Sample application: biologically relevant metallorganic systems are computationally accessible
Car-Parrinello molecular dynamics is used to study the electronic and the dynamical properties of a reduced (picture below) and an extended (right picture on the right) model of the active site of myoglobin.
The problem: The modeling of complex biological molecules, which is essential to understand e.g. enzymatic and/or biomimetic catalysis, is very challenging because a proper description of the active site needs the inclusion of a large number of atoms (from several tens to a few hundreds) treated at a high level of quantum chemical theory.
Results: · This simulation of the manganese and iron porphyrines, contained in the active site of myoglobin, shows that the Quantum Espresso implementation of Car-Parrinello first principle molecular dynamics, combined with Density Functional Theory, allows to optimize molecular structures, study dynamical and finite temperature properties, and model reaction paths of large molecular systems containing transition metal centers, leveraging on just moderate computational resources.
· Additionally, using the Makov-Payne technique, the correct electronic and structural properties of highly charged species (generally hard to tread within the plane wave method) can be reproduced. As an example it has been possible to obtain the correct energy ordering for the 2-Pyp (upper panel) and 4-Pyp (lower panel) isomers of the oxo-aquo (left panel) and oxo-hydroxo (right panel) Mn(V) porphyrins.
Tools: Car-Parrinello code, available within Quantum Espresso package for first-principle molecular dynamics.
References: · P. Giannozzi, F. de Angelis, and R. Car,First-principle molecular dynamics with ultrasoft pseudopotentials: Parallel implementation and application to extended bioinorganic systems: J. Chem. Phys. Rev. 120 (2004) 5903.