A comparative study on the vibrational spectroscopy of pyridazine, pyrimidine and pyrazine

Journal of Molecular Structure (Theochem) 423 (1998) 225–234

A comparative study on the vibrational spectroscopy of pyridazine, pyrimidine and pyrazine Ferenc Billes a,*, Hans Mikosch b, Sa´ndor Holly c a

Institute for Physical Chemistry, Technical University of Budapest, Budafoki u´t 8., H-1521 Budapest, Hungary b Institute for General Chemistry, Technical University of Vienna, Gumpendorferstr. 1a, A-1060 Wien, Austria c Central Research Institute for Chemistry, Hungarian Academy of Sciences, Pusztaszeri u´t 59–67., H-1025 Budapest, Hungary Received 18 March 1997; accepted 27 March 1997

Abstract In this work, the authors deal with the vibrational spectroscopy of the three diazine parent compounds, i.e. that of pyridazine, pyrimidine and pyrazine. Infrared spectra were recorded in vapour and condensed phases, and Raman spectra were measured in condensed phase using both parallel and perpendicular polarization of light. The vibrational fundamental frequencies were calculated applying ab initio quantum-chemical methods: Møller–Plesset perturbation and local density functional methods. The results of the calculations were applied to the assignment of the vibrational fundamentals and the measured fundamental frequencies were used to refine the vibrational force constants. The main deviations between the recalculated and the measured frequencies are about 2.5% or smaller. q 1998 Elsevier Science B.V. Keywords: Vibrational spectra; Diazines; Møller–Plesset; DFT; Vibrational frequencies

1. Introduction The diazine rings are important parts of a series of both natural and synthetic compounds, e.g. mononucleotides. The aim of our work was a comparison of the three diazines from the viewpoint of vibrational spectroscopy. Therefore, we recorded their infrared vapour and condensed phase spectra, and their normal and polarized Raman spectra. Also ab initio quantumchemical calculations were carried out using Hartree–Fock (HF), Møller–Plesset (MP) and charge * Corresponding author.

density functional (DFT) methods. These calculations helped in the assignment of the spectra. The vibrational spectra of the three compounds were measured earlier by various authors. Publications of the last 20 years are: for pyridazine [1–3], for pyrimidine [4–12] and for pyrazine [13–17]. Quantum-chemical calculations of the harmonic vibrational frequencies of the diazines have already been published; for pyridazine calculations see Refs. [2,3,18–21], for the calculated pyrimidine frequencies see Refs. [4,8,19,22,23], and for the calculated pyrazine fundamentals see Refs. [19,24–28]. These calculations were either experimental, semiempirical or ab initio ones at HF level but not at

0166-1280/98/$19.00 Copyright q 1998 Elsevier Science B.V. All rights reserved PII S 0 16 6- 1 28 0 (9 7 )0 0 14 3 -7

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post-HF level, excluding our work on pyridazine using MP2 and LDFT methods.

2. Experimental details The compounds used were: pyridazine (EGAChemie; 97% purity), pyrimidine (Fluka; . 98% purity) and pyrazine (Fluka; . 98% purity). The liquids (pyridazine and pyrimidine) were freshly distilled before recording the spectra. The measurement of the pyrazine spectra was difficult, since this compound sublimates. Infrared spectra of the three compounds were recorded on a Nicolet Magna 750 spectrometer. Vapour spectra were measured in a 10 cm cell (pyrazine and pyrimidine) and a 1 m cell (pyridazine) with 0.125 cm −1 resolution and printed to a file in 0.0625 cm −1 steps. Pyridazine and pyrimidine film spectra were recorded with 2 cm −1 resolution and printed to a file in 1 cm −1 steps. Problems arose with the measurements of the solid state spectrum of pyrazine. A great amount of the substance was necessary to obtain an acceptable spectrum in KBr pellet (effect of sublimation). For the measurement of liquid Raman spectra, a Nicolet FT-Raman 950 spectrometer was applied using 2 cm −1 resolution and printed to a file in 1 cm −1 steps (pyridazine and pyrimidine). The Raman spectrum of pyrazine was recorded in the molten state but the sublimation makes difficulties here also. The spectrum was measured on a Cary 82 spectrometer. Both normal (non-polarized) and polarized spectra (with both parallel and perpendicular polarizers) were recorded.

