Systematic quantum chemical study of DNA‐base tautomers

Abstract

The relative energies of the energetically low-lying tautomers of pyridone, cytosine, uracil, thymine, guanine, and iso-cytosine are studied by a variety of different quantum chemical methods. In particular, we employ density functional theory (DFT) using the six functionals HCTH407, PBE, BP86, B-LYP, B3-LYP, and BH-LYP, and the ab initio methods Hartree-Fock (HF), standard second-order Møller-Plesset perturbation theory (MP2), an improved version of it (SCS-MP2), and quadratic configuration interaction including single and double excitations (QCISD) and perturbative triple corrections [QCISD(T)]. A detailed basis set study is performed for the formamide/formamidic acid tautomeric pair. In general, large AO basis sets of at least valence triple-zeta quality including f-functions (TZV) are employed, which are found to be necessary for an accurate energetic description of the various structures. The performance of the more approximate methods is evaluated with QCISD(T)/TZV(2df,2dp) data taken as reference. In general it is found that DFT is not an appropriate method for the problem. For the tautomers of pyridone and cytosine, most density functionals, including the popular B3-LYP hybrid, predict a wrong energetic order, and only for guanine, the correct sequence of tautomers is obtained with all functionals. Out of the density functionals tested, BH-LYP, which includes a rather large fraction of HF exchange, performs best. A consistent description of the nonaromatic versus aromatic tautomers seems to be a general problem especially for pure, nonhybrid functionals. Tentatively, this could be assigned to the exchange potentials used while the functional itself, including the correlation part, seems to be appropriate. Out of the ab initio methods tested, the new SCS-MP2 approach seems to perform best because it effectively reduces some outliers obtained with standard MP2. It outperforms the much more costly QCISD method and seems to be a very good compromise between computational effort and accuracy.

Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

“…The energy difference between the lowest-energy diketo form of T and other tautomers is even higher. Piacenza and Grimme [57] have reported 9.4 and 9.9 kcal/mol energy gap between the lowest energy and the second stable tautomer [computed by QCISD(T)/TZV(2df,2pd) and MP2/TZV(2df,2dp), respectively].…”

Scaled opposite-spin second order Møller–Plesset correlation energy: An economical electronic structure method

“…For a given (large) basis, Grimme's new approach showed clear statistical improvements in the quality of geometries (of diatomics), and a wide range of relative energies of reactions, and atomization energies. Additionally, an application of this approach to problems that contain long-range correlation such as stacking complexes has been recently reported [35], as well as an extension to yield a scaled MP3 correlation energy [36].…”

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“…9 The odds of having two individuals the same specific STR regions profile is about one in a billion or even higher. 10 …”

“…These include the following light (UV), humidity has more of an effect on the quality of the DNA, rather than the quantity, elevated temperatures and moisture will degrade DNA and will make it difficult to obtain a profile, fungal contamination and length of the postmortem interval. 6,7,9,10,17 The survival of DNA depends on several factors and environmental conditions, hence, the purpose of the present study was to investigate mainly the effect of various temperatures and humidity on DNA survival over time.…”