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An experimental and theoretical study of vibrational spectra of picolinamide, nicotinamide, and isonicotinamide
Journal of Molecular Structure 826 (2007) 6–16 www.elsevier.com/locate/molstruc
An experimental and theoretical study of vibrational spectra of picolinamide, nicotinamide, and isonicotinamide Meric Bakiler a b
a,*
, Olcay Bolukbasi b, Ayberk Yilmaz
b
Mimar Sinan Fine Art University, Department of Physics, Besiktas, 34347 Istanbul, Turkey Istanbul University, Science Faculty, Physics Department, Vezneciler, 34118 Istanbul, Turkey
Received 20 January 2006; received in revised form 13 April 2006; accepted 17 April 2006 Available online 5 June 2006
Abstract The molecular structures and vibrational spectra of the three isomers of pyridinecarboxamide (picolinamide, nicotinamide, isonicotinamide) were calculated with the Density Functional Theory (DFT) method using the B3LYP function and the 6-31++G(d,p), Z2PolX, Z3PolX basis sets. The calculations were performed by using the Gaussian98W packet program set. The total energy distributions (TED) of the vibrational modes of these molecules were calculated by using the Scale 2.0 program and the vibrational modes of the molecules were determined. The Scaled Quantum Mechanical (SQM) method was used in the scaling procedure. In the experimental part of the study, the solid phase FT-IR and Micro Raman spectra of the three isomers of pyridinecarboxamide have been recorded in the range of 4000–650 and 1200–100 cm 1, respectively. The calculated wavenumbers were compared to the corresponding experimental values. As a result, the observed bands of the three isomers of pyridinecarboxamide were assigned with good accuracy. 2006 Elsevier B.V. All rights reserved. Keywords: DFT calculations; Picolinamide; Nicotinamide; Isonicotinamide; Z3PolX basis set; SQM; Vibrational spectra
1. Introduction The three isomers of pyridinecarboxamide; picolinamide (2-pyridinecarboxamide; 2-NH2COpy), nicotinamide (3pyridinecarboxamide; 3-NH2COpy), and isonicotinamide (4- pyridinecarboxamide; 4-NH2COpy) are a class of medicinal agents with activity that includes the reduction of iron-induced renal damage [1]. The structure of picolinamide and nicotinamide has been determined by experimental methods and reported in previous papers [2–5]. In the present paper, we report a complete description of the molecular geometry and the molecular vibrations of the three isomers of pyridinecarboxamide. For that purpose, quantum chemical computations were performed on the three isomers of pyridinecarboxamide by using the Density Functional Theory (DFT). Experimental information on the molecular vibrations was obtained from the FT-IR and Micro Raman spectra measured. Our assignments *
Corresponding author. Tel.: +902122366936; fax: +902122611121. E-mail address: [email protected] (M. Bakiler).
0022-2860/$ - see front matter 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2006.04.021
were made by using the advantages of theoretical computations. 2. Experimental details The solid phase FT-IR spectra of the powdered three isomers of pyridinecarboxamide were recorded with the ATR unit by using the Perkin-Elmer FT-IR spectrometer in the range of 4000–650 cm 1. In these experiments a resolution of 4 cm 1 was applied. The Raman spectra of the powdered samples were recorded on a Micro Raman Jobin YVON Horiba HR800 UV instrument using 632.8 nm excitation from a He–Ne laser in the range of 1200– 100 cm 1, 1800 grating, 5 scans per 30 s pulse and with 10· zoom. 3. Computational details The geometry optimizations and calculated wavenumbers have been carried out at the Density Functional Theory (DFT) method with the B3LYP exchange-correlation
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
functional [6,7] by using the Gaussian 98W program [8]. The 6-31++G(d,p) basis set and the new highly compact Pol-type basis sets, Z2PolX and Z3PolX [9,10], for the three molecules and their conformers were used in the DFT calculations. The vibrational modes of all these molecules were determined by using total energy distribution (TED) and the calculated wavenumbers were scaled by using the scaled quantum mechanical (SQM) analysis method, with the help of the Scale 2.0 program [11,12] for the results of B3LYP/6-31++G(d,p) basis set. The natural internal coordinates were used for SQM procedure and 10 scaling factors were classified according to different types of internal coordinates. The scaling factors were taken from previous studies for each group [13–15]. Only the scaling factors related to the out of plane bendings and NH2 rocking were refined. The diagonal force constants were scaled by the factor associated with the internal coordinates and the off-diagonal force constants were scaled by the geometric mean of the associated scaling factors. As Oakes et al. have stated, [9,10] wavenumbers calculated with the Z2PolX and Z3PolX basis sets showed to be in conformity with the
7
experimental wavenumbers. For this reason, SQM method was not used on the results obtained from the Z2PolX and Z3PolX basis sets. 4. Results and discussion The optimized geometries for the E- and Z-forms of the three molecules were calculated and their total energies are given in Table 1. In addition to the calculated wavenumbers and the total energy distribution results for the Eforms of the three molecules were obtained by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX and Z3PolX basis sets. The calculated data for the Eand Z-forms of the three molecules are very similar. However, it was found to be that the E-forms of these molecules are more stable than the Z-forms. Therefore, we gave a detailed explanation only for the E-form. The E-form structures of these molecules with the atomic numbering used in this study are shown in Fig. 1. The optimized geometry parameters were obtained by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX, and Z3PolX basis sets according to these atom numberings are given
Table 1 The total energies (in hartree) of the optimized geometry for the E- and Z-forms of the three isomers of pyridinecarboxamide Picolinamide E-Form B3LYP/6-31G++(d,p) B3LYP/Z2POLX B3LYP/Z3POLX
417.0289 416.9806 417.0202
Nicotinamide Z-Form 417.0156 416.9648 417.0038
E-Form 417.0199 416.9712 417.0104
Isonicotinamide Z-Form 417.0195 416.9694 417.0088
Fig. 1. The atom numbering of three isomers of pyridinecarboxamide.
E-Form 417.0198 416.9699 417.0091
Z-Form 417.01978 416.9698 417.0090
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M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
Table 2 The optimized geometry parameters obtained by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX, and Z3PolX basis sets of the three isomers of pyridinecarboxamide Atoms
Picolinamide 6-31++G(d,p) ˚ /deg) (A
R(1,2) R(2,3) R(3,4) R(4,5) R(5,6) R(6,1) R(6,7) R(5,8) R(4,9) R(3,10) R(2,11) R(2,10) R(3,9) R4,11) R(3,11) R(11,12) R(11,13) R(13,14) R(13,15) A(11,13,14) A(11,13,15) A(14,13,15) A(13,11,12) A(13,11,2) A(13,11,3) A(13,11,4) A(12,11,2) A(12,11,3) A(12,11,4) A(11,2,3) A(11,4,3) A(11,4,5) A(11,2,1) A(10,2,1) A(10,2,3) A(3,2,1) A(2,3,4) A(2,3,10) A(4,3,10) A(4,3,11) A(2,3,11) A(2,3,9) A(4,3,9) A(2,1,6) A(3,4,5) A(5,4,9) A(3,4,9) A(1,6,5) A(1,6,7) A(5,6,7) A(4,5,6) A(4,5,8) A(6,5,8) D(14,13,11,12) D(14,13,11,2) D(14,13,11,3) D(14,13,11,4) D(15,13,11,12) D(15,13,11,2) D(15,13,11,3) D(15,13,11,4)
1.3432 1.3977 1.3941 1.3959 1.3979 1.3378 1.0876 1.0854 1.086 1.0839 1.5133 –. – – – 1.2295 1.3564 1.0101 1.0081 119.6839 118.978 121.3381 124.0067 114.5465 – – 121.4467 – – 119.0911 – – 117.6005 – – 123.3084 118.3056 119.0192 122.6751 – – – – 117.8589 118.8381 120.6538 120.5081 123.1628 116.2019 120.6353 118.5262 121.3385 120.1353 179.9369 0.0532 – – 0.0577 179.9415 – –
Nicotinamide Z2POLX ˚ /deg) (A 1.3542 1.401 1.3988 1.4015 1.4022 1.3471 1.0902 1.0889 1.0893 1.0873 1.5084 – – – – 1.2532 1.3595 1.0112 1.0088 119.0827 119.531 121.3863 124.0116 114.5365 – – 121.4519 – – 119.7337 – – 117.4448 – – 122.8215 118.4752 119.025 122.4998 – – – – 118.3733 118.992 120.5368 120.4712 122.5937 116.5838 120.8226 118.7444 121.1597 120.0959 180.0 0.0139 – – 0.0036 180.0175 – –
