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Abstract
Stacking interactions play an important role in stabilizing DNA and RNA secondary structure. To select a computational level to study the stacking interactions, both energy and geometric criteria, as well as the time necessary to optimize the system, should be taken into account. In this work, an attempt was made to find the most optimal level of theory describing the stacking interactions in adenine dimers. The obtained results have shown that for this purpose, wB97XD/6-311G(p,d), wB97XD/aug-cc-pvdz, or B97D3/aug-cc-pvdz should be used. What is more, geometry of the most preferable arrangements of molecules was also pointed out, ensuring an optimal starting system for further analyses.
Highlights
It is a trivial statement to say that DNA and RNA biopolymers are of fundamental importance for life
Our research focuses on assessing the impact of a substitution on the structure and energy of stacking interactions of adenine dimers
The research focused on the selection of the most optimal computational level to study stacking interactions in 9H adenine dimers
Summary
It is a trivial statement to say that DNA and RNA biopolymers are of fundamental importance for life. Hbonding is a well-recognized type of interaction [3,4,5,6] and— in principle—does not present any particular problem in computational descriptions of the interactions between pairs and other complexes of nucleic acids [7]. Summarizing, noncovalent interactions govern the structure and conformational dynamics of molecular systems, and they are crucial for their chemical properties. The ability to understand and predict noncovalent interactions is very important. Due to the size of the studied systems, it is very important to choose the appropriate level of calculation (methods and basis sets). The aim of this paper is to present the most effective computational approach which can reliably describe the abovementioned interactions
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