Density functional study of various thiouracil tetrads

Journal of Molecular Structure: THEOCHEM 806 (2007) 159–164 www.elsevier.com/locate/theochem

Density functional study of various thiouracil tetrads Fancui Meng

*

State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, PR China Tianjin State Key Laboratory of Pharmacokinetics and Pharmacodynamics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, PR China Received 21 September 2006; received in revised form 20 November 2006; accepted 20 November 2006 Available online 1 December 2006

Abstract In this paper the substituent effects caused by thiouracil (TU) on uracil tetrad have been investigated. The results of geometries, energies, frequencies and electronic structures have been presented. The outcomes show that the tetrads become more and more unstable as from U4 to 24TU4 through 2TU4 and 4TU4 (BSSE corrected binding energies), at the same time, both the vertical electron affinity and the adiabatic electron affinity increase as from U4 to 24TU4, which indicates that it turns to be easier and easier to inject an electron on the tetrad as from U4 to 24TU4. The stabilization energies and N3–H3 harmonic frequencies of U4 and 2TU4 are similar, while those of 4TU4 and 24TU4 are alike. The HOMO orbital of 2TU4 is different from U4 while 4TU4 and 24TU4 have similar constituents for both HOMO and LUMO orbitals. Ó 2006 Elsevier B.V. All rights reserved. Keywords: Thiouracil; Uracil tetrad; Theoretical study; Anion

1. Introduction Chemically modified bases, such as 5-halouracils, 6-thioguanine, 2-thiouracil, and 4-thiouracil etc., have attracted extensive interests due to their numerous pharmacological, biochemical, and biological capabilities [1–4]. The nucleic acid bases with sulfur atom instead of oxygen atom have been a subject of considerable interest since they have been detected in natural tRNA [5]. Numerous sulfur-substituted bases have been used as drugs and they are important from the clinical point of view. Although the thiobases have the same distribution of hydrogen donors and acceptors as the standard bases, the sulfur atom may induce changes in the properties of bases and their interactions, and further influence the structure of DNA base. For example, the partial incorporation of deoxy-6-SG is effective in inhibiting the formation of G tetrads in guanine-rich oligodeoxyribonucleotides [6]. Thiouracil’s derivatives attract attention not only because of their unclear role in nucleic acid structures but also because of their exhibited pharmacological *

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0166-1280/$ - see front matter Ó 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.theochem.2006.11.023

activities [7]. 2-Thiouracil and 4-thiouracil can be used as anticancer and antithyroid drugs [8] and 2,4-dithiouracil analogues were tested for anti-conflict and anaesthetic activity in rats or mice [9]. Uracil tetrads have been detected experimentally [10] and have been studied theoretically [11–13]. In this paper the effect that thiouracil caused on uracil tetrad has been investigated. The existence of the anions of uracil has been theoretically and experimentally studied in recent years [14– 16].Various experiments on the uracil anion system [17] show evidence of nuclear motion in DNA, which is triggered by electron attachment. The stability of excess electrons in uracil clusters can lead to an insight into electron transfer reactions in DNA, which has many applications when studying its potential to act as an electrical conduct [18]. Therefore, in this paper besides the various thiouracil tetrads, their anions have also been calculated. 2. Calculation schemes Uracil bases could form hydrogen bonds through N3– H3  O4 and N1–H1  O4 linkages with neighboring uracil molecules(The atom labels see Fig. 1) [19]. However,

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The stabilization energy was defined as the energy difference between the tetrad and its corresponding monomers,

H H

H5

N

X2

X2

N3 H3

H5 H

N X4

X2

H

X4 X4

N H

H3 N3

X4 N3 H3

DE ¼ EðXU4Þ  4EðXUÞ

H

H5

H3 N3

X2 N

H5

H H

Fig. 1. Structure and atom labels of various tetrads.

