Molecular dynamics Born-Oppenheimer

With the characterized mechanism, the next key question is the origin of its catalytic power. A prerequisite for this investigation is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio QM/MM approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyltransferase SET7/9... 

The idea of a classical treatment of the nuclear motion within the molecular dynamics (MD) scheme with ab initio determined, quantum-mechanical forces acing on nuclei is as old as quantum mechanics.11,12 The commonly used Born-Oppenheimer approximation12 introduces the concept of potential energy surface (PES). Different time-scales for nuclear and electronic motion allows for the adiabatic separation of the nuclear and electronic wave-function. In the Born-Oppenheimer molecular dynamics (BO-MD) the nuclei move according to Newton laws, while the quantum mechanics is required to determine the potential for this motion ... 

Born-Oppenheimer Molecular Dynamics of Proton Transfer in Phenol-Water Clusters... 

Born-Oppenheimer molecular dynamics simulations for neutral and ionized phenol-water clusters are reported. The results for [C6H50D-(H20)4],+ illustrate how the PT dynamics is coupled to fluctuations of the solvent. The kinetics of PT/recombination in [C6H50D-(H20)4] + clusters is related to strong fluctuations of the electrostatic field of the water molecules and this relationship points out the relevance of investigating the electronic properties of the HB network for understanding chemical reaction in solution. 

G.A. Worth, L.S. Cederbaum, Beyond Born-Oppenheimer Molecular dynamics through a conical intersection. Annual Rev. Chem. Phys. 55 (127) (2004) 127-158. 

In most cases, as in the Born-Oppenheimer Molecular Dynamics scheme discussed earlier (see Sect. 2.3) what is given to us is the external potential vq (r ) instead of the ground state density. In its turn, the ground state density no for the external potential vq can be shown to minimize the energy functional [124] ... 

For a large enough system, for which we can assume molecular chaos, the configurations generated by a Born-Oppenheimer Molecular Dynamics should then be representative of the microcanonical distribution ... 

Blumberger, J., Tavernelli, I., Klein, M.L., Sprik, M. Diabatic free energy curves and coordination fluctuations for the aqueous Ag+/Ag2+ redox couple A biased Born-Oppenheimer molecular dynamics investigation. J. Chem. Phys. 2006,124, 064507. 

Generalization of the Car-Parrinello and Born-Oppenheimer Molecular Dynamics Approaches... 

The very nature of the photochemical processes the multi-state multiconfigurational character and the occurrence of non-adiabatic behavior -leads to the fact that the field of computational photochemistry is still far from saturated with respect to computational tools and method developments. The need to treat several excited states, of different electronic character (covalent, ionic, charge-transfer, Rydberg, etc.), without bias requires the applied theory to be developed at a rather high level of sophistication. While TD-DFT to a large extent is attractable for Born-Oppenheimer molecular dynamics and trajectory surface hopping (TSH), due to its speed, it has its limitations in what type of transitions are correctly... 

Ab initio molecular dynamics methods can roughly be divided into two classifications Born-Oppenheimer Molecular Dynamics and Car-Parrinello Molecular Dynamics . In both simulations, the wavefunction is propagated with the changes in the nuclear coordinates. In the Born-Oppenheimer MD approach, the forces on each of ions are explicitly calculated at each MD time step. As such, the system directly follows the Bom-Oppenheimer surface. The primary drawback of the Born-Oppenheimer MD approach relates to the fact that time-intensive electronic structure calculations must be converged... 

In the ab initio Born-Oppenheimer molecular dynamics approach, the force field is defined on-the-fiy . A static electronic structure optimization is carried out at every time step within the molecular dynamics simulations. MD provides the positions for ions at each step in time. These coordinates are subsequently used as the input to the QM calculation which provides the energy and the forces which act upon each ion. Newton s equation of motion can then be described for the ground-state system as ... 

Recent advances in first-principles molecular dynamics (MD) calculations, which follow the Newtonian dynamics of classically treated nuclei, have made electronic-structure calculations applicable to the study of large systems where previously only classical simulations were possible. Examples of quantum-mechanical (QM) simulation methods are Born-Oppenheimer molecular dynamics (BOMD), Car-Parrinello molecular dynamics (CPMD), tight-binding molecular dynamics (TBMD), atom-centered density matrix propagation molecular dynamics (ADMPMD), and wavepacket ab idtb molecular dynamics (WPAIMD). 

---