Z3POLX ˚ /deg) (A 1.3534 1.4014 1.4013 1.4032 1.4042 1.3457 1.0943 1.0918 1.0926 1.0903 1.5095 – – – – 1.2493 1.3631 1.0157 1.0105 117.9942 120.0128 121.9930 124.2953 114.0045 – – 121.7002 – – 119.6291 – – 117.0388 – – 123.3321 118.3207 118.9831 122.6961 – – – – 117.8598 118.8357 120.6132 120.5511 122.9989 116.3788 120.6223 118.6527 121.2474 120.0999 180.0000 0.0079 – – 0.0075 180.0000 – –
6-31++G(d,p) ˚ /deg) (A 1.3383 1.4025 1.4004 1.3915 1.3984 1.3398 1.0877 1.0854 1.0851 – – 1.0883 – – 1.5031 1.2277 1.3696 1.0077 1.0101 122.2195 116.6389 117.8266 121.7543 – 116.8525 – – 121.3864 – – – – – 115.1379 120.9163 123.9241 117.7444 – – 118.2621 123.9788 – – 117.3681 118.9226 122.1098 118.9674 123.4783 115.9815 120.5394 118.5477 121.1519 120.3004 164.4174 – 16.5246 – 5.4448 – 175.4972 –
Isonicotinamide Z2POLX ˚ /deg) (A 1.3490 1.4058 1.4057 1.3959 1.4025 1.3505 1.0903 1.089 1.0875 – – 1.0902 – – 1.5023 1.2531 1.3691 1.007 1.0101 123.5099 117.6356 118.8545 121.1288 – 117.8414 – – 121.0298 – – – – – 114.6825 121.9127 123.4048 117.7735 – – 117.7991 124.4274 – – 118.0455 119.2708 122.1284 118.6008 122.7444 116.3245 120.9311 118.761 120.9935 120.2455 180.0145 – 0.0258 – 0.0332 – 180.0445 –
Z3POLX ˚ /deg) (A 1.3480 1.4069 1.4069 1.3982 1.4043 1.3499 1.0945 1.0918 1.0913 – – 1.0955 – – 1.5018 1.2490 1.3728 1.0109 1.0122 123.296 117.9044 118.799 121.1198 – 117.771 – – 121.1092 – – – – – 114.4778 121.6566 123.8656 117.7515 – – 117.7965 124.452 – – 117.4645 119.0445 122.2685 118.687 123.2168 115.9926 120.7905 118.6571 121.0803 120.2626 179.8022 – 0.2138 – 0.1041 – 179.912 –
6-31++G(d,p) ˚ /deg) (A 1.3387 1.3973 1.4001 1.3985 1.3951 1.3413 1.0875 1.0844 – – – 1.0878 1.0857 1.5077 – 1.2262 1.3693 1.0079 1.0102 121.8300 116.695 117.767 122.0911 – – 116.4342 – – 121.4674 – 123.8514 118.213 – 116.1544 120.146 123.6991 118.7247 – – – – 119.3905 121.8511 117.1373 117.9268 – – 123.7231 116.0192 120.2577 118.7802 119.7488 121.4708 163.8062 – – 17.1629 6.0024 – – 174.9666
Z2POLX ˚ /deg) (A 1.3496 1.4004 1.4051 1.404 1.3982 1.3524 1.0897 1.0870 – – – 1.0899 1.0885 1.5069 – 1.2518 1.3685 1.0068 1.0102 123.3605 117.7494 118.8901 121.2751 – – 117.6682 – – 121.0566 – 124.4989 117.5675 – 116.4706 120.4776 123.0519 119.0682 – – – – 118.4175 122.5143 117.7617 117.9336 – – 123.0342 116.3148 120.6510 119.1504 119.1370 121.7126 179.9867 – – 0.0148 0.0045 – – 179.9970
Z3POLX ˚ /deg) (A 1.3486 1.4033 1.4060 1.4049 1.4008 1.3515 1.0943 1.0904 – – – 1.0945 1.0923 1.5071 – 1.2477 1.3720 1.0106 1.0122 123.1941 118.0125 118.7934 121.3221 – – 117.5558 – – 121.1221 – 124.6230 117.5815 – 116.1916 120.3911 123.4174 119.0286 – – – – 118.5479 122.4235 117.2374 117.7954 – – 123.5037 115.9949 120.5014 119.0175 119.3303 121.6521 179.9592 – – 0.0439 0.0131 – – 179.9900
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
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Table 2 (continued) Atoms
Picolinamide 6-31++G(d,p) ˚ /deg) (A
D(13,11,2,3) D(13,11,3,4) D(13,11,4,5) D(13,11,2,1) D(13,11,3,2) D(13,11,4,3) D(12,11,2,3) D(12,11,3,4) D(12,11,4,5) D(12,11,2,1) D(12,11,3,2) D(12,11,4,3) D(11,2,3,4) D(11,3,4,5) D(11,4,5,6) D(11,2,3,10) D(11,3,2,10) D(11,3,4,9) D(11,4,5,8) D(1,2,3,11) D(1,2,3,4) D(1,2,3,10) D(1,2,3,9) D(11,2,1,6) D(11,4,3,2) D(11,4,3,9) D(3,2,1,6) D(2,3,4,5) D(2,3,4,9) D(4,3,2,10) D(9,3,2,10) D(10,3,4,5) D(9,3,4,5) D(10,3,4,9) D(9,4,5,8) D(10,2,1,6) D(8,5,6,7) D(2,1,6,5) D(2,1,6,7) D(3,4,5,6) D(3,4,5,8) D(9,4,5,6) D(1,6,5,4) D(1,6,5,8) D(7,6,5,4)
179.946 – – 0.0593 – – 0.0589 – – 179.9464 – – 179.9936 – – 0.0042 – – – – 0.0008 179.9986 – 179.9924 – – 0.0021 0.0001 179.9996 – – 179.9978 – 0.0018 0.0008 – 0.0005 0.0027 179.9995 0.0007 179.9995 179.999 0.0021 179.9981 179.9997
Nicotinamide Z2POLX ˚ /deg) (A 180.0492 – – 0.0063 – – 0.0627 – – 179.9928 – – 180.0094 – – 0.067 – – – – 0.068 179.998 – 180.0155 – – 0.0419 0.0547 180.0244 – – –179.9821 – 0.0482 0.0029 – 0.0174 0.0035 180.0195 0.0194 180.0274 180.0108 0.0071 179.9992 180.0096
Z3POLX ˚ /deg) (A 179.9891 – – 0.0028 – – 0.0055 – – 179.9917 – – 179.9866 – – 0.0000 – – – – 0.0000 179.9872 – 179.9879 – – 0.0000 0.0000 180.0000 – – 179.9871 – 0.0120 0.0046 – 0.0062 0.0028 179.9907 0.0000 179.9946 180.0000 0.0000 179.9935 0.00622
6-31++G(d,p) ˚ /deg) (A – 163.1349 – – 18.2965 – – 17.8034 – – 160.7652 – – 179.8916 – – 1.5115 0.0397 – 179.7362 1.1607 – – – – – 0.1679 1.2326 178.6192 177.0640 – – – – 0.5246 178.1497 0.3439 0.7561 179.55683 0.4083 179.6285 179.4387 0.6341 179.3295 179.6925
Isonicotinamide Z2POLX ˚ /deg) (A – 179.9988 – – 0.0001 – – 0.0101 – – 180.0112 – – 180.0033 – – 0.0376 0.0089 – 180.0068 0.0056 – – – – – 0.0163 0.0044 180.0079 180.0387 – – – – 0.028 180.0252 0.0285 0.0172 179.98065 0.0035 180.0152 179.9907 0.0076 179.9738 179.990
Z3POLX ˚ /deg) (A – 179.853 – – 0.1509 – – 0.163 – – 179.833 – – 179.9894 – – 0.0514 0.0073 – 179.9638 0.0322 – – – – – 0.0268 0.0069 179.9963 179.9446 – – – – 0.0094 179.9448 0.0309 0.0039 179.96215 0.0207 179.994 179.9759 0.0274 179.9872 179.9837
6-31++G(d,p) ˚ /deg) (A – – 159.1972 – – 21.9052 – – 21.7653 – – 157.1323 – – 179.9795 – – – 0.1554 – 0.3005 – 178.2303 – 179.4685 1.5920 0.6776 0.5679 – 179.4103 1.4805 – 177.3085 – – 179.0438 0.7547 0.1834 179.7273 1.0157 178.8084 – 0.6685 179.1524 179.4244
Z2POLX ˚ /deg) (A – – 179.996 – – 0.0040 – – 0.0055 – – 179.9944 – – 179.9998 – – – 0.0004 – 0.0006 – 179.9995 – 179.9996 0.0007 0.0002 0.0004 – 179.9999 0.0009 – 179.9993 – – 179.9997 0.0004 0.0005 179.9993 0.0002 179.9996 – 0.0007 179.9992 179.9994
Z3POLX ˚ /deg) (A – – 179.9777 – – 0.0259 – – 0.0254 – – 179.971 – – 179.9994 – – – 0.001 – 0.0028 – 179.9953 – 179.9968 0.0046 0.0021 0.0004 – 179.9978 0.0053 – 179.9918 – – 179.9985 0.001 0.0019 179.9978 0.004 179.9957 – 0.005 179.9947 179.9993
R, A, and D stand for bond, angle and dihedral angle, respectively.
in Table 2. The dihedral angles between the ring plane and CONH2 group for picolinamide, nicotinamide, and isonicotinamide are marked in bold. These angles show that nicotinamide and isonicotinamide have a non-planar environment, and picolinamide has a planar environment. It was reported that the substitution of the amide group into the pyridine ring does not affect the dimensions of the ring very much [2]. The results of optimized geometry parameters were found to support this. The optimized geometry parameters obtained by using the DFT/B3LYP method with the 6-31++G(d,p) basis set were found to
be in better agreement with the experimental ones than the Z2PolX and Z3PolX basis sets. The assignments of experimental wavenumbers, the calculated wavenumbers by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX, and Z3PolX basis sets compared with experimental wavenumbers and total energy distribution results for each molecule are given in Tables 3–5. When compared with experimental spectra the results showed that the Z2PolX and Z3PolX basis sets gave accurate relative band intensities and band positions better than 6-31++G(d,p) basis set
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M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
without scaling. The simulated IR and Raman spectra and the experimental spectra are shown in Figs. 2–4 for picolinamide, nicotinamide, and isonicotinamide, respectively. IR and Raman intensities, scaled wavenumbers obtained from the SQM procedure, were found to
be in good agreement with the Z2PolX and Z3PolX basis sets. We found that the Z3PolX basis set gives the best results for predicting experimental IR and Raman spectra. Scaled wavenumbers at the 6-31++G(d,p) basis set were calculated by using the scaling factors which were
Table 3 The assignments of experimental wavenumbers, the calculated wavenumbers by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX, and Z3PolX basis sets compared with the experimental wavenumbers and the total energy distribution results for picolinamide Experimental
Calculation 6-31++G(d,p)
Assign.
