Analysis of vibrational spectra of 5-fluoro, 5-chloro and 5-bromo-cytosines based on density functional theory calculations

Spectrochimica Acta Part A 61 (2005) 1001–1006

Analysis of vibrational spectra of 5-fluoro, 5-chloro and 5-bromo-cytosines based on density functional theory calculations V. Krishnakumara,∗ , V. Balachandranb a

Department of Physics, Nehru Memorial College, Puthanampatti, Triuchirapalli 621007, India b Department of Physics, Thanthai Hans Roever College, Perambalur 621212, India Received 4 May 2004; accepted 18 May 2004

Abstract The geometry, frequency and intensity of the vibrational bands 5-fluoro, 5-chloro and 5-bromo-cytosines (5-FC, 5-ClC and 5-BrC) were obtained by the density functional theory (DFT) calculations with Becke3–Lee–Yang–Parr (B3LYP) functional and 6-31G* basis set. The effects of fluorine, chlorine and bromine substituents on the vibrational frequencies of cytosines have been investigated. The assignments have been proposed with the aid of the results of normal coordinate analysis. The observed and the calculated spectra are found to be in good agreement. © 2004 Elsevier B.V. All rights reserved. Keywords: DFT calculations; Vibrational spectra; 5-Fluoro, 5-chloro and 5-bromo-cytosines

1. Introduction Cytosine and its derivatives are the compounds of great biological importance because they are one of the constituents of nucleic acids [1,2]. The vibrational spectrum of cytosine was also predicted theoretically at different levels of approximation [3–5]. The inclusion of halogen atoms at the fifth position of the cytosine molecule leads to the variation of charge distribution in the molecule and consequently this greatly affects the structural, electronic and vibrational parameters. The vibrational spectra of the 5-fluoro, 5-chloro and 5-bromo-cytosines (5-FC, 5-ClC and 5-BrC) had already been interpreted by us [6] on the basis of normal coordinate analysis based on semiempirical methods. The philosophy of computational methods of vibrational spectroscopy [7–9] changed significantly after the introduction of quantum chemical calculations. Harmonic force fields obtained from quantum mechanics are widely used at present for the calculation of frequencies and the normal modes of vibrations. Now-a-days, sophisticated electron correlation and density ∗

Corresponding author. Tel.: +91 431 2769224; fax: +91 431 2791300. E-mail address: vkrishna [email protected] (V. Krishnakumar).

1386-1425/$ – see front matter © 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.saa.2004.05.044

functional theory calculations are increasingly available and deliver force fields of high accuracy even for large polyatomic molecules. Hence, in this study, an attempt has been made to interpret the vibrational spectra of 5-FC, 5-ClC and 5-BrC by applying the density functional theory calculations based on Becke3–Lee–Yang–Parr (B3LYP) and 6-31G* basis set. The IR and Raman intensities were also predicted theoretically. Based on that, the simulated infrared and Raman spectra were also obtained. The experimentally observed spectral data of the title compounds are found to be well comparable to that of the spectral data obtained by quantum chemical methods.

2. Experimental details The fine samples of 5-FC, 5-ClC and 5-BrC were obtained from M/s. Sigma Chemical Co., USA and used as such for the spectral measurements. The FT-Raman spectra were recorded on a computer interfaced BRUKER IFS model interferometer equipped with FRA 106 FT-Raman accessories. The spectra were recorded in the region 3500–100 cm−1 with Nd:YAG laser operating at 200 mW power continuously with 1064 nm

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V. Krishnakumar, V. Balachandran / Spectrochimica Acta Part A 61 (2005) 1001–1006

excitation. The room temperature mid infrared spectra of the title compounds were measured in the region 4000–200 cm−1 at a resolution of ±1 cm−1 using BRUKER IFS 66V vacuum Fourier transform spectrometer equipped with an MCT detector, a KBr beam splitter and globar source. Boxcar apodization was used for the 250 averaged interferogrames collected for the samples.

