On heteroaromaticity of nucleobases. Bond lengths as multidimensional phenomena

Journal of Chemical Information and Computer Sciences

Volumn 43, Issue 3, 2003, Pages 787-809

  Kiralj, R ^a   Ferreira, M M C ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL PACKINGS; HETEROAROMATICITY;

AROMATIC COMPOUNDS; CHEMICAL BONDS; CRYSTAL ATOMIC STRUCTURE; LEAST SQUARES APPROXIMATIONS; MATHEMATICAL MODELS; NUCLEIC ACIDS; PRINCIPAL COMPONENT ANALYSIS; QUANTUM THEORY; REGRESSION ANALYSIS;

BIOCHEMICAL ENGINEERING;

PURINE NUCLEOSIDE; PYRIMIDINE NUCLEOSIDE;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; FACTUAL DATABASE;

DATABASES, FACTUAL; MODELS, CHEMICAL; MODELS, MOLECULAR; PURINE NUCLEOSIDES; PYRIMIDINE NUCLEOSIDES;

EID: 0037708619     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci0200523     Document Type: Article

References (82)

1. Hurst, D. T. An Introduction to the Chemistry and Biochemistry of Pyrimidines, Purines and Pteridines; Wiley: Chichester. UK, 1980; p 104.
2. Chaudhuri, N. C.; Ren, R. X.-F.; Kool, E. T. C-Nucleosides Derived from Simple Aromatic Hydrocarbons. Synlett 1997, 341-347.
3. Saenger, W. Principles of Nucleic Acid Structure; Springer: New York, 1984.
4. Barciszewski, J.; Barciszewska, M. Z.; Siboska, G.; Rattan, S. I, S.; Clark, B. F. C. Some unusual nucleic acid bases are products of hydroxyl radical oxidation of DNA and RNA. Mol. Biol. Rep. 1999, 26, 231-238.
5. Ray, A.; Norden, B. Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future. Faseb J. 2000, 14, 1041-1060.
6. Barnes, T. W., III.; Turner, D. H. Long-Range Cooperativity in Molecular Recognition of RNA by Oligodeoxynucleotides with Multiple C5(1-Propynyl) Pyrimidines. J. Am. Chem. Soc. 2001, 123, 4107-4118.
7. Matulic-Adamic, J.; Beigelman, L.; Portmann, S.; Egli, M.; Usman, N. Synthesis and Structure of l-Deoxy-l-phenyl-β-D-ribofuranose and Its Incorporation into Oligonucleotides. J. Org. Chem. 1996, 61, 3909-3911.
8. Ren, R. X.-F.; Chaudhuri, N. C.; Paris, P. L.; Rumney, S., IV.; Kool, E. T. Naphthalene, Phenanthrene, and Pyrene as DNA Base Analogues: Synthesis, Structure, and Fluorescence in DNA. J. Am. Chem. Soc. 1996, 118, 7671-7678.
9. Guckian, K. M.; Krugh, T. R.; Kool, E. T. Solution Structure of a Nonpolar, Non-Hydrogen-Bonded Base Pair Surrogate in DNA. J. Am. Chem. Soc. 2000, 722, 6841-6847.
10. Schwogler, A.; Carell, T. Toward catalytically active oligonucleotides: Synthesis of a flavin nucleotide and its incorporation into DNA. Org. Lett. 2000, 2, 1415-1418.
11. Clowney, L.; Jain, S. C.; Srinivasan, A. R.; Westbrook, J.; Olson, W. K.; Berman, H. M. Geometric Parameters in Nucleic Acids: Nitrogenous Bases. J. Am. Chem. Soc. 1996, 118, 509-518.
12. Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S. H.; Srinivasan, A. R.; Schneider, B. The Nucleic-Acid Database: A Comprehensive Relational Database of 3-Dimensional Structures of Nucleic-Acids. Biophys. J. 2000, 63, 751759. Website: The Nucleic Acid Database. The Nucleic Acid Database Project. Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 1995-2001. [http://ndbserver.rutgers.edu/structure-finder/ndb/].
13. The NMR-Nucleic Acid Database. The Nucleic Acid Database Project. Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 1995-2001. [http://ndbserver.rutgers.edu/structure-finder/nmr/].
14. The DNA-Binding Protein Database. The Nucleic Acid Database Project. Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 1995-2001. [http://ndbserver.rutgers.edu/structure-finder/dnabind/].
15. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242. Website: PDB - Protein Data Bank. The Research Collaboratory for Structural Bioinformatics (RCSB): Rutgers, the State University of New Jersey; the San Diego Supercomputer Center at the University of California, San Diego; the National Institute of Standards and Technology; and the University of Wisconsin-Madison, [http://www.rcsb.org/pdb/].
16. Alen, F. H.; Kennard, O. 3D Search and Research Using the Cambridge Structural Database. Chem. Design Autom. News 1993, 8, 31-37. Website: The Cambridge Structural Database. Cambridge Crystallographic Data Centre, University of Cambridge, Cambridge, UK. [http://www.ccdc.cam.ac.uk/prods/csd/osd.html].
17. Guckian, K. M.; Schweitzer, B. A.; Ren, R. X.-F.; Sheils, C. J.; Paris, P. L.; Tahmassebi, D. C.; Kook, E. T. Experimental Measurement of Aromatic Stacking Affinities in the Context of Duplex DNA. J. Am. Chem. Soc. 1996, 118, 8182-8183.
18. Guckian, K. M.; Schweitzer, B. A.; Ren, R. X.-F.; Sheils, C. J.; Paris, P. L.; Tahmassebi, D. C.; Kook, E. T. Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA. J. Am. Chem. Soc. 2000, 118, 2213-2222.
19. Voet, D.; Voet, J. O. Biochemistry, 2nd ed.; J. Wiley: New York, 1995; p 868.
20. Lemieux, S.; Oldziej, S.; Major, F. Nucleic Acids: Qualitative Modeling. In Encyclopedia of Computational Chemistry; von Ragué Schleyer, P., Ed.; Wiley: Chichester, UK, 1998; Vol. 3, pp 1930-1941.
21. Bondi, A. van der Waals Volumes and Radii. J. Phys. Chem. 1964, 65, 441-451.
22. Burgi, H. B. Structure correlation and chemistry. Acta Crystallogr. 1998, A54, 873-885.
23. von Ragué Schleyer, P.; Jiao, H. What is aromaticity? Pure Appl. Chem. 1996, 68, 209-218.
24. Lewis, D.; Peters, D. Facts and Theories of Aromaticity, 1st ed.; MacMillan Press: London, 1975; pp 10-14.
25. Bird, C. W. Heteroaromaticity. 13. Bond Alternation and Its Consequences for Conjugation Energies and Other Criteria of Aromaticity. Tetrahedron 1998, 54, 4641-4646.
26. Cramer, C. J. Hyperconjugation. In Encyclopedia of Computational Chemistry; von Ragué Schleyer, P., Ed.; Wiley: Chichester, UK, 1998; Vol. 2, pp 1294-1298.
27. Pauling, L. The Nature of the Chemical Bond, 3rd ed.; Cornell University Press: Ithaca, NY, 1972.
28. Whealand, G. W. The Theory of Resonance; Wiley: New York, 1953.
29. 1]heptacene and Other Condensed Aromatic Hydrocarbons: A Valence-Bond Treatment. Acta Crystallogr. 1980, B36, 1898-1901.
30. Herndon, W. C.; Párkányi, C. π Bond Orders and Bond Lengths. J. Chem. Educ. 1976, 53, 689-691.
31. 4O,O′,O″,O‴] sodium Iodide Dichloromethane Solvate. Acta Crystallogr. 1996, B52, 823-837.
32. Kiralj, R.; Kojić-Prodić, B.; Nikolić, S.; Trinajstić, N. Bond lengths and bond orders in benzenoid hydrocarbons and related systems: a comparison of valence bond and molecular orbital treatments. J. Mol. Struct. (THEOCHEM) 1998, 427, 25-37, and the references therein.
33. Kiralj, R.; Kojić-Prodić, B.; Piantanida, I.; Žinić, M. Crystal and molecular structures of diazapyrenes and a study of π...π interactions. Acta Crystallogr. 1999, B55, 55-69.
34. Stoicheff, B. P. Variation of Carbon-Carbon Bond Lengths With Environment as Determined by Spectroscopic Studies of Simple Polyatomic Molecules. Tetrahedron 1962, 17, 135-145.
35. Kiralj, R. Structural Investigations of Macrocyclic Receptors with Phenanthridine Subunits. Master Thesis, University of Zagreb, Zagreb, Croatia, 1994.
36. Krygowski, T. M.; Anulewicz, R.; Kruszewski, J. Crystallographic Studies and Physicochemical Properties of π-Electron Compounds. III. Stabilization Energy and the Kekulé Structure Contributions Derived from Experimental Bond Lengths. Acta Crystallogr. 1983, B39, 732-739.
37. Kiralj, R. Structural Studies of 4,9-Diazapyrene Derivatives. Doctoral Thesis, University of Zagreb, Zagreb, Croatia, 1999.
