Ground‐ and excited‐state properties of DNA base molecules from plane‐wave calculations using ultrasoft pseudopotentials

We present equilibrium geometries, vibrational modes, dipole moments, ionization energies, electron affinities, and optical absorption spectra of the DNA base molecules adenine, thymine, guanine, and cytosine calculated from first principles. The comparison of our results with experimental data and results obtained by using quantum chemistry methods show that in specific cases gradient‐corrected density‐functional theory (DFT‐GGA) calculations using ultrasoft pseudopotentials and a plane‐wave basis may be a numerically efficient and accurate alternative to methods employing localized orbitals for the expansion of the electron wave functions. © 2003 Wiley Periodicals, Inc. J Comput Chem 1: 112–122, 2004

[1]  N. Hush,et al.  Ionization potentials and donor properties of nucleic acid bases and related compounds , 1975 .

[2]  N. Rösch,et al.  Energetics of hole transfer in DNA , 2000 .

[3]  D. Turnbull,et al.  Solid State Physics : Advances in Research and Applications , 1978 .

[4]  Ignacio Tinoco,et al.  Vapor Spectra and Heats of Vaporization of Some Purine and Pyrimidine Bases1 , 1965 .

[5]  Kress,et al.  Geometrical and electronic structure of the reconstructed diamond (100) surface. , 1994, Physical review. B, Condensed matter.

[6]  Paul Doty,et al.  Absorption spectra of nucleotides, polynucleotides, and nucleic acids in the far ultraviolet , 1963 .

[7]  I. Tinoco,et al.  Correlations in the Ultraviolet Spectra of the Purine and Pyrimidine Bases1 , 1965 .

[8]  M. Schlüter,et al.  Density-Functional Theory of the Energy Gap , 1983 .

[9]  Jerzy Leszczynski,et al.  Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases , 2001, Biopolymers.

[10]  Madhulata Shukla,et al.  A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil , 1999 .

[11]  Ludwik Adamowicz,et al.  Matrix-Isolation FT-IR Studies and ab Initio Calculations of Hydrogen-Bonded Complexes of Molecules Modeling Cytosine or Isocytosine Tautomers. 5. 1-CH3-Cytosine Complexes with H2O in Ar Matrices , 1996 .

[12]  J. Šponer,et al.  Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study , 1994 .

[13]  A. R. Srinivasan,et al.  Geometric parameters in nucleic acids: Nitrogenous bases , 1996 .

[14]  R. K. Robins,et al.  Vicinal effects on the optical activity of some adenine nucleosides. , 1968, The Journal of physical chemistry.

[15]  Jeppe Olsen,et al.  Direct iterative RPA calculations. Applications to ethylene, benzene and cytosine , 1988 .

[16]  James F. Annett.  Vieweg, Braunschweig/Wiesbaden 1999 , 1999 .

[17]  F. Bechstedt,et al.  Excitation energies and radiative lifetimes of Ge1-xSix nanocrystals: alloying versus confinement effects. , 2003, Physical review letters.

[18]  Donald G. Truhlar,et al.  Accurate dipole moments from Hartree-Fock calculations by means of class IV charges , 1999 .

[19]  Scheffler,et al.  Adsorbate-substrate and adsorbate-adsorbate interactions of Na and K adlayers on Al(111). , 1992, Physical review. B, Condensed matter.

[20]  Markus P. Fülscher,et al.  A Theoretical Study of the Electronic Spectra of Adenine and Guanine , 1997 .

[21]  A. Zunger,et al.  A new method for diagonalising large matrices , 1985 .

[22]  G. Kresse,et al.  Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set , 1996 .

[23]  Ab initio study of model guanine assemblies: The role of π − π coupling and band transport , 2001, cond-mat/0110636.

[24]  A. Zunger,et al.  Self-interaction correction to density-functional approximations for many-electron systems , 1981 .

