Stability of Nucleic Acid Base Pairs in Organic Solvents: Molecular Dynamics, Molecular Dynamics/Quenching, and Correlated Ab Initio Study
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- 作者：Lucie Zendlová ; Pavel Hobza ; Martin Kabelá ;
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- 刊名：Journal of Physical Chemistry B
- 出版年：2007
- 出版时间：March 15, 2007
- 年：2007
- 卷：111
- 期：10
- 页码：2591 - 2609
- 全文大小：1445K
- 年卷期：v.111,no.10(March 15, 2007)
- ISSN：1520-5207
文摘
The dynamic structure and potential energy surface of adenine···thymine and guanine···cytosine base pairsand their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents(methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches startingfrom simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantumchemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamicssimulation, the molecular dynamics in combination with quenching technique was also used. The moleculardynamics simulations presented here have confirmed previous experimental and theoretical results from thebulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, inmethanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures ofthe base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroformmolecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The largevolume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded andstacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine···thymine base pairs, was observed. These results provide clear evidence that the preference of eitherthe stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulkproperties or the solvent polarity but rather by specific interactions of the base pair with a small number ofthe solvent molecules. These conclusions obtained at the empirical level were verified also by high-level abinitio correlated calculations.