38. Kiralj, R.; Ferreira, M. M. C. Predicting Bond Lengths in Planar Benzenoid Polycyclic Aromatic Hydrocarbons: A Chemometric Approach. J. Chem. Inf. Comput. Sci. 2002, 42, 508-523.
39. Beebe, K. R.; Pell, R. J.; Seasholtz, M. B. Chemometrics: A Practical Guide; Wiley: New York, 1998.
40. Beebe, K. R.; Kowalski, B. P. An Introduction to Multivariate Calibration and Analysis. Anal. Chem. 1987, 59, 1007A-1017A.
41. 4X Ring Systems: "Classical" and "Magnetic" Concepts May Not Be "Orthogonal". Angew. Chem., Int. Ed. Engl. 1995, 34, 337-340.
42. Lewis, D.; Peters, D. Facts and Theories of Aromaticity, 1st ed.; The MacMillan Press Ltd.: London, 1975; pp 10-14.
43. Clowney, L.; Westbrook, J. D.; Berman, H. M. CIF applications. XI. A La Mode: a ligand and monomer object data environment. I. Automated construction of mmCIF monomer and ligand models. J. Appl. Crystallogr. 1999, 32, 125-133. See the Internet update of the nucleic acid standards at the following: A la mode: A Ligand And Monomer Object Data Environment. The Nucleic Acid Database. The Nucleic Acid Database Project. Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 1995-2001. http://ndbserver.rutgers.edu/alamode/index.html [last accessed on 30 June 2001].
44. Cambridge Structural Database, October Release 2001. The Chemistry Visualization Program (NCSA Chem Viz) at the National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign. http://chemviz.ncsa.uiuc.edu.
45. Spek, A. L. PLATON, A Multipurpose Crystallographic Tool, v. 31000, Utrecht University: Utrecht, The Netherlands, 2000. http://www.cryst.chem.uu.nl/platon/.
46. CRC Handbook of Chemistry and Physics, 74th ed.; Lide, D. R., Ed.; CRC Press: Boca Raton, FL, 1993; Section 9.
47. Titan, v. 1, Wavefunction, Inc.: Irvine, CA, 2000.
48. Kiralj, R.; Ferreira, M. M. C. A priori molecular descriptors in QSAR: A case of HIV-1 protease inhibitors. II. Molecular graphics and modeling. J. Mol. Graph. Mod., in press.
49. Allen, F. H.; Kennard, O.; Watson, D. G.; Brammer, L.; Orpen, A. G.; Taylor, R. Tables of Bond Lengths determined by X-ray and Neutron Diffraction. Part 1. Bond Lengths in Organic Compounds. J. Chem. Soc., Perkin Trans. 2 1987, S1-S19.
50. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Fields for the Simulation of Protein, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
51. Dewar, M. J. S.; Gleicher, G. J. Ground States of Conjugated Molecules. VII. Compounds Containing Nitrogen and Oxygen. J. Chem. Phys. 1966, 44, 759-773.
52. Cieplak, P. Nucleic Acid Force Fields. In Encyclopedia of Computational Chemistry; von Ragué Schleyer, P., Ed.; Wiley: Chichester. UK, 1998; Vol. 3, pp 1922-1930.
53. Hobza, P.; Kabelac, M.; Sponer, J.; Mejzlik, P.; Vondrasek, J. Performance of Empirical Potentials (AMBER, CFF95, CBF, CHARMM, OPLS, POLTEV), Semiempirical Quantum Chemical Methods (AMI, MNDO/M, PM3), and Ab Initio Hartree-Fock Method for Interaction of DNA Bases: Comparison with Nonempirical Beyond Hartree-Fock Results. J. Comput. Chem. 1997, 18, 1136-1150.
54. Bludsky, O.; Sponer, J.; Leszczynski, J.; Spirko, V.; Hobza, P. Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazines are nonplanar: Results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion calculation. J. Chem. Phys. 1996, 105, 11042-11050.
55. Kiralj, R. RESON. A program for determination of weights of Kekulé structures by the method of Krygowski. Rudjer Boskovic Institute: Zagreb, Croatia, 1998.
56. Halgren, T. A. Merck molecular force field. 1. Basis, form, scope, parametrization, and performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.