as N1 is the atom that connects the uracil base and the ribose ring, N1–H1 is blocked as a donor group in uracil nucleotide. As shown in PDB 1rau [10], uracil tetrad have two structures one is the N3–H3  O4 bonded tetrad at the 3 0 -terminus, the other is the C5–H5  O2 bonded tetrad at the 5 0 -terminus. The N3–H3  O4 type is a little more stable than the C5–H5  O2 type [11], so the N3–H3  O4 type is the one we studied. Conventional ab initio and DFT methods have been used to predicate the interactions between nucleic acid bases [20–22] and have been proved to be useful since they can get data that are not available by experiments, such as information about the interaction energies and cooperative effects. DFT method has proved to be successful in the close agreement between calculated and experimental geometrical parameters. Uracil tetrad (U4), 2-thiouracil tetrad (2TU4), 4-thiouracil tetrad (4TU4), and 2,4-thiouracil tetrad (24TU4) and their corresponding anions have been optimized using density functional method B3LYP, which is the Becke’s hybrid three-parameter functional combined with the Lee–Yang–Parr non-local correlation functional. The basis set used is 6-31G(d). Vibrational frequency calculations have been performed on the optimized geometries at the same level and the analysis show that all the obtained structures have no imaginary frequencies, which indicates that all are local minima. Frequency outcomes have been saved every 10 cm1 in Gaussview program and the saved data have been used to plot the vibrational frequency spectrum. Considering that such system is hydrogen-bonded system and its negatively charged tetrad is anionic system, the obtained minima have been further optimized with a larger basis set including both polarization function and diffuse function 6-31++G(d,p). Natural bond orbital (NBO) analysis have been calculated using B3LYP method at 6-311++G(d,p) level. The optimized geometries and the frontier orbitals are all viewed by Gaussview program. All calculations have been performed using Gausssian 98 package.

All stabilization energies have been corrected for basis set superposition error (BSSE) using the counterpoise procedure of Boys and Bernardi [23]. In addition to the stabilization energy, the approach considered above allows for an estimation of the vertical electron affinity (VEA) of neutral tetrad. VEA was predicted as the energy difference between the neutral and anionic species at their neutral geometries. It is given by VEA ¼ E0 ðXU4Þ  E ðXU4Þ The adiabatic electron affinity (AEA) was predicted as the energy difference between the neutral and anionic species at their respective optimized geometries. It could be expressed by AEA ¼ E0 ðXU4Þ  E ðXU4 Þ Positive values of AEA suggest stability towards ionization, and a negative value tells us that there is instability in the anion formation, relative to the neutral system at its equilibrium structure. Previous experimental and theoretical calculations revealed a correlation between the EA and the size of molecule [24,25]. 3. Results and discussions According to a previous study of uracil tetrad [12], both the planar and nonplanar forms of the uracil tetrad (U4) have been optimized at both the HF/6-311G(d,p) and B3LYP/6-311G(d,p) levels and the outcomes show that the nonplanar structure of U4 is a little more stable than the planar structure. Considering that the thiobases have the same distribution of hydrogen donors and acceptors as the standard bases, the various thiouracil tetrads have also been arranged to the nonplanar structure with C4 symmetry as uracil tetrad. Optimizations of 2TU4 starting from C4 symmetry converged to practically planar C4hsymmetric structures. Thus 2TU4 has C4h symmetry and the other tetrads have C4 symmetry. The consequent harmonic frequency analysis shows that all the obtained local minima are real minima. The corresponding anions have been found to be local minima with the same symmetry as their neutral system except 24TU4, which has C2 symmetry. 3.1. Geometric structure of various substituted tetrads and its anions Fig. 2 is the optimized geometries of various substituted uracil tetrads and the atom labels are shown in Fig. 1. From Fig. 2 we can see that all the tetrads have bowlshaped geometry except 2TU4, which is predicted to be planar. As to U4, every uracil molecule is connected with two neighboring uracil molecules through two kinds of pair

F. Meng / Journal of Molecular Structure: THEOCHEM 806 (2007) 159–164

161

Fig. 2. Optimized geometries of various tetrads (a) U4 (b) 2TU4 (c) 4TU4 (d) 24TU4.

