The Amino Group in Adenine: MP2 and CCSD(T) Complete Basis Set Limit Calculations of the Planarization Barrier and DFT/B3LYP Study of the Anharmonic Frequencies of Adenine (original) (raw)
Related papers
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.
Anharmonic vibrational spectroscopy and investigation of intramolecular mode couplings in adenine
Vibrational Spectroscopy, 2011
Vibrational frequencies for the nucleobase adenine are calculated by the vibrational self-consistent field (VSCF) and correlation corrected vibrational self-consistent field (CC-VSCF) methods using Hartree-Fock (HF), density functional theory (DFT) and second order Møller-Plesset (MP2) theories. A large number of potential energy surface (PES) points were computed in the anharmonic calculations corresponding to each method. The quartic force field (QFF) approximation was used to generate the full grid of points for the VSCF solver. We have implemented our new procedure for computing the mode-mode coupling integrals in the 2-mode coupling representations of the quartic force field (2MR-QFF) for prediction of coupling magnitudes. Calculations were performed using the 6-31G(d,p) basis set. Comparison of the calculated ab initio anharmonic spectra with Ar matrix experimental data of adenine reported in the literature reveals that, the CC-VSCF (DFT) wavenumbers show the best agreement. The experimental geometric parameters of adenine are compared with the theoretically optimized molecular structural parameters. These are found to be in good agreement. Vibrational assignments are based on the calculated potential energy distribution (PED) values.
Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study
Physical Chemistry Chemical Physics, 2010
The self-organized adenine ribbon is studied theoretically. The experimental evidence for the formation of such a ribbon has been found in the crystal structure of the supramolecular system [Dobrzyn´ska and Jerzykiewicz, J. Am. Chem. Soc., 2004, 126, 11118], and the striking structural feature is the fact that both the Watson-Crick and Hoogsteen faces of adenine are involved in the hydrogen bonding within the ribbon. The structure and physical properties of the monomer and five clusters of adenine (Ade) n (where n = 2, 3, 4, 5, 6) with AA2 2 configuration have been studied by means of the B3LYP, RI-TPSS, RI-TPSS-D (augmented with the dispersion term) and RI-MP2 methods using the 6-311+G(d,p), cc-pVTZ and TZVP basis sets. It is shown that among the investigated adenine clusters only the dimer has the planar structure. The evaluation of the three-body contribution to the total binding energy of adenine trimer has been performed at different levels of theory. All the methods consistently indicate that this term is positive and small (less than 0.5 kcal mol À1 ) which corresponds to a weak anti-cooperative effect, in adenine trimer. The differences between the total electronic energies obtained at the RI-TPSS/TZVP-D and RI-TPSS/TZVP levels of theory have shown that the London dispersion forces stabilize the adenine cluster containing 12 or more molecules by about À8 kcal mol À1 per molecule. The results from the DFT symmetry adapted perturbation theory analysis have revealed that the contribution of dispersion to the binding energy of the adenine ribbon is about 25%.
Influence of hydrogen bonding on the geometry of the adenine fragment
Journal of Molecular Structure, 1996
The crystal structures of two adenine derivatives, N(6),9-dimethyl-8-butyladenine (I) and its hydrate (1 : 1) (II), have been determined by single-crystal X-ray diffraction. The geometrical features of both structures are discussed. The influence of protonation, substitution and hydrogen bond formation on the geometry of the adenine fragment was studied, based on data retrieved from the Cambridge Structural Database. Total correlation analysis showed mutual correlation between the structural parameters in the adenine ring system; partial correlation calculations for the adenine nucleoside fragments suggest intercorrelation between the parameters of the hydrogen bonding involved in base pairing and the N(adenine)-C(sugar) bond through the adenine fragment; few such correlations were found for fragments without the sugar substituent.
Theoretical Chemistry Accounts, 2010
The equilibrium structures, binding energies, vibrational harmonic frequencies, and the anharmonic corrections for two different (cyclic and asymmetric) urea dimers and for the adenine-thymine DNA base pair system have been studied using the second-order Møller-Plesset perturbation theory (MP2) method and different density functional theory (DFT) exchange-correlation (XC) functionals (BLYP, B3LYP, PBE, HCTH407, KMLYP, and BH and HLYP) with the D95V, D95V**, and D95V??** basis sets. The widely used a posteriori Boys-Bernardi or counterpoise correction scheme for basis set superposition error (BSSE) has been included in the calculations to take into account the BSSE effects during geometry optimization (on structure), on binding energies and on the different levels of approximation used for calculating the vibrational frequencies. The results obtained with the ab initio MP2 method are compared with those calculated with different DFT XC functionals; and finally the suitability of these DFT XC functionals to describe intermolecular hydrogen bonds as well as harmonic frequencies and the anharmonic corrections is assessed and discussed.
