Quantum Mechanical, Molecular Mechanics, and Molecular Dynamics computation in chemistry

The project deals with modeling of molecular structure and mechanism of chemical reactions. Quantum mechanical, ab-initio, and DFT calculations will be applied for molecules that consist up to 250 atoms. Molecular mechanics and molecular dynamics simulation will be used for examination of ligands interaction with proteins and other biomacromolecules, as well as for conformational sampling of small molecules in explicit solvent cluster. In such simulations size of ligands should be up to 300 atoms; while biomacromolecule can have size of more than ten thousands of atoms. In the present stage, simulations were done by NAMD2.8.

Our research is directed toward:

a) examination of the free-energy landscapes of highly potent and very selective antitumor agents, named CSAB, in explicit solvent clusters, having different dielectric constants, H-bonding ability, and polarity, by medium lasting (~ 30ns) molecular dynamic simulations coupled with adaptive biasing force calculation;

b) Molecular dynamics simulations (~ 80 ns each) for “approach and entrance” of the group of compounds, which act as dual acetylcholine esterase (AChE) inhibitors, to enzyme active site. Whole systems (enzyme + inhibitor) for each compound are embedded in properly sized (large) solvent cluster. Last stage of each simulation includes adaptive biasing force calculation.

Several components of this approach require massive study of the vast parameter space and include tightly-coupled simulations with large memory requirements. Testing, benchmarking and production runs of some of the components can be done on standard Grid-type Linux clusters, but the core components require low-latency parallel environment. Post-processing of trajectories, as well as output of (coupled) free-energy calculations, are also often memory demanding, so it is suitable to do such analysis on the nodes associated with the cluster where simulation were performed.

Application's name: Quantum Mechanical, Molecular Mechanics, and Molecular Dynamics computation in chemistry (CompChem)
Scientific contact: Ivan Juranic, (ijuranic at chem.bg.ac.rs)
Technical contact: Ivan Juranic, (ijuranic at chem.bg.ac.rs)
Developers: Ivan Juranic, University of Belgrade, Faculty of Chemistry, Republic of Serbia
Web sitehttp://www.chem.bg.ac.rs/~ijuranic/prezengl.htm
 

Scientific papers:

  • Budimir Marjanović, Ivan Juranić, and Gordana Ćirić-Marjanović
    "Revised Mechanism of Boyland Sims Oxidation"
    J. Phys. Chem. A 2011, 115(15), 3536-3550, 
    DOI: 10.1021/jp111129
  • B.J. Drakulić, A.D. Marinković, I.O. Juranić
    "On the choice of optimal conformation in linear free-energy relationships. Reactivity of 2-[(carboxymethyl)sulfanyl]-4-oxo-4-arylbutanoic acids with diphenyldiazomethane"
    Tetrahedron Lett. 53 (2012) 553–556;
    DOI: 10.1016/j.tetlet.2011.11.097

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HP-SEE receives EC support through FP7 under the "Research Infrastructures" action