Stability of nucleic acid base pairs in organic solvents: Molecular dynamics, molecular dynamics/quenching, and correlated ab intio study

Article Abstract:

Various theoretical techniques are applied to study the dynamic structure and potential energy surface of adenine***thymine and guanine***cytosine base pairs and their methylated analogues interacting with small number of organic solvents like methanol, dimethylsulfoxide, and chloroform. It is inferred that the choice of either the stacked or the hydrogen-bonded structures of base pairs in the solvent is decided by the specific interactions of the base pairs with a small number of the solvent molecules and not only by bulk properties or the solvent polarity.

Analysis, Electric properties, Mechanical properties

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Potential energy and free energy surfaces of all ten canonical and methylated nucleic acid base pairs: molecular dynamics and quantum chemical ab initio studies

Article Abstract:

A molecular dynamics/quenching (MD/Q) technique with the Cornell empirical force field, and a correlated ab initio quantum chemical method were used to study the potential energy surfaces (PESs) and free energy surfaces (FESs) of all ten canonical and methylated nucleic acid base pairs. It was found that the PESs and FESs of most base pairs are very complex and characterized by the coexistence of several structures.

Usage, Quantum chemistry, Methylation, Nucleic acid bases

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Potential energy surfaces of an adenine-thymine base pair and its methylated analogue in the presence of one and two water molecules: Molecular mechanics and correlated ab intio study

Article Abstract:

A potential energy surface of monohydrated ad dehydrated adenine-thymine and 9-methyladenine-1-methylthymine base pairs are examined by the molecular dynamic/quenching technique. The most stable and populated structures found were fully reoptimized at the correlated ab intio level employing the resolution of identity Moller-Plesset method.

Chemical properties

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