57. Dewar, M. J. S.; Thiel, W. Ground-States of Molecules. 38. MNDO Method: Approximations and Parameters. J. Am. Chem. Soc. 1977, 99, 4899-4907.
58. Dewar, M. J. S.; Zoebisch, E. G.; Healy, G. F.; Stewart, J. J. P. The Development and Use of Quantum-Mechanical Molecular Models. 76. AMI: A New General-Purpose Quantum-Mechanical Molecular Model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
59. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods. 1. Methods. J. Comput. Chem. 1989, 10, 209-220.
60. Allen, F. H.; Motherwell, W. D. S. Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry. Acta Crystallogr. 2002, B58, 407-422.
61. Bobadova-Parvanova, P.; Galabov, B. Ab Initio Molecular-Orbital Study on Hydrogen-Bonded Complexes of Carbonyl Aliphatic Compounds and Hydrogen Fluoride. J. Phys. Chem. 1998, A102, 1815-1819.
62. Kiralj, R.; Ferreira, M. M. C. A Combined Computational and Chemometric Study of Indole-3-Acetic Acid. Int. J. Quantum Chem. submitted for publication.
63. Kiralj, R.; Ferreira, M. M. C. A Molecular and Quantum Mechanical Study of Indole-3-Acetic Acid. XI Simpósio Brasileiro de Química Teórica; Caxambu, MG, Brazil, 18-21 November 2001. Poster P302.
64. Bertolasi, V.; Gilli, P.; Ferreti, V.; Gilli, G. Intermolecular N-H⋯O Hydrogen Bonds Assisted by Resonance. Heteroconjugated Systems as Hydrogen-Bond-Strengthening Functional Groups. Acta Crystallogr. 1995, B51, 1004-1015.
65. Taylor, R.; Kennard, O. Accuracy of Crystal Structure Error Estimates. Acta Crystallogr. 1986, B42, 112-120.
66. Allen, F. H. A Systematic Pairwise Comparison of Geometric Parameters Obtained by X-ray and Neutron Diffraction. Acta Crystallogr. 1986, B42, 515-522.
67. Pauling, L. Atomic Radii and Interatomic Distances in Metals. J. Am. Chem. Soc. 1947, 69, 542-553.
68. Gordy, W. Dependence of Bond Order and of Bond Energy Upon Bond Length. J. Chem. Phys. 1947, 75, 305-310.
69. Pirouette 3.01. Infometrix, Inc.; Seattle: WA, 2001.
70. Matlab 6.1. Math Works, Inc.; Natick, MA, 2001.
71. Ferreira, M. M. C.; Montanari, C. A.; Gaudio, A. C. Variable Selection in QSAR. Quím. Nova 2002, 25, 439-448.
72. Ferreira, M. M. C.; Antunes, A. M.; Melgo, M. S.; Volpe, P. L. O. Chemometrics I: Multivariate calibration, a tutorial. Quím. Nova 1999, 22, 724-731.
73. Kubinyi, H. Evolutionary Variable Selection in Regression and PLS Analyses. J Chemometrics 1996, 10, 119-133.
74. Cho, S. J. The QSAR Server: Partial Least Squares (PLS), Laboratory for Molecular Modeling, School of Pharmacy, University of North Carolina, Chapel Hill, NC. http://mmlinl.pha.unc.edu/̃jin/QSAR/PLS/pls.html [last accessed on 23 July 2002].
75. a Reunião Anual da Sociedade Brasileira de Química; Poços de Caldas, MG, Brazil, 20-23 May 2002. Poster QT040.
76. Krygowski, T. M. Crystallographic Studies of Inter- and Intramolecular Interactions Reflected in Aromatic Character of π-Electron Systems. J. Chem. Inf. Comput. Sci. 1993, 33, 70-78.
77. Frisch, M. J.; G. W. Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Salvador, P.; Dannenberg, J. J.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, L; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98 - Revision A.11, Gaussian, Inc., Pittsburgh, PA, 2001.
78. 2. J. Mol. Biol. 2000, 296, 787-801.
79. Glusker, J. P.; Lewis, M.; Rossi, M. Crystal Structure Analysis for Chemists and Biologists; VCH Publishers: New York, 1994; pp 429-431.
80. Trinajstic, N. Chemical Graph Theory, 2nd ed.; CRC Press: Boca Raton, FL, 1992.
81. Gavezzotti, A. Are Crystal Structures Predictable? Acc. Chem. Res. 1994, 27, 309-314.
82. Slowikowska, J. M.; Wozniak, K. Influence of hydrogen bonding on the geometry of the adenine fragment. J. Mol. Struct.-Theochem 1996, 374, 327-337.