coupling hydrogen bonds: N3–H3 in one uracil and O4 in the neighboring uracil form one hydrogen bond and C5– H5 and O2 form a C–H  O type hydrogen bond. At the same time each uracil is a donor and an acceptor in four hydrogen bonds of the N–H  O type [26]. Sulfur atom has larger atomic radium and less electronegativity than oxygen atom, so it is not as a good hydrogen bond acceptor as oxygen atom. Therefore, the sulfur atom makes the hydrogen bond weak and the hydrogen bond distance enlarged, which could be seen from the listed geometrical parameters in Table 1. As to 2TU4, the hydrogen bond C5–H5  S2 is weaker than C5–H5  O2 in U4, and on

the other hand, sulfur atom has larger radius than oxygen atom, thus make the bond distance S2  H5 much larger, which further cause the bowl-shaped structure to be planar. As to 4TU4, the hydrogen bond N3–H3  S4 is much weaker than N3–H3  O4 and at the same time C5– H5  O2 is much stronger than C5–H5  S2, thus make the bowl-shaped structure much deeper. The H3  X4 distance increases in the sequence of ˚ in U4 U4 < 2TU4 < 4TU4 < 24TU4, which is 1.803 A ˚ in 24TU4. Comparing the geometric parameand 2.532 A ters of the four tetrads, one can find that U4 and 2TU4 have similar hydrogen bond parameters while those of

Table 1 ˚ and A is bond angle in °) Selected bond distances and bond angels of various substituted uracil tetrads (R indicates bond distance in A R(H3  X4) d

U4 2TU4 4TU4 24TU4

a b c d e

1.803[1.816] 1.801b 1.836[1.838] 2.483[2.514] 2.532[2.518]e [2.512] 2.523c

R(N3–H3)

A(N3–H3  X4)

R(X2  H5)

R(X4  X4 0 )a

R(X4  X2 0 )a

1.034[1.035]

170.9[169.6] 169.0 173.7[173.8] 158.6[158.0] 158.9[157.6] [158.8] 159.5

2.642[2.542] 2.827 2.827[2.847] 2.468[2.405] 2.945[2.893] [2.897]

3.597[3.630] 3.578 3.473[3.478] 4.052[4.140] 3.818[3.822] [3.812] 3.805

3.656[3.663] 3.654 3.984[4.011] 4.236[4.230] 4.604[4.611] [4.622] 4.602

1.034[1.034] 1.027[1.027] 1.026[1.027] [1.027] 1.026

Measured between the X atoms of the two neighboring bases. Calculated at B3LYP/6-311G(d,p) level from Ref. [12]. Calculated at B3LYP/6-31G(d,p) level from Ref. [13]. Values in brackets are the corresponding parameters of the anions. 24TU4 anion has C2 symmetry and geometrical parameters of both two types are listed.

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4TU4 and 24TU4 are alike. For example, the hydrogen bond angle of N3–H3  X4 is 170.9° and 173.7° in U4 and 2TU4, while it is 158.6° and 158.9° in 4TU4 and 24TU4, respectively. Table 1 also lists the optimized geometrical parameters of the four tetrads at their anionic states. When injecting an electron, the bond distance of H3  X4 increased as for U4, 2TU4, and 4TU4 and the increase are 0.013, ˚ , respectively, while it decreased as for 0.002, and 0.031 A ˚ , which may be 24TU4 and the decrease is 0.014/0.02 A due to the symmetry change of the tetrad. The variation of bond distance X2  H5 is more obvious than H3  X4 ˚ as for U4 from neutral state and it is shortened by 0.1 A to anionic state, while the variation in the other three tetr˚ . The bond length of N3–H3 and ads is from 0.02 to 0.06 A bond angle of N3–H3  X4 are almost unchanged as from neutral state to anionic state. The change of bond length ˚ and that of bond angle N3–H3 is less than 0.001 A N3–H3  X4 is 1° or so. 3.2. Relative stability of various substituted uracil tetrads The stabilization energy of U4 of our results at B3LYP/ 6-31++G(d,p) level is 27.03 kcal/mol without BSSE correction and 24.87 kcal/mol after BSSE correction, while the corresponding values at B3LYP/6-311G(d,p) level of Gu and Leszczynski [12] are 30.73 and 24.93 kcal/ mol, respectively. This imply that B3LYP/6-31++G(d,p) method with BSSE correction is enough to obtain suitable energy outcomes. Table 2 lists the energetic properties of various tetrads and from it we could find that U4 and 2TU4 have similar binding energies while 4TU4 and 24TU4 have much higher binding energies of about 10 kcal/mol. BSSE listed in Table 2 indicates that as for this system, the B3LYP method with 6-31++G(d,p) basis set results BSSE value as little as 2 kcal/mol or so, which is much smaller than that for B3LYP method with 631G(d,p) basis set whose range of BSSE is 4–11 kcal/mol [13]. BSSE corrected binding energies show that the tetrads become more and more unstable as from U4 to 24TU4. In order to examine the quantitative stability of the anions, the vertical electron affinity (VEA) and the adiabatic electron affinity (AEA) for the various substituted uracil tetrads were represented in Table 2. From this table, we notice that excess electron attachment is favored for the

