- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
ISRN Physical Chemistry
Volume 2013 (2013), Article ID 146401, 10 pages
Structure and Stability of Chemically Modified DNA Bases: Quantum Chemical Calculations on 16 Isomers of Diphosphocytosine
1Faculty of Science, King Khalid University, Abha, Saudi Arabia
2Faculty of Science, Jazan University, Jazan, Saudi Arabia
3Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
4Department of Structural Biology and Biomolecular Chemistry, Max F Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
Received 17 December 2012; Accepted 6 January 2013
Academic Editors: E. B. Starikov and A. Tilocca
Copyright © 2013 Abdullah G. Al-Sehemi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- J. March, Advanced Organic Chemistry, Reaction, Mechanism and Structure, John Wiley & Sons, New York, NY, USA, 4th edition, 1993.
- J. Elguero, C. Marzin, A. R. Katritzky, and P. Linda, The Tautomerism of Heterocycles, Advances in heterocyclic chemistry: Supplement I, Academic Press, 1976.
- M. Dreyfus, O. Bensaude, G. Dodin, and J. E. Dubois, “Tautomerism in cytosine and 3-methylcytosine. A thermodynamic and kinetic study,” Journal of the American Chemical Society, vol. 98, no. 20, pp. 6338–6349, 1976.
- R. Stolarski, M. Remin, and D. Shugar, “Studies on prototropic tautomerism in neutral and monoanionic forms of pyrimidines by nuclear magnetic resonance spectroscopy,” Zeitschrift Für Naturforschung C, vol. 32, no. 5, pp. 894–900, 1977.
- J. Lin, C. Yu, S. Peng et al., “Ultraviolet photoelectron studies of the ground-state electronic structure and gas-phase tautomerism of hypoxanthine and guanine,” The Journal of Physical Chemistry, vol. 84, no. 9, pp. 1006–1012, 1980.
- R. S. Norton, R.P. Gregson, and R.J. J. Quinn, “13C n.m.r. spin-lattice relaxation time measurements determining the major tautomer of 1-methylisoguanosine in solution,” Journal of the Chemical Society, Chemical Communications, pp. 339–341, 1980.
- M. J. Nowak, K. Szczepaniak, A. Barski, and D. Shugar, “Spectroscopic studies on vapour phase tautomerism of natural bases found in nucleic acids,” Zeitschrift fur Naturforschung, vol. 33, no. 11-12, pp. 876–883, 1978.
- P. O. LÖwdin, “Quantum genetics and the aperiodic solid: some aspects on the biological problems of heredity, mutations, aging, and tumors in view of the quantum theory of the DNA molecule,” Advances in Quantum Chemistry, vol. 2, pp. 213–360, 1966.
- P. O. LÖwdin, Quantum Genetics and Aperiodic Solids, Preprint No 32. Quantum Theory Project for Research in Atomic, Molecular and Solid state, Chemistry and Physics, University of Florida, Gainesville, Fla, USA, 1962.
- J. Leszczynski, Ed., Computational Molecular Biology, vol. 8 of Theoretical and Computational Chemistry Book Series, Elsevier, 1999.
- S. Kwiatkowski and J. Leszczynski, “An ab Initio quantum-mechanical study of tautomerism of purine, adenine and guanine,” Journal of Molecular Structure, vol. 208, no. 1-2, pp. 35–44, 1990.
- J. Leszczynski, “The potential energy surface of guanine is not flat: an ab Initio study with large basis sets and higher order electron correlation contributions,” Journal of Physical Chemistry A, vol. 102, no. 13, pp. 2357–2362, 1998.
- E. D. Radchenko, A. M. Plohotnichenko, G. G. Sheina, Blagoi, and P. Yu, “ab Initio study of the prototropic tautomerism of cytosine and guanine and their contribution to spontaneous point mutations,” Biophysics, vol. 28, p. 559, 1983.
- Szczepaniak and K. Szczepaniak M, “Matrix isolation infrared studies of nucleic acid constituents: Part 4. Guanine and 9-methylguanine monomers and their keto-enol tautomerism,” Journal of Molecular Structure, vol. 156, no. 1-2, pp. 29–42, 1987.