3. Calculations Our quantum-chemical calculations using post-HF second-order Møller–Plesset perturbation (MP2) [29] with the 6-31G * basis set were based on the gaussian 92 [30] (pyrimidine and pyrazine) and gaussian 90 [31] (pyridazine) program packages. After a geometry optimization, frequency calculations were carried out using the same basis set. Force constants were calculated by twice differentiation of the molecular energy. Harmonic vibrational frequencies and IR-intensities were calculated. The calculated geometry and force field were applied for the further frequency refinement and the potential energy distribution (PED) calculations using our own program. For DFT [32] calculations the demon program package, developed at the Universite´ de Montre´al, was applied. This program uses linear combinations of Gaussian-type orbitals (LCGTO). In this work the following basis sets have been used: •

Auxiliary bases:

•

• •

carbon: 5 s-type Gaussians, 2 s-p-d-GTOs constrained to have the same exponent for CD; 4 s-, 5 s-p-d-GTOs for XC (in short notation: 5,2;4,5); nitrogen: 4,1,2; 4,1,2; hydrogen: 5,1; 5,1.

•

Orbital bases:

•

carbon: 5 2 1 1 contractions for s-type, 4 1 1 contractions for p-type, 1 contraction for d-type (Huzinaga’s notation: 5211/411/1); nitrogen: 7111/411/1 *; hydrogen: 41/1.

• •

Fig. 1. The structures of the diazines: (a) pyridazine, (b) pyrimidine, (c) pyrazine.

227

F. Billes et al./Journal of Molecular Structure (Theochem) 423 (1998) 225–234 Table 1 Geometric parameters of pyridazine Parameter a

N(1)–N(2) N(2)–C(3) C(3)–C(4) C(4)–C(5) C(3)–H(7) C(4)–H(8) N(1)-N(2)-C(3) N(2)-C(3)-C(4) C(3)-C(4)-C(5) N(2)-C(3)-H(7) C(5)-C(4)-H(8)

Experimental

Calculated

ED b

MW c

ED + MW + LC-NMR c

X-ray d

STO-3G e

6-31G f

MP2/6-31G *

DFT

133.0 134.1 139.3 137.5

133.8 133.8 140.0 138.4 107.5 107.5 119.3

133.7 133.8 140.0 138.5 107.5 107.5 119.4

135.5 131.6 139.5 136.5

114.9 120.7

114.9 120.7

134.6 133.0 139.5 137.1 97.8 93.3 118.9 115.5 117.1 115.5 122.8

132.4 132.5 139.2 137.6 106.9 107.9 120.1 122.6 117.3 115.4 122.0

140.0 136.9 141.5 140.2 108.8 108.9 118.5 122.7 118.8 114.2 121.9

132.4 133.1 139.2 138.2 110.6 110.4 119.5 123.8 116.7 114.9 122.4

119.3 123.7 117.1

119.0 123.0 117.0

a

Distances in pm, valence angles in degrees. Ref. [33]. c Ref. [34]. d Ref. [35]. e Ref. [36]. f Ref. [37]. b

Electron densities were calculated at 32 randomly chosen radial and at 12 to 110 angular grid points. A local Vosko–Wilk–Nusair potential was used. The vibrational frequencies were calculated for the energy-optimized geometry from a (mass weighted) Hessian matrix derived by numerical differentiation.

4. Results and discussion 4.1. Geometric parameters All the three molecules have planar structure. While pyridazine (I; Fig. 1(a)) and pyrimidine (II;

Table 2 Geometric parameters of pyrimidine Parameter a

Experimental ED

N(1)–C(2) N(3)–C(4) C(4)–C(5) C(2)–H(7) C(4)–H(8) C(5)–H(9) N(1)-C(2)-N(3) C(2)-N(3)-C(4) N(3)-C(4)-C(5) C(4)-C(5)-C(6) N(1)-C(2)-H(7) C(5)-C(4)-H(8) C(6)-C(5)-H(9) a

b

134.0 134.0 139.3 109.9 109.9 109.9 127.6 115.5 122.3 116.8 116.2 122.4 121.6

Distances in pm, valence angles in degrees. Ref. [38]. c Ref. [36]. d Ref. [39]. e Ref. [23]. b