Table 2 Energetic properties of various substituted uracil tetrads

U4 2TU4 4TU4 24TU4

DE

BSSE

DEBSSE

VEA

AEA

27.04[30.73]a 26.84 12.01 12.34[15.35]b

2.17 2.49 2.07 1.94

24.87[24.93]a 24.35 12.01 10.40[11.18]b

5.45 15.69 24.82 31.32

7.51 15.97 26.70 33.34

All energies are in kcal/mol. a Calculated at B3LYP/6-311G(d,p) level from Ref. [12]. b Calculated at B3LYP/6-31G(d,p) level from Ref. [13].

uracil tetrad as shown by a positive electron affinity (EA) of 7.51 kcal/mol as computed by the B3LYP method with 6-31++G(d,p) basis set. This system is also stable relative to vertical electron attachment yielding a B3LYP result of 5.45 kcal/mol. This latter value is of importance due to the fact that it is an experimentally observable value from PES experiments [27]. The vertical electron detachment energies reveal stability for the other thiouracil substituted tetrads. Both the VEA values and the AEA values increase according to the sequence of U4 < 2TU4 < 4TU4 < 24TU4, which indicates that it turns easier and easier to inject an electron as from U4 to 24TU4 and the stability sequence of the tetrad anions is U4 < 2TU4 < 4TU4 < 24TU4. Our results suggest that thiouracil tetrads are expected to be the major electron capture after RNA that containing these modified bases is exposed to ionizing radiation. Interestingly, the energy difference between the calculated VEA and AEA for various uracil tetrads is between 0.28 and 2.02 kcal/mol, which indicates that although the geometries of the four tetrads are different the energy gained from the nuclear relaxation following anion formation is nearly identical. 3.3. Frequency analysis Harmonic frequency analysis shows that none of the tetrads has imaginary frequencies, which indicates that all the tetrads are local minima. From Fig. 3, we could see that the stretching vibration mN3–H3 of U4 and 2TU4 are alike, both the vibrational frequencies and the IR intensities are close to each other. At the same time, mN3–H3 of 4TU4 and 24TU4 are similar. As we known, the X–H bond usually elongates (or the X–H stretching vibration is red shifted) in the formation of hydrogen bond because of the charge transfer from Y to X–H orbital (where X–H is a hydrogen bond donor and Y is a hydrogen bond acceptor) [28]. The mN–H is red shifted from 3603.85 cm1 in U to 3277.14 cm1 in U4 and the red shift is 426.71 cm1, the red shift of mN3–H3 in uracil dimmer is 375 cm1 from FT-IR spectroscopic study [29], from which we can see that the experimental result is close to ours. The IR intensity increased from 57.53 km/mol in U to 2542.82 km/mol in U4. The same thing happened to the other tetrads, however, due to the fact that the electronegativity of sulfur atom is weaker than oxygen, the frequency shifts decreased as compared with that of U4, and they are 313.51, 225.06, and 197.84 cm1 in 2TU4, 4TU4, and 24TU4, respectively. This is in accord with the N3–H3 bond length changes [30]. The changes of N–H bond lengths are 0.020, 0.019, 0.012, ˚ in U4, 2TU4, 4TU4, and 24TU4 as compared and 0.010 A with the corresponding bond lengths in their monomers, respectively. On the other hand, the IR intensity of 2TU4 is a little larger than that of U4 and is 2696 km/mol, while those of 4TU4 and 24TU4 are much weaker as compared with that of U4 and they are 1200 km/mol or so. In

