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Evaluation of Proton Transfer in DNA Constituents: Development and Application of Ab Initio Based Reaction Kinetics

  • Dmytro Kosenkov
  • Yana Kholod
  • Leonid Gorb
  • Jerzy Leszczynski
Chapter
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 12)

Abstract

The kinetics of chemical reactions characterizes the rates of chemical processes, i.e. distribution of all reactants, intermediates and products over time. This information is of vital importance for all areas of chemistry: chemical technology to control organic or inorganic syntheses, chemical construction of nanomaterials, as well as for the investigation of biochemical processes. The chemical kinetics data provide a possibility to investigate the effect of different chemical, physical and environmental factors on the rate of a reaction, final products and by-products distribution, and even the direction of a chemical process. In the first part of the chapter the general introduction to the kinetics of chemical reactions is given. The classical kinetics of chemical reactions uses the outcome from experimental measurement of reaction rates. However, currently available reliable computational ab initio methods provide an alternative efficient way for estimation of the rate constants even for stepwise and multidirectional reactions. Another benefit of the computational investigations is the possibility to simulate a wide range of processes with duration from picoseconds to hours, days, or even for much longer time scales. Contemporary ab initio methods have been used for estimation and prediction of reaction rates for a number of different chemical reactions. Until recently most of the theoretical studies on kinetic parameters have not been extended beyond the calculations of the rate constants of chemical reactions. In the present review we describe the simulation of the chemical kinetics of proton transfer (tautomerization) in nucleic acid bases and their complexes with metal ions, also in the presence of water molecules. The considered models are based on the ab initio calculated rate constants of chemical reactions. Then, such predicted rate constants are used for further kinetic simulations. Biological consequences of investigated processes are also discussed.

Keywords

Chemical reactivity Gas-phase experiments Nucleobases Laser desorption Tautomerization Point mutations 

Notes

Acknowledgements

Support has been provided by NSF CREST grant HRD-0833178. The authors are grateful to the Mississippi Center for Supercomputer Research for the computational facilities. The authors would thank to Professor Michel Mons, Professor Oleg V. Shishkin, Professor Dmytro M. Hovorun and Dr. Andrea Michalkova for the collaboration and active discussion of the kinetic project.

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Copyright information

© Springer Netherlands 2010

Authors and Affiliations

  • Dmytro Kosenkov
    • 1
    • 2
  • Yana Kholod
    • 1
    • 3
  • Leonid Gorb
    • 1
    • 4
  • Jerzy Leszczynski
    • 1
    • 5
  1. 1.Interdisciplinary Center for Nanotoxicity, Department of Chemistry and BiochemistryJackson State UniversityJacksonUSA
  2. 2.Department of ChemistryPurdue UniversityWest LafayetteUSA
  3. 3.US DoE Ames LaboratoryIowa State UniversityAmesUSA
  4. 4.Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and GeneticsNational Academy of Sciences of UkraineKyivUkraine
  5. 5.Army Engineering Research and Development CenterVicksburgUSA

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