- E. Nir, C. Janzen, P. Imhof, K. Kleinermanns, and M. S. de Vries, “Guanine tautomerism revealed by UV-UV and IR-UV hole burning spectroscopy,” Journal of Chemical Physics, vol. 115, no. 10, pp. 4604–4611, 2001.
- M. J. Nowak, L. Lapinski, and J. Fulara, “Matrix isolation studies of cytosine: the separation of the infrared spectra of cytosine tautomers,” Spectrochimica Acta A, vol. 45, no. 2, pp. 229–242, 1989.
- W. Saenger, Principles of Nucleic Acid Structure, Springer, New York, NY, USA, 1994.
- T. Shimanouchi, M. Tsuboi, and Y. Kyogoku, “The structure and properties of biomolecules and biological systems,” Advances in Chemical Physics, vol. 7, p. 435, 1964.
- R. C. Lord and G. J. Thomas Jr., “Raman spectral studies of nucleic acids and related molecules-I Ribonucleic acid derivatives,” Spectrochimica Acta Part A, vol. 23, no. 9, pp. 2551–2591, 1967.
- G. Lauer, W. Schäfer, and A. Schweig, “Functional subunits in the nucleic acid bases uracil and thymine,” Tetrahedron Letters, vol. 16, no. 45, pp. 3939–3942, 1975.
- D. Dougherty, K. Wittel, J. Meeks, and S. P. McGlynn, “Photoelectron spectroscopy of carbonyls. Ureas, uracils, and thymine,” Journal of the American Chemical Society, vol. 98, no. 13, pp. 3815–3820, 1976.
- A. Padva, T. G. O’Donnell, and P. R. LeBreton, “UV photoelectron studies of biological pyrimidines: the valence electronic structure of methyl substituted uracils,” Chemical Physics Letters, vol. 41, no. 2, pp. 278–282, 1976.
- M. Fujii, T. Tamura, N. Mikami, and M. Ito, “Electronic spectra of uracil in a supersonic jet,” Chemical Physics Letters, vol. 126, no. 6, pp. 583–587, 1986.
- Y. Tsuchiya, T. Tamura, M. Fujii, and M. Ito, “Keto-enol tautomer of uracil and thymine,” Journal of Physical Chemistry, vol. 92, no. 7, pp. 1760–1765, 1988.
- B. B. Brady, L. A. Peteanu, and D. H. Leavy, “The electronic spectra of the pyrimidine bases uracil and thymine in a supersonic molecular beam,” Chemical Physics Letters, vol. 147, no. 6, pp. 538–543, 1988.
- M. Kubota and T. J. Kobayashi, “Electronic structure of uracil and uridine derivatives studied by photoelectron spectroscopy,” Journal of Electron Spectroscopy and Related Phenomena, vol. 82, no. 1-2, pp. 61–70, 1996.
- D. Shugar and K. Szczepaniak, “Tautomerism of pyrimidines and purines in the gas phase and in low-temperature matrices, and some biological implications,” International Journal of Quantum Chemistry, vol. 20, no. 2, pp. 573–585, 1981.
- M. Szczesniak, M. J. Nowak, H. Rostkowska, K. Szczepaniak, W. B. Person, and D. Shugar, “Matrix isolation studies of nucleic acid constituents,” Journal of the American Chemical Society, vol. 105, no. 19, pp. 5969–5976, 1983.
- S. Chin, I. Scot, K. Szczepaniak, and W. B. Person, “Matrix isolation itudies of nucleic acid constituents,” Journal of the American Chemical Society, vol. 106, pp. 3415–3422, 1984.
- Y. D. Radchenko, G. G. Scheina, N. A. Smorygo, Blagoi, and P. Yu, “Experimental and theoretical studies of molecular structure features of cytosine,” Journal of Molecular Structure, vol. 116, no. 3-4, pp. 387–396, 1984.
- R. D. Brown, P. D. Godfrey, D. McNaughton, and A. P. Pierlot, “Microwave spectrum of uracil,” Journal of the American Chemical Society, vol. 110, no. 7, pp. 2329–2330, 1988.