IR
Ra
Gasa
sring
754
dring
794
c (CH)
825
c (CH) c (CH) c (CH) mring mring NH2rock d (CH) d (CH) mring mring d (CH) m (CN)
909
d (CH) d (CH) NH2scis mring mring m (CO) m (CH) m (CH) m (CH) m (CH) m (NH2) m (NH2)
996 1043 1095 1143 1164 1254 1284 1387 1442 1468 1603 1568 1587 1658
Z2POLX
Z3POLX
U
U
TED(%)
100 sCCCO 52 c (CC), 40 sring 62 d (CC), 25 d (CN) 99 NH2wag
77 157 219 335
100 sCCCO 47 c (CC), 46 sring 62 d (CC), 25 d (CN) 96 NH2wag
93 170 216 373
379
373
379
399 428
414 451
29 m (CC), 26 dring, 19 d (CO), 16 d (CN) 100 sring 69 sring, 21 c (CC)
425
414 451
32 m (CC), 25 dring, 18 d (CO), 15 d (CN) 100 sring 76 sring, 16 c (CC)
495
490
43 d (CN), 22 d (CC), 12 mring
495
42 d (CN), 23 d (CC), 11 mring
498
680
612 629 640 717
604 608 636 679
69 44 76 41
612 629 640 717
42 78 76 51
597 632 671 724
747
763
735
60 sring, 34 c (CH)
763
57 c (CH), 37 sring
776
781
765
43 dring, 21 m (CC), 21 mring
780
42 dring, 23 m (CC), 19 mring
795
832
781
832
896 954 988 996 1032 1065 1085 1140 1148 1267 1287 1346
1471 1505 1594 1620 1637 1760 3176 3194 3213 3233 3589 3738
1429 1461 1528 1570 1588 1702 3037 3054 3072 3091 3431 3574
34 c (CO), 28 c (CH), 25 c (CC), 13 sring 100 c (CH) 100 c (CH) 54 dring, 45 mring 100 c (CH) 68 mring, 22 d (CH) 51 NH2rock, 18 m (CN) 43 d (CH), 36 mring 67 d (CH), 21 mring 32 mring, 28 d (CH), 13 dring 65 mring, 29 d (CH) 47 mring, 44 d (CH) 28 m (CN), 16 m (CC), 12 d (CH), 12 d (CO), 11 mring 55 d (CH), 35 mring 54 d (CH), 38 mring 81 NH2scis 73 mring, 15 d (CH) 67 mring, 20 d (CH) 75 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 100 m (CH) 100 m (NH2) 100 m (NH2)
870
928 988 1016 1022 1064 1091 1115 1172 1178 1310 1324 1386
46 c (CH), 20 c (CC), 20 c (CO), 14 sring 100 c (CH) 100 c (CH) 100 c (CH) 59 mring, 39 dring 60 mring, 23 d (CH), 14 dring 43 NH2rock, 21 m (CN), 12 mring 39 d (CH), 35 mring 74 d (CH), 21 mring 29 mring, 22 dring, 16 d (CH) 76 mring, 18 d (CH) 54 d (CH), 36 mring 25 m (CN), 16 m (CC), 13 d (CO), 12 d (CH), 12 NH2scis 57 d (CH), 33 mring 56 d (CH), 36 mring 78 NH2scis 71 mring, 16 d (CH) 65 mring, 21 d (CH) 74 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
996 1030 1086 1156 1244 1291 1362 1433 1472 1567 1645 1722 3020
3061 3075 3164 3414
TED (%)
75 147 219 301
817
998 1043 1083 1100 1142 1168
S
77 157 219 335
602
c (CO)
U
3415 3552
NH2twist, 15 c (CO), 11 sring d (CO), 38 dring dring c (CO), 29 NH2twist, 29 sring
928 988 1016 1022 1064 1091 1115 1171 1178 1310 1324 1386 1471 1505 1594 1620 1637 1760 3176 3194 3213 3233 3589 3738
d (CO), 41 dring NH2twist dring sring, 33 c (CO), 19 NH2twist
438 486
978 1000 1057 1061 1065 1110 1134 1170 1178 1305 1326 1378 1461 1490 1551 1611 1629 1707 3153 3178 3202 3220 3519 3691
TED (%) 100 sCCCO 51 sring, 41 c (CC) 62 d (CC), 26 d (CN) 24 m (CC), 24 dring, 22 d (CO), 19 d (CN) 100 sring 45 NH2wag, 40 sring 39 d (CN), 24 d (CC), 11 mring 55 NH2wag, 31 sring, 12 c (CC) 45 d (CO), 36 dring 83 dring 81 NH2twist 54 sring, 36 c (CO), 16 NH2twist 42 dring, 23 m (CC), 21 mring 47 c (CH), 36 sring, 12 c (CO) 44 c (CH), 24 c (CC), 22 c (CO) 100 c (CH) 57 dring, 41 mring 59 mring, 19 d (CH) 100 c (CH) 48 NH2rock, 15 mring 45 d (CH), 40 mring 100 c (CH) 48 d (CH), 24 mring 49 d (CH), 27 mring 54 d (CH), 40 mring 70 mring, 18 d (CH) 23 m (CN), 17 m (CC), 15 mring, 14 d (CH) 59 d (CH), 33 mring 51 d (CH), 37 mring 74 NH2scis 74 mring, 15 d (CH) 70 mring, 18 d (CH) 71 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
IR, experimental IR solid phase wavenumbers; Ra, the experimental Raman wavenumbers; Gas, experimental IR gas phase wavenumbers; U, unscaled wavenumbers; S, scaled wavenumbers; TED, total energy distribution of picolinamide obtained by using the Scale 2.0 program; s, torsion; d, in plane bending; m, stretching; c, out of plane bending vibrations. a Taken from Ref. [19].
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
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Table 4 The assignments of experimental wavenumbers, the calculated wavenumbers by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX and Z3PolX basis sets compared with the experimental wavenumbers and the total energy distribution results for nicotinamide Experimental
Calculation 6-31++G(d,p)
Assign.
IR
Ra
a
Gas
U
S
Z2POLX TED(%)
U
52 153 212 314
50 147 210 284
97 52 63 90
sCCCO c (CC), 38 sring d (CC), 18 d (CN) NH2wag
38 165 227 385
378
370
733
387 418 495 559 616 643 717 747
374 404 488 537 611 639 689 698
26 22 58 93 43 76 49 61 71 35 30 44 22 68
m (CC), 20 dring, sring, 15 d (CO) sring, 12 d (CN) sring d (CN), 15 d (CC) NH2twist dring, 28 d (CO) dring, 22 d (CO) sring, 33 c (CO) c (CO), sring, 26 c (CH) dring, mring, 18 m (CC) c (CH), 12 c (CC)
Z3POLX
TED(%)
U
TED(%)
sCCCO sring, 46 c (CC) d (CC), 23 d (CN) m (CC), 27 dring, d (CO), 12 d (CN) sring, 14 c (CC)
33 164 227 342
98 51 67 83
sCCCO sring, 42 c (CC) d (CC), 23 d (CN) NH2wag, 12 NH2twist
397
99 47 66 30 18 78
381
443 467 477 602 614 645 740 759
88 76 50 64 39 74 96 50
sring NH2wag, 18 NH2twist d (CN), 18 d (CC), 11 mring NH2twist, 22 NH2wag dring, 38 d (CO) dring, 14 d (CO) sring, 12 c (CO) c (CO), 35 c (CH)
400 444 466 571 600 631 725 758
27 18 89 74 47 78 40 74 95 53
dring, 27 m (CC), d (CO), 15 d (CN) sring sring, 16 c (CC) d (CN), 18 d (CC) NH2twist dring, 37 d (CO) dring, 14 d (CO) sring, 14 c (CO) c (CO), 31 c (CH)
780
45 dring, 22 mring, 19 m (CC)
773
875
886 969 1023 1041 1047
NH2twist dring dring sring c (CO)
701
dring
776
788
777
781
766
c (CH)
828
833
812
841
808
c (CH) c (CH) c (CH) dring
936 996
940
947 990 1015 1037
915 957 981 1022
100 c (CH) 100 c (CH) 100 c (CH) 45 dring, 37 mring, 16 d (CH)
973 1038 1046 1056
65 c (CH), 15 c (CC), 14 c (CO) 100 c (CH) 43 mring, 42 dring, 12 d (CH) 100 c (CH) 65 mring, 25 dring
mring NH2rock
1029 1091
1042 1093
1025 1077
1061 1083
1027 1057
50 NH2rock, 22 m (CN), 14 m (CO) 100 c (CH)
1056 1104
1124 1154
1123 1161
1107 1135
1135 1157
1101 1127
mring, 28 dring NH2rock, m (CN), 10 m (CO) d (CH), 43 mring mring, 26 d (CH), 17 dring
1087 1118
d (CH) mring
63 52 24 45 27
1128 1165
1123 1155
d (CH) mring d (CH) m (CN)
1202 1231 1340 1393
1193 1261 1347
1231 1308 1365 1374
1195 1263 1330 1337
1422 1486 1615
1417 1476 1587
1454 1514 1614
1412 1470 1555
d (CH), 44 mring mring d (CH) m (CN), 20 m (CC), d (CO), 10 NH2rock d (CH), 43 mring d (CH), 34 mring NH2scis
1228 1303 1370 1389
d (CH) d (CH) NH2scis
48 90 86 31 15 50 59 85
1439 1506 1590
46 30 13 54 95 85 36 14 52 58 59
mring
1575
1625
1565
65 mring, 22 d (CH)
1627
68 mring, 20 d (CH)
1601
mring
1593
1638
1589
1643
1674
1722 3016
3061
3050 3088 3436 3554
1753 3165 3177 3206 3222 3598 3732
1695 3026 3038 3065 3080 3440 3568
38 m (CO), 36 NH2scis, 11 mring 58 NH2scis, 24 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
1630
m (CO) m (CH) m (CH) m (CH) m (CH) m (NH2) m (NH2)
66 mring, 21 d (CH), 10 dring 76 m (CO) 100 m (CH) 100 m (CH) 100 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
48 32 13 54 93 87 35 12 52 55 63 12 58 16 70
1691 3133 3155 3191 3214 3550 3698
68 m (CO) 100 m (CH) 100 m (CH) 100 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
627
3150 3358
1684 3158 3176 3201 3223 3570 3713
mring, 41 d (CH) d (CH), 27 mring, 14 dring, NH2rock d (CH), 37 mring mring d (CH) m (CN), 18 m (CC), d (CH), 12 d (CO) d (CH), 41 mring d (CH), 32 mring mring, 16 d (CH), 15 d (CO)
1225 1315 1353 1376 1439 1501 1586
45 dring, 21 mring, 20 m (CC) 70 c (CH), 13 c (CC) 100 c (CH) 67 dring, 23 mring 100 c (CH) 58 NH2rock, 16 m (CN), 11 m (CO) 79 mring, 13 d (CH) 100 c (CH) d (CH), 42 mring mring, 29 d (CH), m (CN), 10 dring d (CH), 40 mring mring d (CH) m (CN), 22 m (CC), d (CH), 11 d (CO) d (CH), 41 mring d (CH), 34 mring NH2scis, m (CO), 12 mring mring, 16 NH2scis, d (CH) mring, 18 d (CH)
IR, experimental IR solid phase wavenumbers; Ra, experimental Raman wavenumbers; Gas, experimental IR gas phase wavenumbers; U, unscaled wavenumbers; S, scaled wavenumbers; TED, total energy distribution of nicotinamide obtained by using the Scale 2.0 program; s, torsion; d, in plane bending; m, stretching; c, out of plane bending vibrations. a Taken from Ref. [20].
determined by Pulay and Pongor [13–15]. Only the scaling factors related to the out of plane bendings and NH2 rocking were refined. The final scaling factors are given
in Table 6. They were used without making any changes for the three isomers. In this way we showed that these scaling factors are transferable.
12
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
Table 5 The assignments of experimental wavenumbers, the calculated wavenumbers by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX and Z3PolX basis sets compared with the experimental wavenumbers and the total energy distribution results for isonicotinamide Experimental
Calculation 6-31++G(d,p)
Assign.
