Cytosine Dipoles

The components of nucleic acids have been the subject of continuous DFT stud-ies61 S5,67 69. Jasien and Fitzgerald calculated dipole moments and polarizabilities for a series of molecules of biological interest including nucleic acid bases (adenine, thymine, cytosine, and guanine) and their pairs (adenine-thymine and cytosine-guanine)61. A good correlation between DFT(HL), experimental, and MP2 results was obtained for dipole moments and polarizabilities. More detailed analyses of DFT(SVWN) and DFT(B88/P86) results, which included vibrational frequencies, were reported for isolated bases and their... 

The dipole moment of cytosine has been calculated many times by different methods. Until very recently, no experimental data were available on this subject. A short time ago, an attempt was undertaken at the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, to measure the dipole moments of cytosine, of a number of its derivatives, and of some cytidines. Table X collects the preliminary results of these measurements. As we see, the value of the dipole moment of cytosine is relatively large (> 6.0 D), probably about... 

D higher than the dipole moment of uracil or thymine. All the quantum-mechanical calculations predicted a greater moment for cytosine (and guanine) than for uracil or thymine (and adenine). The agreement between the experimental dipole moment of cytosine and the values calculated by different methods is satisfactory (cf. Table XI)... 

From past experience,3 the direction of the calculated dipole moment of cytosine (see Tables XI and XII) is reliable. 

Dipole moment of guanine-cytosine base pair has also been calculated. h Hybridization moment. 

See Table XII for the dipole moments of different tautomers of cytosine and its derivatives as calculated in the present paper. For other CNDO/2 calculations on dipole moment of cytosine, see refs. 153, 215, 239. k CNDO/2 method modified by Del Bene and Jafife.240,241... 

Jasien and Fitzgerald62 demonstrated that the LDA dipole moments of such molecules as HF, H20, NH3, formamide, imidazole, pyridine, cytosine, match very closely the experimental ones (the relative errors between 1 and 7%). For uracil and thymine, and adenine, the differences between LDA and experimental dipole moments are slightly larger (relative errors up to 12%) and compared better to the ones derived from second-order Mpller-Plesset calculations. The authors underlined the noticeable effect the inclusion of the hydrogen 2p polarization... 

Since the suggestion of the sequential QM/MM hybrid method, Canuto, Coutinho and co-authors have applied this method with success in the study of several systems and properties shift of the electronic absorption spectrum of benzene [42], pyrimidine [51] and (3-carotene [47] in several solvents shift of the ortho-betaine in water [52] shift of the electronic absorption and emission spectrum of formaldehyde in water [53] and acetone in water [54] hydrogen interaction energy of pyridine [46] and guanine-cytosine in water [55] differential solvation of phenol and phenoxy radical in different solvents [56,57] hydrated electron [58] dipole polarizability of F in water [59] tautomeric equilibrium of 2-mercaptopyridine in water [60] NMR chemical shifts in liquid water [61] electron affinity and ionization potential of liquid water [62] and liquid ammonia [35] dipole polarizability of atomic liquids [63] etc. 

The quantities involved in these predictions are directly obtained in allvalence and all-electrons calculations. The results indicated for the dipole moments by EHT, CNDO/2 and non-empirical calculations are shown in Fig. 3 and Table III. It is rather striking that all methods predict greater dipole moments for guanine and cytosine than for uracil, which in turn should have a slightly greater moment than adenine. What is still more striking is the similarity in the directions of the moments predicted for the bases by all methods. Obviously the overall polarity of the molecules is well indicated by all procedures. A more... 

For cytosine two DBEA are reported 0.230 eV and 0.085 eV. Interestingly, the dipole bound states are observed in the PES of the dihydrates due to two-photon absorption. The first photon removes the waters and then a second photon detaches the electron from the dipole bound state. These spectra for cytosine are shown in Figure 12.3. The spectrum of the bare cytosine is shown in the inset offset by 1.5 eV. The peak at 0.230 eV is assigned to the dipole bound anion of keto-cytosine, whereas the peak at 0.085 eV is assigned to the enol form of the anion. The dipole moment of the enol form is about 4 Debye, while that for the keto form is about 6.5 Debye. The two peak intensities are quite different in the spectrum for the monomer. In the spectrum for the dihydrate the intensities are about the same. The double-photon process explains this difference. The absorption of the initial photon by the dihydrate leaves equal concentrations of two forms that are then photode-tached. In the spectrum of the bare anion the distribution reflects the equilibrium concentrations. The extra structure in the spectrum of the dihydrate can be attributed to excited states of the anion and offers a different interpretation of the onset. 

Predicted based on the value for cytosine and the similarity of the dipole moments of cytosine and guanine. 

On the basis of the present calculations on simplified hydrated models we can safely suggest that cytosine tautomerization reactions should take place at room temperature, and that the Cl Cl conversion is kinetically unfavoured by 2-4 kcal mof with respect to the Cl C3 and C4 C5 processes. Bulk solvent effects, which are not included in the present study, are expected to provide only a fine tuning of the activation energies, as variations of the dipole moment from minima to transition states are generally less than 1 Debye (Table 2). 

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