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Comparative Molecular Mechanics and Quantum Mechanics Study of Microhydration of Nucleic Acid Bases by Lino, J.; González, E.; Deriabina, A.; Velasco, M.; Poltev, V. is a scholarly article available to read on EtoBox.

What is Comparative Molecular Mechanics and Quantum Mechanics Study of Microhydration of Nucleic Acid Bases about?

DNA is the most important biological molecule, and its hydration contributes essentially to the structure and functions of the double helix. We analyze the microhydration of the individual bases of nucleic acids and their methyl derivatives using methods of molecular mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values obtained with QM. For Adenine and Thymine the QM local minima energy values are closer to those obtained by the PM potential (average of 0.72 kcal/mol) than by the AMBER force

Author

Lino, J.; González, E.; Deriabina, A.; Velasco, M.; Poltev, V.

Published

2013

Language

EN