Calculated 3-21G c

4-21G * d

4-21G e

MP2/6-31G *

DFT

132.9 133.2 138.2

132.6 132.8 138.0 107.4 107.3 106.9 127.7 115.4 122.4 116.4 116.1 121.6 121.7

133.4 133.9 139.3 107.3 107.5 107.4 125.1 117.5 121.6 116.7 117.4 121.6 121.6

133.6 136.2 138.9 108.8 108.7 108.7 125.4 117.2 121.3 117.5 117.3 134.9 121.3

133.3 133.4 138.9 110.8 110.8 110.4 127.1 116.0 122.1 116.8 116.5 121.0 121.7

125.0 118.0 122.0 117.0

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F. Billes et al./Journal of Molecular Structure (Theochem) 423 (1998) 225–234

Table 3 Geometric parameters of pyrazine Parameter a

Experimental X-ray

N(1)–C(2) C(2)–C(3) C(2)–H(7) N(1)-C(2)-C(3) C(6)-N(1)-C(2) N(1)-C(2)-H(7)

b

133.4 137.8 105.0 122.4 115.1 118.7

ED

Calculated c

133.9 140.3 111.5 122.1 115.6 113.9

CNDO/2 d STO-3G e

3-21G f

4-21G g

4-21G * g

DZV d

MP2/ 6-31G *

DFT

134.5 138.0 111.8 123.3 113.4 115.4

133.1 138.1

133.3 138.1 106.9 121.1 117.9 117.5

132.6 138.3 107.2 122.2 115.5 117.5

133.4 140.3 107.6 120.9 118.2 117.3

134.5 139.6 108.8 122.4 115.3 116.6

133.3 139.1 110.8 122.1 115.9 117.4

135.5 139.0 108.6 123.0 114.1 116.8

118.0 121.0

a

Distances in pm, valence angles in degrees. Ref. [40]. c Ref. [41]. d Ref. [42]. e Ref. [43]. f Ref. [36]. g Ref. [39]. b

Table 4 Ring stretching force constants, MP2/6-31G *, scaled (F, 10 2 N m −1) Pyridazine

Pyrimidine

Pyrazine

Bond

F

Bond

F

Bond

F

N(1)–N(2) C(3)–C(4) C(4)–C(5)

5.604 6.773 6.559

N(1)–C(2) N(3)–C(4) C(4)–C(5)

5.972 7.898 6.879

N(1)–C(2) C(2)–C(3)

7.208 6.647

Fig. 1(b)) belong to the C 2v point group, the symmetry of pyrazine (III; Fig. 1(c)) is D 2h. The experimental and calculated geometric parameters of the molecules are listed in Table 1, Table 2 and Table 3 for I, II and III, respectively. The experimental and the calculated parameters are in good agreement. Only one exception exists:

the C(5)-C(4)-H(8) angle in pyrimidine, in the MP2/6-31G * calculations. The deviation is more than 128. The calculated charge on N(3) is −0.529 a.u., on H(8) it is + 0.238 a.u. The calculated N(3)–H(8) distance is 193.5 pm. The deviation of the C(4)–H(8) bond is the effect of the large electrostatic attraction between the atoms N(1) and H(8).

Fig. 2. Part of the pyridazine infrared vapour spectrum: the C band at 745 cm −1.

Fig. 3. Part of the pyrimidine infrared vapour spectrum: the C band at 719 cm −1; the Q branch is truncated.

F. Billes et al./Journal of Molecular Structure (Theochem) 423 (1998) 225–234

Fig. 4. Part of the pyrazine infrared vapour spectrum: the C band at 785 cm −1.

229

Fig. 7. Part of the pyrazine infrared vapour spectrum: the C band at 1413 cm −1.

Fig. 5. Part of the pyridazine infrared vapour spectrum: the B band at 1412 cm −1. Fig. 8. Pyridazine infrared liquid spectrum (400–1700 cm −1).

Fig. 6. Part of the pyrimidine infrared vapour spectrum: the B band at 1411 cm −1. Fig. 9. Pyrimidine infrared liquid spectrum (400–1700 cm −1).

