Spectrochimica Acta Part A 67 (2007) 342–349

Molecular structures and vibrational frequencies of xanthine and its methyl

derivatives (caffeine and theobromine) by ab initio Hartree–Fock
and density functional theory calculations
Fatih Ucun ∗ , Adnan Sağlam, Vesile Güçlü
Department of Physics, Faculty of Arts and Sciences, Süleyman Demirel University, Isparta, Turkey
Received 31 January 2006; received in revised form 7 June 2006; accepted 14 July 2006

Abstract
The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine
and theobromine) have been calculated using ab initio Hartree–Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis
set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric
parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been
obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations
well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.
© 2006 Elsevier B.V. All rights reserved.

Keywords: Xanthine; Caffeine; Theobromine; Vibration; IR spectra; Raman spectra; HF; DFT

1. Introduction stituted analogues of xanthine prototropic tautomers is rather

Xanthine (2,6-dihydroxy purine) is a white crystalline
solid. Caffeine (1,3,7-trimethyl xanthine), and thebromine (3,7-
dimethyl xanthine) are its methyl derivatives. These molecules
are common agrochemical and therapeutic agents and easily oxi-
dised to uric acid and methyl uric acid [1].
Xanthine and its methyl derivatives have been studied as
experimental (IR and R) and theoretical (normal coordinate anal-
ysis) by some authors, but authors, in their study, have only
considered 27 normal modes of vibration for all the molecules
[2]. Caffeine has become the subject of many studies as exper-
imental and theoretical [3–5]. Guarine, a complex of caffeine
and tannins, has been studied by FT-Raman spectroscopy [6].
Marco et al. have investigated the geometries and struc-
tural changes of the neutral, protonated and coordinated purine
derivatives xanthine, hypoxanthine, allopurinol and alloxanthine
as quantum chemical and X-ray crystallographic [7]. The tau-
tomers of xanthine [8] and hypoxanthine [9] have been studied
as theoretical. Platonov et al. have found the use of methyl sub-
∗ Corresponding author. Tel.: +90 246 2114032; fax: +90 246 2371106.
E-mail address: fucun@fef.sdu.edu.tr (F. Ucun).
good approach to experimental study of the prototroic tau-
tomeric equilibrium in nucleotide basis if relative energies of
high-energy tautomers are not less than a few kcal/mol [10].
Some authors have described that in the preparation of xan-
thine and its methyl derivatives some care should be taken since
sample handling may affect the water content of these sam-
ples which causes pseudopolymorphic transformations affecting
their biavailability and stability [11].
In the present study we wish to report the vibrational analysis
and optimised molecular geometries of xanthine and its methyl
derivatives caffeine and theobromine having a central impor-
tance for the study of these pharmacologically active molecules
by means of ab inito Hartree–Fock (HF) and density functional
theory (B3LYP) methods.
2. Computational methods
Gaussian 03-program package was used in calculations [12].
The optimised structure parameters and vibrational frequencies
for all the molecules were calculated by using HF and B3LYP
methods at 6-31G(d, p) basis set level. The vibrational modes
were assigned on the basis of visual inspection of each of the
vibrational modes by Gauss-View molecular visualization pro-

1386-1425/$ – see front matter © 2006 Elsevier B.V. All rights reserved.
doi:10.1016/j.saa.2006.07.029
 F. Ucun et al. / Spectrochimica Acta Part A 67 (2007) 342–349 343

gram [13]. The calculated vibrations were scaled with some scale • for theobromine (N = 21)
factors, which we have found by the ratio of the frequency val-
ues of the strongest peaks in the experimental and calculated Γvib. = 39A + 18A ,
spectra. Such obtained scale factors are seen to cause the gained
vibrations well agreement with the experimental data. respectively.
3. Results and discussion
3.2. Molecular geometries
3.1. Vibrational symmetries
The calculated optimised structures of all the molecules are
Xanthine and its methyl derivatives caffeine and theobromine illustrated in Fig. 1 and their calculated geometry parameters
belong to the point group CS . For an N-atomic molecule the are summarized in Tables 1–3. The available experimental data
three Cartesian displacements of the N-atoms provide 3N inter-
nal modes, namely:
Table 1
Γinter. = 3N. Experimental and theoretical optimised geometric structure parameters of
xanthine
From the character table for the CS point group, since
Γ trans. = 2A + A and Γ rot. = A + 2A , we get Parameters Experimentala Calculated [6-31 G(d, p)]
HF B3LYP
Γvib. = Γinter. − Γtrans. − Γrot. = Γinter. − 3A − 3A
Bond lengths (Å)
normal modes of vibration. All the vibrations are active both C(1) O(9) 1.223 1.194 1.217
infrared (IR) and Raman (R). 2N-3 of all these vibrations is in C(1) N(10) 1.384 1.384 1.402
plane, and N-3 is out of plane [14]. Since the molecules are in C(1) N(11) 1.364 1.300 1.389
the CS group, the vibrations being anti-symmetric through the C(2) C(3) 1.368 1.354 1.380
C(2) N(11) 1.369 1.369 1.375
mirror plane σ h will belong to the species A and the ones being C(2) N(13) 1.364 1.348 1.360
symmetric through σ h to the species A . Thus, the vibrations of C(3) C(4) 1.421 1.437 1.438
the A species will be in plane and those of the A species will C(3) N(12) 1.376 1.379 1.381
be out of plane. For all the molecules the numbers of vibration C(4) O(8) 1.229 1.196 1.222
modes are as follows: C(4) N(10) 1.387 1.391 1.411
H(5) N(10) 0.997 1.012
H(6) N(11) 0.995 1.010
• for xanthine (N = 15)
C(7) N(12) 1.326 1.333 1.358
  C(7) N(13) 1.341 1.306 1.329
Γvib. = 27A + 12A , C(7) H(15) 1.070 1.080
N(12) H(14) 0.994 1.009
• for caffeine (N = 24)
Bond angles (◦ )
 