IR
Ra
U
S
TED(%)
Z2POLX
Z3POLX
U
U
56 151 211 341
54 141 209 309
98 57 64 91
368
365
387
375
30 dring, 28 m (CC), 14 d (CO), 12 d (CN) 100 sring
415 510
400 501
565 614 681
542 610 675
720
683
766 769 855
731 761 812
61 38 14 71 49 52 25 36 27 82 35 85
100 c (CH) 100 c (CH) 100 c (CH)
928 996 1053
sCCCO c (CC), 33 sring d (CC), 18 d (CN) NH2wag
sring, 11 d (CN) d (CN), d (CC), 10 sring NH2twist d (CO), 28 dring dring, c (CO), 10 sring dring, c (CO), 22 sring sring, 15 c (CO) dring, 25 m (CC), 17 mring c (CH), 14 c (CC)
32 166 229 383 391
445
98 48 66 83
374
31 dring, 26 m (CC), 16 d (CO), 15 d (CN)
sCCCO sring, 45 c (CC) d (CC), 23 d (CN) NH2wag, 13 NH2twist
393
100 sring
472 476
461 468
58 sring, 19 c (CC), 15 c (CO) 47 d (CN), 18 d (CC)
606 610 686
53 d (CO), 24 dring 60 NH2twist, 21 NH2wag 88 dring
582 595 670
74 NH2twist, 10 NH2wag 53 d (CO), 28 dring 89 dring
735
49 sring, 40 c (CO)
724
57 sring, 41 c (CO)
760 780 883
40 dring, 24 m (CC), 18 mring 59 sring, 22 c (CH), 15 c (CO) 66 c (CH), 19 c (CC), 18 c (CO) 97 c (CH) 64 mring, 34 dring 100 c (CH)
760 778 892
1052
38 dring, 25 m (CC), 17 mring 49 sring, 24 c (CH), 20 c (CO) 70 c (CH), 18 c (CC), 15 c (CO) 99 c (CH) 51 mring, 48 dring 58 NH2rock, 17 m (CN), 11 m (CO) 100 c (CH)
1081
46 mring, 33 d (CH), 21 dring
1085
100 c (CH)
1116 1146
47 mring, 40 d (CH) 37 mring, 15 d (CH), 15 m (CN), 12 dring, 10 m (CC) 65 d (CH), 33 mring 95 mring 78 d (CH), 17 mring 35 m (CN), 21 m (CC), 12 d (CO), 10 d (CH) 59 d (CH), 36 mring 62 d (CH), 32 mring 70 NH2scis, 12 m (CO) 70 mring 66 mring, 20 d (CH) 69 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
c (CO)
708
dring sring c (CH)
754 776 795
783
c (CH) c (CH) c (CH)
852
867
896 984 1007
865 950 973
mring
994
995
1011
1004
56 mring, 43 dring
1084
NH2rock
1065
1063
1083
1067
1085
mring
1086
1084
1091
1076
d (CH) mring
1122 1148
1128 1152
1116 1151
1097 1138
d (CH) mring d (CH) m (CN)
1219 1263 1322 1390
1246 1297 1352 1371
1221 1284 1322 1352
d (CH) d (CH) NH2scis mring mring m (CO) m (CH) m (CH) m (CH) m (CH) m (NH2) m (NH2)
1408 1496 1622 1551 1596 1655 3042
1444 1527 1606 1623 1642 1759 3173 3180 3200 3226 3596 3731
1417 1497 1559 1589 1621 1740 3044 3050 3070 3095 3450 3578
46 NH2rock, 20 m (CN), 11 mring 41 mring, 34 d (CH), 20 dring 43 d (CH), 38 mring 32 mring, 20 dring, 12 m (CN), 12 m (CC), 11 d (CH) 64 d (CH), 34 mring 94 mring 79 d (CH), 15 mring 32 m (CN), 19 m (CC), 14 d (CO) 55 d (CH), 40 mring 59 d (CH), 35 mring 85 NH2scis 77 mring 67 mring, 20 d (CH) 80 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
3178 3362
35 168 228 350
sring, NH2twist, 23 NH2wag NH2wag, 31 sring d (CN), 17 d (CC)
668
3066
TED (%)
98 sCCCO 48 c (CC), 44 sring 65 d (CC), 23 d (CN) 33 dring, 29 m (CC), 15 d (CO) 100 sring
34 26 52 49
NH2twist dring dring
664
TED(%)
1091 1121 1161 1243 1292 1356 1387 1429 1507 1588 1628 1646 1684 3174 3179 3194 3221 3568 3714
31NH2rock, 16 m (CN), 16 mring, 12 m (CO) 100 c (CH) 38 21 40 32 18 64 97 72 36 14 57 65 66 65 38 54 99 99 99 99 99 99
mring, 27 dring, d (CH) mring, 35 d (CH) mring, 18 dring, NH2rock, 13 m (CC) d (CH), 32 mring mring d (CH), 13 mring m (CN), 19 m (CC), d (CH), 12 d (CO), 10 NH2rock d (CH), 37 mring d (CH), 30 mring mring, 15 d (CO) mring, 21 d (CH) NH2scis, 37 m (CO) NH2scis, 26 m (CO) m (CH) m (CH) m (CH) m (CH) m (NH2) m (NH2)
936 994 1045
1241 1302 1341 1372 1428 1508 1584 1599 1630 1696 3150 3158 3181 3218 3552 3701
IR, experimental IR solid phase wavenumbers; Ra, experimental Raman wavenumbers; U, unscaled wavenumbers; S, scaled wavenumbers; TED, total energy distribution of isonicotinamide obtained by using the Scale 2.0 program; s, torsion; d, in plane bending; m, stretching; c, out of plane bending vibrations.
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
13
c
a
0,14
8000
Absorbance
0,12
Intensity
6000
4000
0,10 0,08 0,06 0,04
2000
0,02 0
0,00 0
200
400
600
800
1000
4000
1200
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
-1
Wavenumbers (cm )
b
d 100
Absorbance
Relative Intensity
80 20
60
40
20 0 0 400
800
1200
4000
3500
3000
e
2500
2000
1500
1000
Wavenumbers (cm-1)
Wavenumbers (cm-1) 100
Transmittance
90
80
70
60
50 4000
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Fig. 2. (a) The experimental Raman spectrum, (b) the simulated Raman spectrum, (c) the experimental IR gas phase spectrum, (d) the simulated IR gas phase spectrum, (e) the IR solid phase spectrum of picolinamide.
In the present work, TED calculations indicate a very significant mixing of all ring and bending vibrations. Such mixing was indicated in previous studies [16,17] and it should increase with respect to the pyridine case due to the lowering of molecular symmetry and presence of an amide group which is a heavy group. For example, the ring breathing mode includes ring vibrations and ring bond
stretching in different proportions. Therefore, it does not resemble the ring breathing mode of the pyridine. In this study, the ring breathing modes of picolinamide, nicotinamide, and isonicotinamide were assigned in Raman spectra 998, 1042, 995 cm 1, respectively. Also, it was reported that the ring breathing mode of coordinated nicotinamide was found to be at 1033 cm 1 in Raman spectra [18].
14
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
a
12000
c
0,018 0,016
10000 0,014 0,012
Absorbance
Intensity
8000
6000
0,010 0,008 0,006
4000 0,004 0,002
2000
0,000 0 0
200
400
600
800
1000
-0,002 4000
1200
3500
3000
Wavenumbers (cm-1)
2500
2000
1500
1000
Wavenumbers (cm-1)
b
d
80
Absorbance
Relative Intensity
100
20
60
40
20 0 0 400
800
1200
4000
3500
Wavenumbers (cm-1)
e
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
100 95
Transmittance
90 85 80 75 70 65 60 55 4000
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Fig. 3. (a) The experimental Raman spectrum, (b) the simulated Raman spectrum, (c) the experimental IR gas phase spectrum, (d) the simulated IR gas phase spectrum, (e) the IR solid phase spectrum of nicotinamide.
5. Conclusion The combination of good intensity and wavenumber data made it possible for the isomers of pyridinecarboxamide to have a close correspondence between the simulated IR and Raman spectra and experimental data. The
results of 6-31++G(d,p) basis set, which were obtained by applying the SQM procedure and the results of Z3PolX basis set, showed us that the observed bands could easily be assigned. We found that the Z3PolX basis set gave the best results for predicting experimental IR and Raman spectra.
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
a
15
c
20000
100
18000 16000
80
Absorbance
14000
Intensity
12000 10000 8000
60
40
6000 20
4000 2000
0
0 0
200
400
600
800
1000
4000
1200
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Wavenumbers (cm-1)
b
d
100
Relative Intensity
Transmittance
90
80
70
60
50
0
40 400
800
1200
Wavenumbers (cm-1)
4000
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Fig. 4. (a) The experimental Raman spectrum, (b) the simulated Raman spectrum, (c) the simulated IR gas phase spectrum, (d) the IR solid phase spectrum of isonicotinamide.
Table 6 The scaling factors for the isomers of pyridinecarboxamide Internal coordinates
Scaling factors
X–Y stretching X–H stretching X–Y–Z in plane bending X–Y–H in plane bending CO/CC out of plane bending CH out of plane bending All torsion NH2 scissoring NH2 rocking NH2 wagging
0.9300 0.9140 0.9950 0.9500 0.8300 0.9340 0.9350 0.9130 0.9672 0.8000
H means hydrogen; X, Y, and Z mean first-row heavy atoms C, N, O.
Acknowledgement The authors thank Prof. Dr. Mustafa Urgen and Assoc. Prof. Dr. Gultekin Goller for Raman and FT-IR measurements at the Istanbul Technical University, Istanbul, Turkey.
References [1] T. Kawabata, T. Ogino, M. Mori, M. Awai, Acta Pathol. Jpn. 42 (1992) 469–475. [2] T. Takano, Y. Sasada, M. Kakudo, Acta Crystallogr. 21 (1966) 514– 522. [3] T. Takeshima, H. Takeuchi, T. Egawa, S. Konaka, J. Mol. Struct. 644 (2003) 197. [4] E.A. Velcheva, L.I. Daskalova, J. Mol. Struct. 741 (2005) 85–92. [5] W.B. Wright, G.S.D. King, Acta Crystallogr. 7 (1954) 283. [6] A.D. Becke, J. Chem. Phys. 98 (1993) 5648. [7] C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1988) 785. [8] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.J. Montgomery, 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. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andres, C. Gonzalez, M. Head-Gordon, E.S. Raplogle, J.A. Pople, GAUSSIAN 98, Revision A.9, Gaussian, Inc., Pittsburgh PA, 1998.