4.2. Vibrational force constants The output files of the quantum-chemical calculations contain the force constant matrix in Cartesian coordinates and in Hartree/Bohr 2 units. These force constants were transformed into internal

coordinates using the usual 10 18 N m −1, 10 10 N and 10 2 N m units, respectively. Internal coordinates were chosen according to Pulay’s recommendations [44]. The force constants were refined to the experimental frequencies. The most important diagonal

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F. Billes et al./Journal of Molecular Structure (Theochem) 423 (1998) 225–234

Fig. 10. Pyrazine infrared solid spectrum (450–1700 cm −1).

force constants, the ring stretching ones, are listed in Table 4 for I, II and III. 4.3. Vibrational frequencies Some interesting parts of the recorded spectra are presented in the figures in this section. They are condensed phase infrared and polarized Raman spectra, and some well-defined bands of the infrared vapour spectra. The C bands in the 700 cm −1 region are the best resolved bands of the IR vapour spectra. Fig. 2 shows the 745 cm −1 band of the infrared vapour spectrum of pyridazine with its well-resolved rotational structure. The structure of the band was investigated. Two overtones and a combination band were found (2 p 369 cm −1, 2 p 375 cm −1 and 369 + 375 cm −1). Fig. 3 shows the 719 cm −1 band in the IR vapour spectrum of pyrimidine. The Q band is very intense, therefore it is truncated in the figure,

Fig. 11. Pyridazine polarized Raman spectra, upper line parallel, lower line perpendicular (240–1650 cm −1).

Fig. 12. Pyrimidine polarized Raman spectra, upper line parallel, lower line perpendicular (240–1690 cm −1).

otherwise the rotational structure of the band would not be observable. The 785 cm −1 band of the IR vapour spectrum of pyrazine is presented in Fig. 4. Here also, the rotational structure is very well observable. The three C-type bands in Fig. 2, Fig. 3 and Fig. 4 are possibly the best parts of the vapour spectra. The next three figures contain B bands of the infrared vapour spectra in the 1410 cm −1 region. Fig. 5 shows a B band of the pyridazine IR vapour spectrum (1412 cm −1). It is of very low intensity but the band structure can be followed. The 1411 cm −1 band of pyrimidine is stronger but the rotational lines are not resolved at the actual resolution (Fig. 6). The 1413 cm −1 B band of pyrazine is again well defined with its resolved rotational structure (Fig. 7). The infrared spectra in condensed states are shown in Fig. 8, Fig. 9 and Fig. 10 for I, II and III, respectively (400–1700 cm −1).

Fig. 13. Pyridazine polarized Raman spectra, parallel: upper, perpendicular: lower curve (500–1700 cm −1); the most intense band of the parallely polarized spectrum is truncated.

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F. Billes et al./Journal of Molecular Structure (Theochem) 423 (1998) 225–234 Table 5 Measured and calculated vibrational frequencies of pyridazine (cm −1) Measured a

Calculated

A1 A1 B2 A2 A2 A1 B2 B2 A1 B2 A1 B1 B1 B2 B2 A1 A1 A2 B1 A2 B2 B2 A1 A1

1 2 3 4 5 6a 6b 7b 8a 8b 9a 10a 11 12 13 14 15 16a 16b 17a 18a 19a 19b 20b

PED b (%)

DFT c deMon

MP2 d 6-31G *

MP2 e 6-31G *

IR vapour

IR liquid

RA liquid

1019 3130 1264 767 894 663 617 3118 1592 1583 1077 935 722 1046 3101 1240 1128 342 334 978 1063 1390 1434 3096

1003 3260 1327 935 906 678 629 3252 1636 1632 1110 951 764 1070 3237 1318 1202 361 371 948 1106 1455 1504 3252

950 3099 1255 937 764 598 646 3089 1558 1567 1063 956 706 1045 3075 1300 1146 342 350 950 1125 1398 1475 3080

969A 3082A

962

963p 3076p 1282dp 785 765 622 665dp 3082 1563 1568dp 1235p 985? 755

1281

622A 673?

