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

  1. Judit E. Šponer Dr.1,
  2. Álvaro Vázquez-Mayagoitia Dr.2,
  3. Bobby G. Sumpter Dr.3,
  4. Jerzy Leszczynski Prof.4,
  5. Jiří Šponer Prof.1,
  6. Michal Otyepka Dr.5,
  7. Pavel Banáš Dr.5,
  8. Miguel Fuentes-Cabrera Dr.6

Article first published online: 29 JAN 2010

DOI: 10.1002/chem.200902068

Issue

Chemistry - A European Journal

Chemistry - A European Journal

Volume 16, Issue 10, pages 3057–3065, March 8, 2010

Additional Information

How to Cite

Šponer, Judit E., Vázquez-Mayagoitia, Á., Sumpter, Bobby G., Leszczynski, J., Šponer, J., Otyepka, M., Banáš, P. and Fuentes-Cabrera, M. (2010), Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chem. Eur. J., 16: 3057–3065. doi: 10.1002/chem.200902068

Author Information

  1. 1

    Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, (Czech Republic), Fax: (+420) 541-211-293

  2. 2

    Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, TN 37996-1600 (USA)

  3. 3

    Center for Nanophase Materials Sciences and Computer Sciences and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, P. O. Box 2008, Oak Ridge, TN 37831-6494 (USA)

  4. 4

    Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217 (USA)

  5. 5

    Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. Listopadu 12, 77146 Olomouc (Czech Republic)

  6. 6

    Joint Institute for Computational Sciences, University of Tennessee, Center for Nanophase Materials Sciences and Computer Sciences and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, P. O. Box 2008, Oak Ridge, TN 37831-6494 (USA), Fax: (+1) 865-241-0381

Publication History

  1. Issue published online: 1 MAR 2010
  2. Article first published online: 29 JAN 2010
  3. Manuscript Revised: 4 NOV 2009
  4. Manuscript Received: 24 JUL 2009

Funded by

  • Ministry of Education of the Czech Republic. Grant Numbers: AVOZ50040507, AVOZ50040702, MSM0021622413, LC06030, MSM6198959216, LC512
  • Grant Agency of the Academy of Sciences of the Czech Republic. Grant Numbers: 1QS500040581, IAA400550701, IAA400040802
  • Grant Agency of the Czech Republic. Grant Numbers: 203/09/1476, 203/09/H046
  • Center for Nanophase Materials Sciences
  • Department of Energy
  • National Center for Computational Sciences, ORNL
  • Office of Science, USDOE
  • National Energy Research Scientific Computing Center
  • Office of Science of the U.S. Department of Energy. Grant Number: DEAC02-05CH11231
  • National Science Foundation
  • National Institute for Computational Sciences
  • USDOE
  • Basic Energy Science and Advanced Scientific Computing Research
  • SciDac program

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Keywords:

  • ab initio calculations;
  • base pairing;
  • molecular dynamics;
  • origin of life;
  • prebiotic chemistry

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 N[BOND]H⋅⋅⋅O hydrogen bonds separated by one N[BOND]H⋅⋅⋅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 orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.

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