Density functional calculations on the structure, vibrational frequencies and normal modes of 7-Azaindole

Spectrochimica Acta Part A 64 (2006) 1083–1087

Density functional calculations on the structure, vibrational frequencies and normal modes of 7-Azaindole B. Karthikeyan ∗ Department of Chemistry, Annamalai University, Annamalai Nagar 608002, Tamil Nadu, India Received 12 July 2005; received in revised form 14 September 2005; accepted 14 September 2005

Abstract The structure, harmonic frequencies and vibrational mode assignments for 7-Azaindole monomer and its isotopic analogous are calculated using BP86 method employing the 6-31G* basis set. The results of the optimized molecular structure obtained on the basis of these calculations are presented and critically compared with the experimental IR data recorded in gas phase. The Raman and IR spectral data of 7-Azaindole obtained in solid phase have also been included. The normal mode analysis has been carried out for all the modes. The analysis of vibrational data for 7-Azaindole has been qualitative both in terms of assignments as well as the description of the normal modes. Potential energy distribution has been calculated for the perfect assignment of the vibrational modes. © 2005 Elsevier B.V. All rights reserved. Keywords: Density functional calculations; Vibrational frequencies; 7-Azaindole

1. Introduction 7-Azaindole is an important bicyclic aza-aromatic molecule, it is iso-electronic to purine and has a close relationship with the nucleic bases adenine and guanine [1]. 7-Azaindole can create two hydrogen bonds by donating the pyrrole proton and accepting a proton at the pyridine nitrogen [2]. 7-Azaindole whose molecular structure has received considerable attention since its dimer has been recognized as a simple model for the hydrogenbonded base pair of DNA and could provide information on the possible role of tautomerism in mutation [3]. There are no density functional theoretical (DFT) reports on the 7-Azaindole monomer to the best of our knowledge, though there are so many theoretical and experimental studies reported on its dimer. In this paper, we report the structure and vibrational analysis of 7-Azaindole monomer by means of ab initio DFT calculations. DFT methods are widely used for the computation of molecular structure and vibrational frequencies. In particular, for polyatomic molecules, the DFT methods assist in the prediction of more accurate molecular structure and vibrational frequencies than the conventional ab initio calculations [4]. DFT calcula-

∗

Tel.:+91 4364 280 514. E-mail address: bkarthi [email protected].

1386-1425/$ – see front matter © 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.saa.2005.09.019

tions, being accurate and consistent with the experimental data, have been successfully used to predict the vibrational frequencies for polyatomic systems [5]. Computed frequencies using the method BP86 are relatively close to experimental results due to the inclusion of electron correlation has been reported in many results. The present investigation has been carried out with the following objectives: (a) to study the optimized structure of 7-Azaindole, (b) to obtain PEDs and exact normal mode descriptions with BP86/6-31G* , which are not available in the literature for 7-Azaindole monomer but are necessary for the accurate assignment of the vibrational spectra of the compound, (c) to clarify the deviations in the calculated frequencies for various isotopes of 7-Azaindole with respect to the experimental data and (d) to compare the calculated IR intensities with those obtained from experiments. 2. Computational methods The density functional calculations presented here were performed with the Gaussian-94/DFT [6] program on an IBMRS6000 computer system. The molecular geometry of 7Azaindole was optimized using the method BP86 with the basis set 6-31G* . A complete geometry optimization was carried out employing Berny’s optimization algorithm, which resulted in CS symmetry. The vibrational frequencies and corresponding

