Density functional theory studies on tautomeric stability and infrared and Raman spectra of some purine derivatives

Spectrochimica Acta Part A 68 (2007) 823–832

Density functional theory studies on tautomeric stability and infrared and Raman spectra of some purine derivatives V. Krishnakumar a,∗ , S. Dheivamalar b a

b

Department of Physics, Peiryar University, Salem 636011, India Department of Physics, Cauvery College for Women, Tiruchirappalli, India Received 19 November 2006; accepted 14 December 2006

Abstract The molecular vibrations of 6-hydroxy-purine (6HP) and 6-amino-purine (6AP) were investigated in polycrystalline sample, at room temperature by Fourier transform infrared (FTIR) and FT-Raman spectroscopy. The spectra of the above compounds have been recorded in the region 4000–50, 3500–100 cm−1 , respectively. They were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on density functional theory (DFT) using HF/6-31G* and B3LYP/6-311+G** methods and basis set combinations. The results of the calculations were applied to simulated infrared and Raman spectra of the title compounds, which showed excellent agreement with the observed spectra. The dipole moment and the tautometric stability of purine derivatives were also studied. © 2007 Elsevier B.V. All rights reserved. Keywords: 6-Hydroxy-purine; 6-Amino-purine; FTIR; FT-Raman; DFT methods

1. Introduction In the past decade, IR and Raman spectroscopy has become an important technique, which supplies information about the structures and tautomers of nucleic acid bases and their derivatives. To study the vibrational spectral properties and the spectrum–conformation correlation for biochemical and biological systems involving purine, it is necessary to analyze its vibrational spectrum. In the present paper we report the results of HF/6-31G* and DFT (B3LYP)/6-311+G** calculations on tautomers of 6HP, 6AP. In addition, the combination of B3LYP/6-311+G** theory with the scaled quantum mechanical (SQM) force field method introduced by Rahut and Pulay [1] is applied to study the IR and Raman spectra of 6HP, 6AP. The new reliable vibrational force field of these molecules has been obtained for the lowest energy tautomer of amino-N(9)H form. 2. Experimental The polycrystalline sample of 6HP, 6AP were kindly provided by Lancaster Synthesis (UK) and used as such for the ∗

Corresponding author. E-mail address: vkrishna [email protected] (V. Krishnakumar).

1386-1425/$ – see front matter © 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.saa.2006.12.066

spectral measurements. The room temperature FTIR spectra of the title compounds were measured in the region 4000–50 cm−1 at a resolution of 1 cm−1 using a Bruker IFS 66V FTIR spectrometer equipped with dual detection, a cooled MCT detector for the mid-IR and a room temperature pyroelectric detector for the far IR range. The samples used in these measurements were KBr and polyethylene pellets, respectively. Boxcar apodization was used for the 250 averaged interferograms collected for both the sample and background. The FT-Raman spectra of 6HP and 6AP were recorded on a Bruker IFS 66V model interferometer equipped with an FRA106 FT-Raman accessory in the 3500–100 cm−1 stokes region using 1064 nm line of a Nd:YAG laser for excitation operating at 200 mW power. The reported wave numbers are believed to be accurate within ±1 cm−1 . 3. Computational details All calculations were performed using GAUSSIAN program package [2] and the vibrational modes were assigned by means of visual inspection using GAUSSVIEW program [3] and also from the results of normal coordinate calculations. The geometry optimizations and energy calculations of tautomers of 6HP (Fig. 1(a)) and 6AP (Fig. 1(b)) were carried out with Hartree-Fork (HF) and DFT (B3LYP) methods [4,5]

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with6-31G* and 6-311+G** basis sets, respectively. In geometry optimization it was assumed that in 6AP, other atoms are coplanar except NH2 group because numerous work indicated that DNA bases could adopt non-planar geometry in amino group [6–9]. The normal coordinate analysis of molecular vibration was then performed for the most stable tautomer of 6HP (Fig. 1(a, 1), and 6AP (Fig. 1(b, 1)). At this optimized structure, the

absolute IR and Raman intensities were calculated at the B3LYP/6-311+G** level. In order to express the normal modes in molecular fixed coordinate system, a set of local symmetry internal coordinates for 6HP, and 6AP were defined as recommended by Rahut and Pulay [1]. These coordinates can be found in Tables 1 and 2 and the atom numbering was shown in Fig. 1(a and b), respectively. The theoretical DFT force field was transformed from Cartesian coordinates into the local

Fig. 1. (a) Structure and atomic numbering of 6-hydroxy-purine. (b) Structure and atomic numbering of 6-amino-purine.

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Fig. 1. (Continued ).

internal coordinates and then scaled empirically according to SQM procedure [10]. Fijscaled = (Ci Cj )1/2 FijB3LYP where Ci is the scale factor of coordinate i, FijB3LYP is the B3LYP/6-311+G** force constant in the local internal coordinates and Fijscaled is the scaled force constant. These scale factors were optimized using least-squares procedure [11] by fitting the calculated frequencies to the observed frequencies.