F. Meng / Journal of Molecular Structure: THEOCHEM 806 (2007) 159–164

163

5000 U4

4000

ν N3 -H 3

3000 2000 1000 0

0

1 000

2 000

3 000

4 000

6000 5000

2T U 4

ν N3 -H 3

4000 3000 2000 1000 0 0

1000

2000

3000

4000

3000

4TU 4

2500

ν N3 -H 3

2000 1500 1000 500 0 0

1000

2 000

3000

4000

2500

24T U 4

ν N3 -H 3

2000 1500 1000 500 0 0

1000

2000

3000

4000

Fig. 3. Vibrational frequency spectrum of various tetrads. X axis is frequency in cm1 and Y axis is IR intensity in km/mol.

conclusion, the frequency shift of stretching vibration mN–H becomes less and less as from U4 to 24TU4, and the IR intensities have been greatly strengthened as compared with their corresponding monomers. 3.4. Bonding analysis of various substituted uracil tetrads Fig. 4 shows the HOMO and LUMO orbitals of various tetrads. The LUMO orbital of U4 are mainly made up of the bonding orbital of C4–C5 and the pz orbital of N3,

Fig. 4. HOMO and LUMO orbitals of various tetrads (HOMO orbitals are on the left side and LUMO orbitals on the right side) (a) U4 (b) 2TU4 (c) 4TU4 (d) 24TU4.

C6, N7, C2, and O2. The constituents of 2TU4’s LUMO orbital are similar as that of U4 but the coefficient are much lower than that of U4. The HOMO orbital of U4 is composed of the pz orbital of N1 and C6 and the s orbital of C4. However, the HOMO of 2TU4 is quite different from that of U4 and it consists of the px orbitals of S2 at the diagonal 2TUs and the py orbitals of the other two S2 atoms. The HOMO orbital of 4TU4 is mainly made up of the p orbitals of S4 atoms and its LUMO orbital is like that of U4 but with larger constituents. The HOMO orbital of 24TU4 is mainly distributed on S4 and S2 of the two

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F. Meng / Journal of Molecular Structure: THEOCHEM 806 (2007) 159–164

diagonal 24TUs, and that on the p orbital of the other two diagonal 24TUs is less. Its LUMO orbital is just like that of 4TU4. The eigenvalues of LUMO orbitals are 1.41, 1.71, 2.21, and 2.42 eV for U4, 2TU4, 4TU4, and 24TU4, respectively, which indicates that it becomes easier and easier to inject an electron on the tetrad as from U4 to 24TU4. This is in accord with the EA outcomes. Generally speaking, the larger the energy gap is, the more stable the compound is. The energy gaps between HOMO and LUMO are 5.46, 4.62, 3.77, and 3.72 eV for U4, 2TU4, 4TU4, and 24TU4, respectively, which is also in consistent with the stabilization energy sequence. 4. Conclusion 2-Thiouracil, 4-thiouracil, and 2,4-thiouracil tetrads have been studied using density functional method at B3LYP/6-31++G(d,p) level. The differences between the aforementioned tetrads and uracil tetrad have been discussed and the main results are as follows: (1) The geometrical structures of 4TU4 and 24TU4 have nonplanar C4 symmetry as U4, but optimization of 2TU4 with C4 symmetry converged to be C4h symmetry. (2) Due to the larger atom radius and less electronegativity of sulfur atom, 2TU4 has similar binding energy as U4 while 4TU4 and 24TU4 are much more unstable than U4. VEA and AEA are all positive for the four tetrads, which suggest that the tetrads are stable towards ionization. (3) Frequency analysis indicates that the stretching vibration mN3–H3 of U4 and 2TU4 are alike while those of 4TU4 and 24TU4 are similar.

Acknowledgements This work was supported by Tianjin Municipal Science and Technology Commission (Grant No. 043185111-7). We are grateful for computer resources support from ISC of Nankai University.

