151
Views
6
CrossRef citations to date
0
Altmetric
Articles

Protonation and deprotonation enthalpies of alloxan and implications for the structure and energy of its complexes with water: a computational study

, , &
Pages 897-910 | Received 08 Feb 2014, Accepted 25 Apr 2014, Published online: 22 May 2014

References

  • Abdel-Rahman, M. S., Elrakhawy, F. I., & Iskander, F. A. (1992). Protection of B cells against the effect of alloxan. Toxicology Letters, 63, 155–164.10.1016/0378-4274(92)90007-7
  • Ahmed, I. T., Soliman, E. S., & Boraei, A. A. (2004). The acidity constants of some pyrimidine bases in various water organic solvent media. Annali di Chimica, 94, 847–856.10.1002/(ISSN)1612-8877
  • Arabi, A. A., & Matta, C. F. (2011). Effects of external electric fields on double proton transfer kinetics in the formic acid dimer. Physical Chemistry Chemical Physics, 13, 13738–13748.10.1039/c1cp20175a
  • Bader, R. F. (1990). Atoms in molecules. Oxford: Wiley Online Library.
  • Becke, A. D. (1988). Density-functional exchange-energy approximation with correct asymptotic behavior. Physical Review A, 38, 3098–3100.10.1103/PhysRevA.38.3098
  • Becke, A. D. (1993). Density-functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98, 5648–5652.10.1063/1.464913
  • Bojarski, J. T., Mokrosz, J. L., Bartoń, H. J., & Paluchowska, M. H. (1985). Recent progress in barbituric acid chemistry. Advances in Heterocyclic Chemistry, 38, 229–297.10.1016/S0065-2725(08)60921-6
  • Bolton, W. (1964). The crystal structure of alloxan. Acta Crystallographica, 17, 147–152.10.1107/S0365110X6400041X
  • Bonaccorsi, R., Pullman, A., Scrocco, E., & Tomasi, J.. (1972). N- versus O-proton affinities of the amide group: Ab initio electrostatic molecular potentials. Chemical Physics Letters, 12, 622–624.10.1016/0009-2614(72)80023-X
  • Boys, S. F., & Bernardi, F. D. (1970). The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Molecular Physics, 19, 553–566.10.1080/00268977000101561
  • Brovarets', O. O., & Hovorun, D. M. (2014). Can tautomerization of the A.T Watson–Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis. Journal of Biomolecular Structure and Dynamics, 32, 127–154.10.1080/07391102.2012.755795
  • Brovarets’, O. O., & Hovorun, D. M. (2013a). Why the tautomerization of the G C Watson–Crick base pair via the DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis. Journal of Biomolecular Structure and Dynamics, 32, 1474–1499. doi:10.1080/07391102.2013.822829
  • Brovarets’, O. O., & Hovorun, D. M. (2013b). The physicochemical essence of the purine·pyrimidine transition mismatches with Watson–Crick geometry in DNA: A·C* versa A*·C. A QM and QTAIM atomistic understanding. Journal of Biomolecular Structure and Dynamics, 33, 28–55. doi:10.1080/07391102.2013.852133
  • Brovarets’, O. O., Yurenko, Y. P., & Hovorun, D. M. (2014). Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: A thorough quantum-chemical study. Journal of Biomolecular Structure and Dynamics, 32, 993–1022.10.1080/07391102.2013.799439
  • Car, R., & Parrinello, M. (1985). Unified approach for molecular dynamics and density-functional theory. Physical Review Letters, 55, 2471–2474.10.1103/PhysRevLett.55.2471
  • Chai, J. D., & Head-Gordon, M. (2008). Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections. Physical Chemistry Chemical Physics, 10, 6615–6620.10.1039/b810189b
  • Chandra, A. K., Nguyen, M. T., & Zeegers-Huyskens, T. (1998). Theoretical study of the interaction between thymine and water. Protonation and deprotonation enthalpies and comparison with uracil. The Journal of Physical Chemistry A, 102, 6010–6016.10.1021/jp981259v
  • Cho, S. J., Cui, C., Lee, J. Y., Park, J. K., Suh, S. B., Park, J., Kim, H., & Kim, K. S. (1997). N-protonation vs O-protonation in strained amides: Ab Initio study. The Journal of Organic Chemistry, 62, 4068–4071.10.1021/jo962063z
  • Dunitz, J. D., & Schweizer, W. B. (2007). Alloxan: Is it really a problem structure? CrystEngComm, 9, 266–269.10.1039/b700475c
  • Dunn, J. S., Sheehan, H. L., & Mcletchie, N. G. B. (1943). Necrosis of the islets of Langerhans produced experimentally. The Journal of Pathology and Bacteriology, 55, 245–257.10.1002/(ISSN)1555-2039
  • Foresman, J. B., Keith, T. A., Wiberg, K. B., Snoonian, J., & Frisch, M. J. (1996). Solvent effects. 5. Influence of cavity shape, truncation of electrostatics, and electron correlation on ab initio reaction field calculations. The Journal of Physical Chemistry, 100, 16098–16104.10.1021/jp960488j
  • Frisch, M. J. (2009). Gaussian 09 version D. Wallingford, CT: Gaussian Inc.
  • Frisch, A. E., Dennington, R. D., II, et al. (2009). GaussView. Wallingford, CT: Gaussian Inc.
  • Iyengar, S. S., Schlegel, H. B., & Voth, G. A. (2003). Atom-centered density matrix propagation (ADMP): Generalizations using bohmian mechanics. The Journal of Physical Chemistry A, 107, 7269–7277.10.1021/jp034633m