3. Computational details Quantum chemical density functional calculations were carried out with the 1998 versions of the GAUSSIAN suite of programs [10] using the B3LYP functionals [11,12] supplemented with the standard 6-31G* basis set (referred to as density functional theory (DFT) calculations). The normal grid (50, 194) was used for numerical integration. The Cartesian representation of the theoritical force constants have been computed at the fully optimized geometry by assuming Cs point group symmetry. The multiple scaling of the force constants was performed by the quantum chemical method with selective scaling in the local symmetry coordinate representation [13] using transferable scale factors available in the literature [14]. The transformation of force field from Cartesian to symmetry coordinate, the scaling, the subsequent normal coordinate analysis, calculations of potential energy distribution (PED) and IR and Raman intensities were done on a PC with the version. V7.0–G77 of the MOLVIB program written by Tom Sundius [15,16]. To achieve a close agreement between observed and calculated frequencies, the least square fit refinement algorithm was used. The force field obtained this way was then used to recalculate the normal modes, PEDs and the corresponding theoretically expected IR and Raman intensities to predict the full IR and Raman spectra. For the plots of simulated IR and Raman spectra pure Lorentzian band shapes were used with a bandwidth (FWHH) of 10 cm−1 . The prediction of Raman intensities was carried out by following the procedure outlined below. The Raman activities (Si ) calculated by the GAUSSIAN-98 program and adjusted during the scaling procedure with MOLVIB were converted

Fig. 1. Molecular model of 5-fluoro, 5-chloro and 5-bromo-cytosines. X: F, Cl, Br.

by relative Raman intensities (Ii ) using the following relationship derived from the basic theory of Raman scattering [17]. Ii =

f (ν0 − νi )4 Si νi [1 − exp(−hcνi /kT )]

where ν0 is the exciting frequency (in cm−1 units), νi the vibrational wave number of the ith normal mode, h, c and k are the universal constants and f the suitability chosen common normalization factor for all peak intensities.

4. Results and discussion 4.1. Geometrical parameters The labeling of atoms of 5-FC, 5-ClC and 5-BrC are given in Fig. 1. The bond lengths and bond angles determined at

Fig. 2. FT-IR spectra of 5-fluoro, 5-chloro and 5-bromo cytosines: (a) observed; (b) calculated.

V. Krishnakumar, V. Balachandran / Spectrochimica Acta Part A 61 (2005) 1001–1006

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Table 1 Optimized geometrical parameters of 5-fluoro,5-chloro and 5-bromo cytosines obtained by B3LYP/6-31G* density functional calculations Bond length

N(1) C(2) C(2) N(3) N(3) C(4) C(4) C(5) C(5) C(6) C(6) N(1) C(2) O(7) N(3) H(8) C(4) H(9) C(5) X(10) C(6) N(11) N(11) H(12) N(11) H(13)

˚ Value (A)

Value (◦ )

Bond angle

5-FCa

5-ClCa

5-BrCa

1.360 1.360 1.350 1.400 1.410 1.340 1.400 0.990 1.100 1.350 1.470 1.000 1.000

1.360 1.360 1.350 1.400 1.410 1.340 1.400 0.990 1.100 1.760 1.470 1.000 1.000

1.360 1.360 1.350 1.400 1.410 1.340 1.400 0.990 1.100 1.910 1.470 1.000 1.000

N(1) C(2) N(3) C(4) C(5) C(6) N(1) N(3) C(2) C(4) N(3) C(5) C(4) C(6) N(1) C(5)

C(2) N(3) C(4) C(5) C(6) N(1) C(2) C(2) N(3) N(3) C(4) C(4) C(5) C(5) C(6) C(6)

N(3) C(4) C(5) C(6) N(1) C(2) O(7) O(7) H(8) H(8) H(9) H(9) X(10) X(10) N(11) N(11)

5-FCa

5-ClCa

5-BrCa

126.7 115.6 122.4 116.8 122.2 116.0 116.7 116.5 122.1 122.1 116.1 121.3 121.5 121.6 116.3 121.6

126.7 115.6 122.4 116.8 122.3 115.9 116.7 116.5 122.1 122.1 116.1 121.3 121.5 121.6 116.2 121.6

