Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment

Theory of dipole-bound anions

The problem of the binding of an excess electron to polar molecules and their clusters has long fascinated researchers. Although excess electrons bound to such species tend to be very extended spatially and to have little spatial overlap with the valence electrons of the neutral molecules, inclusion of electron correlation effects is essential for quantitatively describing the electron binding. The major electron correlation contribution may be viewed as a dispersion interaction between the excess electron and the electrons of the molecule or cluster. Recent work using a one-electron Drude model to describe excess electrons interacting with polar molecules is reviewed.

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

We compare the conformational distributions of Ace-Ala-Nme and Ace-Gly-Nme sampled in long simulations with several molecular mechanics (MM) force fields and with a fast combined quantum mechanics/molecular mechanics (QM/MM) force field, in which the solute's intramolecular energy and forces are calculated with the self-consistent charge density functional tight binding method (SCCDFTB), and the solvent is represented by either one of the well-known SPC and TIP3P models. All MM force fields give two main states for Ace-Ala-Nme, beta and alpha separated by free energy barriers, but the ratio in which these are sampled varies by a factor of 30, from a high in favor of beta of 6 to a low of 1/5. The frequency of transitions between states is particularly low with the amber and charmm force fields, for which the distributions are noticeably narrower, and the energy barriers between states higher. The lower of the two barriers lies between alpha and beta at values of psi near 0 for all MM simulations except for charmm22. The results of the QM/MM simulations vary less with the choice of MM force field; the ratio beta/alpha varies between 1.5 and 2.2, the easy pass lies at psi near 0, and transitions between states are more frequent than for amber and charmm, but less frequent than for cedar. For Ace-Gly-Nme, all force fields locate a diffuse stable region around phi = pi and psi = pi, whereas the amber force field gives two additional densely sampled states near phi = +/-100 degrees and psi = 0, which are also found with the QM/MM force field. For both solutes, the distribution from the QM/MM simulation shows greater similarity with the distribution in high-resolution protein structures than is the case for any of the MM simulations.

Fast approximate methods for calculating nucleic acid base pair interaction energies

Interaction enthalpies for six base pairs have been computed at a variety of efficient levels of electronic structure theory and compared to experiment. In addition to previously defined levels of theory, modified Hamiltonians with adjusted parameters in hybrid Hartree-Fock/density functionals and semiempirical neglect-of-diatomic-differential-overlap models were examined. Of the pure and hybrid density functional levels, mPWPW91/MIDI! performed most satisfactorily, as judged by comparison not only to the available experimental data, but also to data from more robust electronic structure methods for 22 additional base pairs. The low computational cost of the mPWPW91/MIDI! model was further exploited in an investigation of various base trimers, tetramers, and one base pentamer. A carefully reparameterized semiempirical model, PM3(BP), was able to achieve similar levels of accuracy at a still greater savings in terms of computational effort.

Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies

Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most important findings are introduced in the present overview: structures and energies of hydrogen bonded base pairs, nature of base stacking, interactions between metal cations and nucleobases, nonplanarity of isolated nucleobases and other monomer properties, tautomeric equilibria of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions. The role of selected molecular interactions in nucleic acids is discussed and representative examples where these interactions occur are given. Also, accuracy of density functional theory, semiempirical methods, distributed multipole analysis and empirical potentials is commented on. Special attention is given to our very recent reference calculations on base stacking and H-bonding. Finally, we briefly comment on the relationship between advanced ab initio quantum-chemical methods and large-scale explicit solvent molecular dynamics simulations of nucleic acids.

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

Stacking energies in low-energy geometries of pyrimidine, uracil, cytosine, and guanine homodimers were determined by the MP2 and CCSD(T) calculations utilizing a wide range of split-valence, correlation-consistent, and bond-functions basis sets. Complete basis set MP2 (CBS MP2) stacking energies extrapolated using aug-cc-pVXZ (X = D, T, and for pyrimidine dimer Q) basis sets equal to -5.3, -12.3, and -11.2 kcal/mol for the first three dimers, respectively. Higher-order correlation corrections estimated as the difference between MP2 and CCSD(T) stacking energies amount to 2.0, 0.7, and 0.9 kcal/mol and lead to final estimates of the genuine stacking energies for the three dimers of -3.4, -11.6, and -10.4 kcal/mol. The CBS MP2 stacking-energy estimate for guanine dimer (-14.8 kcal/mol) was based on the 6-31G(0.25) and aug-cc-pVDZ calculations. This simplified extrapolation can be routinely used with a meaningful accuracy around 1 kcal/mol for large aromatic stacking clusters. The final estimate of the guanine stacking energy after the CCSD(T) correction amounts to -12.9 kcal/mol. The MP2/6-31G(0.25) method previously used as the standard level to calculate aromatic stacking in hundreds of geometries of nucleobase dimers systematically underestimates the base stacking by ca. 1.0-2.5 kcal/mol per stacked dimer, covering 75-90% of the intermolecular correlation stabilization. We suggest that this correction is to be considered in calibration of force fields and other cheaper computational methods. The quality of the MP2/6-31G(0.25) predictions is nevertheless considerably better than suggested on the basis of monomer polarizability calculations. Fast and very accurate estimates of the MP2 aromatic stacking energies can be achieved using the RI-MP2 method. The CBS MP2 calculations and the CCSD(T) correction, when taken together, bring only marginal changes to the relative stability of H-bonded and stacked base pairs, with a slight shift of ca. 1 kcal/mol in favor of H-bonding. We suggest that the present values are very close to ultimate predictions of the strength of aromatic base stacking of DNA and RNA bases.