Transformation of force field and subsequent normal coordinate analysis including least square refinement of scale factors, total energy distribution (TED) and IR, Raman intensities were done on a PC with MOLVIB programme (Version 7.0–G77) written by Sundius [12,13]. The scale factor involving C(2)–H group in 6HP, 6AP were assumed to be same as those of C(6)–N group because both belong to X–Y bond (X and Y represent heavy atoms). The set of scale factors for 6HP, 6AP are listed in Table 3.

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Table 1 Local internal coordinates of 6-hydroxy-purine (atom numbering as in Fig. 1(a)) S1 = r(1,2) S2 = r(2,3) S3 = r(3,4) S4 = r(4,5) S5 = r (5,6) S6 = r(1,6) S7 = r(5,7) S8 = r(7,8) S9 = r(8,9) S10 = r(4,9) S11 = r(6,10) S12 = r(2,11) S13 = r(8,13) S14 = r(9,12) S15 = r(10,14) S16 = (1/6(α(2,3,4) − α(1,2,3) + α(6,1,2) − α(5,6,1) + α(4,5,6) − α(3,4,5)) S17 = (1/12)1/2 (2α(2,3,4) − α(1,2,3) − α(6,1,2) + 2α(5,6,1) − α(4,5,6) − α(3,4,5)) S18 = 0.5(−α(1,2,3) + α(6,1,2) − α(4,5,6) + α(3,4,5)) S19 = 0.632456α(7,8,9) − 0.511667 α(4,9,8) + 0.195439α(5,4,9) + 0.195439α(4,5,7) − 0.511667α(5,7,8) S20 = −0.371748α(4,9,8) + 0.601501α(5,4,9) − 0.601501α(4,5,7) + 0.371748(5,7,8) S21 = (1/2)1/2 (α(1,6,10) − α(5,6,10)) S22 = (1/2)1/2 (α(3,2,11) − α(1,2,11)) S23 = (1/2)1/2 (α(7,8,13) − α(9,8,13)) S24 = (1/2)1/2 (α(8,9,12) − α(4,9,12)) S25 = γ(6,5,1,10) S26 = γ(2,1,3,11) S27 = γ(8,9,7,13) S28 = γ(9,4,8,12) S29 = (6–1/2 ) (τ(6,1,2,3) − 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)) S30 = (12–1/2 ) (2τ(6,1,2,3) − τ(1,2,3,4) − 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)) S31 = 0.5(τ(1,2,3,4) − τ(2,3,4,5) + τ(4,5,6,1) − τ(5,6,1,2)) S32 = 0.1195439τ(7,8,9,4) − 0.511667τ(8,9,4,5) + 0.632456τ(9,4,5,7) − 0.511667τ(4,5,7,8) + 0.195439(5,7,8,9) S33 = −0.601501τ(7,8,9,4) + 0.371748(8,9,4,5) − 0.371748τ(4,5,7,8) + 0.601501τ(5,7,8,9) S34 = (1/2)1/2 (τ(3,4,5,7) − τ(9,4,5,6)) S35 = 1/2(τ(14,10,6,1) + τ(14,10,6,5)) S36 = 1/2(τ(14,10,6,1) − τ(14,10,6,5))

The Raman activities (Si ) calculated with GAUSSIAN 98 program and adjusted during the scaling procedure with MOLVIB and were subsequently converted to relative Raman intensities (Ii ) using the following relationship derived from the intensity theory of Raman scattering [14–16] Ii =

f (νo − νi )4 Si   νi 1 − exp (hcνi /KT )

(1)

where νo is the exciting frequency in cm−1 , νi the vibrational wave number of the ith normal mode, h, c and k fundamental constants, and f is a suitably choosen common normalization factor for all peak intensities. 4. Results and discussion 4.1. Energies and dipolemoment In the molecules 6HP and 6AP, the hydrogen attached at the imidazole ring and the nitrogen N(9) may be rearranged to N(7) position, i.e. N(9)H N(7)H equilibrium. Thus there are 4 iso-

mers of 6HP and 12 isomers of 6AP and they were depicted in Fig. 1(a and b), respectively. In 6AP, one of the NH2 group hydrogen atoms may remain either attached at the substituent N atom or migrate to one of the six or five membered ring nitrogen causing NH2 NH tautomerism. In addition, the H atom of NH group may point towards N(7) or be close to N(1). The total energies and dipolemoments of 6HP and 6AP for different tautomers were calculated at HF/6-31G* and B3LYP/6-311+G** levels and they are given in Table 4. It is evident for the energy calculations that the conformers shown in Fig. 1(a, 1) for 6HP and Fig. 1(b, 1) for 6AP produces the global minimum energy and hence they are the most stable conformers and these stable conformers were considered for further calculations. The lowest and highest dipole moments of the title compounds shows the presence of the least polar tautomer in the crystal instead of one of the more polar forms is indeed surprising. It must be a result of packing in 6HP, 6AP to fulfill the best hydrogen bonding pattern between the molecules in their structure and clearly overpowers the electrostatic dipole–dipole forces usually thought to dictate the predominant tautomer expected in polar medium [17].