[25]  Zhongli Cai,et al.  DFT Calculations of the Electron Affinities of Nucleic Acid Bases: Dealing with Negative Electron Affinities , 2002 .

[26]  Stefan Albrecht Lucia Reining Rodolfo Del Sole Giovanni Onida.  Ab Initio Calculation of Excitonic Effects in the Optical Spectra of Semiconductors , 1998 .

[27]  Nino Russo,et al.  Theoretical determination of electron affinity and ionization potential of DNA and RNA bases , 2000 .

[28]  P. Pulay.  Convergence acceleration of iterative sequences. the case of scf iteration , 1980 .

[29]  Friedhelm Bechstedt,et al.  Optical properties of semiconductors using projector-augmented waves , 2001 .

[30]  Jerzy Leszczynski,et al.  Molecular Structure and Infrared Spectra of Adenine. Experimental Matrix Isolation and Density Functional Theory Study of Adenine 15N Isotopomers , 1996 .

[31]  C Djerassi,et al.  Magnetic circular dichroism studies. VI. Investigation of some purines, pyrimidines, and nucleosides. , 1968, Journal of the American Chemical Society.

[32]  Francesco Luigi Gervasio,et al.  Electronic structure of wet DNA. , 2002, Physical review letters.

[33]  L. Paglieri,et al.  A Density Functional Study of Tautomerism of Uracil and Cytosine , 1994 .

[34]  L. Reining,et al.  Electronic excitations: density-functional versus many-body Green's-function approaches , 2002 .

[35]  K. Kubulat,et al.  Matrix isolation infrared studies of nucleic acid constituents. 5. Experimental matrix-isolation and theoretical ab initio SCF molecular orbital studies of the infrared spectra of cytosine monomers , 1988 .

[36]  N. Rösch,et al.  Energetics of excess electron transfer in DNA , 2001 .

[37]  Francois Gygi,et al.  An ab initio study of DNA base pair hydrogen bonding: a comparison of plane-wave versus Gaussian-type function methods , 1999 .

[38]  Y. Varshavsky,et al.  Ionization potentials and electron-donor ability of nucleic acid babes and their analogues , 1976 .

[39]  G. Gallup,et al.  ELECTRON ATTACHMENT ENERGIES OF THE DNA BASES , 1998 .

[40]  Electrostatic properties of cytosine monohydrate from diffraction data. , 1990, Acta crystallographica. Section B, Structural science.

[41]  Johan Lorentzon,et al.  Theoretical Study of the Electronic Spectra of Uracil and Thymine , 1995 .

[42]  Georg Kresse,et al.  Extreme softening of Vanderbilt pseudopotentials: General rules and case studies of first-row and d-electron elements , 2000 .

[43]  L. E. Ramos,et al.  Substitutional carbon in group-III nitrides: Ab initio description of shallow and deep levels , 2002 .

[44]  C. Desfrançois,et al.  Valence and Dipole Binding of Electrons to Uracil , 1998 .

[45]  Payne,et al.  Periodic boundary conditions in ab initio calculations. , 1995, Physical review. B, Condensed matter.

[46]  E. Starikov.  Nucleic acids as objects of material science: Importance of quantum chemical and quantum mechanical studies , 2000 .

[47]  Srivastava,et al.  III-V(110) surface dynamics from an ab initio frozen-phonon approach. , 1995, Physical review. B, Condensed matter.

[48]  S. F. Boys,et al.  The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors , 1970 .

[49]  Kendall N. Houk,et al.  EFFECT OF GUANINE STACKING ON THE OXIDATION OF 8-OXOGUANINE IN B-DNA , 1998 .

[50]  Steven G. Louie,et al.  Excitonic Effects and the Optical Absorption Spectrum of Hydrogenated Si Clusters , 1998 .

[51]  M. Geller,et al.  Dipole moments of 2,4-diketopyrimidines. II. Uracil, thymine and their derivatives. , 1974, Biochimica et biophysica acta.

