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Title: Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

Abstract

Recent experimental studies on the Watson–Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH···O hydrogen bonds separated by one NH···N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitalsand with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.

Authors:
 [1];  [2]; ORCiD logo [3]; ORCiD logo [3];  [3]
  1. Computational Center for Molecular Structure and Interactions, Jackson, MS
  2. Academy of Sciences of the Czech Republic
  3. ORNL
Publication Date:
Research Org.:
Oak Ridge National Laboratory, Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
979350
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Chemistry—A European Journal
Additional Journal Information:
Journal Volume: 16; Journal Issue: 10
Country of Publication:
United States
Language:
English
Subject:
08 HYDROGEN; ELECTRON CORRELATION; EXTRAPOLATION; HYDROGEN; MELTING POINTS; ORIGIN; PHYSICAL CHEMISTRY; TRIAZINES

Citation Formats

Leszczynski, Jerzy, Sponer, Jiri, Sumpter, Bobby, Fuentes-Cabrera, Miguel A., and Vazquez Mayagoitia, Alvaro. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. United States: N. p., 2010. Web. doi:10.1002/chem.200902068.
Leszczynski, Jerzy, Sponer, Jiri, Sumpter, Bobby, Fuentes-Cabrera, Miguel A., & Vazquez Mayagoitia, Alvaro. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. United States. doi:10.1002/chem.200902068.
Leszczynski, Jerzy, Sponer, Jiri, Sumpter, Bobby, Fuentes-Cabrera, Miguel A., and Vazquez Mayagoitia, Alvaro. Sat . "Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues". United States. doi:10.1002/chem.200902068.
@article{osti_979350,
title = {Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues},
author = {Leszczynski, Jerzy and Sponer, Jiri and Sumpter, Bobby and Fuentes-Cabrera, Miguel A. and Vazquez Mayagoitia, Alvaro},
abstractNote = {Recent experimental studies on the Watson–Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH···O hydrogen bonds separated by one NH···N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitalsand with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.},
doi = {10.1002/chem.200902068},
journal = {Chemistry—A European Journal},
number = 10,
volume = 16,
place = {United States},
year = {2010},
month = {5}
}

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