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Table 2 Local internal coordinates of 6-amino-purine (atomic numbering as in Fig. 1(b)) S1 = r(1,2) S2 = r(2,3) S3 = r(3,4) S4 = r(4,5) S5 = r(5,6) S6 = r(1,6) S7 = r(5,7) S8 = r(7,8) S9 = r(8,9) S10 = r(4,9) S11 = r(6,10) S12 = r(2,11) S13 = r(8,13) S14 = r(9,12) S15 = (1/2)1/2 (r(10,14) + r(10,15)) S16 = (1/2)1/2(r(10,14) − r(10,15)) S17 = (1/6(α(2,3,4) − α(1,2,3) + α(6,1,2) − α(5,6,1) + α(4,5,6) − α(3,4,5)) S18 = (1/12)1/2(2α(2,3,4) − α(1,2,3) − α(6,1,2) + 2α(5,6,1) − α(4,5,6) − α(3,4,5)) S19 = 0.5(−α(1,2,3) + α(6,1,2) − α(4,5,6) + α(3,4,5)) S20 = 0.63245α(7,8,9) − 0.511667α(4,9,8) + 0.194539α(5,4,9) + 0.195439α(4,5,7) − 0.511667α(5,7,8) S21 = −0.3717α(4,9,8) + 0.60150α(5,4,9) − 0.60150 α(4,5,7) + 0.37174α(5,7,8) S22 = (1/2)1/2(α(1,6,10) − α(5,6,10)) S23 = (1/2)1/2(α(3,2,11) − α(1,2,11)) S24 = (1/2)1/2(α(7,8,13) − α(9,8,13)) S25 = (1/2)1/2(α(8,9,12) − α(4,9,12)) S26 = (1/2)1/2(α(14,10,6) − α(15,10,6)) S27 = (1/6)1/2(2α(14,10,15) − α(14,10,6) − α(15,10,6)) S28 = γ(6,5,1,10) S29 = γ(2,1,3,11) S30 = γ(8,9,7,13) S31 = γ(9,4,8,12) S32 = (6−1/2 )(τ(6,1,2,3) − 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)) S33 = (12−1/2 )(2τ(6,1,2,3) − 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)) S34 = 0.5(τ(1,2,3,4) − τ(2,3,4,5) + τ(4,5,6,1) − τ(5,6,1,2)) S35 = 0.11954τ(7,8,9,4) − 0.511667τ(8,9,4,5) + 0.632456τ(9,4,5,7) − 0.511667τ(4,5,7,8) + 0.195439(5,7,8,9) S36 = −0.601501τ(7,8,9,4) + 0.371748(8,9,4,5) − 0.371748τ(4,5,7,8) + 0.601501τ(5,7,8,9) S37 = (1/2)1/2 (τ(3,4,5,7) − τ(9,4,5,6)) S38 = 0.5(τ(14,10,6,1) + τ(14,10,6,5) + τ(15,10,6,1) + τ(15,10,6,5)) S39 = 0.5 (τ(14,10,6,1) + τ(14,10,6,5) − τ(15,10,6,1) − τ(15,10,6,5))

4.2. Geometric parameters The optimized geometries of 6HP, 6AP (most stable form) are given in Table 5 together with the theoretical results of some

purine derivatives from B3LYP/6-31G* calculation. The calculated geometric parameters for 6HP and 6AP are quite close to adenine obtained at the same theoretical level except for bond lengths and angles involving OH, NH2 , group, respectively. At

Table 3 Scale factors for 6AP, 6HP No.

Factors

Internal coordinatesa

1. X–Y (six-membered ring) stretch 2. X–Y (five-membered ring) stretch 3. X Y (five-membered ring) stretch 4. X–H stretch 5. Ring deformation 6. X–Y deformation 7. X–H deformation 8. X–Y out-of-plane 9. X–H (six-membered ring) 10. X–H (five-membered ring) 11. Ring torsion 12. NH2 , OH torsion 13. NH2 out-of-plane

0.925 0.962 0.919 0.920 0.971 0.995 0.951 0.997 0.959 1.017 0.948 1.200 0.850

S1 , S2 , S3 , S4 , S5 , S6 , S11 , S12 S7 , S9 , S10 S8 S13 , S14 , S15 , S16 S17 , S18 , S19 , S20 , S21 S22 S23 , S24 , S25 , S26 , S27 S28 S29 S30 , S31 S32 , S33 , S34 , S35 , S36 , S37 S38 S39

a

The internal coordinates used here are defined in Tables 1 and 2.

