H-bonded DNA base pairs

There is another physical phenomenon which appears at the correlated level which is completely absent in Hartree-Fock calculations. The transient fluctuations in electron density of one molecule which cause a momentary polarization of the other are typically referred to as London forces. Such forces can be associated with the excitation of one or more electrons in molecule A from occupied to vacant molecular orbitals (polarization of A), coupled with a like excitation of electrons in B within the B MOs. Such multiple excitations appear in correlated calculations their energetic consequence is typically labeled as dispersion energy. Dispersion first appears in double excitations where one electron is excited within A and one within B, but higher order excitations are also possible. As a result, all the dispersion is not encompassed by correlated calculations which terminate with double excitations, but there are higher-order pieces of dispersion present at all levels of excitation. Although dispersion is not necessarily a dominating contributor to H-bonds, this force must be considered to achieve quantitative accuracy. Moreover, dispersion can be particularly important to geometries that are of competitive stability to H-bonds, for example in the case of stacked versus H-bonded DNA base pairs. ... 

H-bonded DNA base pairs. The ability to reproduce the ab initio MP2 interaction energies for neutral H-bonded... 

Table 5 Harmonic (H) and Anharmonic (A) Vibrational Frequencies (cm ), and Stabilization Energies (A . kcal mol ) for Selected H-bonded DNA Base Pairs Evaluated at the Hartree-Fock Level with Various Basis Sets...

Calculated thermodynamic characteristics for the formation of H-bonded DNA base pairs in the gas phase are presented... 

This is because the DNAs have different amounts of G C and A T base pairs, and the former confer the greater stability to the helix, perhaps through the presence of three H bonds per base pair rather than two (Fig. 7-1). Thus, the higher the GC content, the higher is the Tm. The value of Tm under standard conditions can be used, therefore, to obtain an estimate of the G + C content of an unknown DNA. This is obvious from Fig. 7-9, which shows a plot of Tm versus G + C content for a number of DNAs. 

A. Hesselmann, G. Jansen, M. Schtitz, Interaction energy contributions of H-bonded and stacked structures of the AT and GC DNA base pairs from the combined density functional theory and intermolecular perturbation theory approach. J. Am. Chem. Soc. 128,11730-11731 (2006)... 

Rigid rotor-harmonic oscillator-ideal gas approximation. The AMBER 4.1 free energy values are summarized in Table 7. The entropy term is important and compensates for the interaction energy (enthalpy) term. A similar type of compensation has also been found in the case of DNA base pairs [40]. FI-bonded structure 4 remains the most stable and also HB6 and HBl structures remain as the second and third most stable ones. The following order of stability is however, changed. The H-bonded structure 7 and the T-shaped structure are surprisingly more stable than H-bonded structures 2, 3 and 5. Analyzing veirious... 

The stabilizing role of C-H- O = C contacts in base pairs was evaluated for the Watson Crick adenine-uracil (AU) pair by Starikov and Steiner [125]. Their ab initio calculations indicated these bonds contributed only about 6% to the total interaction energy. A better estimate might be achieved via the correlated calculations of the dimer of pyrimidine [126] (related to DNA base pairs) like that shown in Fig. 3. This dimer does not contain any conventional H-bonds,... 

---