1084

B. Karthikeyan / Spectrochimica Acta Part A 64 (2006) 1083–1087

normal modes were then evaluated at the optimized geometry using analytical differentiation algorithms contained within the program. The assignment of the calculated normal modes were made from the corresponding potential energy distributions (PEDs) and isotopic shifts. The PEDs and frequencies of the isotopically labeled species were calculated from the quantum mechanically derived Cartesian force constant matrix using MOLVIB program [7]. The normal modes were analysed by transforming the calculated displacements from Cartesian to internal coordinate basis using a program, NMODES [8]. The assignments of the calculated frequencies were clarified by visual inspection of the normal modes using the program MOLVIB. The vibrational frequencies obtained are reported without scaling. 3. Results and discussion 3.1. Geometrical structure The definition of the geometrical parameters and the numbering of atoms in the molecule are shown in Fig. 1. Optimized geometry of the compound in the ground state corresponds to CS symmetry. The optimized parameters have been compared with the microwave spectral data available in the literature [9]. Table 1 shows the bond lengths and bond angles obtained from the BP86/6-31G* optimization for 7-Azaindole monomer along with the microwave spectral data. The obtained geometry is found to be planar. The electron or X-ray diffraction values in previous literature are available only for the dimer form of the molecule due to its existence as dimer in nature. Since this report restricts our discussion to monomer, the ED/XD data could not be reported for comparison with the theoretical results. The C H bond distance (C2 H1 , C3 H5 , C6 H7 , C10 H11 ˚ is overestimated compared to and C12 H13 ) obtained (1.0962 A) ˚ The distance of the C C the microwave spectral data (1.082 A). ˚ on comparison with (C2 C3 ) bond in pyridine ring (1.4001 A), ˚ is found to be highly overthe microwave spectral data (1.382 A), estimated. At the same time, the C C (C2 C4 ) bond distance in ˚ The value the same ring is slightly underestimated by 0.0154 A. ˚ of C C (C12 C10 ) bond distance (1.3834 A) in the pyrrole ring ˚ is in good agreement with the microwave spectral data (1.382 A). ˚ The N H bond distance (1.0173 A) is found to be highly over-

Fig. 1. Structure of 7-Azaindole and numbering of atoms.

Table 1 Optimized parameters of 7-Azaindole by BP86/6-31G* calculation Structural parametersa Bond distances H1 C2 C2 C3 C2 C4 C6 C3 C6 N8 C9 N8 C10 C4 C12 C10 N14 C12 H15 N14 Bond angles C 3 C2 H1 C4 C2 C3 C6 C3 C2 N8 C6 C3 C9 N8 C6 C10 C4 C9 C12 C10 C4 N14 C12 C10 a b

˚ BP86/6-31G* (A) 1.0962 1.4001 1.4096 1.4155 1.3479 1.3403 1.4377 1.3834 1.3882 1.0173 121.0432 117.6525 120.2058 124.4948 113.8013 106.9537 106.8909 109.7362

˚ Microwave datab (A) 1.082 1.382 1.425 – 1.338 1.370 – 1.382 1.370 0.996 – – – – 114.8 – – –

For definition of parameters, see Fig. 1. Experimental values taken from ref. [9].

estimated when compared to the experimental one and similar is the trend with the distance of the bond C N (C9 N8 ) in the pyridine ring. The C N (C12 N14 ) bond distance is found to ˚ As seen in Table 1, be overestimated by a value of 0.0182A. the distance of the C N (C6 N8 ) bond compares well with the experimental data. The corresponding microwave spectral data for comparison with the two C C bond distances, i.e., C3 C6 and C4 C10 in the pyridine and pyrrole rings, respectively, were not available and similar is the case with the optimized bond angles except for the angle C9 N8 C6 whose value (113.8013◦ ) fairly agrees with the experimental value of 114.8◦ . 3.2. Vibrational frequencies and assignments The assignments of the calculated vibrational frequencies of 7-Azaindole, based on normal mode analysis, isotopic shifts and a comparison with the reported experimental results [1] are listed in Table 2. The reported experimental IR intensities for the compound are comparable with the ones obtained theoretically, though there are some discrepancies noted for a few. 3.2.1. Fundamental frequencies of 7-Azaindole 7-Azaindole has 39 fundamental vibrations. Among these, 27 vibrations are in-plane and 12 vibrations are out-of-plane. All the 39 modes are IR active and Raman active as well. As mentioned earlier, the frequencies are reported without scaling. The calculated frequencies and normal mode descriptions of the 39 normal vibrations of 7-Azaindole from the BP86 method with 6-31G* basis set have been compared with the reported gas phase IR results. In general, the IR gas-phase spectrum is found advantageous over the solution or solid-phase spectra in the sense that the symmetry of most vibrational coordinates is easily determined from the rotational profiles of the IR bands and