- I. Kulakowska, M. Geller, B. Lesyng, K. L. Wierzchowski, and K. Bolewska, “Barrier to rotation and conformation of the -NR2 group in cytosine and its derivatives. Part II. Experimental and theoretical dipole moments of methylated cytosines,” Biochimica Et Biophysica Acta, vol. 407, no. 4, pp. 420–429, 1975.
- B. B. Brady, L. A. Peteanu, and D. H. Levy, “The electronic spectra of the pyrimidine bases uracil and thymine in a supersonic molecular beam,” Chemical Physics Letters, vol. 147, no. 6, pp. 538–543, 1981.
- P. Beak and J. M. White, “Relative enthalpies of 1, 3-dimethyl-2, 4-pyrimidinedione, 2, 4-dimethoxypyrimidine, and 4-methoxy-1-methyl-1-2-pyrimidinone: estimation of the relative stabilities of two protomers of uracil,” Journal of the American Chemical Society, vol. 104, no. 25, pp. 7073–7077, 1982.
- J. S. Kwiatkowski, R. J. Bartlett, and W. B. Person, “Contributions from electron correlation to the relative stabilities of the tautomers of nucleic acid bases,” Journal of the American Chemical Society, vol. 110, no. 8, pp. 2353–2358, 1988.
- H. Basch, D. R. Garmer, P. G. Jasien, M. Krauss, and W. J. Stevens, “Electrical properties of nucleic acid bases,” Chemical Physics Letters, vol. 163, no. 6, pp. 514–522, 1989.
- A. Les, L. Adamowicz, and R. J. Bartlett, “Relative stability of cytosine tautomers with the coupled cluster method and first-order correlation orbitals,” Journal of Physical Chemistry, vol. 93, pp. 4001–4005, 1989.
- I. R. Gould and I. H. Hillier, “Accurate Calculations of the Oxo-Hydroxy Tautomers of UracilParaaaa,” Journal of the Chemical Society, Perkin Transactions 2, vol. 2, pp. 329–330, 1990.
- A. Les and L. Adamowic, “Theoretical ab Initio study of the protomeric tautomerism of 2-hydroxypyrimidine, 4-hydroxypyrimidine, and their derivatives,” Journal of Physical Chemistry, vol. 94, no. 18, pp. 7021–7032, 1990.
- P. G. Jasien and G. Fitzgerald, “Molecular dipole moments and polarizabilities from local density functional calculations: Application to DNA base pairs,” The Journal of Chemical Physics, vol. 93, no. 4, pp. 2554–2560, 1990.
- J. Leszczynśki, “Structure and properties of uracil and its sulfur analogs: a systematic study of basis set effects in Ab Initio SCF calculations,” Physical Chemistry, vol. 40, supplement 18, pp. 9–21, 1991.
- A. R. Katritzky and M. Karelson, “Am1 calculations of reaction field effects on the tautomeric equilibria of nucleic-acid pyrimidine and purine-bases and their 1-methyl analogs,” Journal of the American Chemical Society, vol. 113, no. 5, pp. 1561–1566, 1991.
- J. Leszczynski, “Tautomerism of uracil: the final chapter? Fourth-order electron correlation contributions to the relative energies of tautomers,” Journal of Physical Chemistry, vol. 96, no. 4, pp. 1649–1653, 1992.
- D. A. Estrin, L. Paglieri, and G. Corongiu, “A density functional study of tautomerism of uracil and cytosine,” Journal of Physical Chemistry, vol. 98, no. 22, pp. 5653–5660, 1994.
- I. R. Gould, N. A. Burton, R. J. Hall, and I. H. Hillier, “Tautomerism in uracil, cytosine and guanine: a comparison of electron correlation predicted by ab Initio and density functional theory methods,” Journal of Molecular Structure, vol. 331, no. 1-2, pp. 147–154, 1995.
- L. Paglieri, G. Corongiu, and D. A. Estrin, “Solvent effects in density functional calculations of uracil and cytosine tautomerism,” International Journal of Quantum Chemistry, vol. 56, no. 5, pp. 615–625, 1995.
