Electronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis

References

• Bader, R. F. W. , MacDougall, P. J. , & Lau, C. D. H. (1984). Bonded and nonbonded charge concentrations and their relation to molecular geometry and reactivity. Journal of the American Chemical Society , 106 , 1594–1605.10.1021/ja00318a009
   Web of Science ®Google Scholar
• Becke, A. D. (1988). Density-functional exchange-energy approximation with correct asymptotic behavior. Physical Review A , 38 , 3098–3100.10.1103/PhysRevA.38.3098
   PubMed Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Ben Fredj, A. , Ben Lakhdar, Z. , & Ruiz-López, M. F. (2009). Six-coordination in Chlorophylls: The fundamental role of dispersion energy. Chemical Physics Letters , 472 , 243–247.10.1016/j.cplett.2009.03.025
   Web of Science ®Google Scholar
• Bolton, W. (1964). The crystal structure of alloxan. Acta Crystallographica , 17 , 147–152.10.1107/S0365110X6400041X
   Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Brovarets, O. O. , & Hovorun, D. M. (2013). Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: An exhaustive quantum-chemical analysis. Journal of Biomolecular Structure and Dynamics , 31 , 913–936.
   PubMed Web of Science ®Google Scholar
• Brovarets, O. O. , & Hovorun, D. M. (2014a). 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.
   PubMed Web of Science ®Google Scholar
• Brovarets, O. O. , & Hovorun, D. M. (2014b). 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.
   PubMed Web of Science ®Google Scholar
• Brovarets, O. O. , Zhurakivsky, R. O. , & Hovorun, D. M. (2014). Does the tautomeric status of the adenine bases change upon the dissociation of the A*·Asyn Topal–Fresco DNA mismatch? A combined QM and QTAIM atomistic insight. Physical Chemistry Chemical Physics , 16 , 3715–3725.10.1039/c3cp54708f
   PubMed Web of Science ®Google Scholar
• Bunker, D. L. (1971). Classical Trajectory Methods. Methods in Computational Physics , 10 , 287–325.
   Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Carroll, M. T. , Cheeseman, J. R. , Osman, R. , & Weinstein, H. (1989). Nucleophilic addition to activated double bonds: Predictions of reactivity from the Laplacian of the charge density. The Journal of Physical Chemistry , 93 , 5120–5123.10.1021/j100350a019
   Web of Science ®Google Scholar
• Chai, J. , & 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
   PubMed Web of Science ®Google Scholar
• Cortés Guzmán, F. , & Bader, R. F. W. (2005). Complementarity of QTAIM and MO theory in the study of bonding in donor–acceptor complexes. Coordination Chemistry Reviews , 249 , 633–662.10.1016/j.ccr.2004.08.022
   Web of Science ®Google Scholar
• Dunitz, J. D. , & Schweizer, W. B. (2007). Alloxan: Is it really a problem structure? CrystEngComm , 9 , 266–269.10.1039/b700475c
   Web of Science ®Google Scholar
• Frisch, E. , Hratchian, H. P. , Dennington II, R. D. , Keith, T. A. , Millam, J. with Nielsen, A. B. , … Hiscocks, J. (2009). GaussView (Version 5.0.8). Wallingford, CT: Gaussian, Inc., 235.
   Google Scholar
• Frisch, M. J. , Trucks, G. W. , Schlegel, H. B. , Scuseria, G. E. , Robb, M. A. , Cheeseman, J. R. , … Fox, D. J. (2009). Gaussian 09. Wallingford, CT: Gaussian.
