137
Chapter 5
Molecular Structures, Relative Stability, and
Proton Affinities of Nucleotides: Broad View
and Novel Findings
Tetiana A. Zubatiuk, Gennady V. Palamarchuk, Oleg V. Shishkin,
Leonid Gorb and Jerzy Leszczynski
© Springer Science+Business Media Dordrecht 2014
L. Gorb et al. (eds.), Application of Computational Techniques in Pharmacy and Medicine,
Challenges and Advances in Computational Chemistry and Physics 17,
DOI 10.1007/978-94-017-9257-8_5
T. A. Zubatiuk () · G. V. Palamarchuk · O. V. Shishkin
SSI “Institute for Single Crystals” of National Academy of Science of Ukraine,
Lenina Ave., 60, Kharkiv 61001, Ukraine
e-mail: tklimenko@xray.isc.kharkov.com
G. V. Palamarchuk
e-mail: dandygp@list.ru
O. V. Shishkin
e-mail: shishkin@xray.isc.kharkov.com
L. Gorb
Laboratory of Computational Structural Biology, Department of Molecular Biophysics,
Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Key
State Laboratory in Molecular and Cell Biology, Zabolotnogo Str., 150, Kyiv 03143, Ukraine
e-mail: lgorb@icnanotox.org
J. Leszczynski
Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry,
Jackson State University, P.O. Box 17910, Lynch Str., 1325, Jackson, MS 39217, USA
e-mail: jerzy@icnanotox.org
Abstract In this chapter we analyze and systematize the data related to intramolecular hydrogen bonds and their impact on molecular geometry of nucleotides. The
application of various non-empirical methods of quantum chemistry to determination
of conformational characteristics of anions of the canonical 2′-deoxyribonucleotides
and their methyl esters, as well as their energetics, is discussed. We revealed an existence of novel intramolecular interactions of the canonical 2′-deoxyribonucleotide
anions. They are caused by incorporation of 2′-deoxyribonucleotide anions into DNA
as well as by the impact of the nucleobases on the conformational features of the
nucleotides and intramolecular interactions of these molecules. The efficient strategy
of the evaluation of proton affinity for the different types of nucleotides is described.
To the memory of Dr. Oleg Shishkin, our friend and colleague,
for all inspiration he had continuously provided.
Chapter 5
Molecular Structures, Relative Stability, and
Proton Affinities of Nucleotides: Broad View
and Novel Findings
Tetiana A. Zubatiuk, Gennady V. Palamarchuk, Oleg V. Shishkin,
Leonid Gorb and Jerzy Leszczynski
© Springer Science+Business Media Dordrecht 2014
L. Gorb et al. (eds.), Application of Computational Techniques in Pharmacy and Medicine,
Challenges and Advances in Computational Chemistry and Physics 17,
DOI 10.1007/978-94-017-9257-8_5
T. A. Zubatiuk () · G. V. Palamarchuk · O. V. Shishkin
SSI “Institute for Single Crystals” of National Academy of Science of Ukraine,
Lenina Ave., 60, Kharkiv 61001, Ukraine
e-mail: tklimenko@xray.isc.kharkov.com
G. V. Palamarchuk
e-mail: dandygp@list.ru
O. V. Shishkin
e-mail: shishkin@xray.isc.kharkov.com
L. Gorb
Laboratory of Computational Structural Biology, Department of Molecular Biophysics,
Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Key
State Laboratory in Molecular and Cell Biology, Zabolotnogo Str., 150, Kyiv 03143, Ukraine
e-mail: lgorb@icnanotox.org
J. Leszczynski
Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry,
Jackson State University, P.O. Box 17910, Lynch Str., 1325, Jackson, MS 39217, USA
e-mail: jerzy@icnanotox.org
Abstract In this chapter we analyze and systematize the data related to intramolecular hydrogen bonds and their impact on molecular geometry of nucleotides. The
application of various non-empirical methods of quantum chemistry to determination
of conformational characteristics of anions of the canonical 2′-deoxyribonucleotides
and their methyl esters, as well as their energetics, is discussed. We revealed an existence of novel intramolecular interactions of the canonical 2′-deoxyribonucleotide
anions. They are caused by incorporation of 2′-deoxyribonucleotide anions into DNA
as well as by the impact of the nucleobases on the conformational features of the
nucleotides and intramolecular interactions of these molecules. The efficient strategy
of the evaluation of proton affinity for the different types of nucleotides is described.
To the memory of Dr. Oleg Shishkin, our friend and colleague,
for all inspiration he had continuously provided.