Table 2 Vibrational frequencies, PED’s and normal mode descriptions of 7-Azaindole as obtained by BP86/ 6-31G* calculations S. no.

a b

Symmetry

218 234 408 417 450 544 577 602 613 700 753 761 783 809 873 883 901 926 1035 1064 1082 1114 1194 1240 1294 1339 1351 1413 1425 1492 1504 1576 1605 3086 3105 3127 3178 3198 3564

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 a a a a a a

Vapour IRa (cm−1 )

IR intensity

216.5(m) 204 420.3(m) 456.08(s) 468.8(s) 552 580.6(w) 605(vw) 623.6(w) 718.1(vs) 758.3 774.29(s) 798.49(m) 869.6(w) 898.24(m) 925(m) 944.1(m) 960.5(w) 1032 1063.9(w) 1083.3(w) 1115.5(w) 1200.6(w) 1252 1284.3(s) 1308.5(m) 1350.3(m) 1413.3(s) 1425.3(s) 1495.0(w) 1509.5(m) 1579.7(m) 1607.4(m) 3042(w) 3066(m) 3085(w) 3100(w) 3142.1(w) 3517.5(s)

12.77 0.03 24.76 8.09 49.98 1.29 3.57 1.60 2.27 62.88 3.70 22.80 12.85 9.96 3.11 8.75 0.17 1.24 0.36 7.19 23.36 0.53 1.43 1.96 6.42 25.85 26.50 46.71 2.95 9.76 11.35 16.51 12.88 22.00 15.01 27.40 2.96 4.86 60.93

Experimental IR (cm−1 )

432 566(vw) 598(w) 618(w) 725(s)

561

765(s)

767

624

806(w) 879 895(m) 959(vw) 1044

1278(s) 1338(s)

1072 1120 1206 1254 1284 1338

1421(s) 1437 1499(m) 1588(s)

3067(sh) 3124(sh)

Approximate descriptionb

CCC (71) + NH (24) NH (34) NH (52) CCC (72) NH (72) CH (44) + CNC (19) + CCC (18) CCC (45) + CH (44) CH (55) CCC (42) + CH (38) CH (94) CH (16) + CN (15) + CC (14) CH (76) CH (60) CH (98) CH (55) CH (65) CH (89) CH (78) CC (41) + CN (40) CH (68) + CC (12) + CN (11) CH (40) + NH (28) + CN (11) CH (75) CH (53) + NH (12) CH (68) + NH (12) CH (36) + NH (16) + CC (12) CH (61) + CN (12) CN (26) + CC (21) + NH (15) + CH (14) CH (41) + CC (16) + CN (13) CH (43) + NH (25) + CN (16) CH (51) + CC (16) + NH (12) CN (31) + CH (27) + NH (8) CC (25) + CH (22) CC (31) + CH (21) + CN (11) CH (92) CH (96) CH (95) CH (99) CH (99) NH (99)