Normal coordinate analysis and vibrational spectra of adenosine
Biospectroscopy, 1997
The Fourier transform infrared and Fourier transform Raman spectra of adenosine in the polycrystalline state were recorded in the 4000-to 30-cm 01 spectral region as part of a series of normal coordinate analyses of nucleic acid components and their analogues carried out in our laboratory. The harmonic frequencies and potential energy distributions (PED) of the vibrational modes of adenosine are calculated by two different methods: a classical molecular mechanics method and the semiempirical molecular orbital (MO) method, PM3. The results of both computational methods, based on Wilson's matrix method, are compared with observed spectra, and an assignment of the vibrational modes of adenosine is proposed on the basis of the PED and the results of calculations for the 1,3-15 N 2 , 2-13 C, 8-2 H, and 1-2 H isotopomers. It is found that the wavenumbers can be calculated with remarkable accuracy (É1% deviation in most cases), with the classical mechanics method, by transferring a sufficiently large set of available harmonic force constants, thus permitting a reliable assignment. The semiempirical MO method, PM3, is found to be useful for the assignment of experimental frequencies, although it is less accurate (É10% deviation). Infrared intensities calculated by this method did not coincide with the experimental values. Certain out-ofplane vibrations in the base, not reported in previous studies, have been observed. The performance of both methods was related to the crystallographic and ab initio data available. Previous normal coordinate calculations for the adenine base and the nucleoside 5-dGMP are compared with the present results and discussed.
Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study
New Journal of Chemistry, 2013
A full conformational study of solid-state anhydrous adenine is reported, using vibrational spectroscopy techniques coupled to DFT calculations, for the isolated molecule and the solid. In both cases, the N9Hamino tautomer was found to be the predominant species, followed by the N7H-amino form. An excellent agreement was achieved between experiment and theory, both for wavenumbers and intensities (without the need for scaling). A complete spectral assignment was performed, since all vibrational spectroscopic techniques were available to this study -FTIR, Raman and INS -allowing us to detect and interpret even the lowest frequency vibrational bands, not previously accessed. The quantum mechanical calculations presently carried out represent the highest theoretical level applied so far to the study of nucleobases.
Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine
2006
In this study, we have investigated 12 tautomers of the DNA base adenine at the BP86/TZ2P and BP86/QZ4P levels of density functional theory. The vertical and adiabatic ionization energies of all tautomers were determined as the difference in energy between the radical cation and the corresponding neutral system. Furthermore, an evaluation is made for the eigenvalue spectra calculated with the SAOP functional, which is shown to lead to substantial improvements for orbital energies compared to BP86.
A Theoretical Investigation of Excited-State Properties of the Adenine−Uracil Base Pair
Journal of Physical Chemistry A - J PHYS CHEM A, 2002
Molecular geometries of adenine-uracil (AU) base pair were optimized in the ground and selected low-lying singlet ππ* and nπ* excited states. The ground-state geometry optimized at the Hartree-Fock level of theory without symmetry restrictions was found to be planar; the predicted planarity was validated by harmonic vibrational frequency calculations. Excited states were generated employing the configuration interaction technique involving singly excited configurations (CIS method) using a ground-state-optimized geometry, and this was followed by excited-state geometry optimizations under planar symmetry. The 6-31++G(d,p) basis set was used in all calculations. The computed electronic transitions of adenine and uracil after linear scaling were found to be in good agreement with the corresponding experimental data. Electronic excitations were found to be localized at either of the monomeric units. It is predicted that among the states studied here the AU base pair has one charge transfer type singlet excited state lying slightly higher in energy. This state is characterized by the excitation of an electron from the occupied orbitals of the adenine moiety to the virtual orbitals of the uracil moiety. In the S 4 (ππ*) singlet excited state where the excitation is localized at the uracil moiety of the AU base pair, a large increase in the C′5-C′6 bond length of uracil is revealed. Such a large increase can account for the photophysical reactivity of pyrimidines in view of photodimerization. The base pair geometry is predicted to be largely destabilized under nπ* excitations.