Specific Solvation Effects on Structures and Properties of Isocytosine−Cytosine Complexes:  A Theoretical ab Initio Study

Abstract

Ab initio quantum chemical studies at the Hartree−Fock (HF) level with the 6-31G* basis set were performed for four different hydrogen-bonded isocytosine−cytosine (iCC) complexes in the gas phase and in a water solution. Full geometry optimizations without any constraints on the planarity of these complexes were carried out. The water solution was modeled by explicit inclusion of different numbers of water molecules, up to six, which creates the first coordination sphere around the iCC base pair. Single point calculations were also performed at the correlated MP2/6-31G*//HF/6-31G* level. The interaction and solvation energies were corrected for the basis set superposition error by using the full Boys−Bernardi counterpoise correction scheme. It was shown that the base pair corresponding to the standard Watson−Crick pair (denoted as iCC1) is the global minimum on the potential energy surface both in the gas phase and in a water solution. Inclusion of six instead of four water molecules has crucial effects both on the geometries and relative stabilities of iCC complexes. Complexes involving six water molecules become strongly nonplanar, whereas in the case of four or fewer water molecules, only a slight deviation from planarity is observed. Moreover, the relative stability order changes when one considers six water molecules, and the zwitterionic form (denoted as iCC4) becomes the second most stable species after the Watson−Crick iCC1 base pair. Since the structure of isocytosine mimics the six-membered parts of guanine, the results of this study could provide important insights into the structures and properties of analogous guanine−cytosine complexes in a water solution.

Influence of the - interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

“…Similarly, the effect of bound water molecules may also be taken into account. Although most water molecules in X-ray structures of polynucleotides are situated in the vicinity of the phosphate group, a significant number of close contacts with nucleobases do occur (103–105). These interactions are not discussed in the present work but may be investigated in a future study.…”

Polymorphism of hydrogen bonding in the short double helixes of oligonucleotides: Semiempirical quantum chemical study

“…Media effect is usually significant and should be taken into account when the calculated geometries are compared with the X‐ray data. Many different methods to model such type effects are known 18–22, 26, 28–41. The most comprehensive approach is the supermolecule approximation 33, 42.…”

“…The most comprehensive approach is the supermolecule approximation 33, 42. In this case, media molecules surrounding the DNA constituents are considered explicitly and are optimized together with the whole complex 21, 22, 29–32, 34. A more simple method of media effect calculations, like the polarized continuum model (PCM) 19, 33, 35, 42, self‐consistent reaction field (SCRF) methods 19, 36, 42, Langevin dipoles solvation model (LD) 4, 37, solvation models (SMx) 19, 38, 42, and conductor‐like screening models (COSMO) 39–42 are also in use.…”

Solution‐Phase Organic Chemistry

“…These values were then corrected for BSSE. 110 A systematic survey of 10 stacked nucleic acid base pairs was reported by Sponer et al 113 by using the MP2-optimized base geometries and an empirical force field to locate the dimer structures. These hydrogen-bonded Watson-Crick pairs were also optimized at B3LYP/6-31G** and PW91/6-31G**, and the interaction energies are listed in Table 7.18.…”