Stacking of nucleic acid bases: optimization of the computational approach—the case of adenine dimers

Paulina Marek , Halina Szatyłowicz , Tadeusz Marek Krygowski

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.
Author Paulina Marek (FC / CofIC)
Paulina Marek,,
- Chair Of Inorganic Chemistry
, Halina Szatyłowicz (FC / DPC)
Halina Szatyłowicz,,
- Department Of Physical Chemistry
, Tadeusz Marek Krygowski
Tadeusz Marek Krygowski,,
-
Journal seriesStructural Chemistry, ISSN 1040-0400, (N/A 70 pkt)
Issue year2019
Vol30
No1
Pages351-359
Publication size in sheets0.5
Keywords in EnglishAdenine Stacking interaction Hydrogen bond Computational method
ASJC Classification1606 Physical and Theoretical Chemistry
DOIDOI:10.1007/s11224-018-1253-7
URL https://link.springer.com/article/10.1007%2Fs11224-018-1253-7
Languageen angielski
File
Marek2019_Article_StackingOfNucleicAcidBasesOpti.pdf 1.32 MB
Score (nominal)70
Score sourcejournalList
ScoreMinisterial score = 70.0, 20-10-2019, ArticleFromJournal
Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2017 = 0.525; WoS Impact Factor: 2017 = 2.019 (2) - 2017=1.526 (5)
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