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Original Articles

Hydrogen Bonding and Stacking of DNA Bases: A Review of Quantum-chemical ab initio Studies

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Pages 117-135 | Received 14 Apr 1996, Published online: 21 May 2012

References and Footnotes

  • Aida , M. and Nagata , C. 1986 . Int. J. Quantum Chem. , 29 : 1253
  • Hobza and Sandorfy , C. 1987 . J. Am. Chem. Soc. , 109 : 1302
  • Aida , M. 1988 . J. Theor. Biol. , 130 : 327
  • Nagata , C. and Aida , M. 1988 . J. Mol. Struct. (Theochem) , 179 : 451
  • Aida , M. 1988 . J. Comput. Chem. , 9 : 362
  • Czerminski , R. , Kwiatkowski , J. S. , Person , W. B. and Szczepaniak , K. 1989 . J. Mol. Struct. , 198 : 297
  • Anwander , E. H.S. , Probst , M. M. and Rode , B. M. 1990 . Biopolymers , 29 : 757
  • Colson , A. O. , Besler , B. , Close , D. M. and Sevilla , M. D. 1991 . J. Phys. Chem. , 96 : 661
  • Colson , A. O. , Besler , B. and Sevilla , M. D. J. Phys. Chem. , 96 9767 (1991)
  • Colson , A. O. , Besler , B. and Sevilla , M. D. J. Phys. Chem. , 97 13852 (1991)
  • Sponer , J. and Hobza , P. 1994 . J. Am. Chem. Soc. , 116 : 709
  • Gould , I. R. and Kollman , P. A. 1994 . J. Am. Chem. Soc. , 116 : 2493
  • Sponer , J. and Hobza , P. 1994 . J. Biomol. Struct. Dyn. , 12 : 671
  • Hobza , P. , Sponer , J. and Polásek , M. 1995 . J. Am. Chem. Soc. , 117 : 792
  • Florián , J. and Leszczynski , J. 1995 . J. Biomol. Struct. Dyn. , 12 : 1055
  • Jiang , S.-P. , Raghunathan , G. , Ting , K.-L. , Xuan , J. C. and Jernigan , R. L. 1994 . J. Biomol. Struct. Dyn. , 12 : 367
  • Sponer , J. , Leszczynski , J. and Hobza , P. 1996 . J. Phys. Chem. , 100 : 1965
  • Sponer , J. , Leszczynski , J. and Hobza , P. 1996 . J. Comput. Chem. , 17 : 841
  • Sponer , J. , Hobza , P. and Leszczynski , J. 1996 . Computational Chemistry. Reviews of Current Trends Edited by: Leszczynski , J. 185 Singapore : World Scientific Publisher .
  • Sponer , J. and Hobza , P. 1996 . Chem. Phys. , 294 : 5590
  • Elorián , J. and Leszczynski , J. 1996 . J. Am. Chem. Soc. , 118 : 3010
  • Sponer , J. , Florián , J. , Leszczynski , J. and Hobza , P. 1996 . J. Biomol. Struct. Dyn. , 13 : 827
  • Sponer , J. , Leszczynski , J. , Vetterl , V. and Hobza , P. 1996 . J. Biomol. Struct. Dyn. , 13 : 695
  • Sponer , J. , Leszczynski , J. and Hobza , P. 1996 . J. Phys. Chem. , 100 : 5590
  • Leszczynski , J. 1992 . Int. J. Quantum Chem. Quantum Biol. Symp. , 19 : 43
  • Sponer , J. and Hobza , P. 1994 . J. Mol. Struct. (THEOCHEM) , 304 : 35
  • Sponer , J. and Hobza , P. 1994 . J. Phys. Chem. , 98 : 3161
  • Bludsky , O. , Sponer , J. , Leszczynski , J. , Hobza , P. and Spirko , V. submitted to . J. Chem. Phys. ,
  • Szabo , A. and Ostlund , N. S. 1989 . Modern Quantum Chemistry. Introduction to Advanced Electronic Structure Theory. New York : McGraw-Hill Inc. .
  • In order to speed up the numerical evaluation of integrals, the atomic orbitals are approximated by fixed combinations of Gauss-type functions
  • Hehre , W. J. , Radom , L. , Schleyer , P. v.R. and Pople , J. A. 1986 . Ab initio Molecular Orbital Theory New York : John Wiley & Sons. Inc. .
