Accurate Structures and Binding Energies for Stacked Uracil Dimers

Leininger, Matthew L.; Nielsen, Ida M. B.; Colvin, Michael E.; Janssen, Curtis L.

doi:10.1021/jp013866f

Cited by 72 publications

(101 citation statements)

References 31 publications

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“…The higher correlation energy contributions are rather significant, ranging from +2.45 to +3.43 kcal · mol -1 in B-DNA and from +2.57 kcal · mol -1 to +3.23 kcal · mol -1 in A-RNA and can thus be never neglected. 98,99 The differences between ∆CCSD (T) corrections in B-DNA and A-RNA are only marginal, not exceeding 0.35 kcal · mol -1 . The comparison of the RI-DFTD/TPSS method with the high level CBS(T) calculations on the B-DNA system reveals ( Table 3) that, while the RI-DFTD/TPSS/TZVP calculations yield the base pair step stacking energies on average higher (less stabilizing) by 1.8 kcal · mol -1 compared to CBS(T) results, this error is reduced about 2-fold when using the larger LP basis set.…”

Section: 59mentioning

confidence: 95%

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Svozil¹,

Hobza²,

Šponer³

2010

J. Phys. Chem. B

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High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal · mol, which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the CG/CG step that is well separated from the second most stable step GC/GC. Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal · mol -1 per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of ∆G°3 7 free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.

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Section: 59mentioning

confidence: 95%

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Svozil¹,

Hobza²,

Šponer³

2010

J. Phys. Chem. B

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“…[26] Recent developments in computer hardware and software enable major improvements in calculations of aromatic stacking. [37][38][39][40] Stabilization energies can be evaluated to the complete basis set (CBS) limit with the MP2 method. The CBS limit is obtained by extrapolation from series of MP2 calculations with large basis sets of atomic orbitals.…”

Section: Introductionmentioning

confidence: 99%

Nature of Base Stacking: Reference Quantum‐Chemical Stacking Energies in Ten Unique B‐DNA Base‐Pair Steps

Šponer

Jurečka

Marchán

et al. 2006

Chemistry A European J

213

306

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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 A 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.

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“…Nielsen and coworkers 53 recently reported an analysis of the uracil dimer (UU) PES at the MP2 level, finding two minima for the parallel (p) and antiparallel (ap) isomers. CCSD(T) binding energies for these isomers were then calculated to be 40.60 and 36.84 kJ mol Ϫ1 , respectively.…”

mentioning

confidence: 99%

Hybrid density functional theory for π‐stacking interactions: Application to benzenes, pyridines, and DNA bases

et al. 2006

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The suitability of a hybrid density functional to qualitatively reproduce geometric and energetic details of parallel pi-stacked aromatic complexes is presented. The hybrid functional includes an ad hoc mixture of half the exact (HF) exchange with half of the uniform electron gas exchange, plus Lee, Yang, and Parr's expression for correlation energy. This functional, in combination with polarized, diffuse basis sets, gives a binding energy for the parallel-displaced benzene dimer in good agreement with the best available high-level calculations reported in the literature, and qualitatively reproduces the local MP2 potential energy surface of the parallel-displaced benzene dimer. This method was further critically compared to high-level calculations recently reported in the literature for a range of pi-stacked complexes, including monosubstituted benzene-benzene dimers, along with DNA and RNA bases, and generally agrees with MP2 and/or CCSD(T) results to within +/-2 kJ mol(-1). We also show that the resulting BH&H binding energy is closely related to the electron density in the intermolecular region. The net result is that the BH&H functional, presumably due to fortuitous cancellation of errors, provides a pragmatic, computationally efficient quantum mechanical tool for the study of large pi-stacked systems such as DNA.

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Accurate Structures and Binding Energies for Stacked Uracil Dimers

Cited by 72 publications

References 31 publications

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Nature of Base Stacking: Reference Quantum‐Chemical Stacking Energies in Ten Unique B‐DNA Base‐Pair Steps

Hybrid density functional theory for π‐stacking interactions: Application to benzenes, pyridines, and DNA bases

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