modeling of an enzyme catalytic reaction ... biological systems, such as enzymes. ... MD and in particular CPMD: "Ab Initio molecular dynamics: Theory and.
Quantum Mechanics Molecular Mechanics modeling of an enzyme catalytic reaction Hans Ågren and Håkan Hugosson Division of Theoretical Chemistry KTH Biotechnology KTH, Stockholm
Quantum mechanical (QM) electronic structure calculations are frequently used to model reaction centers in biological systems, such as enzymes. While QM methods can treat molecular complexes of the size up to 100 atoms, most biological systems, such as proteins and nucleic acids, are much larger than that. In order to realistically model the biological system one also needs to consider a larger surrounding or a medium, e.g. water, further increasing the size of the simulation model. Using multiscale (QM/MM) extensions, the active site region can be treated fully quantum mechanically, while the evolution and interaction from the remainder of the system is determined using a more expedient classical forcefield (MM) model. In this project we will setup and simulate the time evolution of a biological system using a QM/MM method and study reaction paths in terms of equilibria and transition states and explore the roles of the different forces in the system. An introductory text concerning AbInitio MD and in particular CPMD: "Ab Initio molecular dynamics: Theory and Implemenation", D. Marx and J. Hutter, pages 133 especially. pdffile Classical (force field) molecular dynamics: "AMBER, a package for .... molecular dynamics ....", D.A. Pearlman, D.A. Case, P. Kollman et. al, pdffile On the QM/MM implementation used together with CPMD: "A Hamiltonian electrostatic coupling scheme for hybrid CarParrinello molecular dynamics simulations" and "DRESP: Dynamically Generated Electrostatic Potential Derived Charges from Quantum Mechanics/Molecular Mechanics Simulations", both by A. Laio, J. VandeVondele and U. Röthlisberger. pdffile , pdffile