2.971 6.7119 3.01 2.073 2.609 7.376 4.25 9.410 5.57 5.05 4.57 3.3363 10.8034 3.701 11.205 5.20 3.04 7.32 5.02 5.76 2.19 5.98 2.84 1.50 12.03 3.665 4.82 6.59

Fig. 2. Comparison of observed and calculated infrared spectra of 6-hydroxypurine. (a) Observed in solid phase; (b) calculated with B3LYP/6-31G*; (c) calculated with B3LYP/6-311+G**.

the optimized equilibrium geometry the vibrational harmonic force field of purine derivatives (6HP, 6AP) were calculated with B3LYP/6-311+G** method and scaled by Pulay’s SQM technology. The scale factors of C(2)–H stretching, bending and out-of-plane bending were taken to be equal to those of corresponding modes of C(6)–N group. 4.3. Analysis of spectra and theoretical spectrum simulations The title compounds 6HP, 6AP have Cs symmetries and the 36 and 39 normal modes of 6HP and 6AP are distributed amongst the symmetry species as Γ3N–6 = 25A (planar) + 11A (out-of-plane) Γ3N–6 = 27A (planar) + 12A (out-of-plane)

c

From Ref. [21]. 6-Amino-purine (present work). 6-Hydroxy-purine (present work). a

b

1 2 3 4 5 6 7 8 9 10 11 12

4.41 8.88 3.30 7.95 3.62 3.66 3.80 4.62 8.66 9.69 3.05 5.94

4.28 8.64 2.95 7.81 3.21 3.46 3.78 4.54 8.25 9.23 2.92 5.53 −926.915143 −926.901662 −926.896886 −926.880748 −926.882158 −926.892191 −926.8857 −926.8848 −926.8634 −926.8630 −926.8850 −926.8735 −923.420199 −923.404737 −923.396978 −923.379915 −923.382424 −923.393790 −923.38573 −923.384958 −923.363744 −923.36318 −923.38514 −923.37285

−464.340 −464.329 −464.289 −464.311 −463.681 −464.276 −464.281 −464.272 −464.250 −463.691 −464.278 −464.261

−467.257 −467.229 −467.201 −467.221 −467.184 −467.193 −466.531 −467.188 −467.163 −467.187 −467.153 −467.165

−484.035 −487.0857 3.403 −484.013 −487.063 6.920 −484.033 −487.0843 3.43 −484.035 −487.0855 5.001 Only four isomers are possible for 6HP

HF/6-31G* HF/6-31G* B3LYP/ 6-311+G* HF/6-31G* HF/6-31G* B3LYP/ 6-31G* HF/6-31G*

B3LYP/ 6-31G*

HF/6-31G*

B3LYP/ 6-311+G*

B3LYP/ 6-311+G*

Dipole moment (debye) Total energy (Hartree) Dipole moment (debye) Total energy (Hartree) Dipole moment (debye) Total energy (Hartree)

6-Amino-purineb 2-Chloro-adeninea S. no.

Table 4 Energies and dipolemoments of different isomers of tautomers of purine derivatives

B3LYP/ 6-311+G*

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6-Hydroxy-purinec

828

i.e. all the vibrations are active both in infrared absorption and Raman scattering. In the Raman spectrum the in plane vibrations (A ) give rise to polarised bands while the out-of-plane ones (A ) give rise to depolarised bands. The measured FT-IR and FT-Raman spectra of poly crystalline samples of 6HP, 6AP were presented in Figs. 2–5. The assignments of bands proposed in this study for the tile compounds were given Tables 6 and 7. These assignments are in agreement with known group frequency correlations and they are also supported by the normal mode calculations. The vibrational frequencies calculated with the unscaled B3LYP/6-31G* force field are known for over estimation than the experimental values by 2–5% on average. The RMS error of frequencies (unscaled/B3LYP/6-31G*) observed for 6HP and 6AP were found to be 73.50 and 81.65 cm−1 , respectively. Root mean square (RMS) values were obtained in this study using the following expression:   n  1  exp 2 RMS =  (νical − νi ) n−1 i

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Table 5 Optimized geometries of some purine derivatives (at B3LYP/6-31G* level) Bond length

6HPa

6APb

Cl Adec

Aded

Bond angles

6HPa

6APb

Cl Adec

Aded

N1 –C2 C2 N3 N3 –C4 C4 C5 C5 –C6 N1 C6 C5 –N7 N7 C8 C8 –N9 C4 –N9 C6 –N10 C2 –H11 C–O O–H N9 –H12 C2 –Cl11 C8 –H13 N10 –H14 N10 –H15

1.351 1.349 1.332 1.392 1.410 1.342 1.372 1.310 1.372 1.372 1.360 1.070 1.208 0.960 1.000 – 1.064 – –

1.326 1.340 1.326 1.398 1.394 1.340 1.389 1.312 1.389 1.382 1.359 1.070 – – 1.000 – 1.082 1.082 –

1.332 1.326 1.340 1.398 1.411 1.346 1.384 1.310 1.382 1.375 1.352 – – – 1.010 1.761 1.082 1.009 1.009

1.343 1.337 1.339 1.400 1.411 1.345 1.386 1.310 1.381 1.378 1.357 1.088 – – 1.010 – 1.082 1.009 1.009