  • Jardetzky, O. (1963). Proton magnetic resonance studies of purine and pyrimidine derivatives. IX. The protonation of pyrimidines in acid solution. Journal of the American Chemical Society, 85, 1657–1658.10.1021/ja00894a027
  • Kakkar, R., Bhandari, M., & Gaba, R. (2012). Tautomeric transformations and reactivity of alloxan. Computational and Theoretical Chemistry, 986, 14–24.10.1016/j.comptc.2012.01.038
  • Kasende, O., & Zeegers-Huyskens, T. (1984). Infrared spectra of protonated pyrimidine derivatives in the solid state. Spectroscopy Letters, 17, 783–801.10.1080/00387018408075706
  • Keith, T. A. (2012). AIMAll. Overland Park, KS: TK Gristmill software.
  • Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785–789.10.1103/PhysRevB.37.785
  • Lenzen, S. (2008). The mechanisms of alloxan- and streptozotocin-induced diabetes. Diabetologia, 51, 216–226.10.1007/s00125-007-0886-7
  • Lenzen, S., & Munday, R. (1991). Thiol-group reactivity, hydrophilicity and stability of alloxan, its reduction products and its N-methyl derivatives and a comparison with ninhydrin. Biochemical Pharmacology, 42, 1385–1391.10.1016/0006-2952(91)90449-F
  • Lenzen, S., & Panten, U. (1988). Alloxan: History and mechanism of action. Diabetologia, 31, 337–342.10.1007/BF02341500
  • Lewis, T. C., & Tocher, D. A. (2004). Redetermination of 5,5-dihydroxybarbituric acid trihydrate (alloxan tetrahydrate). Acta Crystallographica Section E Structure Reports Online, 60, o1748–o1750.10.1107/S1600536804022019
  • Lozynski, M., Rusinska-Roszak, D., & Mack, H.-G. (1998). Hydrogen bonding and density functional calculations: The B3LYP approach as the shortest way to MP2 results. The Journal of Physical Chemistry A, 102, 2899–2903.10.1021/jp973142x
  • Matta, C. F. (2010). How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree-Fock, DFT, and MP2 on a biologically relevant set of molecules. Journal of Computational Chemistry, 31, 1297–1311.
  • Mizushima, S. I., Simanouti, T., Nagakura, S., Kenji, K., Masamichi, T., Baba, H., & Fujioka, O. (1950). The molecular structure of n-methylacetamide. Journal of the American Chemical Society, 72, 3490–3494.10.1021/ja01164a048
  • Naik, T., & Chikhalia, K. (2007). Studies on synthesis of pyrimidine derivatives and their pharmacological evaluation. Journal of Chemistry, 4, 60–66.
  • Patterson, J. W., Lazarow, A., & Levey, S. (1949). Alloxan and dialuric acid: Their stabilities and ultraviolet absorption spectra. Journal of Biological Chemistry, 177, 187–196.
  • Reed, A. E., Curtiss, L. A., & Weinhold, F. (1988). Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chemical Reviews, 88, 899–926.10.1021/cr00088a005
  • Refat, M. S., EL-Korashy, S. A., Kumar, D. N., & Ahmed, A. S., (2008). Spectral and thermal studies of alloxan complexes. Journal of Coordination Chemistry, 61, 1935–1950.10.1080/00958970701793636
  • Rohwedder, T., & Schneider, R. (2011). An analysis for the DIIS acceleration method used in quantum chemistry calculations. Journal of Mathematical Chemistry, 49, 1889–1914.10.1007/s10910-011-9863-y
  • Russo, N. (1998). Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory. Journal of Computational Chemistry, 19, 989–1000.10.1002/(ISSN)1096-987X
  • Schlegel, H. B., Li, X., Millam, J. M., Gregory, A. V., Scuseria, G. E., & Frisch, M. J. (2002). Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals. III. Comparison with Born–Oppenheimer dynamics. The Journal of Chemical Physics, 117, 8694–8704.10.1063/1.1514582
  • Singh, C. (1965). The structure of the pyrimidines and purines. VIII. The crystal structure of alloxan C4H4N2O5. Acta Crystallographica, 19, 759–767.10.1107/S0365110X65004334
  • Steneteg, P., Abrikosov, I. A., Weber, V., & Niklasson, A. M. N. (2010). Wave function extended Lagrangian Born-Oppenheimer molecular dynamics. Physical Review B, 82, 075110.10.1103/PhysRevB.82.075110
  • Stewart, R., & Harris, M. G. (1977). Amino group acidity in nucleotide bases. Canadian Journal of Chemistry, 55, 3807–3814.10.1139/v77-537
  • Sun, L., & Hase, W. L. (2003). Born-Oppenheimer direct dynamics classical trajectory simulations. Reviews in Computational Chemistry, 19, 79–128.
  • Tapia, O., & Goscinski, O. (1975). Self-consistent reaction field theory of solvent effects. Molecular Physics, 29, 1653–1661.10.1080/00268977500101461
  • Nguyen, M. T., & Chandra, A. K. (1998). Protonation and deprotonation energies of uracil Implications for the uracil–water complex. Journal of the Chemical Society, Faraday Transactions, 94, 1277–1280.10.1039/a708804c
  • Ventura, O. N., Rama, J. B., Turi, L., & Dannenberg, J. J. (1995). Gas-phase structure and acidity of formohydroxamic acid and formamide: A comparative Ab Initio study. The Journal of Physical Chemistry, 99, 131–136.10.1021/j100001a023

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.