Ring C C + δNH (butterfly mode) δNH (asymmetric torsion) δNH Ring C C δNH δCH + C N C + Ring C C Ring C C + δCH δCH (␴) + Ring C C Ring C C + δCH (␳) + δCH (␴) δCH (␴) δCH (␳) + νCN (␳) + νCC δCH (␳) + δCH (␴) δCH (␳) + δCH (␴) δCH (␴) δCH (␳) + δCH (␴) δCH (␳) + δCH (␴) δCH (␳) δCH (␳) νCC (␳) + νCN (␴) νCH (␳) + νCC (␴) + νCN (␴) δCH (␴) + δNH + νCN (␴) δCH (␳) + δCH (␴) δCH (␳) + δCH (␴) + δNH δCH (␳) + δCH (␴) + δNH δCH (␳) + δNH + νCC (␴) δCH (␳) + δCH (␴) + νCN (␳) νCN (␳) + νCC (␳) + δNH + δCH (␳) δCH (␳) + νCC (␴) + νCN (␳) δCH (␳) + δCH (␴) + δNH + νCN (␴) δCH (␳) + δCH (␴) + νCC (␳) + δNH νCN (␳) + δCH (␴) + δNH νCC (␳) + δCH (␳) νCC (␳) + δCH (␳) + νCN (␳) νCH (␳) νCH (␳) νCH (␳) νCH (␴) νCH (␴) νNH

Raman (cm−1 )

430(w)

1207(vw)

PED (%)

1509 1586 1603 3013 3065 3130

B. Karthikeyan / Spectrochimica Acta Part A 64 (2006) 1083–1087

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 34 35 36 37 38 39

DFT BP86/6-31G* (cm−1 )

Values taken from ref. [1]. ν: stretch; δ: bend; ␳: pyridine ring; ␴: pyrrole ring. 1085

1086

B. Karthikeyan / Spectrochimica Acta Part A 64 (2006) 1083–1087

Fig. 3. Raman spectrum of 7-Azaindole in solid. Fig. 2. IR spectrum of 7-Azaindole in solid.

that hydrogen bond formation and other inter-molecular interactions are mostly avoided. A comparative study of these computed frequencies with the vapour IR data are given in Table 2. As it is observed from the table, the computed frequencies are slightly underestimated, particularly in the structure sensitive region 400–1700 cm−1 with the exception of only a few vibrational modes. The overestimation of the frequencies observed in the region 3000–3200 cm−1 can be attributed to the fact that the DFT methods are known to overestimate the C H stretching frequencies. Comparison with experimental Raman and IR spectral frequencies of 7-Azaindole solid has also been included for the comparison. As it is observed from the table, there are many discrepancies in the agreement between theoretical and experimental could be accounted to the most probable spent existence of the molecule in the form of a dimer in its solid state. 3.2.2. Frequency assignments With our calculations, we predict the out-of-plane butterfly motion at 218 cm−1 and an asymmetric torsion of the pyridine and pyrrole rings at 234 cm−1 . Since the latter vibration carries almost zero density and based on the computed frequencies and intensities, we assign the band at 216.5 cm−1 in the vapour IR spectrum to this mode. Our calculations predict three fundamentals in the region around 450 cm−1 viz., two strong a symmetry, at 408 and 450 cm−1 and an a of medium intensity at 417 cm−1 . The comparison between computed and experimental intensities is the basis for the proper assignments of the modes. The fundamental at 544 cm−1 is found to deform the pyridine ring asymmetrically as shown in Fig. 2 and has been assigned to the band at 552 cm−1 , whose intensity is very less. The C H wagging vibrations at 700 and 761 cm−1 are assigned to the intense bands at 718.1 and 774.29 cm−1 , respectively. Similar kind of vibrations are observed at two more fundamentals of a symmetry and of very less intensity at 901 and 926 cm−1 to which two IR bands at 944.1 and 960.5 cm−1 can plausibly be assigned, respectively. The totally symmetric modes in the interval between 1030 and 1250 cm−1 are commonly weak in nature and are with C H rocking and C C stretching in both