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[9] R.E. Oakes, S.E.J. Bell, Z. Benkova, A.J. Sadlej, J. Comput. Chem. 26 (2004) 154. [10] Z. Benkova, A.J. Sadlej, R.E. Oakes, S.E.J. Bell, J. Comput. Chem. 26 (2004) 145. [11] G. Pongor, Scale2, Department of Theoretical Chemistry, Eotvos Lorand University, Budapest, 1978. [12] G. Pongor, G. Fogarasi, I. Magdo, J.E. Boggs, G. Keresztury, I.S. Ignatyev, Spectrochim. Acta 48A (1992) 111. [13] G. Rauhut, P. Pulay, J. Phys. Chem. 99 (1995) 3093. [14] G. Rauhut, P. Pulay, J. Am. Chem. Soc. 117 (1995) 4167.
[15] F. Kalincsak, G. Pongor, Spectrochim. Acta Part A 58 (2002) 99– 1011. [16] M. Bakiler, I.V. Maslov, S. Akyuz, J. Mol. Struct. 475 (1999) 83– 92. [17] M. Bakiler, I.V. Maslov, S. Akyuz, J. Mol. Struct. 476 (1999) 21–26. [18] O. Bolukbasi, S. Akyuz, J. Mol. Struct. 744–747 (2005) 961–971. [19]. [20] .
An experimental and theoretical study of vibrational spectra of picolinamide, nicotinamide, and isonicotinamide Meric Bakiler a b
a,*
, Olcay Bolukbasi b, Ayberk Yilmaz
b
Mimar Sinan Fine Art University, Department of Physics, Besiktas, 34347 Istanbul, Turkey Istanbul University, Science Faculty, Physics Department, Vezneciler, 34118 Istanbul, Turkey
Received 20 January 2006; received in revised form 13 April 2006; accepted 17 April 2006 Available online 5 June 2006
Abstract The molecular structures and vibrational spectra of the three isomers of pyridinecarboxamide (picolinamide, nicotinamide, isonicotinamide) were calculated with the Density Functional Theory (DFT) method using the B3LYP function and the 6-31++G(d,p), Z2PolX, Z3PolX basis sets. The calculations were performed by using the Gaussian98W packet program set. The total energy distributions (TED) of the vibrational modes of these molecules were calculated by using the Scale 2.0 program and the vibrational modes of the molecules were determined. The Scaled Quantum Mechanical (SQM) method was used in the scaling procedure. In the experimental part of the study, the solid phase FT-IR and Micro Raman spectra of the three isomers of pyridinecarboxamide have been recorded in the range of 4000–650 and 1200–100 cm 1, respectively. The calculated wavenumbers were compared to the corresponding experimental values. As a result, the observed bands of the three isomers of pyridinecarboxamide were assigned with good accuracy. 2006 Elsevier B.V. All rights reserved. Keywords: DFT calculations; Picolinamide; Nicotinamide; Isonicotinamide; Z3PolX basis set; SQM; Vibrational spectra
1. Introduction The three isomers of pyridinecarboxamide; picolinamide (2-pyridinecarboxamide; 2-NH2COpy), nicotinamide (3pyridinecarboxamide; 3-NH2COpy), and isonicotinamide (4- pyridinecarboxamide; 4-NH2COpy) are a class of medicinal agents with activity that includes the reduction of iron-induced renal damage [1]. The structure of picolinamide and nicotinamide has been determined by experimental methods and reported in previous papers [2–5]. In the present paper, we report a complete description of the molecular geometry and the molecular vibrations of the three isomers of pyridinecarboxamide. For that purpose, quantum chemical computations were performed on the three isomers of pyridinecarboxamide by using the Density Functional Theory (DFT). Experimental information on the molecular vibrations was obtained from the FT-IR and Micro Raman spectra measured. Our assignments *
Corresponding author. Tel.: +902122366936; fax: +902122611121. E-mail address: [email protected] (M. Bakiler).
0022-2860/$ - see front matter 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2006.04.021
were made by using the advantages of theoretical computations. 2. Experimental details The solid phase FT-IR spectra of the powdered three isomers of pyridinecarboxamide were recorded with the ATR unit by using the Perkin-Elmer FT-IR spectrometer in the range of 4000–650 cm 1. In these experiments a resolution of 4 cm 1 was applied. The Raman spectra of the powdered samples were recorded on a Micro Raman Jobin YVON Horiba HR800 UV instrument using 632.8 nm excitation from a He–Ne laser in the range of 1200– 100 cm 1, 1800 grating, 5 scans per 30 s pulse and with 10· zoom. 3. Computational details The geometry optimizations and calculated wavenumbers have been carried out at the Density Functional Theory (DFT) method with the B3LYP exchange-correlation
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
functional [6,7] by using the Gaussian 98W program [8]. The 6-31++G(d,p) basis set and the new highly compact Pol-type basis sets, Z2PolX and Z3PolX [9,10], for the three molecules and their conformers were used in the DFT calculations. The vibrational modes of all these molecules were determined by using total energy distribution (TED) and the calculated wavenumbers were scaled by using the scaled quantum mechanical (SQM) analysis method, with the help of the Scale 2.0 program [11,12] for the results of B3LYP/6-31++G(d,p) basis set. The natural internal coordinates were used for SQM procedure and 10 scaling factors were classified according to different types of internal coordinates. The scaling factors were taken from previous studies for each group [13–15]. Only the scaling factors related to the out of plane bendings and NH2 rocking were refined. The diagonal force constants were scaled by the factor associated with the internal coordinates and the off-diagonal force constants were scaled by the geometric mean of the associated scaling factors. As Oakes et al. have stated, [9,10] wavenumbers calculated with the Z2PolX and Z3PolX basis sets showed to be in conformity with the
7
experimental wavenumbers. For this reason, SQM method was not used on the results obtained from the Z2PolX and Z3PolX basis sets. 4. Results and discussion The optimized geometries for the E- and Z-forms of the three molecules were calculated and their total energies are given in Table 1. In addition to the calculated wavenumbers and the total energy distribution results for the Eforms of the three molecules were obtained by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX and Z3PolX basis sets. The calculated data for the Eand Z-forms of the three molecules are very similar. However, it was found to be that the E-forms of these molecules are more stable than the Z-forms. Therefore, we gave a detailed explanation only for the E-form. The E-form structures of these molecules with the atomic numbering used in this study are shown in Fig. 1. The optimized geometry parameters were obtained by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX, and Z3PolX basis sets according to these atom numberings are given
Table 1 The total energies (in hartree) of the optimized geometry for the E- and Z-forms of the three isomers of pyridinecarboxamide Picolinamide E-Form B3LYP/6-31G++(d,p) B3LYP/Z2POLX B3LYP/Z3POLX
417.0289 416.9806 417.0202
Nicotinamide Z-Form 417.0156 416.9648 417.0038
E-Form 417.0199 416.9712 417.0104
Isonicotinamide Z-Form 417.0195 416.9694 417.0088
Fig. 1. The atom numbering of three isomers of pyridinecarboxamide.
E-Form 417.0198 416.9699 417.0091
Z-Form 417.01978 416.9698 417.0090
8
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
Table 2 The optimized geometry parameters obtained by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX, and Z3PolX basis sets of the three isomers of pyridinecarboxamide Atoms
Picolinamide 6-31++G(d,p) ˚ /deg) (A
R(1,2) R(2,3) R(3,4) R(4,5) R(5,6) R(6,1) R(6,7) R(5,8) R(4,9) R(3,10) R(2,11) R(2,10) R(3,9) R4,11) R(3,11) R(11,12) R(11,13) R(13,14) R(13,15) A(11,13,14) A(11,13,15) A(14,13,15) A(13,11,12) A(13,11,2) A(13,11,3) A(13,11,4) A(12,11,2) A(12,11,3) A(12,11,4) A(11,2,3) A(11,4,3) A(11,4,5) A(11,2,1) A(10,2,1) A(10,2,3) A(3,2,1) A(2,3,4) A(2,3,10) A(4,3,10) A(4,3,11) A(2,3,11) A(2,3,9) A(4,3,9) A(2,1,6) A(3,4,5) A(5,4,9) A(3,4,9) A(1,6,5) A(1,6,7) A(5,6,7) A(4,5,6) A(4,5,8) A(6,5,8) D(14,13,11,12) D(14,13,11,2) D(14,13,11,3) D(14,13,11,4) D(15,13,11,12) D(15,13,11,2) D(15,13,11,3) D(15,13,11,4)
1.3432 1.3977 1.3941 1.3959 1.3979 1.3378 1.0876 1.0854 1.086 1.0839 1.5133 –. – – – 1.2295 1.3564 1.0101 1.0081 119.6839 118.978 121.3381 124.0067 114.5465 – – 121.4467 – – 119.0911 – – 117.6005 – – 123.3084 118.3056 119.0192 122.6751 – – – – 117.8589 118.8381 120.6538 120.5081 123.1628 116.2019 120.6353 118.5262 121.3385 120.1353 179.9369 0.0532 – – 0.0577 179.9415 – –
