Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine (original) (raw)
Related papers
Tautomeric forms of adenine: Vertical ionization energies and Dyson orbitals
International Journal of Quantum Chemistry, 2009
For the MP2/6-311ϩϩg(2df,p) optimized geometry of all the 14 adenine tautomers, the first three vertical ionization energies have been calculated using several electron propagator decouplings. The corresponding Dyson orbitals provide detailed insight into the role of structural variations in different adenine tautomers. Changes in the electron binding energies and the corresponding Dyson orbital amplitudes have been correlated with tautomeric proton shifts and changes in conjugation patterns. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 1911 and ionization energies for HOMO-1 and HOMO-2 are not available from non-EPT theoretical approaches. The HOMO and HOMO-2 Dyson orbitals are of type and resemble closely the 6 and 5 orbitals, whereas the HOMO-1 Dyson orbital has the same topological features as the 29 orbital seen
Journal of Molecular Structure, 2009
The Raman (3700-100 cm À1 ), infrared (4000-200 cm À1 ), mass spectrum and 1 H NMR temperaturedependent study of adenine have been recorded. Quantum chemical calculations were carried out for N(9)H-amino, N(7)H-amino, N(9)H-imino and N(7)H-imino adenine tautomers using RHF, B3LYP and MP2 with full electron correlation up to 6-311++G(d,p) basis set. The computational results reveal the non-planar N(9)H-amino conformer of adenine to be the most stable structure of adenine. The planar (C s ) form of N(9)H-amino adenine is found to represent a transition state, lying 8 cm À1 above the non-planar conformer and with one imaginary frequency. Comparison between theoretical and experimental 1 H NMR spectra favors the assignment of the signals to N9(H) and N7(H)-amino tautomers over the corresponding imino tautomers. On the other hand, the recorded IR, Raman and 13 C NMR spectra were fully consistent with N9(H)-amino adenine tautomer, therefore it is the only tautomer in both the gas and solid phases and in solution. Moreover, the results of NH 2 potential surface scans utilizing B3LYP and MP2 = full methods at 6-31G(d) basis also support the non-planarity of N(9)H-amino adenine. The mass spectral measurements indicate the presence of 3% adenine dimmer which indicates weak inter-molecular hydrogen bonding interactions in adenine. Additionally, intramolecular hydrogen bonding is also predicted between N 1 and H 15 atoms. The theoretical infrared and Raman spectra have been successfully simulated by means of both DFT and MP2 calculations, allowing the interpretation of the complex bands observed. Aided by normal coordinate analysis, potential energy distributions and the calculated force constants, a revised and accurate vibrational assignment for all fundamentals has been provided for the non-planar N(9)H-adenine tautomer. The results are reported herein and compared with similar molecules whenever appropriate.
Outer valence orbital response to proton positions in prototropic tautomers of adenine
Journal of Computational Methods in Sciences and Engineering, 2007
Orbital response to proton positions in the prototropic tautomers of adenine (Ade-N1, Ade-N3, Ade-N7 and Ade-N9) has been studied in position space and momentum space using dual space analysis (DSA). Based on the electronic structures of our previous density functional theory (DFT-BP86/TZ2P and BP86/QZ4P) study of adenine tautomers (J. Phys. Chem. A, 110(2006)4012), variations in properties such as ring perimeters, dipole moments, Hirshfeld charges, vertical ionization spectra and orbital theoretical momentum distributions (MDs) of these tautomers are compared, in order to understand the impact of the mobile proton positions in the purine ring. It is found that the proton relocation causes only small perturbations in isotropic properties such as geometries and vertical ionization energies in the outer valence space of adenine. Molecular polarity and dipole moments differentiate the tautomers. Hirshfeld charges divide the nitrogen sites of the tautomers into amino (single bonds) and imino (at least one double bond) nitrogen sites. Adenine tautomerization is essentially a σ-bonding phenomenon with little perturbation to the π-bonding framework. That is, the π (or a) orbitals, including the frontier orbitals such as the highest occupied molecular orbital (HOMO), 6a , and the third HOMO (HOMO-2), 5a , do not respond apparently to the proton relocation (note that the next HOMO (HOMO-1) is 29a , a σ orbital). Only relevant σ or a orbitals residing within the purine plane, such as 21a − 24a and orbital 27a , respond significantly to the proton positions. The present study demonstrates that the tautomer electronic structures depend not only on three dimensional geometries but also on the electron density distributions.
Systematic quantum chemical study of DNA-base tautomers
Journal of Computational Chemistry, 2004
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 triplequality 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.
