Thymine dipole moments

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... 

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)... 

The second experimental measure of the orientation of the dipole moment in the ground state of the bases was made by Seibold and Labhart405 for uracil and thymine. The direction of the ground state dipole moment with respect to the transition moment in the lowest excited singlet state has been determined from the influence of an... 

It is interesting to look at the effect of substituents on the dipole moment of uracil (or thymine). An examination of the data collected in Table XX shows that among the four positions (N-l, N-3, C-5, C-6) available for substitution, the one at C-6 is the most sensitive. An alkyl substituent at C-6 of uracil (or thymine) increases the dipole moment by about 0.4 0.5 D, while the same substituent at N-l, N-3, or C-5 has only a small effect. Similarly, a halogen does not greatly alter the dipole moment of the molecule when at C-5 whereas 6-halogen decreases the value of the dipole moment considerably (cf. the data for 1,3- dimethyl-uracil and for its 5- and 6-chloro derivatives, Table XX). An attempt has been made by Kufakowska and Wierzchowski402 to interpret these... 

For dipole moments of derivatives of dihydrouracils and dihydrothymines, see ref. 368, and for dipole moments of dimers of thymine and dihydrothymine, see ref. 367. 

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... 

Dipole moment of the adenine-thymine base pair has also been calculated. 

Table 13. Vertical singlet mt and nK excitation energies (AE, eV), oscillator strengths (f), transition moment directions ( ,°) and dipole moments ([i, Debye) of thymine in the isolated and hydrated forms at the CIS/6-31 lG(d,p)//HF/6-31 lG(d,p) level.

Among the computer-efficient yet reliable methods for geometry optimization of NABs are the MP2 and DFT (B3LYP) approximations with the 6-31G(d,p) basis set. The latter level also proves to be extremely valuable for predicting the IR harmonic frequencies and intensities. Tables 2 and 3 present experimental and calculated rotational constants and dipole moments for the normal tautomers of uracil and thymine and three experimentally characterized forms of... 

Table 2 Rotational Constants (MHz) and Dipole Moment (D) of Uracil and Thymine Calculated with 6-3IG(d,p) Basis Sel ...

Ethyl acetate (dielectric constant = 6.02 at 20 C, Dipole Moment = 1.88 D) and ethanol (dielectric constant = 23.8 at 20°C, Dipole Moment = 1.68 D) are aprotic and nonpolar solvents. The l- -octylth-ymine in these solvents forms hydrogen-bonded pairs, and then form double layers by the stacking interaction of thymine bases. Finally, the double layers aggregate by van der Waals interaction to form... 

In Form III from acetonitrile (Type 2), both stacking of the thymine bases and crystallization of the alkyl chains are found. Acetonitrile (dielectric constant = 37.5 at 20°C, Dipole Moment = 3.44 D) is an aprotic and polar solvent. Also, in acetonitrile, thymines form hydrogen-bonded pairs at first. For the association of the hydrogen-bonded pairs, the stacking interaction of thymine bases and the van der Waals interaction of the long alkyl chains occur at the same time. In this crystal, acetonitrile interacts with C2-0 of thymine to give an inclusion crystal Rotation of the thymine bases in crystal is possible because included acetonitrile is mobile. The formation of the inclusion crystal may be kinetic control, but slow evaporation of acetonitrile gives thermodynamically stable plates. 

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