Quantum Mechanical/Effective Fragment Potential-Molecular Dynamics (QM/EFP–MD) Simulation: A Smart Sampling Technique in Condensed Phase
While non-polarizable force fields such as AMBER, CHARMM, and GROMACS have been extremely successful in the descriptions of biomolecules, they are not applicable to chemical reactions in water and other solvents, where explicit descriptions of electronic structure are necessary. On the other hand, although ab initio molecular dynamics (AIMD) simulation methods such as Car-Parrinello MD (CPMD) or FMO-MD have been recognized to be one of the most direct and accurate computation tools for studying dynamic processes in condensed phases, the AIMD simulation over such a long period (100–200ps) for fairly large (hundreds of atoms) composite systems is still far from the practical. To overcome this difficulty, the quantum mechanical/molecular mechanical (QM/MM) method has been successfully used as an alternative method. It has been shown that the EFP (effective fragment potential) could successfully reproduce full QM results with comparatively low computational cost. Note that the computational speed with EFP is order of magnitude faster that of typical full QM calculations. Therefore, it is quite clear that the advantage of EFP as compared to classical parameters is its chemical accuracy in the calculations of energies and structures. The hybrid quantum mechanical/effective fragment potential (QM/EFP) can be a very effective and practical quantum mechanical molecular dynamics method, when it is properly combined with well-developed traditional molecular dynamics (MD) technique. Recently developed QM/EFP-MD simulation techniques successfully utilized in various solution dynamics include dissociation/association processes, IR spectroscopy, proton transfer mechanism, pKa prediction, rotational dynamics, photochemistry and excited state dynamics, etc. The detailed association/dissociation processes of Na+—Na+, Cl-—Cl-, and NaCl has been described by the various structural conversions with bridging water as solvent, providing detailed structural information for the first time. On the other hand, an interesting yet very stable parallelogram structure of [O-H---H-O]2- without any bridging water was also discovered in like-charge ion pairing of hydroxide using QM/MM-MD simulations. The hydrophobic and hydrophilic attractions between methanol pair in aqueous media shows the direct theoretical evidence of the methanol/water “incomplete mixing” process. Also, various rotational dynamics of glycine and glucopyranose, and excited state dynamics of 1,2-dichloroethane in condensed phase will be discussed.
Manik Kumer Ghosh received his PhD in Chemistry from Kyungpook National University in South Korea where he studied theoretical mechanistic study on silicon surface reactions using QM/MM techniques. He did postdoctoral research with Professor Shigeru Nagase at the Institute for Molecular Sciences and Professor Cheol Ho Choi at Kyungpook National University. His research interests include chemical reaction dynamics in condensed phase and applications of efficient QM and QM/MM methods. Currently, he is working as a research fellow with Dr Stephen Dooley at the University of Limerick.
DATE: Thursday, 14 April 2016
TIME: 12h00, TEA/COFFEE WILL BE AVAILABLE AT 11h45
VENUE: MSG-025 MSSI Building Extension
For further information, please contact: Dr Stephen Dooley, Tel. No: (061) 202746 or Email: email@example.com