pyridine and pyrrole rings. The atomic displacements of these modes are depicted in Fig. 3. These frequencies are found to be well in agreement with the experimental values. A few modes among these exhibit C N stretching and N H bending as well. The interval from 1290 to 1610 cm−1 have only totally symmetric modes among which three are strong and the others are with medium intensity. The C C stretching, C H rocking, C N stretching and N H bending contribute more to these vibrational modes and the assignment of these modes are given in Table 2. Six totally symmetrical modes are computed in the interval between 3030 and 3570 cm−1 which include three modes with medium, two with weak and one with very high intensity. The major contributions are from C H stretching from the pyridine ring, C H stretching in the pyrrole ring and N H stretching. These frequencies agree fairly well with the experimental values as shown in Table 2 except for the one at 3178 cm−1 which is noted to have been deviated from the experimental value by 78 cm−1 and the assignment has been made tentatively. The N H stretching fundamental is observed to be the strongest among all which is computed at 3564 cm−1 and is assigned to the band at 3517.5 cm−1 in the reported IR spectrum. PED have been calculated to support the present assignment and to analyse the coupled modes. The obtained results are also given in Table 2. 3.2.3. Isotopic shifts The frequencies for the isotopic analogues viz., ((13 C)5 C2 NH5 )NH, ((13 C)4 C3 NH5 )NH, (C7 ND3 H2 )NH1 , (C7 ND3 H2 ) NH2 of 7-Azaindole monomer have also been computed and given in Table 3. The isotopic shifts are found to be consistent with the PEDs and assignment of the normal modes. Calculations were carried out with 13 C and 2 H substitutions in both pyridine and pyrrole rings in the fashions given in Table 3 so as to verify the assignments of the normal modes involving C N, C C and C H stretching. Table 3 clearly shows the frequencies which are influenced by the isotopic substitution along with the corresponding isotopic shifts and assignments. As all the carbon atoms in the pyridine ring are substituted with 13 C, the frequencies at 1035, 1294, 1339, 1413, 1425, 1492, 1576 and 1605 cm−1 are shifted by 23, 27, 27, 30, 35, 35, 41 and 44 cm−1 , respectively. From these isotopic shifts and from the calculated

B. Karthikeyan / Spectrochimica Acta Part A 64 (2006) 1083–1087

1087

Table 3 Isotopic shifts for normal modes of 7-Azaindole Frequencies and isotopic shifts (cm−1 ) (C6 CNH5

)NHa

1035 1294 1339 1413 1492 1504 1576 1605 3086 3105 3127 3178 3198 3564

((13 C)

5 C2 NH5

)NHb

1

1012 1267 1312 1383 1457

23 27 27 30 35

1535 1561

41 44

((13 C) 1271 1311 1393 1461 1480 1551 1580

4 C3 NH5

)NHc

2

(C7 ND3 H2 )NH1

d

3

(C7 ND3 H2 )NH2

e

4

23 28 20 31 24 25 25 2277

809

2316

811

2346 2380 2617 3086 3105 3127

740 725 510 92 93 437

Normal mode description νCC + νCN νCC νCN νCC + νCN νCC νCN νCC νCC + νCN νCH νCH νCH νCH νCH νNH

ν: stretch. 1 : (C6 CNH5 )NH ((13 C)5 C2 NH5 )NH, 2 : (C6 CNH5 )NH (13 C)4 C3 NH5 )NH, 3 : (C6 CNH5 )NH (C7 ND3 H2 )NH1 , 4 : (C6 CNH5 )NH (C7 ND3 H2 )NH2 . a Without any isotopic substitutions. b All the carbon atoms in the pyridine ring substituted with 13 C. c All the hydrogen atoms in the pyridine ring substituted with D. d All the carbon atoms in the pyrrole ring substituted with 13 C. e All the hydrogen atoms in the pyrrole ring substituted with D.

