Molecular dynamics of bimolecular reactions : the equilibrium constant of dimerisation of carbon dioxide : rebinding molecular dynamics of nitric oxide to the V68F myoglobin mutant

Abstract

1.1 Carbon dioxide 1.1.1 Significance Theoretical and experimental investigations of weakly bound molecular complexes are of fundamental importance for understanding of molecular interactions responsible for properties of condensed phases. The carbon dioxide clusters provide a simple model for such studies. Carbon dioxide has been a subject of many papers in recent years. Some deal with its role in the biosphere, mainly the greenhouse effect. The greenhouse effect is the rise in temperature that the Earth experiences because certain gases in the atmosphere (water vapor, carbon dioxide, nitrous oxide, and methane, for example) trap energy from the sun. Without these gases, heat would escape back into space and Earth’s average temperature would be lower. Other investigations deal with the significance of carbon dioxide for the nutrition for plants, the supercritical carbon dioxide as a green solvent for extraction and synthesis and the existance of carbon dioxide in the atmospheres of Mars and Venus. 1.1.2 Previous Investigations The carbon dioxide dimer was first detected in 1966 by Leckenby et al.[?]. The slippedparallel( C2h - geometry) structure of the carbon dioxide dimer was shown experimentally in references [?] - [?](high-resolution infrared) and [?](Raman studies) to be the stable one. That the structure of the dimer is slipped-parallel(C2h - geometry) was shown in [?] as a result of quantum-chemical calculations. The dimerisation equilibrium constant was evaluated using partition functions [?]. 1.1.3 Dimer formation A new method is developed to calculate the equilibrium constant of weak dimer complexes and the life time of the dimer in the gas phase. Actually it is not an easy task to define when approaching monomers form a dimer. In the new method the defined time correlation function from the molecular dynamics simulations shows a slow decay corresponding to real dimers and a fast decay corresponding to unstable collisions. The results obtained for the carbon dioxide dimerization are compared to results obtained by two other methods using partition function and second virial coefficient. A possible application is to predict the dimer carbon dioxide concentration in the atmospheres of Mars and Venus. 1.2 Rebinding dynamics of nitric oxide to the V68F Myoglobin mutant In connection with the work on rebinding molecular dynamics of nitric oxide to the V68F Myoglobin mutant I would like to emphasize that the study of reactive processes in chemically and biologically relevant systems is a topic of much current interest. For fast reactions (proton transfer, ligand rebinding) computer simulations are a useful means to investigate and understand the energetics and dynamics of chemical reactions. A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented in [?]. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one.