Nicotinamide Z2POLX ˚ /deg) (A 1.3542 1.401 1.3988 1.4015 1.4022 1.3471 1.0902 1.0889 1.0893 1.0873 1.5084 – – – – 1.2532 1.3595 1.0112 1.0088 119.0827 119.531 121.3863 124.0116 114.5365 – – 121.4519 – – 119.7337 – – 117.4448 – – 122.8215 118.4752 119.025 122.4998 – – – – 118.3733 118.992 120.5368 120.4712 122.5937 116.5838 120.8226 118.7444 121.1597 120.0959 180.0 0.0139 – – 0.0036 180.0175 – –
Z3POLX ˚ /deg) (A 1.3534 1.4014 1.4013 1.4032 1.4042 1.3457 1.0943 1.0918 1.0926 1.0903 1.5095 – – – – 1.2493 1.3631 1.0157 1.0105 117.9942 120.0128 121.9930 124.2953 114.0045 – – 121.7002 – – 119.6291 – – 117.0388 – – 123.3321 118.3207 118.9831 122.6961 – – – – 117.8598 118.8357 120.6132 120.5511 122.9989 116.3788 120.6223 118.6527 121.2474 120.0999 180.0000 0.0079 – – 0.0075 180.0000 – –
6-31++G(d,p) ˚ /deg) (A 1.3383 1.4025 1.4004 1.3915 1.3984 1.3398 1.0877 1.0854 1.0851 – – 1.0883 – – 1.5031 1.2277 1.3696 1.0077 1.0101 122.2195 116.6389 117.8266 121.7543 – 116.8525 – – 121.3864 – – – – – 115.1379 120.9163 123.9241 117.7444 – – 118.2621 123.9788 – – 117.3681 118.9226 122.1098 118.9674 123.4783 115.9815 120.5394 118.5477 121.1519 120.3004 164.4174 – 16.5246 – 5.4448 – 175.4972 –
Isonicotinamide Z2POLX ˚ /deg) (A 1.3490 1.4058 1.4057 1.3959 1.4025 1.3505 1.0903 1.089 1.0875 – – 1.0902 – – 1.5023 1.2531 1.3691 1.007 1.0101 123.5099 117.6356 118.8545 121.1288 – 117.8414 – – 121.0298 – – – – – 114.6825 121.9127 123.4048 117.7735 – – 117.7991 124.4274 – – 118.0455 119.2708 122.1284 118.6008 122.7444 116.3245 120.9311 118.761 120.9935 120.2455 180.0145 – 0.0258 – 0.0332 – 180.0445 –
Z3POLX ˚ /deg) (A 1.3480 1.4069 1.4069 1.3982 1.4043 1.3499 1.0945 1.0918 1.0913 – – 1.0955 – – 1.5018 1.2490 1.3728 1.0109 1.0122 123.296 117.9044 118.799 121.1198 – 117.771 – – 121.1092 – – – – – 114.4778 121.6566 123.8656 117.7515 – – 117.7965 124.452 – – 117.4645 119.0445 122.2685 118.687 123.2168 115.9926 120.7905 118.6571 121.0803 120.2626 179.8022 – 0.2138 – 0.1041 – 179.912 –
6-31++G(d,p) ˚ /deg) (A 1.3387 1.3973 1.4001 1.3985 1.3951 1.3413 1.0875 1.0844 – – – 1.0878 1.0857 1.5077 – 1.2262 1.3693 1.0079 1.0102 121.8300 116.695 117.767 122.0911 – – 116.4342 – – 121.4674 – 123.8514 118.213 – 116.1544 120.146 123.6991 118.7247 – – – – 119.3905 121.8511 117.1373 117.9268 – – 123.7231 116.0192 120.2577 118.7802 119.7488 121.4708 163.8062 – – 17.1629 6.0024 – – 174.9666
Z2POLX ˚ /deg) (A 1.3496 1.4004 1.4051 1.404 1.3982 1.3524 1.0897 1.0870 – – – 1.0899 1.0885 1.5069 – 1.2518 1.3685 1.0068 1.0102 123.3605 117.7494 118.8901 121.2751 – – 117.6682 – – 121.0566 – 124.4989 117.5675 – 116.4706 120.4776 123.0519 119.0682 – – – – 118.4175 122.5143 117.7617 117.9336 – – 123.0342 116.3148 120.6510 119.1504 119.1370 121.7126 179.9867 – – 0.0148 0.0045 – – 179.9970
Z3POLX ˚ /deg) (A 1.3486 1.4033 1.4060 1.4049 1.4008 1.3515 1.0943 1.0904 – – – 1.0945 1.0923 1.5071 – 1.2477 1.3720 1.0106 1.0122 123.1941 118.0125 118.7934 121.3221 – – 117.5558 – – 121.1221 – 124.6230 117.5815 – 116.1916 120.3911 123.4174 119.0286 – – – – 118.5479 122.4235 117.2374 117.7954 – – 123.5037 115.9949 120.5014 119.0175 119.3303 121.6521 179.9592 – – 0.0439 0.0131 – – 179.9900
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
9
Table 2 (continued) Atoms
Picolinamide 6-31++G(d,p) ˚ /deg) (A
D(13,11,2,3) D(13,11,3,4) D(13,11,4,5) D(13,11,2,1) D(13,11,3,2) D(13,11,4,3) D(12,11,2,3) D(12,11,3,4) D(12,11,4,5) D(12,11,2,1) D(12,11,3,2) D(12,11,4,3) D(11,2,3,4) D(11,3,4,5) D(11,4,5,6) D(11,2,3,10) D(11,3,2,10) D(11,3,4,9) D(11,4,5,8) D(1,2,3,11) D(1,2,3,4) D(1,2,3,10) D(1,2,3,9) D(11,2,1,6) D(11,4,3,2) D(11,4,3,9) D(3,2,1,6) D(2,3,4,5) D(2,3,4,9) D(4,3,2,10) D(9,3,2,10) D(10,3,4,5) D(9,3,4,5) D(10,3,4,9) D(9,4,5,8) D(10,2,1,6) D(8,5,6,7) D(2,1,6,5) D(2,1,6,7) D(3,4,5,6) D(3,4,5,8) D(9,4,5,6) D(1,6,5,4) D(1,6,5,8) D(7,6,5,4)
179.946 – – 0.0593 – – 0.0589 – – 179.9464 – – 179.9936 – – 0.0042 – – – – 0.0008 179.9986 – 179.9924 – – 0.0021 0.0001 179.9996 – – 179.9978 – 0.0018 0.0008 – 0.0005 0.0027 179.9995 0.0007 179.9995 179.999 0.0021 179.9981 179.9997
Nicotinamide Z2POLX ˚ /deg) (A 180.0492 – – 0.0063 – – 0.0627 – – 179.9928 – – 180.0094 – – 0.067 – – – – 0.068 179.998 – 180.0155 – – 0.0419 0.0547 180.0244 – – –179.9821 – 0.0482 0.0029 – 0.0174 0.0035 180.0195 0.0194 180.0274 180.0108 0.0071 179.9992 180.0096
Z3POLX ˚ /deg) (A 179.9891 – – 0.0028 – – 0.0055 – – 179.9917 – – 179.9866 – – 0.0000 – – – – 0.0000 179.9872 – 179.9879 – – 0.0000 0.0000 180.0000 – – 179.9871 – 0.0120 0.0046 – 0.0062 0.0028 179.9907 0.0000 179.9946 180.0000 0.0000 179.9935 0.00622
6-31++G(d,p) ˚ /deg) (A – 163.1349 – – 18.2965 – – 17.8034 – – 160.7652 – – 179.8916 – – 1.5115 0.0397 – 179.7362 1.1607 – – – – – 0.1679 1.2326 178.6192 177.0640 – – – – 0.5246 178.1497 0.3439 0.7561 179.55683 0.4083 179.6285 179.4387 0.6341 179.3295 179.6925
Isonicotinamide Z2POLX ˚ /deg) (A – 179.9988 – – 0.0001 – – 0.0101 – – 180.0112 – – 180.0033 – – 0.0376 0.0089 – 180.0068 0.0056 – – – – – 0.0163 0.0044 180.0079 180.0387 – – – – 0.028 180.0252 0.0285 0.0172 179.98065 0.0035 180.0152 179.9907 0.0076 179.9738 179.990
Z3POLX ˚ /deg) (A – 179.853 – – 0.1509 – – 0.163 – – 179.833 – – 179.9894 – – 0.0514 0.0073 – 179.9638 0.0322 – – – – – 0.0268 0.0069 179.9963 179.9446 – – – – 0.0094 179.9448 0.0309 0.0039 179.96215 0.0207 179.994 179.9759 0.0274 179.9872 179.9837
6-31++G(d,p) ˚ /deg) (A – – 159.1972 – – 21.9052 – – 21.7653 – – 157.1323 – – 179.9795 – – – 0.1554 – 0.3005 – 178.2303 – 179.4685 1.5920 0.6776 0.5679 – 179.4103 1.4805 – 177.3085 – – 179.0438 0.7547 0.1834 179.7273 1.0157 178.8084 – 0.6685 179.1524 179.4244
Z2POLX ˚ /deg) (A – – 179.996 – – 0.0040 – – 0.0055 – – 179.9944 – – 179.9998 – – – 0.0004 – 0.0006 – 179.9995 – 179.9996 0.0007 0.0002 0.0004 – 179.9999 0.0009 – 179.9993 – – 179.9997 0.0004 0.0005 179.9993 0.0002 179.9996 – 0.0007 179.9992 179.9994
Z3POLX ˚ /deg) (A – – 179.9777 – – 0.0259 – – 0.0254 – – 179.971 – – 179.9994 – – – 0.001 – 0.0028 – 179.9953 – 179.9968 0.0046 0.0021 0.0004 – 179.9978 0.0053 – 179.9918 – – 179.9985 0.001 0.0019 179.9978 0.004 179.9957 – 0.005 179.9947 179.9993
R, A, and D stand for bond, angle and dihedral angle, respectively.
in Table 2. The dihedral angles between the ring plane and CONH2 group for picolinamide, nicotinamide, and isonicotinamide are marked in bold. These angles show that nicotinamide and isonicotinamide have a non-planar environment, and picolinamide has a planar environment. It was reported that the substitution of the amide group into the pyridine ring does not affect the dimensions of the ring very much [2]. The results of optimized geometry parameters were found to support this. The optimized geometry parameters obtained by using the DFT/B3LYP method with the 6-31++G(d,p) basis set were found to
be in better agreement with the experimental ones than the Z2PolX and Z3PolX basis sets. The assignments of experimental wavenumbers, the calculated wavenumbers by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX, and Z3PolX basis sets compared with experimental wavenumbers and total energy distribution results for each molecule are given in Tables 3–5. When compared with experimental spectra the results showed that the Z2PolX and Z3PolX basis sets gave accurate relative band intensities and band positions better than 6-31++G(d,p) basis set
10
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
without scaling. The simulated IR and Raman spectra and the experimental spectra are shown in Figs. 2–4 for picolinamide, nicotinamide, and isonicotinamide, respectively. IR and Raman intensities, scaled wavenumbers obtained from the SQM procedure, were found to
be in good agreement with the Z2PolX and Z3PolX basis sets. We found that the Z3PolX basis set gives the best results for predicting experimental IR and Raman spectra. Scaled wavenumbers at the 6-31++G(d,p) basis set were calculated by using the scaling factors which were
Table 3 The assignments of experimental wavenumbers, the calculated wavenumbers by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX, and Z3PolX basis sets compared with the experimental wavenumbers and the total energy distribution results for picolinamide Experimental
Calculation 6-31++G(d,p)
Assign.