[52]  Friedhelm Bechstedt,et al.  EfficientO(N2)method to solve the Bethe-Salpeter equation , 2003 .

[53]  Eric L. Shirley,et al.  Optical Absorption of Insulators and the Electron-Hole Interaction: An Ab Initio Calculation , 1998 .

[54]  P. Callis,et al.  Electronic States and Luminescence of Nucleic Acid Systems , 1983 .

[55]  Density-relaxation part of the self energy , 1997, cond-mat/9710129.

[56]  B. Roos,et al.  Theoretical Study of the Electronic Spectrum of Cytosine , 1995 .

[57]  P Hobza,et al.  Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies. , 1996, Journal of biomolecular structure & dynamics.

[58]  D. G. Lister,et al.  The microwave spectrum, structure and dipole moment of aniline , 1974 .

[59]  J. Šponer,et al.  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 , 1996 .

[60]  J. Šponer,et al.  DNA base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations , 1996 .

[61]  F. Bechstedt,et al.  Origin of the different reconstructions of diamond, Si, and Ge(111) surfaces. , 2001, Physical review letters.

[62]  M L Leininger,et al.  Electron affinities of the DNA and RNA bases. , 2001, Journal of the American Chemical Society.

[63]  J. Leszczynski,et al.  An ab Initio Post-Hartree-Fock Comparative Study of 5-Azacytosine and Cytosine and Their Dimers with Guanine , 2000 .

[64]  Jerzy Leszczynski,et al.  A DFT STUDY OF THE WATER-ASSISTED INTRAMOLECULAR PROTON TRANSFER IN THE TAUTOMERS OF ADENINE , 1999 .

[65]  Matthias Scheffler,et al.  Pseudopotential study of binding properties of solids within generalized gradient approximations: The role of core-valence exchange-correlation. , 1998 .

[66]  Walter Kohn,et al.  Nobel Lecture: Electronic structure of matter-wave functions and density functionals , 1999 .

[67]  T Yamada,et al.  Vacuum ultraviolet absorption spectra of sublimed films of nucleic acid bases , 1968, Biopolymers.

[68]  W C Johnson,et al.  Circular dichroism of the nucleic acid monomers , 1977, Biopolymers.

[69]  Steven G. Louie,et al.  Electron-Hole Excitations in Semiconductors and Insulators , 1998 .

[70]  F. Aryasetiawan,et al.  The GW method , 1997, cond-mat/9712013.

[71]  M. Maestre,et al.  Circular dichroism of some mononucleosides , 1975, Biopolymers.

[72]  Jerzy Leszczynski,et al.  Molecular Structure and Vibrational IR Spectra of Cytosine and Its Thio and Seleno Analogues by Density Functional Theory and Conventional ab initio Calculations , 1996 .

[73]  Ab initio calculation of surface phonons in GaAs(110). , 1993, Physical review letters.

[74]  G. Halász,et al.  BSSE-free SCF theories: a comment , 2000 .

[75]  L. Adamowicz,et al.  Anharmonic contributions to the inversion vibration in 2-aminopyrimidine , 1995 .

[76]  J. Leszczynski,et al.  An ab initio post-Hartree–Fock study of vibrational infrared spectra of 5-azacytosine and cytosine* , 2001 .

[77]  J. Sühnel.  Beyond nucleic acid base pairs: From triads to heptads , 2001, Biopolymers.

[78]  Daniel M. Neumark,et al.  Anion spectroscopy of uracil, thymine and the amino-oxo and amino-hydroxy tautomers of cytosine and their water clusters , 1998 .

[79]  Jackson,et al.  Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation. , 1992, Physical review. B, Condensed matter.

[80]  P Hobza,et al.  Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. , 1999, Chemical reviews.

[81]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[82]  I. Tinoco,et al.  The stability of helical polynucleotides: base contributions. , 1962, Journal of molecular biology.

[83]  F. Bechstedt,et al.  Bulk excitonic effects in surface optical spectra. , 2001, Physical review letters.