126.7 115.6 122.4 116.7 122.3 115.9 116.7 116.5 122.1 122.1 116.1 121.3 121.5 121.6 116.2 121.5

X: F, Cl, Br. a 5-Fluoro, 5-chloro, 5-bromo cytosines. Table 2 Local symmetry coordinates of 5-fluoro, 5-chloro and 5-bromo cytosines

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33

Symmetry coordinate

Description

S1 = r2,1 S2 = r2,3 S3 = r4,3 S4 = r4,5 S5 = r5,6 S6 = r6,1 S7 = r2,7 S8 = r3,8 S9 = r4,9 S10 = r5,10 S11 = r6,11 S12 = r11,12 S13 = r11,13 S14 = β12,11,6 − β13,11,6 S15 = 2β12,11,13 − β12,11,6 − β13,11,6 S16 = β1,2,3 + β2,3,4 − 2β3,4,5 + β4,5,6 + β1,6,5 − 2β6,1,2 S17 = β1,2,3 − β2,3,4 + β3,4,5 − β4,5,6 + β1,6,5 − β6,1,2 S18 = β1,2,3 − β2,3,4 + β4,5,6 − β1,6,5 S19 = β3,2,7 − β1,2,7 S20 = β2,3,8 − β4,3,8 S22 = β3,4,9 − β5,4,9 S23 = β6,5,10 − β4,5,10 S21 = β1,6,11 − β5,6,11 S24 = γ 7,2,3,1 S25 = γ 8,3,2,4 S26 = γ 9,4,3,5 S27 = γ 10,5,4,6 S28 = γ 11,6,5,1 S29 = γ 6,11,12 + γ 6,11,13 S30 = γ 11,6,12,13 S31 = τ 1,2,3,4 + τ 2,3,4,5 − 2τ 3,4,5,6 + τ 4,5,6,1 + τ 5,6,1,2 − 2τ 6,1,2,3 S32 = τ 1,2,3,4 − τ 2,3,4,5 + τ 3,4,5,6 − τ 4,5,6,1 + τ 5,6,1,2 − τ 6,1,2,3 S33 = τ 1,2,3,4 − τ 2,3,4,5 + τ 4,5,6,1 − ␶5,6,1,2

ν C2N1 ν C2N3 ν C4N3 ν C4C5 ν C5C6 ν C6N1 ν C2O7 ν N3H8 ν C4H9 ν C5X(10) ν C6N11 ν N11H12 ν N11H13 δ NH2 (rocking) δ NH2 (scissoring) δ ring 1

X: F, Cl, Br.

δ ring 2 δ ring 3 δ C2O7 δ N3H8 δ C4H9 δ C5X(10) δ C6N11 γ C207 γ N3H8 γ C4H9 γ C5X(10) γ C6N11 γ NH2 (twisting) γ NH2 (wagging) τ ring 1 τ ring 2 τ ring 3

Fig. 3. FT-Raman spectra of 5-fluro, 5-chloro and 5-bromo cytosines: (a) observed; (b) calculated.

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Table 3 Detailed assignment of fundamental vibrations of 5-fluoro, 5-chloro, 5-bromo cytosine by normal mode analysis based on SQM force field calculations No.



A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A

5-Fluoro cystosine

5-Chloro cystosine

Observed frequency (cm−1 ) IR Raman

Calculated frequency (cm−1 ) Unscaled Scaled

IR intensity

3462 s 3333 ms 3190 w 3105 m 1734 w 1678 s 1660 b 1613 w 1572 s 1520 ms 1490 sh 1410 m 1355 vs 1292 vs 1280 w 1232 vs 1128 s 1060 w 1010 w 978 s 972 w 900 vs 810 s 800 vs 726 s 615 s – 555 w 512 vs 418 vs 375 sh 485 s 285 b

3740 3601 3507 3393 1913 1872 1758 1696 1653 1590 1573 1481 1422 1353 1336 1281 1172 1097 1042 1004 993 993 837 833 750 636 593 572 524 436 384 492 296