- M. Monshi, K. Al-Farhan, S. Al-Resayes, A. Ghaith, and A. A. Hasanein, “Excited states dipole moments and polarizabilities of uracil and cytosine 5-halo derivatives,” Spectrochimica Acta A, vol. 53, no. 14, pp. 2669–2677, 1997.
- S. X. Tian, C. F. Zhang, Z. J. Zhang, X. J. Chen, and K. Z. Xu, “How many uracil tautomers there are? Density functional studies of stability ordering of tautomers,” Chemical Physics, vol. 242, no. 2, pp. 217–225, 1999.
- S. I. Kawaharaa, T. Uchimarua, and M. Sekineb, “The hydrogen bond energy on mismatched base pair formation between uracil derivatives and guanine in the gas phase and in the aqueous phase,” Journal of Molecular Structure, vol. 530, pp. 1109–2117, 2000.
- M. K. Shukla and J. Leszczynski, “Phototautomerism in Uracil: a quantum chemical investigation,” Journal of Physical Chemistry A, vol. 106, no. 37, pp. 8642–8650, 2002.
- X. Li, L. Sanche, and M. D. Sevilla, “Dehalogenation of 5-halouracils after low energy electron attachment: A density functional theory investigation,” Journal of Physical Chemistry A, vol. 106, no. 46, pp. 11248–11253, 2002.
- M. Di Laudo, S. R. Whittleton, and S. D. Wetmore, “Effects of hydrogen bonding on the acidity of uracil,” Journal of Physical Chemistry A, vol. 107, no. 48, pp. 10406–10413, 2003.
- M. Piacenza and S. Grimme, “Systematic quantum chemical study of DNA-base tautomers,” Journal of Computational Chemistry, vol. 25, no. 1, pp. 83–98, 2004.
- Iwona Dabkowska, Janusz Rak, Maciej Gutowskia, J. Michael Nilles, S. T. Stokes, and K. H. Bowen, “Barrier-free intermolecular proton transfer induced by excess electron attachment to the complex of alanine with uracil,” Journal of Chemical Physics, vol. 120, no. 13, 2004.
- X. Hu, H. Li, W. Liang, and S. Han, “Theoretical study of the proton transfer of uracil and (water) n (n = 0–4): Water stabilization and mutagenicity for uracil,” Journal of Physical Chemistry B, vol. 108, no. 34, pp. 12999–13007, 2004.
- R. Zhang, A. Ceulemans, and Nguyen, “A theoretical study of Uracil and its tautomers in their lowest-lying triplet state,” Molecular Physics, vol. 103, no. 6-8, pp. 983–994, 2005.
- X. Hu, H. Li, W. Liang, and S. Han, “Systematic study of the tautomerism of uracil induced by proton transfer. exploration of water stabilization and mutagenicity,” Journal of Physical Chemistry B, vol. 109, no. 12, pp. 5935–5944, 2005.
- J. K. Wolken and F. Turecek, “Proton affinity of uracil: a computational study of protonation sites,” Journal of the American Society For Mass Spectrometry, vol. 11, no. 12, pp. 1065–1071, 2000.
- V. Esposito, A. Randazzo, G. Piccialli, L. Petraccone, C. Giancola, and L. Mayol, “Effects of an 8-bromodeoxyguanosine incorporation on the parallel quadruplex structure [d(TGGGT)]4,” Organic and Biomolecular Chemistry, vol. 2, no. 3, pp. 313–318, 2004.
- S. D. Wetmore, R. J. Boyd, and L. A. Eriksson, “A theoretical study of 5-halouracils: electron affinities, ionization potentials and dissociation of the related anions,” Chemical Physics Letters, vol. 343, no. 1-2, pp. 151–158, 2001.
- P. U. Civcir, “AM1 and PM3 studies of some thio analogues of pyrimidine bases in the gas and aqueous phases,” Journal of Physical Organic Chemistry, vol. 14, no. 3, pp. 171–179, 2001.
- S. Denifl, S. Matejcik, B. Gstir et al., “Electron attachment to 5-chloro uracil,” Journal of Chemical Physics, vol. 118, no. 9, pp. 4107–4114, 2003.
- W. Saenger and D. Suck, “The Relationship between hydrogen bonding and base stacking in crystalline 4-thiouridine derivatives,” European Journal of Biochemistry, vol. 32, no. 3, pp. 473–478, 1973.