relative atomic displacements of these normal modes, it is reasonable to assign these frequencies to C C and C N stretching vibrations as given in Table 3. Likewise, the isotopic shifts that are observed when all the carbon atoms in the pyrrole ring are substituted with 13 C are 23, 28, 20, 31, 24, 25 and 25 cm−1 for the modes at 1294, 1339, 1413, 1425, 1492, 1504, 1576 and 1605 cm−1 , respectively, and thus the assignments that were made previously are reconfirmed. The C H stretching frequency assignments are reconfirmed by substituting the hydrogen atoms in pyridine and pyrrole rings and computing the isotopic shifts. The frequencies 3086 and 3127 cm−1 , when all the hydrogen atoms in the pyridine ring are substituted with 2 H, are deviated by 809 and 811 cm−1 , respectively. The observation of isotopic shifts by 740, 725, 510, 92, 93 and 437 cm−1 when the hydrogen atoms in the pyrrole ring are replaced by 2 H at the frequencies 3086, 3105, 3127, 3148, 3198 and 3564 cm−1 , respectively, helps double checking the first hand assignments. The final mode at 3564 cm−1 has been assigned to the N H stretching vibration which is confirmed by its shift from the original frequency by 437 cm−1 . 4. Conclusion A systematic study of the vibrational analysis of 7-Azaindole using DFT method has been carried out. It is observed that BP86/6-31G* is very useful in predicting vibrational frequencies for polyatomic systems like 7-Azaindole. The computed frequencies are in good agreement with the experimental gasphase frequencies of the compound. Thus, a complete vibrational assignments of 7-Azaindole is done from this studies in addition to providing normal mode descriptions and PED values for the vibrational frequencies.

Acknowledgement Author thank Prof. Umapathy, Department of Inorganic and Physical Chemistry, I.I.Sc., Bangalore, for providing him with the computing facilities necessary to carry out the present calculations through SERC, I.I.Sc., Bangalore. References [1] E. Can´e, P. Paimieri, R. Tarroni, A. Trombetti, J. Chem. Soc., Faraday Trans. 90 (21) (1994) 3213–3219. [2] P. Ilich, J. Mol. Struct. 354 (1995) 37–47. [3] K. Fuke, H. Yoshiuchi, K. Kaya, J. Phys. Chem. 88 (1984) 5840– 5844. [4] N. Biswas, S. Umapathy, J. Phys. Chem. A 101 (1997) 5555–5566. [5] P. Mohandas, S. Umapathy, J. Phys. Chem. A 101 (1997) 4449–4459. [6] M.J. Frisch, G.W. Trucks, H.B. Schlegal, P.M.W. Gill, B.G. Johnson, M.A. Robb, J.R. Cheeseman, T. Keith, G.A. Peterson, J.A. Montgomery, K. Raghavachari, M.A. Al-Laham, V.G. Zakrzewski, J.V. Ortiz, J.B. Foresman, J. Cioslowski, B.B. Stefanov, A. Nanayakkara, M. Challacombe, C.Y. Peng, P.Y. Ayala, W. Chen, M.W. Wong, J.L. Andres, E.S. Replogle, R. Gonperts, R.L. Martin, D.J. Fox, J.S. Binkley, D.J. Defrees, J. Baker, J.J.P. Stewart, M. Head-Gordon, C. Gonzalez, J.A. Pople, Gaussian 94, Revision C.2, Gaussian Inc., Pittsburgh, PA, 1995. [7] T. Sundius, MOLVIB. Calculation of Harmonic Force Fields and Vibrational Modes of Molecules, QCPE, 1991, QCMP 103. [8] NMODES is a package developed in Prof. Umapathy, Department of IPC, I.I.Sc., Bangalore, Laboratory which gives normal modes and potential energy distributions in internal coordinates. Since the program generates internal coordinate definitions and other necessary information automatically, Gaussian output file can be directly used as the input without any modifications. This package can be used to calculate isotopic frequencies and also to facilitate a visual inspection of the normal modes. NMODES can be run on IBM compatible personal computers as well as mainframe computers. [9] A.C. Borin, L. Serrano-Andr´es, Chem. Phys. 262 (2000) 253–265.