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Computer Simulations of Complex Chemical Systems: Solvation of DNA and Solvent Effects in Conformational Transitions

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1 Author(s)
Clementi, Enrico ; IBM Data Processing Product Group laboratory, Poughkeepsie, New York 12602, USA

As is known, atomic and small molecular systems can be realistically simulated with quantum-mechanical models. In complex chemical systems, however, the natural parameters for a description are not only the electronic density and energy but also entropy, temperature, and time. We have considered as an example for a complex chemical system the structure of water surrounding DNA with counterions. No direct experimental determination of the solvent structure around a single DNA macromolecule is available from experimental data, despite continuous efforts during the last twenty years to obtain both single crystals of DNA and scattering data from solutions. A very detailed representation is now available concerning the structure and interaction energy of water molecules in the first solvation shell or in the “grooves” of the DNA. The data obtained by our computer simulation are in good agreement with indirect data from DNA fibers at different relative humidities and with other indirect evidence. In addition, our simulated results allow us to present a preliminary model for the solvent effects in transition processes between different DNA conformations. The model presented is also in agreement with available experimental data. Finally, our results report the first determination of the position of counterions in DNA at different relative humidities and at room temperature. This application demonstrates the flexibility of the computational approach. The method we have used is very general; namely, it is not limited to a biological system but is valid for any organic or inorganic problem requiring systematic simulation on a class of compounds interacting either as a few molecules or as a large ensemble of molecules.

Note: The Institute of Electrical and Electronics Engineers, Incorporated is distributing this Article with permission of the International Business Machines Corporation (IBM) who is the exclusive owner. The recipient of this Article may not assign, sublicense, lease, rent or otherwise transfer, reproduce, prepare derivative works, publicly display or perform, or distribute the Article.  

Published in:

IBM Journal of Research and Development  (Volume:25 ,  Issue: 4 )