The doctoral dissertations of the former Helsinki University of Technology (TKK) and Aalto University Schools of Technology (CHEM, ELEC, ENG, SCI) published in electronic format are available in the electronic publications archive of Aalto University - Aaltodoc.
Aalto

First-Principles Studies of the Structure and Dynamics of Biomolecules

Ivan Degtyarenko

Dissertation for the degree of Doctor of Science in Technology to be presented with due permission of the Department of Engineering Physics and Mathematics for public examination and debate in Auditorium E at Helsinki University of Technology (Espoo, Finland) on the 8th of June, 2007, at 12 o'clock noon.

Overview in PDF format (ISBN 978-951-22-8806-9)   [756 KB]
Dissertation is also available in print (ISBN 978-951-22-8805-2)

Abstract

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.

This thesis consists of an overview and of the following 5 publications:

  1. 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). © 2005 Elsevier Science. By permission.
  2. 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). © 2006 Biophysical Society. By permission.
  3. 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).
  4. 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. © 2007 by authors and © 2007 American Scientific Publishers (ASP). By permission.
  5. 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. © 2007 by authors and © 2007 Springer Science+Business Media. By permission.

Keywords: biophysics, computational physics, density-functional, vibrational spectroscopy, ab initio simulations, hydration

This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.

© 2007 Helsinki University of Technology

Last update 2011-05-26