Spectra Modelling Combining Molecular Dynamics and Quantum Mechanics

V. Novák1,2, P. Bouř1

1Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague 6, 16610

2University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28


Vibrational spectroscopic methods are powerful tools for studies of biomolecular structure. Such ability of the Raman scattering or infrared absorption is greatly enhanced by interpretation and simulation of the spectra by theoretical calculations. However, quantum mechanical (QM) spectra modelling of big systems, such as large biomolecules, are highly computationally demanding and from certain size practically impossible. Therefore there is a need for simpler, but accurate approaches.

We use the autocorrelation function of the polarizability and dipole moment obtained from dynamical trajectories to calculate Raman scattering and absorption intensity. For example, total polarizability of a single box is generated from molecular ones calculated at the QM level. This approach thus allows calculating spectra of much larger systems compared to usual QM approaches.

To estimate the accuracy, as an initial model a water box was used, different box sizes and approaches to process dynamical trajectories were compared. Molecular dynamics with the Amber99 force field was compared to Amoeba09 force fields and ab‑initio MD using the PBE functional. The simulated spectra were dependent on the method, but in general features agreed with the experiment. As a further application, Raman spectral dependence on pH for water solutions was examined both experimentally and theoretically. In the future, we plan to model spectra of proteins and include molecular chirality.

Computational resources were provided by the MetaCentrum under the program LM2010005 and the CERIT-SC under the program Centre CERIT Scientific Cloud, part of the Operational Program Research and Development for Innovations, Reg. no. CZ.1.05/3.2.00/08.0144.

The present study was undertaken owing to a support from the Grant Agency of the Czech Republic (15‑090‑725, P208/11/105).