   Google Scholar
• Griffiths, M. Z. , & Popelier, P. A. (2013). Characterization of heterocyclic rings through quantum chemical topology. Journal of Chemical Information and Modeling , 53 , 1714–1725.10.1021/ci400235u
   PubMed Web of Science ®Google Scholar
• Glasel, J. A. (1969). Proton magnetic resonance studies of tautomerism in substituted pyrimidines. Organic Magnetic Resonance , 1 , 481–489.10.1002/(ISSN)1097-458X
   Google Scholar
• Grimme, S. , Antony, J. , Ehrlich, S. , & Krieg, H. (2010). A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. The Journal of Chemical Physics , 132 , 154104. doi:10.1063/1.3382344
   PubMed Web of Science ®Google Scholar
• Hall, W. R. (1977). Biological significance of the electronic structure of alloxan and its tautomers. Journal of Medicinal Chemistry , 20 , 275–279.10.1021/jm00212a018
   PubMed Web of Science ®Google Scholar
• Iogansen, A. V. (1999). Direct proportionality of the hydrogen bonding energy and the intensification of the stretching ν(XH) vibration in infrared spectra. Spectrochimica Acta, Part A: Molecular and Biomolecular Spectroscopy , 55 , 1585–1612.10.1016/S1386-1425(98)00348-5
   Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Kakkar, R. , & Sarma, B. K. (2002). Theoretical study of the excited singlet and triplet states of alloxan. International Journal of Quantum Chemistry , 86 , 502–509.10.1002/(ISSN)1097-461X
   Web of Science ®Google Scholar
• Keith, T. A. (2011). AIMAll (Version 11.04.03). Retrieved October 3, from aim.tkgristmill.com
   Google Scholar
• Kondratyuk, I. V. , Samijlenko, S. P. , Kolomiets, I. M. , & Hovorun, D. M. (2000). Prototropic molecular–zwitterionic tautomerism of xanthine and hypoxanthine. Journal of Molecular Structure , 523 , 109–118.10.1016/S0022-2860(99)00385-3
   Web of Science ®Google Scholar
• Lee, C. , Yang, W. , & Parr, R. G. (1998). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B , 37 , 785–789.
   Web of Science ®Google Scholar
• Lenzen, S. , & Panten, U. (1988). Alloxan: History and mechanism of action. Diabetologia , 31 , 337–342.10.1007/BF02341500
   PubMed Web of Science ®Google Scholar
• Lippert, G. , Hutter, J. , & Parrinello, M. (1999). The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) , 103 , 124–140.10.1007/s002140050523
   Web of Science ®Google Scholar
• Masatomo, A. , & Kunio, N. (1982). The normal coordinate analysis of alloxan [2,4,5,6(1H,3H)-pyrimidinetetrone]. Spectrochimica Acta , 38A , 73–83.
   Google Scholar
• Matta, C. F. (Ed.). (2010). Quantum biochemistry: Electronic structure and biological activity , vols. 1 and 2. Weinheim: Wiley-VCH.
   Google Scholar
• Millefiori, S. , & Millefiori, A. (1987). Tautomerism in alloxan. Journal of Heterocyclic Chemistry , 24 , 525–527.10.1002/jhet.v24:2
   Web of Science ®Google Scholar
• Naik, T. , & Chikhalia, K. (2007). Studies on synthesis of pyrimidine derivatives and their pharmacological evaluation. Journal of Chemistry , 4 , 60–66.
   Google Scholar
• Nikolaienko, T. Y. , Bulavin, L. A. , & Hovorun, D. M. (2012). Bridging QTAIM with vibrational spectroscopy: The energy of intramolecular hydrogen bonds in DNA-related biomolecules. Physical Chemistry Chemical Physics , 14 , 7441–7447.10.1039/c2cp40176b
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Rozas, I. , Alkorta, I. , & Elguero, J. (2000). Behavior of ylides containing N, O, and C Atoms as hydrogen bond acceptors. Journal of the American Chemical Society , 122 , 11154–11161.10.1021/ja0017864
   Web of Science ®Google Scholar
• Schlegel, H. B. , Iyengar, S. S. , Li, X. , Millam, J. M. , Voth, G. A. , 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
   Web of Science ®Google Scholar
• Shi, Z. , & Boyd, R. J. (1991). The Laplacian of the charge density as a probe of reaction paths and reactivity: A comparison of SN2 reactions at carbon and silicon. The Journal of Physical Chemistry , 95 , 4698–4701.10.1021/j100165a020
   Web of Science ®Google Scholar
• Sivakova, S. , & Rowan, Stuart J. (2005). Nucleobases as supramolecular motifs. Chemical Society Reviews , 34 , 9–21.10.1039/b304608g
   PubMed Web of Science ®Google Scholar
• Thompson, D. L. (1998). Trajectory simulations of molecular collisions: Classical treatment. In P. v. R. Schleyer , N. L. Allinger , P. A. Kollman , T. Clark , H. F. Schaefer III , J. Gasteiger , P. R. Schreiner (Eds.), Encyclopedia of Computational Chemistry (vol 3., pp. 3056–3073). Chichester: Wiley.
   Google Scholar
• Zhao, Y. , & Truhlar, D. G. (2008a). The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theoretical Chemistry Accounts , 120 , 215–241.10.1007/s00214-007-0310-x
   Web of Science ®Google Scholar
• Zhao, Y. , & Truhlar, D. G. (2008b). Density functionals with broad applicability in chemistry. Accounts of Chemical Research , 41 , 157–167.10.1021/ar700111a
   PubMed Web of Science ®Google Scholar