Differentiation of adenine non-planarity in valence molecular orbitals

Molecular Simulation

Volumn 32, Issue 8, 2006, Pages 667-673

  Downton, M T ^a,b   Wang, F ^a  

^a SWINBURNE UNIVERSITY OF TECHNOLOGY   (Australia)

^b SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Adenine non planarity; Dual space analysis; Theoretical orbital momentum profiles; Valence molecular orbitals

Indexed keywords

AROMATIC COMPOUNDS; CRYSTAL SYMMETRY; FORMABILITY; NITROGEN COMPOUNDS;

ADENINE NON-PLANARITY; DUAL SPACE ANALYSIS; THEORETICAL ORBITAL MOMENTUM PROFILES; VALENCE MOLECULAR ORBITALS;

MOLECULAR DYNAMICS;

EID: 33748862241     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020600860911     Document Type: Article

References (33)

1. The National Academies Press. Board On Chemical Sciences and Technology, National Research Council, Beyond the Molecular Frontier: Challenges For Chemistry and Chemical Engineering, The National Academies Press, Washington, DC (2003).
2. J. Sponer, P. Hobza. Molecular interactions of nucleic acid bases. A review of quantum-chemical studies. Collect. Czech. Chem. Commun., 68, 2231 (2003).
3. J. Leszczynski. Are the amino-groups in the nucleic-acid bases coplanar with the molecular rings? Ab initio HF/6-310* and MP2/6-31G* studies. Int. J. Quant. Chem., Suppl., 19, 43 (1992).
4. J. Sponer, P. Hobza. Nonplanar geometries of DNA bases - ab initio 2nd-order Moller-Plesset study. J. Phys. Chem., 98, 3161 (1994).
5. O.V. Shishkin, L. Gorb, P. Hobza, J. Leszczynski. Structural nonrigidity of nucleic acid bases. Post-Hartree-Fock ab initio study. Int. J. Quant. Chem., 80, 1116 (2000).
6. P. Hobza, J. Sponer. Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chem. Rev., 99, 3247 (1999).
7. F. Dong, R.E. Miller. Vibrational transition moment angles in isolated biomolecules: A structural tool. Science, 298, 1227 (2002).
8. J. Leszcynski. Electron correlation effects in the ah initio study on tautomerism of guanine. Chem. Phys. Lett., 174, 347 (1990).
9. N.V. Riggs. An ab initio study of the stationary structures of the major gas-phase tautomer of adenine. Chem. Phys. Lett., 177, 447 (1991).
10. N. Kurita, V.I. Danilov, V.M. Anisimov. The structure of Watson-Crick DNA base pairs obtained by MP2 optimization. Chem. Phys. Lett., 404, 164 (2005).
11. M.J. Nowak, L. Lapinski, J. Fulara, A. Les, L. Adamowicz. Matrixisolation IR spectroscopy of tautomeric systems and its theoretical interpretation - 2-hydroxypyridin/2(1H)-pyridinone. J. Phys. Chem., 96, 1562 (1992).
12. O. Bludsky, J. Sponer, J. Leszczynski, V. Spirko, P. Hobza. Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are nonplanar: Results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion motion. J. Chem. Phys., 105, 11042 (1996).
13. J. Sponer, J. Florian, P. Hobza, J. Leszczynski. Nonplanar DNA base pairs. J. Biomol. Struct. Dyn., 13, 827 (1996).
14. F. Wang. Assessment of quantum mechanical models based on resolved orbital momentum distributions of n-butane in the outer valence shell. J. Phys. Chem. A, 107, 10199 (2003).
15. F. Wang, M. Downton. Inner valence shell bonding mechanism of n-butane studied using orbital momentum distributions of its conformational isomers. J. Phys. B: At. Mol. Opt. Phys., 37, 557 (2004).
16. M. Downton, F. Wang. Chemical bonding mechanisms of n-butane probed by the core orbitals of conformational isomers in r-space and k-space. Chem. Phys. Lett., 384, 144 (2004).