N1 C2 N3 C2 N3 C4 N3 C4 C5 C4 C5 C6 C5 C6 N1 C6 N1 C2 C4 C5 N7 C5 N7 C8 N7 C8 N9 C8 N9 C4 N9 C4 C5 C5 C6 N10 N1 C2 H11 C8 N9 H12 N7 C8 H13 C6 N10 H14 C6 N10 H15 H14 N10 H15 N10 C6 N1 C2

123.2 118.9 127.21 119.90 120.40 111.82 109.3 115.592 109.5 107.12 127.21 118.9 122.26 112.95 – – – – –

122.32 118.452 121.138 120.4 119.4 118.452 107.183 118.183 109.6 108.18 119.20 132.56 125.20 144.0 110.814 25.766 118.4 180.0

130.2 110.5 127.0 115.6 118.8 117.8 103.9 113.4 106.6 104.5 122.6 114.7 127.5 125.2 118.7 119.7 119.7 119.2 179.0

129.0 111.1 127.0 125.8 118.9 118.3 103.9 113.5 106.7 164.4 122.3 115.2 127.5 125.1 117.9 119.2 119.1 119.2 180.0

a b c d

6HP (the present work). 6AP (the present work). ClAde: 2-chloro-adinine (from Ref. [21]). Ade, adenine (from Ref. [22]).

In order to reproduce the observed frequencies, refinement of scaling factors were applied and optimized via least square refinement algorithm which resulted a weighted RMS deviation of 6.83 and 3.85 cm−1 for 6HP and for 6AP 7.15 and 4.02 cm−1 for the B3LYP/6-31G* (small) and B3LYP/6311+G** (large) basis sets, respectively, between experimental and SQM frequencies. The good agreement allows us to perform the assignments of the IR and Raman bands to the normal modes in the whole studied spectral regions. From high to low wave number the following comments are in order. 4.4. Spectral region over 3000 cm−1 Fig. 3. Comparison of observed and calculated Raman spectra of 6-hydroxypurine. (a) Observed in solid phase; (b) calculated with B3LYP/6-31G*; (c) calculated with B3LYP/6-311+G**.

According to Socrates [18] the stretching of amino group appeared around 3500–3000 cm−1 in absorption spectra. The

Fig. 4. Comparison of observed and calculated infrared spectra of 6-aminopurine. (a) Observed in solid phase; (b) calculated with B3LYP/6-31G*; (c) calculated with B3LYP/6-311+G**.

Fig. 5. Comparison of observed and calculated Raman spectra of 6-aminopurine. (a) Observed in solid phase; (b) calculated with B3LYP/6-31G*; (c) calculated with B3LYP/6-311+G**.

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Table 6 Assignment of fundamental vibrations of 6-hydroxy-purine by normal modes analysis based on SQM force field calculations using selectively scaled B3LYP/6311+G** force field Number

Symmetry species

Observed fundamentals (cm−1 )

Calculated frequencies (cm−1 )

FTIR

Raman

Unscaled B3LYP/6-31G*

Scaledc B3LYP/6-31G*

Scaled B3LYP/ 6-311+G**

3592 w 3378 m 3340 w 3124 w 3014 w 2909 m 2017 w 1843 m 1695 ms 1590 ms

3731 3582 3541 3370 3234 3047

1421 ms 1400 w 1312 w 1320 w 1234 w

1781 1724 1518 1502 1481 1452 1384 1336 1323

3555 3380 3348 3126 3012 2908 2018 1841 1699 1612 1482 1451 1424 1411 1318 1290 1240

1186 w

1309 1231 1207 1148 1036 1024 930 822 794 744

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

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

3543 vs

18 19

A A

1207 s 1186 m

20 21 22 23 24 25 26 27

A A A A A A A A

1112 m 1091 ms 1008 w

28 29 30 31 32 33 34 35 36

A A A A A A A A A

714 vs 690 m 672 m 610 m 585 m 569 m 525 m

3120 w 3010 w 2909 m

1697 vs 1619 m 1488 w 1454 ms 1421 ms 1407 ms 1316 s 1288 s 1246 m

917 w 809 m 779 w 739 m

1110 m

976 s 901 w 790 vs 731 m 707 m 670 m 609 m 524 m 379 m 348 m

731 697 680 622 594 580 427 392 350 73.5 cm−1

AI a

Ii b

TED (%) among types of coordinates

3558 3378 3349 3122 3015 2909 2019 1848 1697 1601 1482 1441 1422 1410 1361 1299 1234

0.861 0.010 0.028 0.110 0.123 0.352 0.030 0.032 0.842 0.412 0.120 0.112 0.551 0.692 0.721 0.420 0.642

4.53 29.25 2.43 3.73 2.12 29.05 1.75 22.05 51.12 52.24 0.73 0.31 52.75 7.05 2.30 2.54 2.78