33.13 27.00 1.76 12.70 3.86 39.06 25.47 2.63 44.37 8.63 1.98 2.93 55.63 48.03 0.89 61.07 43.11 2.10 2.31 1.84 0.51 61.20 42.03 38.03 22.94 17.08 4.31 0.40 51.82 40.00 0.76 0.04 0.49

3459 m 3333 m 3200 m 3091 m 1730 ms 1676 ms 1662 m 1602 ms 1571 ms 1523 ms 1490 m 1414 w 1350 vs 1276 s 1258 w 1235 ms 1128 ms 1062 w 1004 ms 978 m 968 ms 890 m 816 w 792 vs 720 ms 622 ms 573 ms 548 m 494 m 420 vs 378 sh – 286 b

3466 3336 3194 3112 1737 1686 1664 1617 1575 1525 1492 1414 1355 1298 1285 1225 1137 1068 1015 987 975 907 817 804 729 621 573 560 516 419 377 486 286

Raman activity 20.37 7.63 4.00 8.94 15.70 13.36 6.40 17.66 10.70 18.37 1.63 0.03 33.77 18.69 0.63 1.98 8.61 1.86 12.98 3.27 4.43 18.19 0.23 29.62 7.53 0.10 1.67 1.80 6.84 0.84 0.37 1.26 0.33

5-Bromo cystosine

Observed frequency (cm−1 ) IR Raman

Calculated frequency (cm−1 ) Unscaled Scaled

3451 s 3320 w 3182 w 3090 w 1708 w 1655 ms 1630 b 1610 s 1525 ms 1510 ms 1472 s 1405 ms 1342 s 652 ms 1295 s 1227 s 1128 vs 1055 vs 1034 vs 982 w 972 w 890 ms 820 w 785 w 740 s 620 w 595 ms 525 ms 472 m 435 s 395 m 251 ms 290 b

3733 3590 3492 3371 1897 1764 1775 1693 1614 1584 1553 1471 1409 729 1366 1276 1173 1094 1070 1007 955 922 848 819 767 638 612 540 501 444 404 256 301

3448 ms 3320 ms 3174 m 3081 m 1708 ms 1651 ms 1626 ms 1604 s 1538 ms 1512 m 1470 s 1394 w 1342 m 654 vs 1294 m 1220 s 1130 m 1060 w 1028 vs – 962 ms 892 ms – 785 m 748 m 618 m 588 ms 540 ms 482 ms 438 m 390 vw 250 w 295 ms

3457 3325 3184 3096 1715 1658 1634 1617 1534 1506 1475 1413 1347 647 1288 1227 1122 1060 1039 986 969 895 826 792 744 622 594 528 485 439 394 252 292

IR intensity 30.01 17.63 1.56 12.51 3.14 14.15 42.59 1.72 0.34 13.12 6.04 4.38 41.69 36.00 0.73 68.03 22.76 1.91 0.47 2.68 0.31 76.06 22.88 44.37 36.58 29.69 4.38 0.31 48.17 32.81 0.37 0.07 0.43

Raman activity 20.02 9.91 3.21 9.43 11.41 3.21 19.32 4.38 0.84 3.59 0.15 1.80 29.94 28.62 0.31 0.26 7.61 5.95 1.40 1.76 0.37 0.26 7.16 0.98 28.29 2.03 1.80 0.37 4.19 0.17 0.13 1.73 0.63

Observed frequency (cm−1 ) IR Raman

Calculated frequency (cm−1 ) Unscaled Scaled

3429 m 3310 w 3210 w 3095 w 1726 w 1665 w 1625 w 1610 m 1570 ms 1510 w 1472 vs 1455 w 1342 vs 545 ms 1285 ms 1230 m 1140 ms 1065 ms 1015 s 975 ms 955 ms 900 w – 776 ms 725 s 632 m 580 m – 495 w 430 ms 380 w 376 w 280 b

