Nucleic Acid Bases Cytosine Research Articles

Quantum chemical studies of solvent effects on cytosine tautomers

Ab initio and density functional theory methods have been employed to study the molecular properties of tautomers of nucleic acid base cytosine in different environments; gas, water, methanol and chloroform. Molecular geometries and energetics of the tautomeric forms in gaseous phase have been obtained using B3LYP and MP2 levels of theory, implementing 6-311G(2d,2p) atomic basis set. The SCRF theory has been employed by implementing the same basis set to optimize the tautomers both in polar solvent (water, methanol) and apolar solvent (chloroform) and the solvent effect has been studied. The structural and energetical parameters of all the conformers have been analyzed. Chemical hardness and chemical potential have been calculated at HF/6-311G(2d,2p) level of theory for all the optimized structures, and the principle of maximum hardness has been tested. NMR studies have been carried out on the basis of Cheeseman coworker’s method at B3LYP/6-311G(2d,2p) level of theory, to analyze the molecular environment as well as the delocalization activities of electron clouds. Vibrational frequency analyses have been performed and the stationary points corresponding to local minima without imaginary frequencies have been obtained for all the optimized structures.

Modelling the nanoscale patterning of nucleic acid base pairs deposited on graphite

Interactions between graphite and nucleic-acid base pairs are investigated. An existing polarizable potential that uses distributed multipoles up to and including quadrupoles is extended to describe the graphite surface and the nucleic-acid bases cytosine and guanine. Adsorption energies and structures calculated with this potential are compared with data obtained using electronic structure theory. Structures of co-adsorbed cytosine and guanine layers are optimised and two competing arrangements, the ‘dimer-row’ and ‘quartet-row’ patterns, are compared with experimental scanning tunnelling microscopy images. We include two factors not considered in previous studies: the presence of the graphite surface and the inter-row packing. However, our findings agree with previous calculations in that the ‘quartet-row’ is energetically preferred, despite STM experiments suggesting the ‘dimer-row’ structure is observed.

Electron Transfer in Amino Acid·Nucleic Acid Base Complexes: EPR, ENDOR, and DFT Study of X-Irradiated N-Formylglycine·Cytosine Complex Crystals

Single crystals of the 1:1 complex of the nucleic acid base cytosine and the dipeptide N-formylglycine (C.NFG) have been irradiated at 10 and 273 K to doses of about 70 kGy and studied at temperatures between 10 and 293 K using 24 GHz (K-band) and 9.5 GHz (X-band) electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR-induced EPR (EIE) spectroscopy. In this complex, the cytosine base is hydrogen bonded at positions N3 and N4 to the carboxylic group of the dipeptide, and the N3 position of cytosine has become protonated by the carboxylic group. At 10 K, two major radicals were characterized and identified. One of these (R1) is ascribed to the decarboxylated N-formylglycine one-electron oxidized species. The other (R2) is the N3-protonated cytosine one-electron reduced species. A third minority species (R3) appears to be a different conformation or protonation state of the one-electron reduced cytosine radical. Upon warming, the R2 and R3 radicals decay at about 100 K, and at 295 K, the only cytosine-centered radicals present are the C5 and C6 H-addition radicals (R5, R6). The R1 radical decays at about 150 K, and a glycine backbone radical (R4) grows in slowly. Thus, in the complex, a complete separation of initial oxidation and reduction events occurs, with oxidation localized at the dipeptide moiety, whereas reduction occurs at the nucleic acid base moiety. DFT calculations indicate that this separation is driven by large differences in electron affinities and ionization potentials between the two constituents of the complex. Once the initial oxidation and reduction products are trapped, no further electron transfer between the two constituents of the complex takes place.

A theoretical study on cytosine tautomers in aqueous media by using continuum models

B3LYP/6-31++G ∗∗ and MP2/6-31++G ∗∗ calculations have been carried out to study six tautomers of the nucleic acid base cytosine in aqueous media. Solvent effects have been analyzed using the self-consistent reaction field theory with two continuum methods. Relative stabilities and optimized geometries have been calculated for the tautomers and compared with experimental data. The present results show the importance of electrostatic solvent effects in determining observable properties of the cytosine tautomers. The amino-oxo form (C1) is the most abundant tautomer in aqueous media while the other amino-oxo form (C4) is the most energetically favored when solvent effects are included. These results can be justified by the larger values of the dipole moments for both C1 and C4 tautomers. Theoretical and experimental results of the harmonic vibrational frequencies and rotational constants show good agreement.

The Polymorphism of a Cytosine Anion Studied by Electron Paramagnetic Resonance Spectroscopy

Electron addition to the nucleic acid base cytosine and several derivatives was studied in frozen aqueous solution and in aqueous glasses containing 10 M glucose, 7 M BeF2, 10 M LiCl and 8 N NaOH. Electron paramagnetic resonance spectroscopy revealed that three major types of spectra are obtained which can be classified into a group D giving a doublet (ca. 1.6 mT) and a group of triplet patterns T and T1 (ca. 3.0 mT total spread) which differ slightly in coupling values but which are both distinct from D by showing the loss of one sizeable proton coupling (ca. 1.0 mT) in deuterated solvents. Varying the type of glasses and other parameters such as pH, together with modification of the cytosine exocyclic groups, indicated that the triplet patterns represent electron adducts protonated at the amino group, whereas the doublets D should probably involve N3-protonated species. The equilibrium between doublets and triplets was found to depend strongly on the presence of Li+ and Be2+ and less strongly on pH or the presence of Na+, the former group of ions inducing the triplets. It is suggested that the influence of the ions derives mostly from their strength in stabilizing the amino-protonated tautomer of the electron adducts.

Cytosine reflectance measurements using electron energy loss spectra and synchrotron radiation

The reflectivity of thin films of the nucleic acid base cytosine (C 4N 3OH 4) has been calculated from the optical constants determined from electron energy loss spectra. This calculated reflectivity was then compared with the reflectivity as measured using synchrotron radiation in the region 4–24 eV. The agreement of the measured and calculated reflectance confirms the correctness of the optical constants as determined by electron spectroscopy.