1211 1180

1212 1189

0.361 0.382

0.78 4.62

1110 1098 1012 972 919 812 781 742

1111 1096 1009 974 921 808 193 733

0.520 0.114 0.121 0.032 0.540 0.261 0.081 0.263

31.15 0.203 0.214 73.250 2.510 0.230 87.52 37.02

0.882 0.362 0.341 0.312 0.260 0.258 0.212 0.188 0.161

29.54 0.42 37.25 37.34 1.72 26.04 0.368 28.24 28.21

␯ O–H (100) ␯ N9 –H12 (76) ␯ N8 –H13 (81) ␯ C–H (99) ␯ C–H (99) ␯ C–H (82) ␯ O–H (89) ␯ C–O (54) ␯ C–C (36), ␯ C–N (26) ␯ C–C (56), ␯ C–N (14) ␯ Ring ␯ C–N (76), ␯ C–O (19) ␯ Ring ␯ Ring ␯ N–H in-plane (52) ␯ C–O (76), ␯ Ring (23) ␦ N–H in-plane (54), ␦ C–H in-plane (42) ␦ O–H in-plane (76) ␦ C–N in-plane (19) ␦ C–H in-plane (76) ␦ C–H in-plane (54) ␦ C–OH (84), ␯ Ring ␦ C–H out-of-plane (21) ␦ N–H out-of-plane (69) ␦ Ring5 ␦ Ring6 ␦ C–H out-of-plane (66) T Ring5 ␦ C–H out-of-plane (61) ␦ Ring6 ␦ C–O in-plane (71) T Ring5 (15) T Ring6 T Ring6 T Ring5 ␦ N–C–N out-of-plane (61) ␦ C–O out-of-plane (61) ␦ C–H out-of-plane (59) T Ring

716 684 678 612 589 556 516 384 356 6.83 cm−1

710 698 672 606 584 526 416 382 354 3.85 cm−1

Abbreviations: vs, very strong; s, strong; ms, medium strong; w, weak; vw, very weak; ␯, stretching; ␳, rocking; T, torsion; ␻, wagging; ␦, deformation. a Relative absorption intensities normalized with highest peak absorbance equal to 1.0. b Relative Raman intensities calculated by Eq. (1) and normalized to 100. c For optimized values of scale factors applied; see Table 3.

bands at 3625, 3692 and 3479, 3471 cm−1 are usually due to O–H stretching vibrations. The OH compound includes water, alcohol and phenol. The larger bandwidth of O–H band would be due to intra molecular association [19]. In 6HP, the O–H stretching frequency is observed at 3543 cm−1 for IR and 3592 cm−1 for Raman, respectively. The hetero aromatic structure shows the presence of C–H stretching vibrations in the region 3100–3000 cm−1 , which is the characteristic region for the ready identification of C–H stretching vibrations [20]. In this region the nature of the substituent will not affect appreciably the absorption regions. The

6HP molecule gives rise to two in-plane bending and two out-ofplane bending vibrations. Hence in the present investigation, the IR and Raman bands identified at 3120, 3010 cm−1 and 3124, 3014 cm−1 , respectively. In 6AP, C–H stretching modes of vibration were observed for IR and Raman at 3084 and 3034 cm−1 , respectively. 4.4.1. Spectral region 1650–1000 cm−1 In this region, the scissoring vibration of amino group contributes to two observed bands at 1633 and 1507 cm−1 corresponding to the frequencies predicted to be at 1678 and

V. Krishnakumar, S. Dheivamalar / Spectrochimica Acta Part A 68 (2007) 823–832

831

Table 7 Assignment of fundamental vibrations of 6-amino-purine by normal modes analysis based on SQM force field calculations using selectively scaled B3LYP/6-311+G** force field Number Symmetry species

Observed fundamentals (cm−1 )

Calculated frequencies (cm−1 )

FTIR

Raman

Unscaled B3LYP/6-31G*

Scaledc B3LYP/6-31G*

Scaled B3LYP/ 6-311+G**

3471 w

3641 3584 3415 3336

3458 3396 3219 3091

3198 2235

AI a

Ii b

TED (%) among types of coordinates

3482 3389 3219 3038

0.420 0.168 0.126 0.126

10.07 4.28 0.94 12.52

2970 2099

2971 2097

0.072 0.523

10.80 3.88

1639 w 1608 w 1516 w 1459 w 1453 w 1421 m 1384 vs 1315 m 1283 m 1243 s

2166 1932 1874 1830 1735 1697 1606 1549 1481 1456 1416 1356 1320 1298

2058 1898 1770 1745 1678 1614 1518 1470 1446 1426 1369 1332 1302 1252

2052 1890 1792 1749 1648 1601 1579 1462 1450 1426 1392 1311 1308 1247

0.212 0.481 0.120 0.126 0.138 0.120 0.121 0.148 0.156 0.463 0.382 0.189 0.362 0.121