622 665

1568A 1572B 1061A 985? 745C 1058B 3080B 1337-

1564 1571 1062 987 758 1050

1154 369C

372

1412B 1418A 3052A

1131 1413 1444 3057

1335 1160p 377dp 368dp 963 1118 1444p 3051

nrg10bCH90 nCH99 nrg93 gCH98 gCH100 brg93 brg90 nCH99 nrg63bCH28 nrg58bCH33 nrg78bCH20 gCH91 grg95 nrg66brg30 nCH99 nrg48bCH47 nrg20bCH79 grg91 grg91 grg10gCH90 brg92 nrg16bCH82 nrg32bCH63 nCH99

Note: Mean deviation between the experimental and the scaled MP2/6-31G * results: 2.64% (22.14 cm −1), 3 scale factors. a IR: infrared; A, B and C: IR band contours; RA: Raman; p: polarized; dp: depolarized. b MP2/6-31G * scaled, u: stretching, b: in-plane bending, g: out-of-plane deformation, rg: ring. c For the basis sets, see the text. d Quantum-chemical results. e With scaled force field.

The polarized Raman spectra (200–1700 cm −1 for I and II, 400–1700 cm −1 for III) are presented in Fig. 11, Fig. 12 and Fig. 13 for I, II and III, respectively. The first two could be recorded with a very good signal-to-noise ratio. The melt spectra are very noisy, therefore the two spectra are not overlaid in the figure. Also, the most intense band of the parallely polarized spectrum was truncated, since its intensity is very high in comparison to all other bands. The numerical results of the measurements and calculations are presented in Table 5, Table 6 and Table 7 for I, II and III, respectively. The vibrational modes are numbered according to the benzene modes following Wilson [45]. Compared with benzene, the number of atoms is reduced by 2, thus

the number of vibrational modes is only 24, i.e. lowered by 6. The lower symmetry implies an ambiguity in correlating six modes to the analogous species in the higher symmetry, since by neglecting atoms in a given molecule, the components of the normal coordinates for the remaining atoms are identical for different vibrational modes of the same symmetry. Or—the same fact explained the other way round— by increasing the number of atoms in a molecule the number of degrees of freedom increases threefold; the additional vibrations originate from vibrational modes of the former symmetry group. Thus, depending on the molecule, equivalent pairs of vibrations arise, in our case one of the 7-, 9-, 10-, 17-, 18- and 20-type modes, respectively.

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F. Billes et al./Journal of Molecular Structure (Theochem) 423 (1998) 225–234

Table 6 Measured and calculated vibrational frequencies of pyrimidine (cm −1) Measured a

Calculated

A1 A1 B2 B1 B1 A1 B2 B2 A1 B2 A1 B1 B1 A1 A1 B2 B2 A2 B1 A2 B2 A1 B2 A1

1 2 3 4 5 6a 6b 7b 8a 8b 9a 10b 11 12 13 14 15 16a 16b 17a 18b 19a 19b 20b

PED b (%)

DFT c deMon

MP2 d 6-31G *

MP2 e 6-31G *

IR vapour

IR liquid

927 3130 1329 754 948 675 612 3082 1588 1589 1435 986 775 1139 3081 1287 1196 381 290 976 1395 1053 1065 3078

1006 3258 1415 726 928 691 621 3247 1567 1656 1497 982 809 1189 3240 1330 1260 345 374 933 1494 1064 1087 3238

962 3076 1335 754 978 690 624 3066 1566 1575 1451 1032 843 1132 3058 1226 1162 388 357 981 1415 1048 1052 3056

969A 3082A

960 3086 1356 720 980 679 621 3049 1569 1569 1466 1026 810 1160 3049 1226 1158

719C

621? 3047B 1572A 1465A 10338041155A 3053A 1224 1158B

1411B 1065A 1071B 3053A

1399 1071 1071 3053

RA liquid 3087

980d 679 624d 3040 1571p 1565dp 1468

1139p 3054 1228dp 398dp 347dp 960 1398dp 1075p 1075? 3053

nrg10bCH90 nCH98 nrg68bCH30 gCH90 gCH95 nrg12brg87 brg91 nCH99 nrg81bCH10 nrg63bCH26 nrg31bCH67 gCH95 grg20gCH79 nrg40brg52 nCH99 nrg66bCH33 nrg21bCH78 grg99 grg89gCH11 gCH99 nrg15bCH84 nr51br31bCH15 nrg48bCH42 nCH99

Note: Mean deviation between the experimental and the scaled MP2/6-31G * results: 1.17% (10.80 cm −1), 9 scale factors. a IR: infrared; A, B and C: IR band contours; RA: Raman; p: polarized; dp: depolarized. b MP2/6-31G * scaled, n: stretching, b: in-plane bending, g: out-of-plane deformation, rg: ring. c For the basis sets, see the text. d Quantum-chemical results. e With scaled force field.