Electron affinity of the guanine-cytosine base pair and structural perturbations upon anion formation

The adiabatic electron affinity (AEA) for the Watson-Crick guanine-cytosine (GC) DNA base pair is predicted using a range of density functional methods with double- and triple-zeta plus polarization plus diffuse (DZP++ and TZ2P++) basis sets in an effort to bracket the true electron affinity. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chem.Rev. 2002, 102, 231). Optimized structures for GC and the GC anion are compared to the neutral and anionic forms of the individual bases as well as Rich's 1976 X-ray structure for sodium guanylyl-3',5'-cytidine nonahydrate, GpC.9H(2)O. Structural distortions and natural population (NPA) charge distributions of the GC anion indicate that the unpaired electron is localized primarily on the cytosine moiety. Unlike treatments using second-order perturbation theory (MP2), density functional theory consistently predicts a substantial positive adiabatic electron affinity for the GC pair (e.g., TZ2P++/B3LYP: +0.48 eV). The stabilization of C(-) via three hydrogen bonds to guanine is sufficient to facilitate adiabatic binding of an electron to GC and is also consistent with the positive experimental electron affinities obtained by photoelectron spectroscopy of cytosine anions incrementally microsolvated with water molecules. The pairing (dissociation) energy for GC(-) (35.6 kcal/mol) is determined with inclusion of electron correlation and shows the anion to have greater thermodynamic stability; the pairing energy for neutral GC (TZ2P++/B3LYP 23.9 kcal/mol) compares favorably to previous MP2/6-31G (23.4 kcal/mol) results and a debated experiment (21.0 kcal/mol).

The concerted mechanism of photo-induced biprotonic transfer in 7-azaindole dimers: structure, quantum-theoretical analysis, and simultaneity principles

Six stable dimer models for 7-azaindole (including the classic C(2h) doubly hydrogen-bonded, coplanar, centrosymmetric dimer) are considered to be observable in adiabatic nozzle jet molecular beams. They are analyzed by hybrid density functional theory (DFT), the MP2 ab initio method for the ground electronic state, and the single-excitation configuration interaction (CIS) (over frozen ground state optimized geometries obtained from DFT) excited state calculations, for global potential minima and proton-transfer potential energy curves. Three simultaneity principles are stated: (i) intermolecular coherent excitation molecular exciton simultaneity, (ii) intramolecular acid-base change simultaneity at the pyrrolo-N-H and aza-N proton-donor, proton-acceptor sites, and (iii) intermolecular simultaneity of catalytic proton-donor, proton-acceptor action. It is suggested that the formation of the classic C(2h) dimer of 7-azaindole, which is considered exclusively by previous researchers, can be formed from at least one of the several card-pack hydrogen-bonded dimers in a secondary slower step approaching a microsecond scale, instead of the picosecond events at the supersonic nozzle. It is proposed that the complexity of dimerization modes is the basis of the postexcitation, postionization diverse kinetic isotope results.

Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study

Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6'-diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were investigated by means of a nonempirical correlated ab initio method. All intercalators exhibit large charge delocalization, and none of them (including the DAPI dication) exhibits a site with dominant charge. All intercalators have large polarizability and are good electron acceptors, while base pairs are good electron donors. MP2/6-31G*(0.25) stabilization energies of intercalator...base pair complexes are large (E...AT, 22.4 kcal/mol; D...GC, 17.8 kcal/mol; EL...GC, 18.2 kcal/mol; DAPI...GC, 21.1 kcal/mol) and are well reproduced by modified AMBER potential (van der Waals radii of intercalator atoms are enlarged and their energy depths are increased). Standard AMBER potential underestimates binding, especially for DAPI-containing complexes. Because the DAPI dication is the best electron acceptor (among all intercalators studied), this difference is explained by the importance of the charge-transfer term, which is not included in the AMBER potential. For the neutral EL molecule, the standard AMBER force field provides correct results. The Hartree-Fock and DFT/B3LYP methods, not covering the dispersion energy, fail completely to reveal any energy minimum at the potential energy curve of the E...AT complex, and these methods thus cannot be recommended for a study of intercalation process. On the other hand, an approximate version of the DFT method, which was extended to cover London dispersion energy, yields for all complexes very good stabilization energies that are well comparable with referenced ab initio data. Besides the vertical dependence of the interaction, an energy twist dependence of the interaction energy was also investigated by a reference correlated ab initio method and empirical potentials. It is concluded that, despite the cationic (E +1, D +1, DAPI +2) or polar (EL) character of the intercalators investigated, it is the dispersion energy which predominantly contributes to the stability of intercalator...base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation.