Reply to the ‘Comment on “A Fourier transform EPR study of uracil and thymine radical anions in aqueous solution”’ by D. M. Close, Phys. Chem. Chem. Phys., 2002, 4, 43

Concerning the Comment by Close¹ on our recent paper² we emphasize the following points. In our highly resolved FT EPR experiments we have determined the hyperfine coupling constants of some pyrimidine-type base radical anions in aqueous solution for all active hyperfine nuclei with high precision. By comparison of these hfc values with DFT quantum chemical calculations we conclude the uracil and thymine radical anions are nonplanar and the out-of-plane deviation of the C6–H bond is in the order of 10°. By detailed steady state EPR/ENDOR experiments³ of irradiated single crystals of similar nucleotides their radical anions were studied at low temperatures. From the direction cosines of the C6–H hfc tensor the deviation of the C6–H bond direction from the ring plane was obtained lower than 5°. In our opinion these results from two different EPR experiments are not in contradiction. The different environment for the radical anions of different parent molecules (pyrimidine-type bases in aqueous solution and nucleotides in low temperature matrices) can give rise to small changes in radical conformations.

In order to estimate the correctness of our conclusions from DFT quantum chemical calculations⁴ we have to consider three important points, firstly the choice of an appropiate basis set, secondly the influence of the dielectric solvent⁵ and thirdly the correct description of all hfc parameters obtained from the experimental spectra. From the geometry optimization all calculation methods give quite similar geometries with two structures. The first one has an approximately half-chair conformation and the second one is planar. The frequency analysis for the planar structure produces two negative frequencies indicating that this conformation is a second-order saddle point. The half-chair structure produces no negative frequencies and is a minimum in agreement with the results of Wetmore et al.⁶

To find the optimal basis set and method of geometry optimization, respectively, the results for all hfc constants of the uracil radical anion are compared in Table 1.⁴ These calculated hfc constants show us that the best agreement with all experimental values is obtained with a middle level of theory (UBLYP/6-31+G(d,p)//UMP2/6-31G(d)). This is in agreement with the results of Jolibois et al.,⁷ Carmichael,⁸ Gauld et al.⁹ and Bally and Borden.¹⁰

Table 1 UB3LYP with different basis sets calculated hyperfine coupling constants a(MHz) of uracil radical anion

Parameter Basis set	Vacuum 6-31G(d)	Vacuum 6-31+G(d,p)//MP2^a	Vacuum 6-311++G(2df,p)//6-31+G(d,p)	Vacuum 6-311++G(2df,p)//6-311+G(d,p)	ε = 78 IPCM 6-31+G(d,p)//MP2^a	Exp.
a UMP2/6-31G(d) geometry.
a(N,1)	−0.75	−0.01	−0.63	−0.56	−0.20	0
a(N,3)	3.31	3.15	1.25	1.19	3.63	4.1
a(H,1)	8.07	5.81	−0.90	−1.39	5.80	2.4
a(H,3)	−4.64	−4.54	−5.28	−4.98	−5.24	2.4
a(H,5)	−6.16	−6.39	−6.83	−6.79	−2.36	2.5
a(H,6)	16.79	26.05	4.62	1.20	16.70	35.0
∠C4C5C6H	30.0°	29.1°	22.9°	21.6°	29.1°

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The influence of the dielectric solvent water was checked with the same middle level of theory using the self-consistent reaction field (SCRF[double bond, length half m-dash]PCM and SCRF[double bond, length half m-dash]IPCM) models. The results are listed in Table 1. The comparison of all hfc values shows the best agreement between calculated and experimental data for the SCRF[double bond, length half m-dash]IPCM model in aqueous solution. Thereby, we find a strong dependence of the C6–H hfc constant on the dihedral angle C4–C5–C6–H with the maximal value in the molecular plane (a_calc(C6–H) up to 51 MHz) and minimal value at approximately 30°. Consequently, the C6–H bond should be out of the molecular plane, but smaller than 30°. A more detailed presentation of these calculations is in preparation.

References

1. D. M. Close, Phys. Chem. Chem. Phys., 2002, 4, 43.
2. J. M. Lü, J. Geimer, S. Naumov and D. Beckert, Phys. Chem. Chem. Phys., 2001, 3, 952.
3. D. M. Close, Radiat. Res., 1993, 135, 1.
4. M. J. Frisch et al., Gaussian 98, Gaussian, Pittsburgh, PA, 1998..
5. S. Naumov, A. Barthel, J. Reinhold, F. Dietz, J. Geimer and D. Beckert, Phys. Chem. Chem. Phys., 2000, 2, 4207.
6. S. D. Wetmore, R. J. Boyd and L. A. Eriksson, J. Phys. Chem. B, 1998, 102, 5369.
7. F. Jolibois, J. Cadet, A. Grand, R. Subra, N. Rega and V. Barone, J. Am. Chem. Soc., 1998, 120, 1864.
8. I. Carmichael, J. Phys. Chem. A, 1997, 101, 4633.
9. J. W. Gauld, L. A. Eriksson and L. Radom, J. Phys. Chem. A, 1997, 101, 1352.
10. Th. Bally and W. Th. Borden, Rev. Comput. Chem., 1999, 13, 1.

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