- A. G. Lezius and K. H. Scheit, “Enzymatic synthesis of DNA with 4-thio-thymidine triphosphate as substitute for dTTP,” European Journal of Biochemistry, vol. 3, no. 1, pp. 85–94, 1967.
- K. H. Scheit and E. Gartner, “Über die Eigenschaften von polynucleotiden, welche uridin und 4-thiouridin enthalten,” Biochimica Et Biophysica Acta, vol. 182, no. 1, pp. 10–16, 1969.
- E. M. Gottschalk, E. Kopp, and A. G. Lezius, “A synthetic DNA with unusual base-pairing,” European Journal of Biochemistry, vol. 24, no. 1, pp. 168–182, 1971.
- T. M. El-Gogary and A. M. El-Nahas, “Origin of reverse stability of diphosphouracil tautomers compared to their analogue uracil: DFT and ab Initio study,” Journal of Molecular Structure, vol. 851, no. 1-3, pp. 54–62, 2008.
- A. F. Jalbout, B. Trzaskowski, Y. Xia et al., “Structures, stabilities and tautomerizations of uracil and diphosphouracil tautomers,” Chemical Physics, vol. 332, no. 2-3, pp. 152–161, 2007.
- M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., Gaussian 09, Revision A. 1, Gaussian Inc., Wallingford, Conn, USA, 2009.
- A. D. J. Becke, “Density-functional thermochemistry. III. The role of exact exchange,” Chemical Physics, vol. 98, no. 7, pp. 5648–5652, 1993.
- C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Physical Review B 37, pp. 785–789, 1988.
- P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, “ab Initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields,” Journal of Physical Chemistry, vol. 98, no. 45, pp. 11623–11627, 1994.
- G. A. Zhurko and D. A. Zhurko, ChemCraft version 1. 5, 2005.
- A. E. Reed, R. B. Weinstock, and F. Weinhold, “Natural population analysis,” The Journal of Chemical Physics, vol. 83, no. 2, pp. 735–746, 1985.
- S. Miertus, E. Scrocco, and J. Tomasi, “Electrostatic interaction of a solute with a continuum. A direct utilizaion of ab Initio molecular potentials for the prevision of solvent effects,” Journal of Chemical Physics, vol. 55, no. 1, pp. 117–129, 1981.
- J. Tomasi and M. Persico, “Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent,” Chemical Reviews, vol. 94, no. 7, pp. 2027–2094, 1994.
- R. Cammi and J. Tomasi, “Remarks on the use of the apparent surface charges/ASC methods in solvation problems: iterative versus matrix-inversion procedures and the renormalization of the apparent charges,” Journal of Computational Chemistry, vol. 16, pp. 1449–1458, 1995.
- M. Cossi, V. Barone, R. Cammi, and J. Tomasi, “ab Initio study of solvated molecules: A new implementation of the polarizable continuum model,” Chemical Physics Letters, vol. 255, no. 4–6, pp. 327–335, 1996.
- J. Sponer and P. Hobza, “Nonplanar Geometries of DNA Bases. ab Initio Second-Order Moeller-Plesset Study,” Journal of Physical Chemistry, vol. 98, no. 12, pp. 3161–3164, 1994.
- E. L. Stewart, C. K. Foley, N. L. Allinger, and J. P. Bowen, “ab Initio calculations with electronic correlation (MP2) on the nucleic acid bases and their methyl derivatives,” Journal of the American Chemical Society, vol. 116, no. 16, pp. 7282–7286, 1994.
- V. B. Delchev and M. V. Nenkova, “Theoretical Modeling of the Ground State Intramolecular Proton Transfer in Cytosine: DFT Level Study,” Acta Chimica Slovenica, pp. 132–137, 2008.
- T. K. Ha, H. J. Keller, R. Gunde, and H. H. Gunthard, “Energy increment method based on quantum chemical results: a general recipe for approximative prediction of isomerization and tautomerization energies of pyrimidine and purine Nucleic acid bases and related compounds,” Journal of Physical Chemistry A, vol. 103, no. 33, pp. 6612–6623, 1999.