Multiscale methods for nanochemistry and biophysics in solution
Andriy Kovalenko
Department of Mechanical Engineering, University of Alberta, Edmonton, AB, T6G 2G8, Canada
e-mail: andriy.kovalenko
nrc.ca
Predictive modeling of nanosystems in solution should derive their properties from the chemical functionalities of the constituents, while operating at length scale up to hundreds nanometers and time scale up to milliseconds and more, which requires multiscale treatment. Their molecular modeling requires long-time description of millions molecules which is by far not feasible with ab initio methods, challenging for molecular simulations, and problematic for continuum solvation theories that are phenomenological and thus non-transferable. Statistical-mechanical, three-dimensional molecular theory of solvation (a.k.a. 3D-RISM) operates with 3D distributions of species in the statistical ensemble rather than with trajectories of individual molecules and predicts from the first principles the solvation structure and thermodynamics of nanosystems[1]. It properly accounts for chemical functionalities by representing both electrostatic and non-polar features of the solvation structure, such as hydrogen bonding, solvophobicity, salt bridges, structural solvent, associative and electrochemical effects, and is promising as a core part of multiscale modeling of nanosystems in solution. We have coupled the 3D-RISM-KH theory with ab initio quantum chemistry methods in a self-consistent description of electronic structure, optimized geometry, and chemical reactions in solution[1,2] and have extensively validated this multiscale method against experimental data for solvation thermochemistry, conformational equilibria, and activation barriers for various nanosystems in different solvents[2]. We have also coupled the 3D-RISM-KH theory contracting solvent degrees of freedom with MD simulation of biomolecules in the Amber molecular dynamics package[3]. This included several accelerating schemes and multi-time steps up to 20 fs to enable simulation of large biomolecules. The method allows one to study biomolecular processes on extremely long timescales. It also replaces the MM/PB(GB)SA post-processing using empirical non-polar terms with statistical-mechanical, MM/3D-RISM-KH evaluation of the solvation thermodynamics[3,4]. This talk presents the above multiscale methods and their application to explain experimental results for the electronic and solvation structure of ionic liquids[5]; mechanisms of self-assembly, conformational stability and solvent-driven supramolecular chirality of synthetic organic rosette nanotubular architectures[6]; aggregation of β-sheet Amyloid oligomers[4]; and function-related properties of GroEL chaperon[7].
References
- A. Kovalenko, 3D-RISM theory for molecular liquids and solid-liquid interfaces, in: Molecular Theory of Solvation, F. Hirata (ed.), Kluwer, Dordrecht, 2003, pp.169-275; (and refs. therein).
- S. Gusarov, T. Ziegler, A. Kovalenko, J. Phys. Chem. A 110, 6083 (2006); D. Casanova, S. Gusarov, A. Kovalenko, T. Ziegler, J. Chem. Theory Comput. 3, 458 (2007).
- T. Luchko, S. Gusarov, D. R. Roe, C. Simmerling, D. A. Case, J. Tuszynski, A. Kovalenko, J. Chem. Theory Comput., (2010), (in press).
- N. Blinov, L. Dorosh, D. Wishart, A. Kovalenko, Biophys. J. 98, 282 (2010).
- M.Malvaldi,S.Bruzzone,C.Chiappe,S.Gusarov,A.Kovalenko, J.Phys.Chem.B 113, 3536 (2009).
- T. Yamazaki, H. Fenniri, A. Kovalenko, ChemPhysChem. 11, 361 (2010); R. S. Johnson, T. Yamazaki, A. Kovalenko, H. Fenniri, J.Am.Chem.Soc.129, 5735 (2007); J.G.Moralez, J. Raez, T.Yamazaki, R.K.Motkuri, A.Kovalenko, H.Fenniri, J.Am.Chem.Soc.Comm.127, 8307 (2005).
- T. M. Stumpe, V. Pande, N. Blinov, D. Wishart, A. Kovalenko, (submitted).