3726 3591 3489 3363 1909 1770 1722 1690 1659 1586 1551 1523 1501 622 1355 1287 1189 1106 1051 1006 983 935 807 802 749 651 597 680 506 438 386 370 289

3428 m 3313 m 3202 m 3094 w 1707 w 1666 s 1620 m 1606 ms 1572 m 1500 s 1486 w 1454 w 1344 vs 544 s 1290 ms 1222 ms 1134 m 1068 m 1010 ms 962 ms 948 ms 892 ms 786 vs 770 m 720 w – 586 ms 568 ms 502 m 430 s 380 s 374 s –

3436 3315 3215 3399 1730 1671 1628 1614 1578 1507 1479 1464 1347 549 1291 1233 1140 1071 1020 983 959 903 792 780 728 636 582 565 499 432 381 374 279

Characterization of normal modes with PED (%)

IR intensity 16.48 1.81 1.50 0.89 1.91 2.03 1.36 15.48 19.50 1.07 67.70 1.63 44.84 8.73 1.98 3.60 5.62 2.68 42.85 4.38 1.67 0.99 61.38 8.07 4.35 1.98 3.53 0.16 1.98 0.08 0.41 0.67 0.06

Raman activity 41.37 32.08 44.37 0.80 3.94 13.92 1.40 7.86 5.33 28.63 0.43 0.89 2.63 32.36 4.40 1.86 1.21 0.69 18.68 1.46 0.88 8.73 0.26 0.38 0.17 1.84 7.59 0.36 0.26 2.98 0.43 1.98 1.45

νas N11H13 (99) νs N11H12 (99) ν N3H8 (98) ν C4H9 (98) ν C2O7 (86) δ NH2 (sciss) (71); ν C5C6 (18) ν C6NI(82); ν C6NII(14) ν C4C5(88); ν C5C6(11) δ NH2 (rock) (67); ν C5C6(22) δ N3H8(85); ν C2N3(13) ν C5C6(88); δ ring1(11) ν C2N3(82); δ ring3 (13) ν C2N1(80); δ ring2 (14) ν C5X10(89); ν C5C6(10) ν C6NII(74); ν C6N1(12); δ C2O7(10) ν C4N3(76); ν C2N3(12); δ N3H8(10) γ NH2(twist) (54); γ C5X10(25) δ C4H9(58); ν C4N3(21); δ ring1 (11) δ ring1(86); ν C4H9(12) δ ring2(83); ν C5X10(15) δ C6N11(71); δ ring3(21) γ N3H8(56); δ ring1(23) γ C4H9(56); γ N3H8(25) δ ring3(69); δ C2O7(21) δ C2O7(59); γ N3H8(27) γ NH2 (wag)(61); γ C5X10(22) γ C6N11(61); γ C5X10(32) γC2O7(70); τ ring2(18) δ C5X10(58); δ C6N11(21); τ ring2(11) τ ring1(52); τ ring2(28) τ ring2(57); τ ring3(31) γ C5X10(54); γ C6N11(32) τ ring3(51); τ ring1(38)

X: F, Cl, Br; s; strong; vs: very strong; m: medium; w: weak; vw: very weak; sh: shoulder; b: broad; ν: stretching, δ: in-plane bending, γ: out-of-plane bending, τ: ring torsion (out-of-plane).

V. Krishnakumar, V. Balachandran / Spectrochimica Acta Part A 61 (2005) 1001–1006

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33

Symmetry species (Cs )