17. F. Wang, M.T. Downton, N. Kidwani. Adenine tautomer electronic structural signatures studied using dual space analysis. J. Theo. Comp. Chem., 4, 247 (2005).
18. S. Saha, F. Wang, C.T. Falzon, M.J. Brunger. Coexistence of 1,3-butadiene conformers in ionization energies and Dyson orbitals. J. Chem. Phys., 123, 124315 (2005).
19. C.T. Falzon, F. Wang. Understanding glycine conformation through molecular orbitals. J. Chem. Phys., 123, 214307 (2005).
20. S. Knippenberg, K.L. Nixon, H. Mackenzie-Ross, M.J. Brunger, F. Wang, M.S. Deleuze, J.P. Francois, D. A. Winkler. Investigation into the valence electronic structure of norbornene using electron momentum spectroscopy, Green's function, and density functional theories. J. Phys. Chem. A, 109, 9324 (2005).
21. F. Wang. The electronic structural information from core orbitals of norbornadiene, norbonene and norbornane. J. Mol. Struct. THEOCHEM., 728, 31 (2005).
22. N. Godbout, D.R. Salahub, J. Andzelm, E. Wimmer. Optimization of Gaussian-type basis-sets for local spin-density functional calculations.1. Boron through neon, optimization technique and validation. Can. J. Chem., 70, 560 (1992).
23. M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.H. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S.J. Su, T.L. Windus, M. Dupuis, J.A. Montgomery. General atomic and molecular electronic-structure system. J. Camp. Chem., 14, 1347 (1993).
24. E. Weigold, I. McCarthy. Electron Momentum Spectroscopy, Kluwer Academic/Plenum Publishers, New York (1999).
25. P. Duffy, D.P. Chong, M.E. Casida, D.R. Salahum. Assessment of KS density-functional orbitals as approximate Dyson orbitals for the calculation of electron-momentum-spectroscopy scattering cross-sections. Phys. Rev. A, 50, 4707 (1994).
26. S. Knippenberg, K.L. Nixon, M.J. Brunger, T. Maddern, L. Campbell, N. Trout, F. Wang, W.R. Newell, M.S. Deleuze, J.P. Francois, D.A. Winkler. Norbornane: An investigation into its valence electronic structure using electron momentum spectroscopy, and density functional and Green's function theories. J. Chem. Phys., 121, 10525 (2004).
27. K.L. Nixon, F. Wang, L. Campbell, T. Maddern, D. Winkler, R. Gleiter, P. Loeb, E. Weigold, M.J. Brunger. An electron momentum spectroscopy and density functional theory study of the outer valence electronic structure of stella-2,6-dione. J. Phys. B.: At. Mol. Opt. Phys., 36, 3155 (2003).
28. S.A.C. Clark, T.J. Reddish, C.E. Brion, E.R. Davidson, R.F. Frey. The valence orbital momentum distributions and binding energy spectra of methane by electron momentum spectroscopy-quantitative comparisons using near Hartree-Fock limit and correlated wave-functions. Chem. Phys., 143, 1 (1990).
29. F. Wang, H. Mackenzie-Ross, D.A. Winkler, I.E. McCarthy, L. Campbell, M.J. Brunger. A high-resolution electron momentum spectroscopy and density functional theory study into the complete valence electronic structure of allene. J. Camp. Chem., 22, 1321 (2001).
30. Y. Zheng, J.J. Neville, C.E. Brion. Imaging the electron-density in the highest occupied molecular-orbital of glycine. Science, 270, 786 (1995).
31. J.J. Neville, Y. Zheng, C.E. Brion. Glycine valence orbital electron densities: Comparison of electron momentum spectroscopy experiments with Hartree-Fock and density functional theories. J. Am. Chem. Soc., 118, 10533 (1996).
32. W. Saenger. Principles of Nucleic Acid Structure, Springer, New York (1988).
33. G. Schaftenaar, J.H. Noordik. Molden: a pre- and post-processing program for molecular and electronic structures. J. Comput. Aided Mol. Des., 14, 123 (2000).