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Nature of Base Stacking: Reference Quantum‐Chemical Stacking Energies in Ten Unique B‐DNA Base‐Pair Steps
Author(s) -
Šponer Jiří,
Jurečka Petr,
Marchan Ivan,
Luque F. Javier,
Orozco Modesto,
Hobza Pavel
Publication year - 2006
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.200501239
Subject(s) - stacking , extrapolation , force field (fiction) , chemistry , basis set , base (topology) , quantum , computational chemistry , field (mathematics) , molecular physics , crystallography , physics , density functional theory , quantum mechanics , mathematics , mathematical analysis , organic chemistry , pure mathematics
Base‐stacking energies in ten unique B‐DNA base‐pair steps and some other arrangements were evaluated by the second‐order Møller–Plesset (MP2) method, complete basis set (CBS) extrapolation, and correction for triple (T) electron‐correlation contributions. The CBS(T) calculations were compared with decade‐old MP2/6‐31G*(0.25) reference data and AMBER force field. The new calculations show modest increases in stacking stabilization compared to the MP2/6‐31G*(0.25) data and surprisingly large sequence‐dependent variation of stacking energies. The absolute force‐field values are in better agreement with the new reference data, while relative discrepancies between quantum‐chemical (QM) and force‐field values increase modestly. Nevertheless, the force field provides good qualitative description of stacking, and there is no need to introduce additional pair‐additive electrostatic terms, such as distributed multipoles or out‐of‐plane charges. There is a rather surprising difference of about 0.1 Å between the vertical separation of base pairs predicted by quantum chemistry and derived from crystal structures. Evaluations of different local arrangements of the 5′‐CG‐3′ step indicate a sensitivity of the relative stacking energies to the level of calculation. Thus, describing quantitative relations between local DNA geometrical variations and stacking may be more complicated than usually assumed. The reference calculations are complemented by continuum‐solvent assessment of solvent‐screening effects.