IR
Ra
Gasa
sring
754
dring
794
c (CH)
825
c (CH) c (CH) c (CH) mring mring NH2rock d (CH) d (CH) mring mring d (CH) m (CN)
909
d (CH) d (CH) NH2scis mring mring m (CO) m (CH) m (CH) m (CH) m (CH) m (NH2) m (NH2)
996 1043 1095 1143 1164 1254 1284 1387 1442 1468 1603 1568 1587 1658
Z2POLX
Z3POLX
U
U
TED(%)
100 sCCCO 52 c (CC), 40 sring 62 d (CC), 25 d (CN) 99 NH2wag
77 157 219 335
100 sCCCO 47 c (CC), 46 sring 62 d (CC), 25 d (CN) 96 NH2wag
93 170 216 373
379
373
379
399 428
414 451
29 m (CC), 26 dring, 19 d (CO), 16 d (CN) 100 sring 69 sring, 21 c (CC)
425
414 451
32 m (CC), 25 dring, 18 d (CO), 15 d (CN) 100 sring 76 sring, 16 c (CC)
495
490
43 d (CN), 22 d (CC), 12 mring
495
42 d (CN), 23 d (CC), 11 mring
498
680
612 629 640 717
604 608 636 679
69 44 76 41
612 629 640 717
42 78 76 51
597 632 671 724
747
763
735
60 sring, 34 c (CH)
763
57 c (CH), 37 sring
776
781
765
43 dring, 21 m (CC), 21 mring
780
42 dring, 23 m (CC), 19 mring
795
832
781
832
896 954 988 996 1032 1065 1085 1140 1148 1267 1287 1346
1471 1505 1594 1620 1637 1760 3176 3194 3213 3233 3589 3738
1429 1461 1528 1570 1588 1702 3037 3054 3072 3091 3431 3574
34 c (CO), 28 c (CH), 25 c (CC), 13 sring 100 c (CH) 100 c (CH) 54 dring, 45 mring 100 c (CH) 68 mring, 22 d (CH) 51 NH2rock, 18 m (CN) 43 d (CH), 36 mring 67 d (CH), 21 mring 32 mring, 28 d (CH), 13 dring 65 mring, 29 d (CH) 47 mring, 44 d (CH) 28 m (CN), 16 m (CC), 12 d (CH), 12 d (CO), 11 mring 55 d (CH), 35 mring 54 d (CH), 38 mring 81 NH2scis 73 mring, 15 d (CH) 67 mring, 20 d (CH) 75 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 100 m (CH) 100 m (NH2) 100 m (NH2)
870
928 988 1016 1022 1064 1091 1115 1172 1178 1310 1324 1386
46 c (CH), 20 c (CC), 20 c (CO), 14 sring 100 c (CH) 100 c (CH) 100 c (CH) 59 mring, 39 dring 60 mring, 23 d (CH), 14 dring 43 NH2rock, 21 m (CN), 12 mring 39 d (CH), 35 mring 74 d (CH), 21 mring 29 mring, 22 dring, 16 d (CH) 76 mring, 18 d (CH) 54 d (CH), 36 mring 25 m (CN), 16 m (CC), 13 d (CO), 12 d (CH), 12 NH2scis 57 d (CH), 33 mring 56 d (CH), 36 mring 78 NH2scis 71 mring, 16 d (CH) 65 mring, 21 d (CH) 74 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
996 1030 1086 1156 1244 1291 1362 1433 1472 1567 1645 1722 3020
3061 3075 3164 3414
TED (%)
75 147 219 301
817
998 1043 1083 1100 1142 1168
S
77 157 219 335
602
c (CO)
U
3415 3552
NH2twist, 15 c (CO), 11 sring d (CO), 38 dring dring c (CO), 29 NH2twist, 29 sring
928 988 1016 1022 1064 1091 1115 1171 1178 1310 1324 1386 1471 1505 1594 1620 1637 1760 3176 3194 3213 3233 3589 3738
d (CO), 41 dring NH2twist dring sring, 33 c (CO), 19 NH2twist
438 486
978 1000 1057 1061 1065 1110 1134 1170 1178 1305 1326 1378 1461 1490 1551 1611 1629 1707 3153 3178 3202 3220 3519 3691
TED (%) 100 sCCCO 51 sring, 41 c (CC) 62 d (CC), 26 d (CN) 24 m (CC), 24 dring, 22 d (CO), 19 d (CN) 100 sring 45 NH2wag, 40 sring 39 d (CN), 24 d (CC), 11 mring 55 NH2wag, 31 sring, 12 c (CC) 45 d (CO), 36 dring 83 dring 81 NH2twist 54 sring, 36 c (CO), 16 NH2twist 42 dring, 23 m (CC), 21 mring 47 c (CH), 36 sring, 12 c (CO) 44 c (CH), 24 c (CC), 22 c (CO) 100 c (CH) 57 dring, 41 mring 59 mring, 19 d (CH) 100 c (CH) 48 NH2rock, 15 mring 45 d (CH), 40 mring 100 c (CH) 48 d (CH), 24 mring 49 d (CH), 27 mring 54 d (CH), 40 mring 70 mring, 18 d (CH) 23 m (CN), 17 m (CC), 15 mring, 14 d (CH) 59 d (CH), 33 mring 51 d (CH), 37 mring 74 NH2scis 74 mring, 15 d (CH) 70 mring, 18 d (CH) 71 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
IR, experimental IR solid phase wavenumbers; Ra, the experimental Raman wavenumbers; Gas, experimental IR gas phase wavenumbers; U, unscaled wavenumbers; S, scaled wavenumbers; TED, total energy distribution of picolinamide obtained by using the Scale 2.0 program; s, torsion; d, in plane bending; m, stretching; c, out of plane bending vibrations. a Taken from Ref. [19].
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
11
Table 4 The assignments of experimental wavenumbers, the calculated wavenumbers by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX and Z3PolX basis sets compared with the experimental wavenumbers and the total energy distribution results for nicotinamide Experimental
Calculation 6-31++G(d,p)
Assign.
IR
Ra
a
Gas
U
S
Z2POLX TED(%)
U
52 153 212 314
50 147 210 284
97 52 63 90
sCCCO c (CC), 38 sring d (CC), 18 d (CN) NH2wag
38 165 227 385
378
370
733
387 418 495 559 616 643 717 747
374 404 488 537 611 639 689 698
26 22 58 93 43 76 49 61 71 35 30 44 22 68
m (CC), 20 dring, sring, 15 d (CO) sring, 12 d (CN) sring d (CN), 15 d (CC) NH2twist dring, 28 d (CO) dring, 22 d (CO) sring, 33 c (CO) c (CO), sring, 26 c (CH) dring, mring, 18 m (CC) c (CH), 12 c (CC)
Z3POLX
TED(%)
U
TED(%)
sCCCO sring, 46 c (CC) d (CC), 23 d (CN) m (CC), 27 dring, d (CO), 12 d (CN) sring, 14 c (CC)
33 164 227 342
98 51 67 83
sCCCO sring, 42 c (CC) d (CC), 23 d (CN) NH2wag, 12 NH2twist
397
99 47 66 30 18 78
381
443 467 477 602 614 645 740 759
88 76 50 64 39 74 96 50
sring NH2wag, 18 NH2twist d (CN), 18 d (CC), 11 mring NH2twist, 22 NH2wag dring, 38 d (CO) dring, 14 d (CO) sring, 12 c (CO) c (CO), 35 c (CH)
400 444 466 571 600 631 725 758
27 18 89 74 47 78 40 74 95 53
dring, 27 m (CC), d (CO), 15 d (CN) sring sring, 16 c (CC) d (CN), 18 d (CC) NH2twist dring, 37 d (CO) dring, 14 d (CO) sring, 14 c (CO) c (CO), 31 c (CH)
780
45 dring, 22 mring, 19 m (CC)
773
875
886 969 1023 1041 1047
NH2twist dring dring sring c (CO)
701
dring
776
788
777
781
766
c (CH)
828
833
812
841
808
c (CH) c (CH) c (CH) dring
936 996
940
947 990 1015 1037
915 957 981 1022
100 c (CH) 100 c (CH) 100 c (CH) 45 dring, 37 mring, 16 d (CH)
973 1038 1046 1056
65 c (CH), 15 c (CC), 14 c (CO) 100 c (CH) 43 mring, 42 dring, 12 d (CH) 100 c (CH) 65 mring, 25 dring
mring NH2rock
1029 1091
1042 1093
1025 1077
1061 1083
1027 1057
50 NH2rock, 22 m (CN), 14 m (CO) 100 c (CH)
1056 1104
1124 1154
1123 1161
1107 1135
1135 1157
1101 1127
mring, 28 dring NH2rock, m (CN), 10 m (CO) d (CH), 43 mring mring, 26 d (CH), 17 dring
1087 1118
d (CH) mring
63 52 24 45 27
1128 1165
1123 1155
d (CH) mring d (CH) m (CN)
1202 1231 1340 1393
1193 1261 1347
1231 1308 1365 1374
1195 1263 1330 1337
1422 1486 1615
1417 1476 1587
1454 1514 1614
1412 1470 1555
d (CH), 44 mring mring d (CH) m (CN), 20 m (CC), d (CO), 10 NH2rock d (CH), 43 mring d (CH), 34 mring NH2scis
1228 1303 1370 1389
d (CH) d (CH) NH2scis
48 90 86 31 15 50 59 85
1439 1506 1590
46 30 13 54 95 85 36 14 52 58 59
mring
1575
1625
1565
65 mring, 22 d (CH)
1627
68 mring, 20 d (CH)
1601
mring
1593
1638
1589
1643
1674
1722 3016
3061
3050 3088 3436 3554
1753 3165 3177 3206 3222 3598 3732
1695 3026 3038 3065 3080 3440 3568
38 m (CO), 36 NH2scis, 11 mring 58 NH2scis, 24 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
1630
m (CO) m (CH) m (CH) m (CH) m (CH) m (NH2) m (NH2)
66 mring, 21 d (CH), 10 dring 76 m (CO) 100 m (CH) 100 m (CH) 100 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
48 32 13 54 93 87 35 12 52 55 63 12 58 16 70
1691 3133 3155 3191 3214 3550 3698
68 m (CO) 100 m (CH) 100 m (CH) 100 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
627
3150 3358
1684 3158 3176 3201 3223 3570 3713
mring, 41 d (CH) d (CH), 27 mring, 14 dring, NH2rock d (CH), 37 mring mring d (CH) m (CN), 18 m (CC), d (CH), 12 d (CO) d (CH), 41 mring d (CH), 32 mring mring, 16 d (CH), 15 d (CO)
1225 1315 1353 1376 1439 1501 1586
45 dring, 21 mring, 20 m (CC) 70 c (CH), 13 c (CC) 100 c (CH) 67 dring, 23 mring 100 c (CH) 58 NH2rock, 16 m (CN), 11 m (CO) 79 mring, 13 d (CH) 100 c (CH) d (CH), 42 mring mring, 29 d (CH), m (CN), 10 dring d (CH), 40 mring mring d (CH) m (CN), 22 m (CC), d (CH), 11 d (CO) d (CH), 41 mring d (CH), 34 mring NH2scis, m (CO), 12 mring mring, 16 NH2scis, d (CH) mring, 18 d (CH)
IR, experimental IR solid phase wavenumbers; Ra, experimental Raman wavenumbers; Gas, experimental IR gas phase wavenumbers; U, unscaled wavenumbers; S, scaled wavenumbers; TED, total energy distribution of nicotinamide obtained by using the Scale 2.0 program; s, torsion; d, in plane bending; m, stretching; c, out of plane bending vibrations. a Taken from Ref. [20].
determined by Pulay and Pongor [13–15]. Only the scaling factors related to the out of plane bendings and NH2 rocking were refined. The final scaling factors are given
in Table 6. They were used without making any changes for the three isomers. In this way we showed that these scaling factors are transferable.
