Abstract:

Accounting for the quantum mechanical (QM) behavior of large molecular systems together with their bulk and dynamical properties represents an ultimate goal for the comprehensive modeling of chemical phenomena. We recently developed a method capable of running full-QM molecular dynamics simulations of large (bio)molecular systems: SemiEmpirical Born-Oppenheimer Molecular Dynamics (SEBOMD).1 Our approach is based on a semiempirical treatment of the QM wavefunction under the NDDO approximation, which makes the computational time compatible with the requirements of extensive sampling techniques. Our implementation of SEBOMD within the AmberTools program package is now fully integrated and distributed with this molecular modeling suite.2 In addition to standard dynamical properties, SEBOMD offers information about the wavefunction of the system and related quantities (e.g., dipole moments, bond orders, and electronic structure in general), thereby opening a wide range of new perspectives in molecular modeling. Through illustrations of our work using molecular mechanics (MM), QM/MM, and full-QM simulations, the seminar will discuss the place of SEBOMD within the large palette of theoretical chemistry methods together with its potential, current range of application, and future challenges.

References:

1. Marion, Antoine; Gokcan, Hatice; Monard, Gerald (2018): SemiEmpirical Born-Oppenheimer Molecular Dynamics (SEBOMD) Within the Amber Biomolecular Package. ChemRxiv. Preprint. 

2. http://ambermd.org

Short Biography of the Speaker:

Dr. Antoine Marion is a theoretical chemist specialized in the application and development of cutting-edge modelling methods to address challenging biochemical problems. He obtained his PhD degree from the University of Lorraine (Nancy, France) in 2014, and received the “best PhD reward” of the university for his work on the development and applications of semiempirical quantum force fields in molecular dynamics.  He then joined the Life Sciences Department at the Technical University of Munich (TUM, Germany) in 2015 as a post-doctoral researcher for two years. During his scientific career he was involved in a great number of collaborations through which he gained experience in most of the techniques in molecular modelling; from approximate models for the description of large biomolecular assemblies, to more elaborate ab initio quantum mechanics theories.In February 2018, he joined the Chemistry Department at the Middle East Technical University (METU) as a faculty member. His research group at METU focuses on modelling peculiar reaction mechanisms, on the characterization of rare phenomena in nature, and on the development of computational chemistry tools for general and specific usage in the field.