  • Dunning , T. H. Jr . 1989 . J. Chem. Phys. , 90 : 1007
  • Dunning , T. H. Jr and Harrison , R. J. 1992 . J. Chem. Phys. , 96 : 6796
  • Dunning , T. H. Jr . 1993 . J. Chem. Phys. , 98 : 1358
  • Cízek , J. 1969 . Adv. Chem. Phys. , 14 : 35
  • Hobza , P. , Selzle , H. L. and Schlag , E. W. 1994 . Chem. Rev. , 94 : 1767
  • Pople , J. A. , Head-Gordon , M. and Raghavachari , K. 1987 . J. Chem. Phys. , 89 : 5968
  • Watts , J. D. , Urban , M. and Bartlett , R. J. 1995 . Theor. Chim. Acta , 90 : 341
  • Estrin , D. A. , Paglieri , L. and Corongiu , G. 1994 . J. Phys. Chem. , 98 : 5653
  • Sponer , J. and Hobza , P. 1995 . Int. J. Quantum Chem. , 57 : 959
  • Florián , J. and Johnson , B. G. 1994 . J. Phys. Chem. , 98 : 3681
  • Florián , J. and Johnson , B. G. 1995 . J. Phys. Chem. , 99 : 5899
  • Kwiatkowski , J. S. and Leszczynski , J. 1996 . J. Phys. Chem. , 100 : 941
  • Nowak , M. J. , Lapinski , L. , Kwiatkowski , J. S. and Leszczynski , J. 1996 . J. Phys. Chem. , 100 : 3527
  • Lapinski , L. , Rostkowska , H. , Nowak , M. J. , Kwiatkowski , J. S. and Leszczynski , J. Spectrochimica Acta , in press
  • Kwiatkowski , J. S. and Leszczynski , J. Int. J. Quantum. Chem. , in press
  • Kohn , W. and Sham , L. J. 1995 . Phys. Rev. , 140 : A1133
  • Becke , A. D. 1994 . J. Phys. Chem. , 98 : 5684
  • Gould , I. R. , Burton , N. A. , Hall , R. J. and Hillier , I. H. 1995 . J. Mol. Struct. (THEOCHEM) , 331 : 147
  • Kristián , S. and Pulay , P. 1994 . Chem. Phys. Let. , 229 : 175
  • Hobza , P. , Šponer , J. and Reschel , T. 1995 . J. Comput. Chem. , 11 : 1315
  • Sim , F. , St-Amant , A. , Papoi , I. and Salahub , D. R. 1992 . J. Am. Chem. Soc. , 114 : 4391
  • Laasonen , K. , Pannello , M. , Car , R. , Lee , C. and Vanderbilt , D. 1993 . Chem. Phys. Lett. , 207 : 208
  • Novoa , J. J. and Sosa , C. 1995 . J. Phys. Chem. , 99 : 15837
  • The factors mentioned are theoretical factors, which may be somewhat reduced by an effective programming and computer implementation. This is especially well done for the HF approximation, where the actual “computer requirements” factor can be below 3
  • Boys , S. F. and Bernardi , F. 1970 . Mol. Phys. , 19 : 553
  • van Duijneveldt , F. B. , van Duijneveldt - van de Rijdt , J. G.C.M. and van Lenthe , J. 1994 . Chem. Rev. , 94 : 1873
  • Chalasinsky , G. and Szczesniak , M. M. 1994 . Chem. Rev. , 94 : 1723
  • Dewar , M. J.S. , Zoebisch , E. G. , Healy , E. F. and Stewart , J. J.P. 1985 . J. Am. Chem. Soc. , 107 : 3902
  • Stewart , J. J.P. 1989 . J. Comput. Chem. , 10 : 209
  • Dewar , M. J.S. and Thiel , W. 1977 . J. Am. Chem. Soc. , 99 : 4899
  • Pullman , B. and Pullman , A. 1974 . Adv. Prot. Chem. , 28 : 347
  • Aqvist , J. and Warshel , A. 1993 . Chem. Rev. , 93 : 2523
  • 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. and Kollman , P. A. 1995 . J. Am. Chem. Soc. , 117 : 5179
  • Mac Kerell , A. D. Jr. , Wiorkiewicz-Kuczera , J. and Karplus , M. 1995 . J. Am. Chem. Soc. , 117 : 11946
  • Jorgensen , J. and Tirado-Rives , J. J. 1988 . J. Am. Chem. Soc. , 110 : 1657
  • Burkert , U. and Allinger , N. L. 1982 . Molecular Mechanics Washington D.C. : ACS .
  • Allinger , N. L. , Kok , R. A. and Imam , M. R. 1988 . J. Comput. Chem. , 9 : 591
  • 1994 . Comput. Phys. Commun. , 84 : 131 CVFF - Discover, Version 2.9.5&94.0, May 1994, Biosym Technoloogies, San Diego, Ca.; CFF95 - A.T. Hagler and C.S, Ewig,; CFF95 force field has not yet been released
  • Halgren , T. A. 1996 . J. Comput. Chem. , 17 : 490
  • Rein , R. 1979 . Intermolecular Interactions: From Diatomic to Biopolymers Edited by: Pullman , B. 307 New York : Wiley-Interscience .
