Details

Autor(en) / Beteiligte

• Mendieta-Moreno, Jesús I
• Walker, Ross C
• Lewis, James P
• Gómez-Puertas, Paulino
• Mendieta, Jesús
• Ortega, José

Titel

fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems

Ist Teil von

• Journal of chemical theory and computation, 2014-05, Vol.10 (5), p.2185-2193

Ort / Verlag

United States: American Chemical Society

Erscheinungsjahr

2014

Link zum Volltext

Quelle

Alma/SFX Local Collection

Beschreibungen/Notizen

• In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Because of the complexity of biomolecules and the desire to achieve converged sampling, it is important that the QM method presents a good balance between accuracy and computational efficiency. Here, we report on the implementation of a QM/MM technique that combines a DFT approach specially designed for the study of complex systems using first-principles molecular dynamics simulations (fireball) with the amber force fields and simulation programs. We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.