The assignment of the experimental frequencies is not an easy task. The easiest way is to find the vapour band contour and the polarized Raman lines. Otherwise, one has to rely on the former, mostly experimental results. Some bands are very weak and disappear in the noise of the spectra. It is very difficult to decide the polarization state of weak Raman lines. Some bands are very close to each other and therefore they also overlap in the infrared vapour spectrum, e.g. the pyridazine 8a and 12 bands. Here we have a band structure that is not resolvable by usual methods. Overlapping bands in condensed states in both infrared and Raman spectra were resolved. The frequencies calculated with MP2/6-31G * for pyridazine are very close to the experimental ones

(excluding CH stretchings). The deviations from the experimental frequencies are greater for pyrimidine and pyrazine. Scaling of the force constants was applied to decrease the deviations. It was interesting, however, that for pyrimidine the deviations increased in cases where the agreement between the calculated and measured frequencies was quite good. The tables also contain the mean deviation between our scaled MP2/6-31G * and measured results. The frequencies calculated with the DFT method are in better agreement with the experimental frequencies than the MP2 ones. Therefore, this method seems to be a good tool for further work. Regarding the PED, sometimes it was difficult to distinguish between the character of a vibrational mode. For example the 9a, 18b, 19a and 19b modes

233

F. Billes et al./Journal of Molecular Structure (Theochem) 423 (1998) 225–234 Table 7 Measured and calculated vibrational frequencies of pyrazine (cm −1) Measured a

Calculated

Ag Ag B 3g B 2g B 2g Ag B 3g B 3g Ag B 3g Ag B 1g B 3u B 1u B 1u B 2u B 2u Au B 3u Au B 1u B 1u B 2u B 2u

1 2 3 4 5 6a 6b 7b 8a 8b 9a 10a 11 12 13 14 15 16a 16b 17a 18a 19a 19b 20b

DFT c deMon

MP2 d 6-31G *

MP2 e 6-31G *

997 3086 1311 734 952 588 702 3072 1584 1563 1200 897 767 1026 3070 1284 1059 287 407 977 1134 1452 1398 3080

1041 3244 1396 747 949 605 718 3225 1641 1589 1281 944 801 1040 3226 1365 1113 344 424 961 1176 1531 1471 3240

1003 3060 1356 743 946 590 673 3041 1585 1528 1242 941 799 1011 3042 1315 1075 339 420 958 1139 1486 1425 3055

IR vapour

PED b (%) IR solid

RA melt 1015p 3053p 1353 f 755 f 976 f 601 f 698dp 3062dp 1579p 1522dp 1235p 925 f

785C 1020A 3017A 1335B 1063B

790 1019 3015 1339 1065

417C

417

1135A 1484A 1413B 3069B

1128 1485 1411 3060

nrg94 nCH99 nrg11bCH87 gCH90grg10 gCH10grg90 brg92 brg92 nCH99 nrg64bCH28 nrg80bCH12 nrg34bCH66 gCH99 gCH97 nrg24brg70 nCH99 nrg98 nrg66bCH32 grg95 grg97 gCH93 nrg50brg28bCH20 nrg24bCH74 nrg34bCH65 nCH99

Note: Mean deviation between the experimental and the scaled MP2/6-31G * results: 1.88% (23.30 cm −1), 7 scale factors. a IR: infrared; A, B and C: IR band contours; RA: Raman; p: polarized; dp: depolarized. b MP2/6-31G * scaled, n: stretching, b: in-plane bending, g: out-of-plane deformation, rg: ring. c For the basis sets, see the text. d Quantum-chemical results. e With scaled force field. f From non-polarized melt spectrum.

of pyrimidine are strongly mixed. Therefore, the assignment is uncertain in this case. After finishing this work, we discovered the paper by Martin and Alsenoy [46]. They calculated the vibrational frequencies of the same molecules applying the DFT method with the Becke3LYP functional. They did not measure, however, the experimental spectra of the compounds. Acknowledgements Ferenc Billes would like to thank the Hungarian National Scientific Foundation OTKA for supporting this work (project number T 014064).

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