  • Langlet , J. , Claverie , P. , Caron , F. and Boevue , J. C. 1981 . Int. J. Quantum Chem. , 1 : 9 299
  • Kudryatskaya , Z. G. and Danilov , V. I. 1976 . J. Theor. Biol. , 59 : 303
  • Ornstein , R. L. and Fresco , J. R. 1983 . Biopolymers , 22 : 1979
  • Ornstein , R. L. and Fresco , J. R. 1983 . Proc. Natl. Acad. Sci. USA , 80 : 5171
  • Sarai , A. and Saito , M. 1984 . Int. J. Quantum. Chem. , 25 : 527
  • Del Bene , J. 1985 . J. Mol. Struct (THEOCHEM) , 124 : 201
  • Sagarik , K. P. and Rode , B. M. 1983 . Inorg. Chim. Acta , 78 : 177
  • Hobza , P. and Sandorfy , C. 1985 . J. Biomol. Struct. Dyn. , 2 : 1245
  • Hobza , P. and Sandorfy , C. 1984 . Biophys. Chem. , 19 : 201
  • Hobza , P. , Hubálek , F. , Kabeláč , M. , Mejzlík , P. , Sponer , J. and Vondrášek , J. Chem. Phys. Let. in press.
  • Hobza , P. , Hubálek , F. , Kabeláč , M. , Mejzlík , P. , Šponer , J. and Vondrá Šek , J. to be published.
  • Gould , I. R. and Hillier , I. H. 1989 . Chem. Phys. Lett. , 161 : 185
  • Leszczynski , J. 1990 . Chem. Phys. Lett. , 174 : 347
  • Leszczynski , J. and Lammertsma , K. 1990 . J. Phys. Chem. , 95 : 3128
  • Gould , I. R. and Hillier , I. H. 1990 . J. Chem. Soc. Perkin. Trans , 2 : 329
  • Riggs , N. V. 1991 . Chem. Phys. Lett. , 177 : 447
  • Ha , T. K. , Keller , H. J. , Gunde , R. and Gunthard , H. H. 1996 . J. Mol. Struct. , 376 : 375
  • 1995 . J. Chem. Phys. , 103 : 7030 This estimate is based on a comparison of HF/6–31G**-optimized and MP2/6–31G**-optimized geometries of cytosine dimer; the length of hydrogen bonds of the MP2-optimized structure has been corrected for the basis set superposition error (17). Let us note that a comparison with crystal data is not straightforward, because the H-bond lengths may be significantly influenced by the crystal field effects - for more details see S. Suhai
  • MP2 correlation interaction energy covers the intersystem correlation energy, change of intrasystem correlation energy, and the mixing term. The first term covers the second order dispersion energy (i.e., r6, r8, r10, r12,. terms) while the second term includes the change of coulombic energy when passing from HF to MP2 level. Dipole and quadrupole moments are mostly overestimated at HF level by about 10–20%
  • Chem. Phys. Lett. The experimental stabilization energy of the benzene.Ar amounts to about 350 cm−1 (92), the MP2 stabilization energy obtained with medium basis set (4s2p2d/2s2p/7s4p2d If - basis set for C,H, and Ar, respectively) is 396 cm−1 (36), while that obtained with extended basis set (8s5p4d3f/4s3p/15s/10p/5d/5f) is too large (553 cm−1 - 36). The agreement between theory and experiment for the medium-sized basis set is due a compensation of errors: size of basis set on one hand and neglect of higher correlation energy contributions on the other hand. It should be mentioned that the experimental value referred above has been reevaluated. This indicates that outcomes of experimental studies should be taken with care, including the DNA base pairs experiments. For a long time, the only data available were gas phase interaction enthalpies from mass field spectroscopy by Yanson et al. (93). Their reliability could be questioned because determination of enthalpy from the slope of the van't Hoff curve may be ambiguous. However, they are in a good agreement with theoretical results, including MP2 studies (17). Recently, Dey et al. (94) reported gas phase pseudoasociation constants for DNA base pairs. We tried to reproduce their results using the calculated interaction enthalpies and the entropy contribution obtained within the rigid rotor and harmonic oscillator - ideal gas approximations (P. Hobza and J. Šponer, submitted to). The difference between experimental and theoretical values was very large. Taking into account the quality of the theoretical MP2 procedure used the experimental values mentioned are suspicious. In addition it means that the two available gas phase experimental studies on DNA base pairs are mutually inconsistent. We assume that some assumptions given in ref. 94 (reproducibility of the desorption process and/or the thermodynamic equilibrium in the beam expansion) were not fulfilled