3.25 3.78 12.72 2.70 9.54 8.49 8.42 9.56 14.23 32.57 79.06 36.42 21.62 55.84

1164 w 1137 s 1026 m

1184 1150 1041

1154 1129 1025

1168 1143 1028

0.138 0.368 0.361

3.24 52.06 29.05

992 952 983 879 843

989 942 916 878 849

9982 945 915 864 855

0.123 0.142 0.110 0.352 0.152

51.05 59.75 28.02 4.75 0.253

814 758 707 625 618 588 542 274

802 720 678 650 620 570 529 270

806 728 676 642 616 550 532 273

0.623 0.358 0.162 0.622 0.420 0.521 0.123 0.182

0.141 79.03 0.314 29.52 0.568 34.50 0.218 13.12

256 214 182 81.6153 cm−1

244 204 177 7.153 cm−1

224 204 164 4.02 cm−1

0.623 0.212 0.144

53.05 77.52 13.15

␯as NH2 (99) ␯s NH2 (98) ␯ N–H (86) ␯ C–H (21), ␯ N–H (62) ␯ C–H (84) ␯ C–C (21), ␯ N–H (41) ␯ C–N (43) ␯ C–C (89) ␯ C–N (56) ␯ C–N (69) ␾ NH2 (86) ␯ Ring (69) ␾ NH2 (59) ␯ C–N (81) ␯ Ring ␯ Ring ␯ Ring ␯ Ring δ N–H in-plane (59) ␦ C8 –H13 in-plane (53), ␳ NH2 (66) ␯ Ring, ␳ NH2 (56) ␦ C–H (64) ␦ Ring (67), ␳ NH2 (31) ␦ Ring (62) ␦ C–C (59) ␦ Ring ␦ Ring δ C–H out-of-plane (42) ␦ Ring (82) T Ring ␻ NH2 (58) ␦ Ring ␦ Ring ␦ Ring ␦ Ring ␦ C–NH2 out-of-plane (41) T NH2 T Ring Butterfly motion

1 2 3 4

A A A A

3476 m 3449 w 3215 w 3084 w

5 6

A A

2958 w 2091 ms

7 8 9 10 11 12 13 14 15 16 17 18 19 20

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

2046 m 1892 ms 1778 w 1746 w 1633 w 1612 w 1507 vs 1468 w 1450 w 1416 ms 1368 m 1329 ms 1298 m 1250 w

21 22 23

A A A

1156 w 1125 m 1023 m

24 25 26 27 28

A A A A A

985 w 939 w 912 w 870 m 847 vw

29 30 31 32 33 34 35 36

A A A A A A A A

796 s 723 m 670 m 646 s 612 ms 542 s 527 w 276 w

283 ms

37 38 39

A A A

266 s 239 w 197 ms

225 s 201 vs 162 m

3034 w 2973 w

1786 w

945 s 912 m 861 vw 853 w 809 vw 730 vs 637 m 608 w 553 ms

Abbreviations: vs, very strong; s, strong; ms, medium strong; w, weak; vw, very weak; ␯, stretching; ␳, rocking; T, torsion; ␻, wagging; ␦, deformation; ␾, scissoring. a Relative absorption intensities normalized with highest peak absorbance equal to 1.0. b Relative Raman intensities calculated by Eq. (1) and normalized to 100. c For optimized values of scale factors applied; see Table 3.

1518 cm−1 . The bands due to the NH2 rocking are found at 1250 and 1023 cm−1 . The bands at 1298 and 1250 cm−1 are assigned to the N(9)H and C(8)H bending vibrations estimated at 1302 and 1252 cm−1 , respectively. The other eight bands in this spectral region would be assigned to the modes of ring stretching. In 6AP, the calculated vibrations at 1614, 1470, 1446, 1426, 1369,

1332, 1129 and 1025 cm−1 have the dominant characters of the five, and six-membered big stretching, which were observed at 1612, 1468, 1450, 1416, 1368,1329, 1125 and 1023 cm−1 , respectively. In 6HP the calculated vibrations at 1612, 1482, 1451, 1424, 1411, 1318, 1180 and 1110 cm−1 have the dominant char-

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V. Krishnakumar, S. Dheivamalar / Spectrochimica Acta Part A 68 (2007) 823–832

