First-principles studies of the structure and dynamics of biomolecules

No Thumbnail Available
Journal Title
Journal ISSN
Volume Title
Doctoral thesis (article-based)
Checking the digitized thesis and permission for publishing
Instructions for the author
Degree programme
39, [89]
Dissertations of Laboratory of Physics, Helsinki University of Technology, 147
First-principles biosimulations have become an essential tool in the study of atoms and molecules and, increasingly, in modelling complex systems as those arising in biology. With the appearance of density-functional theory, and gradient-corrected exchange-correlation functionals, the ability to obtain an accurate enough solutions to the electronic Schrödinger equation for systems containing hundreds (or even thousands) of atoms has revolutionized biophysics and biochemistry. Biological systems exhibit a far higher degree of complexity than those studied in many other fields of physics. The sizes of the systems, long time scale of processes, the effect of the environment, and the range of intermolecular interactions provide challenging problems for the application of first-principles quantum mechanical simulations to biomolecular studies. This thesis concentrates on first-principles electronic structure calculations of various biological systems and processes. The dynamics of the active center of myoglobin has been studied by means of Born-Oppenheimer molecular dynamics. Similar methodology has been used to investigate the effect of hydration of the L-alanine amino acid and to predict its actual structure in aqueous solution at finite temperature. The effect of the environment, and the actual structure of several biomolecules in water have been investigated by means of vibrational spectra calculations. Different continuum models have been employed in calculations of the vibrational absorption, vibrational dichroism, Raman and Raman optical activity spectra. The treatment of large, biological systems, such as proteins in aqueous solution, entirely by ab initio methods is extremely expensive. The thesis demonstrates various approaches to overcome size and time scale limits. The work presented here is an example of how quantum mechanical techniques can successfully be applied to biologically relevant problems in rather large and complex systems.
biophysics, computational physics, density-functional, vibrational spectroscopy, ab initio simulations, hydration
Other note
  • K. J. Jalkanen, V. Würtz Jürgensen, and I. M. Degtyarenko, Linear response properties required to simulate vibrational spectra of biomolecules in various media: (R)-phenyloxirane (a comparative theoretical and spectroscopic vibrational study), Advances in Quantum Chemistry, Volume 50, pp. 91-124 (2005). [article1.pdf] © 2005 Elsevier Science. By permission.
  • I. Degtyarenko, R. M. Nieminen, and C. Rovira, Structure and dynamics of dioxygen bound to cobalt and iron heme, Biophysical Journal, Volume 91, Issue 6, pp. 2024-2034 (2006). [article2.pdf] © 2006 Biophysical Society. By permission.
  • I. M. Degtyarenko, K. J. Jalkanen, A. A. Gurtovenko, and R. M. Nieminen, L-alanine in a droplet of water: a density-functional molecular dynamics study, The Journal of Physical Chemistry B, Volume 111, Issue 16, pp. 4227-4234 (2007).
  • I. M. Degtyarenko, K. J. Jalkanen, A. A. Gurtovenko, and R. M. Nieminen, The aqueous and crystalline forms of L-alanine zwitterion, Journal of Computational and Theoretical Nanoscience, in press. [article4.pdf] © 2007 by authors and © 2007 American Scientific Publishers (ASP). By permission.
  • K. J. Jalkanen, I. M. Degtyarenko, R. M. Nieminen, X. Cao, L. A. Nafie, F. Zhu, and L. D. Barron, Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N'methylamide in aqueous solution: a combined theoretical and experimental approach, Theoretical Chemistry Accounts, in press. [article5.pdf] © 2007 by authors and © 2007 Springer Science+Business Media. By permission.
Permanent link to this item