Ionization Energy Thresholds of Microhydrated Adenine and Its Tautomers
The Journal of Physical Chemistry A, 2008
In the present work the vertical and adiabatic ionization energy thresholds (IET) of adenine, and its amino and imino tautomers complexed with 1-3 water molecules are presented. The vertical and adiabatic IETs have been calculated at the B3LYP and P3 levels of theory, using the standard 6-31++G(d,p) basis set. The results show that there is hardly any effect of microhydration on the vertical ∆IET of adenine, which is at odds with the experimental values determined by Kim et al. (J. Phys. Chem. 1996, 100, 7933). In an attempt to assign the experimental ∆IET values, calculations have been performed on the microhydrated amino and imino tautomers of adenine. Vertical ∆IET calculations and adiabatic ∆IET calculations on adenine N7H tautomers complexed with water are in better agreement with the experimental results than are calculations involving the canonical (N9H) form of adenine.
Journal of the American Society for Mass Spectrometry, 2020
Cation radicals of adenine (A •+) and 9-methyladenine (MA •+) were generated in the gas phase by collisioninduced intramolecular electron transfer in copper−terpyridine− nucleobase ternary complexes and characterized by collisioninduced dissociation (CID) mass spectra and UV−vis photodissociation action spectroscopy in the 210−700 nm wavelength region. The action spectra of both A •+ and MA •+ displayed characteristic absorption bands in the near-UV and visible regions. Another tautomer of A •+ was generated as a minor product by multistep CID of protonated 9-(2-bromoethyl)adenine. Structure analysis by density functional theory and coupled-clusters ab initio calculations pointed to the canonical 9-H-tautomer Ad1 •+ as the global energy minimum of adenine cation radicals. The canonical tautomer MA1 •+ was also calculated to be a low-energy structure among methyladenine cation radicals. However, two new noncanonical tautomers were found to be energetically comparable to MA1 •+. Vibronic absorption spectra were calculated for several tautomers of A •+ and MA •+ and benchmarked on equation-of-motion coupled-clusters excited-state calculations. Analysis of the vibronic absorption spectra of A •+ tautomers pointed to the canonical tautomer Ad1 •+ as providing the best match with the action spectrum. Likewise, the canonical tautomer MA1 •+ was the unequivocal best match for the MA •+ ion generated in the gas phase. According to potential-energy mapping, MA1 •+ was separated from energetically favorable noncanonical cation radicals by a high-energy barrier that was calculated to be above the dissociation threshold for loss of a methyl hydrogen atom, thus preventing isomerization. Structures and energetics of all four DNA nucleobase cation radicals are compared and discussed.
The Journal of Physical Chemistry B, 2008
The amino group in adenine plays a key role in formation of hydrogen bonds in nucleic acids and in other molecular systems. Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. Ab initio MP2 and density functional B3LYP methods with various basis sets have been used to calculate the optimized structure and the infrared spectrum of adenine (the N9-H tautomer). Calculations at the MP2 level with larger basis sets tend to decrease the degree of pyramidalization of the C-NH 2 group, whereas the B3LYP method consistently yields the planar or nearly planar structure of adenine. MP2 complete basis set (CBS) limit method with the aug-cc-pVTZ f aug-cc-pVQZ (aTZ f aQZ) extrapolation scheme has predicted very small planarization barrier of adenine, 0.015 kcal/mol, which is in very good agreement with the MP2-predicted planarization barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III, J. Chem. . Similar results were obtained in calculations by the coupled cluster CCSD(T) CBS method. Thus, it can be concluded that the amino group in adenine, in the gas phase, is very flexible with a small degree of nonplanarity. Extremely low planarization barrier implies that adenine requires very little energy to conform the structure of the amino group to formation of the complementary hydrogen bonds with other molecules. This fact is very important for base pairing in nucleic acids or other polymers containing adenine residues. The anharmonic frequencies of adenine have been calculated at the B3LYP/6-311++G(df,pd) level of theory. The theoretical results show excellent agreement with the available experimental data. The revised assignment of the infrared spectrum of adenine in Ar matrix has been made. The predicted anharmonic frequency of the NH 2 inversion, 181 cm -1 , is supported by the experimental data. It is demonstrated that the vibrational frequencies and potential energy distribution (PED) obtained from the B3LYP calculations are more reliable than those obtained at the MP2 level.
Electron affinities and ionization potentials of nucleotide bases
Chemical Physics Letters, 2000
Density-functional theory (B3LYP functional) is used to investigate the ionization potentials and electron affinities of the DNA and RNA nucleotide bases. For the first time, anions lying lower in energy than the neutral species have been calculated for both thymine and uracil (i.e., positive adiabatic electron affinities). Additionally, the calculations show that anion formation leads to significant geometrical changes to
Journal of Molecular Structure, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.