Born-Oppenheimer molecular dynamics simulations

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... 

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. 

Kuo, I.-F. W., Mundy, C. J., McGrath, M. J., Siepmann, J. I. (2006). Time-dependent properties of liquid water A comparison of Car-Parrinello and Born-Oppenheimer molecular dynamics simulations. Journal of Chemical Theory and Computation, 2,1274. 

This chapter highlights recent developments in auxiliary density functional theory (ADFT) and their implementation in deMon2k. The simplifications associated with ADFT permit an efficient parallel code structure that is suitable for research applications in the nano-regime with chemical accuracy. The presented Born-Oppenheimer molecular dynamics simulation shows that simulation times on the nanosecond time scale can be reached with ADFT. As the here presented applications show this opens new and exciting perspectives for computational chemistry and material simulations with first-principle methods. 

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). 

The first purpose of the present work is thus to evaluate whether the structural distortions which were proposed by Liu et al. [45] are compatible with thermal fluctuations at or near standard room temperature, that is, at 298 and 310 K, according to Maxwell-Boltzmann (MB) statistics [53, 54] on vibrational energy levels. The analysis is supplemented by Born-Oppenheimer Molecular Dynamical (BOMD) simulations [55-57] at the same temperatures of momentum profiles inferred from vertical (e, 2e) ionization cross-sections. A main advantage of this approach is that, by virtue of ergodicity [58], it enables a complete exploration of phase space which is equivalent to an ensemble... 

Schwenk CF, Loffler HH et al (2001) Molecular dynamics simulations of Ca2+ in water comparison of a classical simulation including three-body corrections and Born-Oppenheimer ab initio and density functional theory quantum mechanical/molecular mechanics simulations. I Chem Phys 115 10808... 

Section 2 of this chapter notes will be devoted to the framework for separation of the ionic and electronic dynamics through the Born-Oppenheimer approximation. Atomic motion, with forces on the ions at each timestep evaluated through an electronic structure calculation, can then be propagated by Molecular Dynamics simulations, as proposed by first-principle Molecular Dynamics. This allows for a description of the electronic reorganisation following the atomic motion, e.g. bond rearrangements in chemical reactions. 

So far, our discussion has focussed on stationary quantum chemical methods, which yield results for fixed atomic nuclei, i.e. for frozen molecular structures like minimum structures on the Born-Oppenheimer potential energy surface. Processes in supramolecular assemblies usually feature prominent dynamical effects, which can only be captured through explicit molecular dynamics or Monte Carlo simulations [95-98]. Molecular dynamics simulations proved to be a useful tool for studying the detailed microscopic dynamic behavior of many-particle systems as present in physics, chemistry and biology. The aim of molecular dynamics is to study a system by recreating it on the computer as close to nature as possible, i.e. by simulating the dynamics of a system in all microscopic detail over a physical length of time relevant to properties of interest. 

In general, molecular dynamics simulations, in the framework of the Born-Oppenheimer or Car-Parrinello approximation, are of great importance for the understanding of materials dedicated to proton transport. Especially for materials, where interactions are dominated by covalent or hydrogen bonds, ab initio molecular dynamics provide a proper description. The results obtained by such methods give details at the atomic level, which are not accessible by experimental investigations. Nevertheless, the choice of the model system has to be done in a very careful way in order to consider the manifold possibilities of structures and mechanisms. 

Tongraar A, Rode BM (2005a) Stmctural arrangement and dynamics of the hydrated Mg " " An ab initio QM/MM molecular dynamics simulation. Chem Phys Lett 409 304-309 Tongraar A, Liedl KR, Rode BM (1998) Born-Oppenheimer ab Initio QM/MM Dynamics Simulations of Na+ and K+ in Water From Stmcture Making to Stmcture Breaking Effects. J Phys Chem A 102 10340-10347... 

Hamiltonian models are classified according to then-level of approximation. The features of Schroedinger (S), Born-Oppenheimer (BO), and McMillan-Mayer (MM) level Hamiltonian models are exemplified in Table I by a solution of NaCl in H2O. The majority of investigations on electrolyte solutions are carried out at the MM level. BO-Level calculations are a precious tool for Monte Carlo and molecular dynamics simulations as well as for integral equation approaches. However, their importance is widely limited to stractural investigations. They, as well as the S-level models, have not yet obtained importance in electrochemical engineering. S-Level quantum-mechanical calculations mainly follow the Car-Parinello ab initio molecular dynamics method. 

Before discussing applications of the SE-SCM (and variants thereof) to the description of cluster fission, we note that for atomic and molecular clusters microscopic descriptions of energetics and dynamics of fission processes, based on modern electronic structure calculations in conjunction with molecular dynamics simulations (where the classical trajectories of the ions, moving on the concurrently calculated Born-Oppenheimer (BO) electronic potential-energy surface, are obtained via integration of the Newtonian... 

Combining a microscopic electronic theory with molecular dynamics simulations in the Born-Oppenheimer approximation, Bennemann, Garcia, and Jeschke presented the first theoretical results for the ultrafast structural changes in the silver trimer [135]. They determined the timescale for the relaxation from the linear to a triangular structure initiated by a photodetachment process and showed that the time-dependent change of the ionization potential (IP) reflects in detail the internal degrees of freedom. 

---