Ab initio (MP2/6-31G*(0.25)) interaction energies were calculated for almost 240 geometries of 10 stacked nucleic acid−base pairs: A···A, C···C, G···G, U···U, A···C, G···A, A···U, G···C, C···U, and G···U; in some cases uracil was replaced by thymine. The most stable stacked pair is the G···G dimer (−11.3 kcal/mol), and the least stable is the uracil dimer (−6.5 kcal/mol). The interaction energies of H-bonded base pairs range from −25.8 kcal/mol (G···C) to −10.6 kcal/mol (T···T). The stability of stacked pairs originates in the electron correlation, while all the H-bonded pairs are dominated by the HF energy. The mutual orientation of the stacked bases is, however, primarily determined by the HF interaction energy. The ab initio base stacking energies are well reproduced by the empirical potential calculations, provided the atomic charges are derived by the same method as used in the ab initio calculations. Some contributions previously postulated to significantly influence base stacking (induction interactions, π−π interactions) were not found. Base stacking was also investigated in six B-DNA and two Z-DNA base pair steps; their geometries were taken from the oligonucleotide crystal data. The many-body correction was estimated at the HF/MINI-1 level. The sequence-dependent variations of the total base pair step stacking energies range from −9.9 to −14.7 kcal/mol. The range of the calculated many-body corrections to the stacking energy is 2 kcal/mol. The ab initio calculations exclude the consideration that the unusual conformational properties of the CpA(TpG) steps might be associated with attractive induction interactions of the exocyclic groups of DNA bases and the aromatic rings of bases.

Hydrogen bonding of DNA bases was investigated by reliable nonempirical ab initio calculations. Gradient optimization was carried out on 30 DNA base pairs using the Hartree-Fock (HF) approximation and the 6-31G** basis set of atomic orbitals. The optimizations were performed within C s symmetry. However, the harmonic vibrational analysis indicates that 13 of the studied base pairs are intrinsically nonplanar. Interaction energies of base pairs were then evaluated at the planar optimized geometries with inclusion of the electron correlation energy using the second-order Møller-Plesset (MP2) method. The stabilization energies of the studied base pairs range from -24 to -9 kcal/mol, and the calculated gas phase interaction enthalpies agree well (within 2 kcal/mol) with the available experimental values. The binding energies and molecular structures of the base pairs are not determined solely by the hydrogen bonds, but they are also strongly influenced by the polarity of the monomers and by a wide variety of secondary long-range electrostatic interactions that also involve the hydrogen atoms bonded to ring carbon atoms. The stabilization of the base pairs is dominated by the Hartree-Fock interaction energy. This result confirms that the stability of the base pairs originates in the electrostatic interactions. For weakly bonded base pairs, the correlation interaction energy amounts to as much as 30-40% of the stabilization. For some other base pairs, however, repulsive correlation interaction energy was found. The latter fact is explained as a result of a reduction of the electrostatic attraction upon inclusion of the electron correlation. The empirical London dispersion energy does not reproduce the correlation interaction energy. For the sake of comparison, results of a first gradient optimization for a DNA base pair at a correlated level (CC base pair, MP2/6-31G** level) are reported. In addition, the ability of the economical density functional theory (DFT) method to reproduce the ab initio data was investigated. The DFT method with present functionals is not suitable to consistently study the whole range of the DNA base interactions. However, it gives good estimates of interaction energies at the reference HF/6-31G** geometries.

Structures and energetics of complexes between the adenine−thymine Watson−Crick (AT WC) and adenine−adenine reverse-Hoogsteen (AA rH) DNA base pairs and hydrated (five water molecules) Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+ metal cations were studied using high-level quantum chemical techniques. Binding of the cations to N7 of adenine does not enhance the strength of the base pairing through polarization effects. This is in stark contrast with the results obtained for the GG and GC base pairs. This finding and other recently published data indicate a qualitative difference between adenine-containing (AA,AT) and guanine-containing (GC,GG) base pairs. There are significant changes in the electronic structure of the guanine aromatic system upon cation binding to N7 which propagate toward the H-bonded partner. No such effect has been observed for any adenine-containing pair. The interaction between hydrated cations and adenine is much weaker than that between hydrated cations and guanine due to the low dipole moment of adenine. Furthermore, the cation and its surrounding polarized water molecules interact with the nitrogen atom of the adenine amino group which then acts as an H-bond acceptor. This can lead to destabilization of the base pairing. The zinc and magnesium groups of divalent cations have a different balance of the water−cation and base−cation interactions. Binding of the zinc-group elements to nucleobases is more efficient. Interaction of large IIa group divalent cations (Ca2+, Sr2+, and mainly Ba2+) with the N7 site of adenine is not likely unless the amino group nitrogen atom serves as a coordination center which may disrupt the base pairing. The complexes were optimized within the Hartree−Fock approximation with the 6-31G* basis set of atomic orbitals and relativistic pseudopotentials for the cations. All atoms of the base pairs were kept coplanar. No other constraints were applied. The interaction energies have been calculated with inclusion of the electron correlation by means of the full second-order Moeller−Plesset perturbational theory.

Simplified cluster models representing cation binding sites in a zeolite of ferrierite structure have been optimized with a series of divalent (MgII, MnII, CoII, NiII) and monovalent (NaI, CuI, AgI) metal cations. It has been found that the coordination of metal cations significantly perturbs the charge distribution over the cation binding sites. The perturbation is of electronic origin and arises from the strong electric field concentrated on the metal cation and from framework to metal charge-transfer effects. Its extent is specific to the type of cation and can be expressed with an empirical formula, which contains the formal charge of the cation and bond distance parameters. A sound correlation has been found between the extent of perturbation and the measured infrared vibrational wavenumbers of the shifted T−O−T antisymmetric skeletal vibrations, appearing in the 1020−780 cm-1 region of the FTIR spectra of ferrierite exchanged with metal cations.