New methods for Born-Oppenheimer molecular dynamics simulations have been developed and used to study protonated water clusters and mechanochemistry of alkanes. The novel algorithms are an efficient coordinate transformation and sampling microcanonical ensembles of trajectories used for generating starting conditions for simulations. In combination with existing techniques as well as with electronic structure methods within DALTON program, they make it a powerful tool to study reaction dynamics, free of charge.
This has been demonstrated by investigation of protonated water clusters relevant for water nucleation in atmospheric chemistry. The structure of the proton salvation shell and evaporation kinetics have been revealed.
Another application is the dynamics of alkanes under mechanical stress. Short-chain alkanes – butane and octane – are model compounds for polymers. Their dynamical behavior was simulated and analyzed under two scenarios mimicking the modes ofmechanochemical activation: slow stretching in the atomic-force microscope and violent action of ultrasound.
List of papers
(1, 2,3 and 4 are removed due to publisher restrictions)
1 Insights into the Dynamics of Evaporation and Proton Migration in Protonated Water Clusters from Large-Scale Born–Oppenheimer Direct Dynamics. Vladimir V. Rybkin, Anton O. Simakov, Vebjørn Bakken, Simen Reine, Thomas Kjærgaard, Trygve Helgaker and Einar Uggerud. Journal of Computational Chemistry 2013, 34, 533–544 DOI: 10.1002/jcc.23162
2 Internal-to-Cartesian Back Transformation of Molecular Geometry Steps Using High-Order Geometric Derivatives. Vladimir V. Rybkin, Ulf Ekström, and Trygve Helgaker. Journal of Computational Chemistry 2013, 34, 1842–1849 DOI: 10.1002/jcc.23327
3 The Dalton quantum chemistry program system. Kestutis Aidas et al. WIREs Comput Mol Sci 2014, 4:269–284. DOI: 10.1002/wcms.1172
4 Mechanochemistry: The Effect of Dynamics. Hans S. Smalø, Vladimir V. Rybkin, Wim Klopper, Trygve Helgaker and Einar Uggerud. J. Phys. Chem. A 2014, 118, 7683−7694 DOI: 10.1021/jp504959z
5 Sampling microcanonical ensembles of trajectories using harmonic approximation in internal coordinates. Vladimir V. Rybkin and Ulf Ekström. Journal of Chemical Physics 141, 064108 (2014) DOI: 10.1063/1.4892109