Cooperative Hydrogen-Bonding in Adenine−Thymine and Guanine−Cytosine Base Pairs. Density Functional Theory and Møller−Plesset Molecular Orbital Study

Abstract

The cooperative contributions to the H-bonding interaction energies of the adenine-thymine and guaninecytosine base pairs have been evaluated using molecular orbital theory. The energies of the individual bonds in each base pair were ascertained by using models structures that keep one H-bond at a time intact by rotating one base with respect to the other about the axis of each H-bond to form structures with the bases perpendicular to each other. The energies of the individual H-bonds calculated in this way are compared with those of the planar base pairs. Optimized geometries were obtained using ab initio molecular orbital theory with electron correlation (MP2/D95**) and density functional theory (B3LYP/D95**). The cooperative contributions are of similar magnitude for each base pair. However, since the A‚T overall interaction is weaker, the cooperative interaction provides 31% of its stability versus only 12-16% for G‚C. The relatively smaller cooperative contribution to G‚C is due to the difficulty of forming three optimal H-bonds between two rigid molecules. Structural modifications that might strengthen one H-bond tend to weaken another. As a result the central H-bond of G‚C appears to be compressed by the attractive interaction in the two outer H-bonds. To the extent that these observations can be generalized, they should be important to the design of materials that utilize H-bonding motifs for self-assembly.

The World of Non-Covalent Interactions: 2006

“…As the A...T interaction energy is smaller, the cooperative interaction (contributing to about 30% of its value) is larger by a factor of two than that with the G...C pair 209 . In connection with electron affinity calculations of the G...C base pair, it was shown (DFT) that the unpaired electron is essentially localized on the cytosine moiety 210 .…”

Trinucleotide duplex formation inside a confined nanospace under supercooled conditions

“…In the nearest-neighbour model 18 , the change in DH for a d-T n /a-A n pair is À 8 kcal mol À 1 per single base pair. The energy of the H-bonds in one A-T base pair was estimated to be B À 12 kcal mol À 1 using ab initio molecular orbital simulation 28 . In the light of these energy values, the difference in DH values between complementary and singlemismatched 3-mer DNA pairs appears to be small, with the maximum difference in DH being 2.3 kcal mol À 1 (Table 3).…”

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

“…Although many theoretical studies performed on the total hydrogen bond energy of the Watson-Crick type base pairs, especially the A-T and G-C base pairs [5,10,16,[25][26][27][28][29][30][31], a few studies performed on the individual hydrogen bond energies [32][33][34][35]. Asensio et al [32] evaluated the cooperative hydrogen bonding in the A-T and G-C base pairs.…”