  • Krausse , H. and Neusser , M. J. 1993 . J. Chem. Phys. , 99 : 6278
  • Yanson , I. K. , Teplitsky , A. B. and Sukhodub , L. F. 1979 . Biopolymers , 18 : 1149
  • Dey , M. , Moritz , F. , Grotemeyer , J. and Schlag , E. W. 1994 . J. Am. Chem. Soc. , 116 : 9211
  • Šponer , J. , Hobza , P. and Leszczynski , J. manuscript in preparation
  • Hobza , P. , Selzle , H. L. and Schlag , E. W. submitted to . J. Chem. Phys. ,
  • Smith , G. D. and Jaffe , R. L. 1996 . J. Phys. Chem. , 100 : 9624
  • Hobza , P. and Šponer , J. J. Mol. Struct. , (THEOCHEM) in press
  • Leszczynski , J. 1992 . J. Phys. Chem. , 96 : 1649
  • Orozco , M. and Luque , F. J. 1995 . J. Am. Chem. Soc. , 117 : 1378
  • leszczynski , J. J. Phys. Chem , submitted
  • Hobza , P. , Selzle , H. L. and Schlag , E. W. 1994 . J. Am. Chem. Soc. , 116 : 3500
  • Šponer , J. and Hobza , P. unpublished data
  • Klopper , W. , Schutz , M. , Luthi , H. P. and Leutwyler , S. 1995 . J. Chem. Phys , 103 : 1085
  • Shiskhin , O. V. 1995 . J. Chem. Soc. Chem. Commun. , 1539
  • Colson , A.-O. and Sevilla , M. D. 1996 . J. Phys. Chem. , 100 : 4420
  • Leszczynski , J. 1990 . Chem. Phys. Lett. , 174 : 347
  • Leszczynski , J. 1994 . J. Mol. Struct. (THEOCHEM) , 311 : 37
  • Florian , J. , Baumruk , V. and Leszczynski , J. 1991 . J. Phys. Chem. , 113 : 2810
  • Pranata , J. , Wierschke , S. C. and Jorgensen , W. L. 1991 . J. Am. Chem. Soc. , 113 : 2810
  • Weiner , S. , Kollman , P. A. , Case , D. , Singh , U. , Ghio , C. , Alagona , G. , Profeta , S. and Weiner , P. 1984 . J. Am. Chem. Soc. , 106 : 765
  • Zhurkin , V. B. , Poltev , V. I. and Florentev , V. L. 1980 . Mol. Biol. (USSR) , 14 : 1116
  • Blizniuk , A. A. and Voityuk , A. A. 1988 . Zh. Str. Chim. , 29 : 31 No. 2
  • Due to the importance of dispersion energy, we do not know whether the stacking energies are overestimated or underestimated. The use of large basis set would increase the stabilization energy, however, higher-order correlation contributions could significantly shift the intermolecular correlation interaction energy in the opposite direction. The balance between these two trends is not known, because it is different for different systems
  • Bugg , C. E. , Thomas , J. M. , Sundaralingam , M. and Rao , S. T. 1971 . Biopolymers , 10 : 175
  • Šponer , J. , Jursa , J. and Kypr , J. 1994 . Nucleosid. Nucleotid. , 13 : 671
  • Hunter , C. A. 1993 . J. Mol. Biol. , 230 : 1025
  • Šponer , J. , Gabb , H. , Leszczynski , J. and Hobza , P. manuscript in preparation
  • Egli , M. and Gessner , R. V. 1995 . Proc. Natl. Acad. Sci. USA , 92 : 180
  • J. Am. Chem. Soc. , 97 6624 These data were obtained at the HF/4–31G level with dispersion energy evaluated by the second-order sum-of-state perturbation method (W. A. Lathan, G. R. Pack and K. Morokuma, (1975)), and represented benchmark values for nearly a decade. Our MP2/6–31G* calculations qualitatively improve these data by addresing two following items. I) The method applied by Aida can evaluate the dispersion attraction, but it does not take into consideration the intrasystem correlation interaction energy. The intrasystem correlation interaction energy reduces the electrostatic (dipole - dipole) interaction compared with the HF level II) To evaluate the interaction energy properly, the basis set of atomic Orbitals must be flexible enough to cover the space between the interacting monomers; i.e., it must contain diffuse and polarization functions. 4–31G basis set does not fulfil any of these conditions, while our basis set contains one set of d-polarization functions especially modified to evaluate the dispersion contributions (diffuse polarization functions with an exponent of 0.25)
  • Gehring , K. , Leroy , J.-L. and Gueron , M. 1993 . Nature , 363 : 561
  • Chen , L. , Cai , L. , Zhang , X. and Rich , A. 1994 . Biochemistry , 33 : 13540

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