Molecular Dynamics Simulations of Vibrational Spectra of Hydrogen-Bonded Systems

  • Mateusz Z. Brela
  • Marek Boczar
  • Łukasz Boda
  • Marek J. Wójcik
Chapter

Abstract

In this chapter, we present current studies on molecular dynamics (MD) simulations of hydrogen-bonded systems with emphasis on vibrational spectra analysis. One of the most informative experimental data are spectroscopic data (infrared and Raman spectroscopy), which give information important in diverse fields, e.g. protein folding, drug design, sensors, nanotechnology, separations, etc. Spectroscopic data are very sensitive on inter- and intramolecular interactions. The processes of melting, boiling, unfolding and strand separation involve disruption of molecular interactions, that engage attractive or repulsive forces between molecules. In this chapter, we focus on calculations of IR spectra of hydrogen-bonded complexes based on linear response theory, in which the spectral density is the Fourier transform of the autocorrelation function of the dipole moment operator involved in the IR transitions. Recently, Born–Oppenheimer molecular dynamics (BOMD), Car–Parrinello molecular dynamics (CPMD), path integral molecular dynamics (PIMD), hybrid molecular dynamics (QM/MM) and other methods which use trajectories from molecular dynamics have been employed to simulate IR spectra of hydrogen-bonded systems. Each of these methods has some advantages and disadvantages which will be discussed in this chapter presenting also recent applications of these methods.

Keywords

Molecular dynamics simulations BOMD CPDM Vibrational spectra IR Hydrogen-bond 

Notes

Acknowledgements

This work was financially supported by National Science Centre, Poland, grant 2016/21/B/ST4/02102.

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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Mateusz Z. Brela
    • 1
  • Marek Boczar
    • 1
  • Łukasz Boda
    • 1
  • Marek J. Wójcik
    • 1
  1. 1.Faculty of ChemistryJagiellonian UniversityKrakowPoland

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