The World of Non-Covalent Interactions: 2006

Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.

The Effects of Hydrogen-Bonding Environment on the Polarization and Electronic Properties of Water Molecules

Adequate representation of the interactions that take place between water molecules has long been a goal of force field design. A full understanding of how the molecular charge distribution of water is altered by adjacent water molecules and by the hydrogen-bonding environment is a vital step toward achieving this task. For this purpose we generated ab initio electron densities of pure water clusters and hydrated serine and tyrosine. Quantum chemical topology enabled the study of a well-defined water molecule inside these clusters, by means of its volume, energy, and multipole moments. Intra- and intermolecular charge transfer was monitored and related to the polarization of water in hydrogen-bonded networks. Our analysis affords a way to define different types of water molecules in clusters.

London dispersion forces by range-separated hybrid density functional with second order perturbational corrections: The case of rare gas complexes

A satisfactory account of the van der Waals (vdW) (London dispersion) forces is, in general not possible by the Kohn-Sham method using standard local, semilocal generalized gradient approximation (GGA), or meta-GGA density functionals. The recently proposed range-separated hybrid (RSH) approach, supplemented by second order perturbational corrections (MP2) to include long-range dynamic correlation effects, offers a physically consistent, seamless description of dispersion forces. It is based on a rigorous generalization of the Kohn-Sham method, where long-range exchange and correlation effects are treated by wave function methods, while short-range electron exchange and correlation are handled by local or semilocal functionals. The method is tested on a series of rare gas dimers in comparison with standard wave function theory and density functional theory approaches. In contrast to the most successful exchange correlation functionals, which describe at best the vdW minimum, the RSH+MP2 approach is valid also in the asymptotic region and the potential curve displays the correct 1/R(6) behavior at large internuclear separations. In contrast to usual MP2 calculations, the basis set superposition error is considerably reduced, making RSH+MP2 an ideal tool for exploring the potential energy surface of weakly bound molecular complexes.

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.

A London-type formula for the dispersion interactions of endohedral A@B systems

A London-type formula is derived for endohedral systems. It involves the static dipole polarisability, alpha(1)(A) of the inner system, A, and a new type of dipole polarisability, alpha(-2)(B) with an r(-2) radial operator, for the outer system, B. The new formula has no explicit dependence on the radius, R, of B. The predicted interaction energies are compared against MP2 supermolecular calculations for A@C(60), A = He-Xe, Zn, Cd, Hg, and CH(4).