtually any color. Finding ways to improve their efficiency in solar cell applications requires a combination of many theoretical methods which makes them ideally suited for the software developed in this project. The second example relates to improving solvents used in industrial processes. Goal of this work is to develop solvent combinations that can be used to replace environmentally undesirable volatile organic liquids by "greener" alternatives. Systematic scans of many different combinations are impossible without the automation that will be realized in this work.
Chris de Graaf receives 500 kEuro NLeSC research grant for Medicinal eChemistry
Dr. Chris de Graaf (Medicinal Chemistry, VU University Amsterdam) has received a 500 kEuro research grant for the development of eScience technologies to improve the integration of chemical and biological data for the prediction of polypharmacological action of drug molecules on multiple proteins.
In the 3D-e-Chem project, Dr. De Graaf will work together with colleagues from CMBI-Radboudumc (Dr. Ritschel, Prof. Vriend) and the Netherlands eScience Center on the design of an eChemistry workflow that allows interoperability of large volumes of heterogeneous life science data and modeling software. As a proof of concept, 3D-e-Chem will identify and optimize molecules that can act on several G Protein-Coupled Receptors (GPCRs, the most important drug targets) simultaneously while avoiding critical side effects via off-target proteins.
The open-source eScience workflow will facilitate collaboration with external partners (including BioAxis Research, Griffin Discoveries, Taros Chemicals, and AstraZeneca Pharmaceuticals) and efficient extrapolation of the knowledge obtained in 3D-e-Chem to other protein classes and research domains.
About the eScience Center: The Netherlands eScience Center (NLeSC) is the national hub for the development and application of domain overarching software and methods for the scientific community.