12
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
Table 5 The assignments of experimental wavenumbers, the calculated wavenumbers by using the DFT/B3LYP method with the 6-31++G(d,p), Z2PolX and Z3PolX basis sets compared with the experimental wavenumbers and the total energy distribution results for isonicotinamide Experimental
Calculation 6-31++G(d,p)
Assign.
IR
Ra
U
S
TED(%)
Z2POLX
Z3POLX
U
U
56 151 211 341
54 141 209 309
98 57 64 91
368
365
387
375
30 dring, 28 m (CC), 14 d (CO), 12 d (CN) 100 sring
415 510
400 501
565 614 681
542 610 675
720
683
766 769 855
731 761 812
61 38 14 71 49 52 25 36 27 82 35 85
100 c (CH) 100 c (CH) 100 c (CH)
928 996 1053
sCCCO c (CC), 33 sring d (CC), 18 d (CN) NH2wag
sring, 11 d (CN) d (CN), d (CC), 10 sring NH2twist d (CO), 28 dring dring, c (CO), 10 sring dring, c (CO), 22 sring sring, 15 c (CO) dring, 25 m (CC), 17 mring c (CH), 14 c (CC)
32 166 229 383 391
445
98 48 66 83
374
31 dring, 26 m (CC), 16 d (CO), 15 d (CN)
sCCCO sring, 45 c (CC) d (CC), 23 d (CN) NH2wag, 13 NH2twist
393
100 sring
472 476
461 468
58 sring, 19 c (CC), 15 c (CO) 47 d (CN), 18 d (CC)
606 610 686
53 d (CO), 24 dring 60 NH2twist, 21 NH2wag 88 dring
582 595 670
74 NH2twist, 10 NH2wag 53 d (CO), 28 dring 89 dring
735
49 sring, 40 c (CO)
724
57 sring, 41 c (CO)
760 780 883
40 dring, 24 m (CC), 18 mring 59 sring, 22 c (CH), 15 c (CO) 66 c (CH), 19 c (CC), 18 c (CO) 97 c (CH) 64 mring, 34 dring 100 c (CH)
760 778 892
1052
38 dring, 25 m (CC), 17 mring 49 sring, 24 c (CH), 20 c (CO) 70 c (CH), 18 c (CC), 15 c (CO) 99 c (CH) 51 mring, 48 dring 58 NH2rock, 17 m (CN), 11 m (CO) 100 c (CH)
1081
46 mring, 33 d (CH), 21 dring
1085
100 c (CH)
1116 1146
47 mring, 40 d (CH) 37 mring, 15 d (CH), 15 m (CN), 12 dring, 10 m (CC) 65 d (CH), 33 mring 95 mring 78 d (CH), 17 mring 35 m (CN), 21 m (CC), 12 d (CO), 10 d (CH) 59 d (CH), 36 mring 62 d (CH), 32 mring 70 NH2scis, 12 m (CO) 70 mring 66 mring, 20 d (CH) 69 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
c (CO)
708
dring sring c (CH)
754 776 795
783
c (CH) c (CH) c (CH)
852
867
896 984 1007
865 950 973
mring
994
995
1011
1004
56 mring, 43 dring
1084
NH2rock
1065
1063
1083
1067
1085
mring
1086
1084
1091
1076
d (CH) mring
1122 1148
1128 1152
1116 1151
1097 1138
d (CH) mring d (CH) m (CN)
1219 1263 1322 1390
1246 1297 1352 1371
1221 1284 1322 1352
d (CH) d (CH) NH2scis mring mring m (CO) m (CH) m (CH) m (CH) m (CH) m (NH2) m (NH2)
1408 1496 1622 1551 1596 1655 3042
1444 1527 1606 1623 1642 1759 3173 3180 3200 3226 3596 3731
1417 1497 1559 1589 1621 1740 3044 3050 3070 3095 3450 3578
46 NH2rock, 20 m (CN), 11 mring 41 mring, 34 d (CH), 20 dring 43 d (CH), 38 mring 32 mring, 20 dring, 12 m (CN), 12 m (CC), 11 d (CH) 64 d (CH), 34 mring 94 mring 79 d (CH), 15 mring 32 m (CN), 19 m (CC), 14 d (CO) 55 d (CH), 40 mring 59 d (CH), 35 mring 85 NH2scis 77 mring 67 mring, 20 d (CH) 80 m (CO) 100 m (CH) 100 m (CH) 99 m (CH) 99 m (CH) 100 m (NH2) 100 m (NH2)
3178 3362
35 168 228 350
sring, NH2twist, 23 NH2wag NH2wag, 31 sring d (CN), 17 d (CC)
668
3066
TED (%)
98 sCCCO 48 c (CC), 44 sring 65 d (CC), 23 d (CN) 33 dring, 29 m (CC), 15 d (CO) 100 sring
34 26 52 49
NH2twist dring dring
664
TED(%)
1091 1121 1161 1243 1292 1356 1387 1429 1507 1588 1628 1646 1684 3174 3179 3194 3221 3568 3714
31NH2rock, 16 m (CN), 16 mring, 12 m (CO) 100 c (CH) 38 21 40 32 18 64 97 72 36 14 57 65 66 65 38 54 99 99 99 99 99 99
mring, 27 dring, d (CH) mring, 35 d (CH) mring, 18 dring, NH2rock, 13 m (CC) d (CH), 32 mring mring d (CH), 13 mring m (CN), 19 m (CC), d (CH), 12 d (CO), 10 NH2rock d (CH), 37 mring d (CH), 30 mring mring, 15 d (CO) mring, 21 d (CH) NH2scis, 37 m (CO) NH2scis, 26 m (CO) m (CH) m (CH) m (CH) m (CH) m (NH2) m (NH2)
936 994 1045
1241 1302 1341 1372 1428 1508 1584 1599 1630 1696 3150 3158 3181 3218 3552 3701
IR, experimental IR solid phase wavenumbers; Ra, experimental Raman wavenumbers; U, unscaled wavenumbers; S, scaled wavenumbers; TED, total energy distribution of isonicotinamide obtained by using the Scale 2.0 program; s, torsion; d, in plane bending; m, stretching; c, out of plane bending vibrations.
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
13
c
a
0,14
8000
Absorbance
0,12
Intensity
6000
4000
0,10 0,08 0,06 0,04
2000
0,02 0
0,00 0
200
400
600
800
1000
4000
1200
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
-1
Wavenumbers (cm )
b
d 100
Absorbance
Relative Intensity
80 20
60
40
20 0 0 400
800
1200
4000
3500
3000
e
2500
2000
1500
1000
Wavenumbers (cm-1)
Wavenumbers (cm-1) 100
Transmittance
90
80
70
60
50 4000
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Fig. 2. (a) The experimental Raman spectrum, (b) the simulated Raman spectrum, (c) the experimental IR gas phase spectrum, (d) the simulated IR gas phase spectrum, (e) the IR solid phase spectrum of picolinamide.
In the present work, TED calculations indicate a very significant mixing of all ring and bending vibrations. Such mixing was indicated in previous studies [16,17] and it should increase with respect to the pyridine case due to the lowering of molecular symmetry and presence of an amide group which is a heavy group. For example, the ring breathing mode includes ring vibrations and ring bond
stretching in different proportions. Therefore, it does not resemble the ring breathing mode of the pyridine. In this study, the ring breathing modes of picolinamide, nicotinamide, and isonicotinamide were assigned in Raman spectra 998, 1042, 995 cm 1, respectively. Also, it was reported that the ring breathing mode of coordinated nicotinamide was found to be at 1033 cm 1 in Raman spectra [18].
14
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
a
12000
c
0,018 0,016
10000 0,014 0,012
Absorbance
Intensity
8000
6000
0,010 0,008 0,006
4000 0,004 0,002
2000
0,000 0 0
200
400
600
800
1000
-0,002 4000
1200
3500
3000
Wavenumbers (cm-1)
2500
2000
1500
1000
Wavenumbers (cm-1)
b
d
80
Absorbance
Relative Intensity
100
20
60
40
20 0 0 400
800
1200
4000
3500
Wavenumbers (cm-1)
e
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
100 95
Transmittance
90 85 80 75 70 65 60 55 4000
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Fig. 3. (a) The experimental Raman spectrum, (b) the simulated Raman spectrum, (c) the experimental IR gas phase spectrum, (d) the simulated IR gas phase spectrum, (e) the IR solid phase spectrum of nicotinamide.
5. Conclusion The combination of good intensity and wavenumber data made it possible for the isomers of pyridinecarboxamide to have a close correspondence between the simulated IR and Raman spectra and experimental data. The
results of 6-31++G(d,p) basis set, which were obtained by applying the SQM procedure and the results of Z3PolX basis set, showed us that the observed bands could easily be assigned. We found that the Z3PolX basis set gave the best results for predicting experimental IR and Raman spectra.
M. Bakiler et al. / Journal of Molecular Structure 826 (2007) 6–16
a
15
c
20000
100
18000 16000
80
Absorbance
14000
Intensity
12000 10000 8000
60
40
6000 20
4000 2000
0
0 0
200
400
600
800
1000
4000
1200
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Wavenumbers (cm-1)
b
d
100
Relative Intensity
Transmittance
90
80
70
60
50
0
40 400
800
1200
Wavenumbers (cm-1)
4000
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Fig. 4. (a) The experimental Raman spectrum, (b) the simulated Raman spectrum, (c) the simulated IR gas phase spectrum, (d) the IR solid phase spectrum of isonicotinamide.
Table 6 The scaling factors for the isomers of pyridinecarboxamide Internal coordinates
Scaling factors
X–Y stretching X–H stretching X–Y–Z in plane bending X–Y–H in plane bending CO/CC out of plane bending CH out of plane bending All torsion NH2 scissoring NH2 rocking NH2 wagging
0.9300 0.9140 0.9950 0.9500 0.8300 0.9340 0.9350 0.9130 0.9672 0.8000
H means hydrogen; X, Y, and Z mean first-row heavy atoms C, N, O.
Acknowledgement The authors thank Prof. Dr. Mustafa Urgen and Assoc. Prof. Dr. Gultekin Goller for Raman and FT-IR measurements at the Istanbul Technical University, Istanbul, Turkey.
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