References [1] V. Esposito, A. Randazzo, G. Piccialli, L. Petraccone, C. Giancola, L. Mayol, Org. Biomol. Chem. 2 (2004) 313. [2] S.D. Wetmore, R.J. Boyd, L.A. Eriksson, Chem. Phys. Lett. 343 (2001) 151. ¨ . Civcir, J. Phys. Org. Chem. 14 (2001) 171. [3] P.U [4] S. Denifl, S. Matejcik, B. Gstir, G. Hanel, M. Probst, P. Scheier, T.D. Ma¨rka, J. Chem. Phys. 118 (2003) 4107. [5] M.N. Lipsett, J. Biol. Chem. 240 (1965) 3975. [6] T.S. Rao, R.H. Durland, D.M. Seth, M.A. Myrick, V. Bodepudi, G. Revankar, Biochemistry 34 (1995) 765. [7] L. Lapinski, M.J. Nowak, R. Kolos, J.S. Kwiatkowski, J. Leszczynski, Spectrochimica Acta Part A 54 (1998) 685. [8] W. Saenger, Principles of Nucleic Acid Structures, Springer-Verlag, New York, Berlin, Heidelberg, Tokyo, 1984, Chapter 7. [9] M. Inazumi, F. Kano, S. Sakata, Chem. Pharm. Bull. 40 (1992) 2147. [10] C. Cheong, P.B. Moore, Biochemistry 31 (1992) 8406. [11] M. Meyer, T. Steinke, M. Brandl, J. Su¨hnel, J. Comput. Chem. 22 (2001) 109. [12] J.-D. Gu, J. Leszczynski, J. Phys. Chem. A 105 (2001) 10366. [13] H. Wang, F. Meng, W. Xu, C. Liu, J. Mol. Struc. (THEOCHEM). 716 (2005) 137. [14] D.M.A. Smith, J. Smets, L. Adamowicz, J. Phys. Chem. A 103 (1999) 5784. [15] C. Defrancois, H. Abdul-Carime, J.P. Schermann, J. Chem. Phys. 104 (1996) 7792. [16] S. Denifl, S. Ptasin´ska, G. Hanel, B. Gstir, M. Probst, P. Scheier, T.D. Ma¨rka, J. Chem. Phys. 120 (2004) 6557. [17] K.A. atooni, G.A. Gallup, P.D. Burrow, J. Phys. Chem. A 102 (1998) 6205. [18] D. Svozil, P. Jungwirth, Z. Havlas, Collection of Czechoslovak Chemical Communications 69 (2004) 1395. [19] M. Rozenberg, G. Shoham, I. Reva, R. Fausto, Spectrochim. Acta Part A 60 (2004) 2323. [20] C.F. Guerra, F.M. Bickelhaupt, Angew. Chem. Int. Ed. 38 (1999) 2942. [21] C.F. Guerra, F.M. Bickelhaupt, Angew. Chem. Int. Ed. 41 (2002) 2092. [22] J. Sponer, J. Leszczynski, P. Hobza, J. Mol. Struct. (Theochem) 573 (2001) 43. [23] S.F. Boys, F. Bernardi, Mol. Phys. 19 (1970) 553. [24] A. Martı´nez, J. Chem. Phys. 123 (2005) 104308. [25] C. Desfrancois, H. Abdoul-Carime, S. Carles, V. Pe´riquet, J.P. Schermann, D.M.A. Smith, L. Adamowicz, J. Chem. Phys. 110 (1999) 11876. [26] M.J. Wo´jcik, M. Boczar, M. Wieczorek, W. Tatara, J. Mol. Struc. 555 (2000) 165. [27] A.F. Jalbout, L. Adamowicz, Chem. Phys. Lett. 420 (2006) 209. [28] T. Steiner, Angew. Chem. Int. Ed. 41 (2002) 48. [29] G. Maes, M. Graindourze, J. Smets, J. Mol. Struct. 248 (1991) 89– 110. [30] F. Meng, C. Liu, W. Xu, Chem. Phys. Lett. 373 (2003) 72.