Effective Atomic Charges of Canonical 2'-Deoxyribonucleotides and Their Conformational Dependences
Effective charges for the atoms of canonical 2'-deoxyribonucleotides (the molecules of 5'-deoxycytidylic, 5'-thymidylic, 5'-deoxyadenylic, and 5'-deoxyguanylic acids) averaged over all of their possible conformers and the corresponding root-mean-square deviations have been obtained. It is shown that the charge deviations for carbon atoms can exceed the average values of the charge itself. A capability of reproducing the conformer dipole moments with the use of averaged charges has been analyzed. It is found that the neglect of the dependence of effective atomic charges on the molecule conformation may result in errors for the dipole moment magnitude exceeding 100%. The results obtained can be used for the improvement of electrostatic components in the existing force fields.
O.P. Chepinoga, The Biological Role of Nucleic Acids (Israel Program for Sci. Transl., Jerusalem, 1962).
E. Chargaff, Essays on Nucleic Acids (Elsevier, Amsterdam, 1963).
R.H. Sarma, Nucleic Acid Geometry and Dynamics (Pergamon Press, New York, 1980).
W. Saenger, Principles of Nucleic Acid Structure (Springer, New York, 1984).
Nucleic Acids in Chemistry and Biology, edited by G.M. Blackburn and M.J. Gait (IRL Press, Oxford, 1990).
R.L.P. Adams, J.T. Knowler, and D.P. Leader, The Biochemistry of the Nucleic Acids (Springer, New York, 1992).
R.R. Sinden, DNA Structure and Function (Academic Press, San Diego, 1994).
V.A. Bloomfield, D.M. Crothers, and I. Tinoco, Nucleic Acids: Structures, Properties, and Functions (Univ. Science Books, Sausalito, CA, 2000).
S. Neidle, Nucleic Acid Structure and Recognition (Oxford Univ. Press, Oxford, 2002).
The Chemical Biology of Nucleic Acids, edited by G. Mayer (Wiley, Chichester, 2011).
L. Yang and B.M. Pettitt, J. Phys. Chem. 100, 2564 (1996).
A. Perez, F.J. Luque, and M. Orozco, J. Am. Chem. Soc. 129, 14739 (2007).
A. Perez, F. Lankas, F.J. Luque, and M. Orozco, Nucleic Acids Res. 36, 2379 (2008).
A.D. Mackerell, J. Comput. Chem. 25, 1584 (2004).
J.W. Ponder and D.A. Case, Adv. Protein Chem. 66, 27 (2003).
J. Sponer, J. Leszczynski, and P. Hobza, J. Phys. Chem. 100, 5590 (1996).
T.Yu. Nikolaienko and D.M. Hovorun, Dopov. Nat. Akad. Nauk Ukr., No. 9, 173 (2010).
T.Yu. Nikolaienko, L.A. Bulavin, and D.M. Hovorun, Ukr. Biokhim. Zh. 82, No. 6, 76 (2010).
T.Yu. Nikolaienko, L.A. Bulavin, and D.M. Hovorun, Ukr. Biokhim. Zh. 83, No. 4, 16 (2011).
T.Yu. Nikolaienko, L.A. Bulavin, and D.M. Hovorun, Biopolym. Cell. 27, 291 (2011).
F. Jensen, Introduction to Computational Chemistry (Wiley, New York, 1999).
R.S. Mulliken, J. Chem. Phys. 23, 1833 (1955).
A.E. Reed, R.B. Weinstock, and F. Weinhold, J. Chem. Phys. 83, 735 (1985).
D.E. Williams, Rev. Comput. Chem. 2, 219 (1991).
U.C. Singh and P.A. Kollman, J. Comp. Chem. 5, 129 (1984).
J. Cioslowski, J. Am. Chem. Soc. 111, 8333 (1989).
R.F.W. Bader, P.M. Beddall, and P.E. Cade, J. Am. Chem. Soc. 93, 3095 (1971).
T.Yu. Nikolaienko, L.A. Bulavin, and D.M. Hovorun, Ukr. Bioorg. Acta 9, 3 (2011).
P.J. Stephens, F.J. Devlin, C.F. Chabalowski, and M.J. Frisch, J. Phys. Chem. 98, 11623 (1994).
R.H. Hertwig and W. Koch, Chem. Phys. Lett. 268, 345 (1997).
G. Bakalarski, P. Grochowski, J. S. Kwiatkowski et al., Chem. Phys. 204, 301 (1996).
How to Cite
License to Publish the Paper
The corresponding author and the co-authors (hereon referred to as the Author(s)) of the paper being submitted to the Ukrainian Journal of Physics (hereon referred to as the Paper) from one side and the Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, represented by its Director (hereon referred to as the Publisher) from the other side have come to the following Agreement:
1. Subject of the Agreement.
The Author(s) grant(s) the Publisher the free non-exclusive right to use the Paper (of scientific, technical, or any other content) according to the terms and conditions defined by this Agreement.
2. The ways of using the Paper.
2.1. The Author(s) grant(s) the Publisher the right to use the Paper as follows.
2.1.1. To publish the Paper in the Ukrainian Journal of Physics (hereon referred to as the Journal) in original language and translated into English (the copy of the Paper approved by the Author(s) and the Publisher and accepted for publication is a constitutive part of this License Agreement).
2.1.2. To edit, adapt, and correct the Paper by approval of the Author(s).
2.1.3. To translate the Paper in the case when the Paper is written in a language different from that adopted in the Journal.
2.2. If the Author(s) has(ve) an intent to use the Paper in any other way, e.g., to publish the translated version of the Paper (except for the case defined by Section 2.1.3 of this Agreement), to post the full Paper or any its part on the web, to publish the Paper in any other editions, to include the Paper or any its part in other collections, anthologies, encyclopaedias, etc., the Author(s) should get a written permission from the Publisher.
3. License territory.
The Author(s) grant(s) the Publisher the right to use the Paper as regulated by sections 2.1.1–2.1.3 of this Agreement on the territory of Ukraine and to distribute the Paper as indispensable part of the Journal on the territory of Ukraine and other countries by means of subscription, sales, and free transfer to a third party.
4.1. This Agreement is valid starting from the date of signature and acts for the entire period of the existence of the Journal.
5.1. The Author(s) warrant(s) the Publisher that:
– he/she is the true author (co-author) of the Paper;
– copyright on the Paper was not transferred to any other party;
– the Paper has never been published before and will not be published in any other media before it is published by the Publisher (see also section 2.2);
– the Author(s) do(es) not violate any intellectual property right of other parties. If the Paper includes some materials of other parties, except for citations whose length is regulated by the scientific, informational, or critical character of the Paper, the use of such materials is in compliance with the regulations of the international law and the law of Ukraine.
6. Requisites and signatures of the Parties.
Publisher: Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine.
Address: Ukraine, Kyiv, Metrolohichna Str. 14-b.
Author: Electronic signature on behalf and with endorsement of all co-authors.