acters of the five- and six-membered ring stretching, which were observed at 1619, 1488, 1454, 1421, 1407, 1316, 1186 and 1091 cm−1 , respectively. The in-plane and out-of-plane bending vibrations have been also identified and presented in Tables 6 and 7. They are also supported by literature [21,22]. 4.4.2. Spectral region 950–500 cm−1 In 6HP the bands at 917, 809, 779, 714, 569 and 525 cm−1 are assigned to the ring deformation vibrations compared with the predicted frequencies at 919, 812, 781, 712, 556 and 516 cm−1 , respectively. In 6AP the bands at 939, 912, 796, 542 and 527 cm−1 are assigned to the ring deformation vibrations comparing with the predicted frequencies at 942, 916, 802, 570 and 529 cm−1 , respectively. The weak bands found at 847 and 542 cm−1 in the experimental IR spectra of 6AP corresponds to the fundamental modes of C(8)–H and N(9)–H out-of-plane modes. 4.5. Spectral region below 500 cm−1 In 6AP, only three experimental bands were found below 500 cm−1 . The bands at 276 cm−1 is assigned to out-of-plane bending vibrations of C(6)–N. The observed strong band at 266 cm−1 is difficult to assign because two strong bands predicted theoretically have too low frequencies of 177 and 167 cm−1 corresponding to the butterfly motion and NH2 out-ofplane vibration, respectively. The three ring torsion vibrations are predicted for 6HP, 6AP and they were given in Tables 6 and 7, respectively. 5. Conclusion It is predicted that the equilibrium geometries of 6HP, 6AP are close, to each other and also to adenine 2-chloro-adenine except for bond length and bond angle. The reliable vibrational frequencies were also calculated by combining density functional theory DFT (B3LYP)/ 6-311+G** method and the SQM force field approach. Refinement of scale factors applied in this study achieved a weighted RMS deviation of 6.83 and 3.85 cm−1 for 6HP and 7.15 and 4.02 cm−1 for 6AP for small and large basis sets, respectively, between the experimental and SQM frequencies. The complete assignments of the vibrational fundamentals of 6HP, 6AP were proposed on the basis of the IR and Raman

intensities determined from DFT calculation and is believed to be unambiguous. References [1] G. Rahut, P. Pulay, J. Phys. Chem. 99 (1995) 3093. [2] M.J. Frisch, G.W. Trucks, H.B. Schlyed, P.M.W. Gill, B.G. Johnson, M.A. Robb, J.R. Cheeseman, T. Keith, G.A. Petersson, J.A. Montgomery, K. Raghavachari, M.A. Allaham, V.G. Zakrzewski, J.V. Ortiz, J.B. Forsman, J. Cioslowski, B.B. Replogle, R. Gomperts, R.L. Martin, D.J. Fox, J.S. Binkley, D.J. Defrees, J. Baker, J.P. Stewart, M. Head-Gordon, C. Gonalez, J.A. Pople, Gaussian 98, Revision A, 11. 4, Gaussian, Inc., Pittsburgh PA, 1995. [3] M.J. Frisch, G.W. Trucks, H.B. Schlegal, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, A.J. Montgomery Jr., R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Menncci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokurma, N. Rega, P. Salvador, J.J. Dannenberg, D.K. Malick, Cioslowski, J.V. Ortiz, A.G. Baboul, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A.A. I-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andress, C. Gonzalez, M. Head-Gordon, E.S. Reploghe, J.A. Pople, Gaussian 98, Revision A, 11. 4, Gaussian, Inc., Pittsburgh, PA, 2002. [4] A.D. Becke, J. Chem. Phys. 98 (1993) 5648. [5] C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1998) 785. [6] J. Leszyzynski, Int. J. Quant. Chem. Quantum Biol. Symp. 19 (1992) 43. [7] J. Sponer, D. Hobza, J. Phys. Chem. 98 (1994) 3161. [8] O. Bludsky, J. Sponer, J. Leszezynski, V. Spirko, D. Hobza, J. Chem. Phys. 105 (1996) 11402. [9] G. Yan, Y. Xue, D. Xie, Int. J. Quantum Chem. 72 (1999) 53. [10] P. Pulay, G. Fogarasi, G. Pongor, J.E. Boggs, A. Vargha, J. Am. Chem. Soc. 105 (1983) 7037. [11] G. Yan, Y. Xue, D. Xie, Sci. China (Ser. B) 41 (1998) 91. [12] T. Sundius, J. Mol. Struct. 218 (1990) 321. [13] (a) T. Sundius, Vib. Spectrosc. 29 (2002) 89; (b) MOLVIB (V.7.0): Calculation of harmonic force fields and vibrational modes of molecules, QCPE Program No. 807 (2002). [14] P.L. Polavarapu, J. Phys. Chem. 94 (1990) 8106. [15] G. Kersztury, S. Holly, J. Varga, G. Bensenyi, A.Y. Wang, J.R. Durig, Spectochim. Acta V 49 A (1993) 2007. [16] G. Kereztruy, Raman spectroscopy theory, in: J.M. Chalmerg, P.R. Griffiths (Eds.), Hand Book of Vibrational Spectroscopy, vol. 1, Wiley, 2002, p. 71. [17] O.E. Kasende, Spetrochim. Acta Part a 58 (2002) 1793. [18] G. Socrates, Infrared and Raman Characteristic Group Frequencies, Tables and Charts, third ed., Wiley, Chichester, 2001. [19] V. Krishnakumar, R.J. Xavier, Indian J. Pure Appl. Phys. 41 (2003) 95. [20] G. Varsanyi, Vibrational Spectra of 700 Benzene Derivatives, vols. (I–II), Akademici Kiaclo, Budapest, 1974. [21] Y. Xue, D. Xu, D. Xie, G. Yan, Spectrochim. Acta Part A 56 (2000) 1929. [22] Y. Xue, D. Xie, G. Yan, Int. J. Quantum Chem. 76 (2000) 686.