V. Krishnakumar, V. Balachandran / Spectrochimica Acta Part A 61 (2005) 1001–1006

the DFT level of theory for the title compounds are listed in Table 1. 4.2. Analysis of vibrational spectra In the crystalline state, cytosine adopts its amino-oxo tautomeric form, in which four planar molecules are arranged into sheets exhibiting a network of H-bonds involving their NH2 , N(3) H, N(1) and C O groups [1]. In the case of the isolated cytosine molecule, the dominant tautomer was found to be the amino-hydroxy form [3,4,18,19]. The preference for different tautomeric forms in the crystal and for the isolated molecule is a clear indication of the importance of the intermolecular interactions, in particular H-bonding, to determine the structure of the condensed phase. Further, the bonding properties of cytosine and its derivatives are also influenced by the rearrangements of electrons during substitution and addition reactions. The halogen atoms (F, Cl and Br) substituted at the fifth position of the cytosine (Ref. Fig. 1) are highly electronegative and hence they withdraw electrons from the neighboring carbon bonds. The properties of cytosine and its derivatives discussed above will greatly influence the vibrational spectral data. The molecules 5-FC, 5-ClC and 5-BrC belongs to the Cs point group symmetry. The 13 atoms of the title compounds gives rise to 33 normal modes of vibrations and they are distributed among the symmetry species as 23A and 10A . The A and A represents the in-plane and out-of-plane vibrations, respectively. The local symmetry coordinates, defined in terms of the internal valance coordinate following the IUPAC recommendation [20] for the title compounds are given in Table 2. These coordinates are practically the same as the so-called natural internal coordinates recommended by Pulay et al. [21]. The force fields thus determined were used to calculate the vibrational potential energy distribution among the normal coordinates using the latest version of MOLVIB program [15,16]. For visual comparison, the observed and calculated (simulated) FT-IR and FT-Raman spectra of 5-FC, 5-ClC and 5-BrC were shown in a common frequency scale in Figs. 2 and 3, respectively. The detailed vibrational analysis along with observed frequencies, calculated frequencies at the DFT level (unscaled) SQM predicted frequencies (scaled) and characterization of normal modes by PED for the title compounds are depicted in Table 3. The multiple scaling (SQM) method performed in this study by using the recommended set of scale factors [14] produced a close agreement between the observed and calculated frequencies. The RMS frequency error between the observed and the scaled frequencies of 5FC, 5-ClC and 5-BrC are found to be 4.3, 4.2 and 4.5 cm−1 , respectively. The fundamental vibrations arising from N H, C H, C C and C O bonds of 5-FC, 5-ClC and 5-BrC are observed in their respective characteristic regions and they are listed in Table 3.

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4.3. C–X vibrations (where X = F, Cl and Br) Strong characteristic absorptions due to the C X stretching vibrations are observed in this study. The positions of the band being influenced by the nature of the halide atoms substituted at the fifth positions of the cytosine derivatives. The larger frequency shift have been observed from Cl and Br. In the organic halogen compounds the band due to C F stretching vibrations may be found over a wide frequency range, 1360–1000 cm−1 , since the vibration is easily influenced by adjacent atoms or groups. The C Cl stretching vibrations give generally strong bonds in the region 760–505 cm−1 . Bromine compounds absorb strongly in the region 650–485 cm−1 due to the C Br stretching vibrations [22]. In this study, the strong IR bands obtained at 1292, 652 and 545 cm−1 for 5-FC, 5-ClC and 5-BrC have been designated to νC F, νC Cl and νC Br, respectively. Vibrational coupling with neighbouring carbon groups may resulted into a shift in the absorption frequencies of the respective compounds.

5. Conclusion A complete vibrational analysis of 5-fluoro, 5-chloro and 5-bromo-cytosines have been made in this study based on the density functional theory calculations at the B3LYP/631G* level. Refinement of the scaling factors applied in this study achieved a weighted mean deviation of 4.3, 4.2 and 4.5 cm−1 between the experimental and scaled frequencies. The assignment of most of the fundamentals provided in this work is believed to be unambiguous. The simulated and observed IR and Raman spectra agrees well with the better frequency fit and intensities. The influence of halogen atoms in the hetroaromatic cytosine compounds and their role in the vibrational spectral data were also discussed.

Acknowledgments The authors are thankful to Sophisticated Analytical Instrumentation Facility (SAIF). IIT Madras, Chennai for the spectral measurements. The authors are also thankful to Dr. Gabor Keresztury, Chemical Research Centre, Hungarian Academy of Sciences (HAS), Budapest, Hungary and Professor Tom Sundius, University of Helsinki, Helsinki, Finland, for providing the software to carryout the computations in this study.

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