Γvib. = 45A + 21A , N(10) C(1) O(9) 120.8 122.0 122.6
N(11) C(1) O(9) 122.8 123.0 123.2
N(10) C(1) N(11) 116.4 115.0 114.2
N(11) C(2) C(3) 121.9 121.5 120.9
N(13) C(2) C(3) 110.7 111.9 112.1
N(11) C(2) N(13) 127.4 126.6 127.0
C(2) C(3) C(4) 122.1 122.9 123.6
C(2) C(3) N(12) 105.5 104.7 104.5
C(4) C(3) N(12) 132.3 132.5 131.9
C(3) C(4) O(8) 127.3 127.5 127.8
C(3) C(4) N(10) 111.7 110.3 109.8
N(10) C(4) O(8) 121.1 122.1 122.3
N(12) C(7) N(13) 112.6 113.5 113.0
N(12) C(7) H(15) 122.3 122.3
N(13) C(7) H(15) 124.2 124.7
C(1) N(10) C(4) 128.0 129.3 129.9
C(1) N(10) H(5) 114.4 114.2
C(4) N(10) H(5) 116.2 115.9
C(1) N(11) C(2) 119.9 121.0 121.6
C(1) N(11) H(6) 117.5 117.1
C(2) N(11) H(6) 121.6 121.4
C(3) N(12) C(7) 107.1 106.0 106.6
C(3) N(12) H(14) 126.4 125.6
C(7) N(12) H(14) 127.6 128.0
C(7) N(13) C(2) 104.1 103.9 103.8
a Taken from Ref. [7].
Fig. 1. Optimised geometrical structures of all the title molecules.
344 F. Ucun et al. / Spectrochimica Acta Part A 67 (2007) 342–349

Table 2 Table 3
Theoretical optimised geometric structure parameters of caffeine Theoretical optimised geometric structure parameters of theobromine
Parameters Calculated [6-31 G(d, p)] Parameters Calculated [6-31 G(d, p)]
HF B3LYP HF B3LYP
Bond lengths (Å) Bond lengths (Å)
C(1) N(8) 1.372 1.392 C(1) N(8) 1.370 1.391
C(1) N(9) 1.391 1.408 C(1) N(9) 1.383 1.400
C(1) O(11) 1.199 1.222 C(1) O(11) 1.196 1.220
C(2) C(3) 1.357 1.381 C(2) C(3) 1.360 1.384
C(2) N(6) 1.346 1.359 C(2) N(6) 1.345 1.359
C(2) N(8) 1.370 1.375 C(2) N(8) 1.373 1.379
C(3) C(4) 1.432 1.433 C(3) C(4) 1.434 1.435
C(3) N(7) 1.383 1.387 C(3) N(7) 1.382 1.386
C(4) N(9) 1.395 1.417 C(4) N(9) 1.387 1.408
C(4) O(10) 1.201 1.228 C(4) O(10) 1.199 1.225
C(5) N(6) 1.310 1.330 C(5) N(6) 1.310 1.330
C(5) N(7) 1.329 1.356 C(5) N(7) 1.328 1.356
C(5) H(24) 1.071 1.081 C(5) H(21) 1.071 1.081
N(7) C(16) 1.451 1.457 N(7) C(16) 1.451 1.457
N(8) C(20) 1.458 1.462 N(8) C(12) 1.458 1.462
N(9) C(12) 1.464 1.466 N(9) H(20) 0.997 1.012
C(12) H(13) 1.080 1.091 C(12) H(13) 1.080 1.092
C(12) H(15) 1.076 1.087 C(12) H(15) 1.077 1.088
C(16) H(17) 1.080 1.092 C(16) H(17) 1.080 1.091
C(16) H(19) 1.081 1.091 C(16) H(19) 1.081 1.091
C(20) H(21) 1.081 1.092
C(20) H(23) 1.078 1.088 Bond angles (◦ )
N(8) C(1) N(9) 116.2 115.4
Bond angles (◦ ) N(8) C(1) O(11) 122.7 122.6
N(8) C(1) N(9) 118.0 117.2 N(9) C(1) O(11) 121.1 122.0
N(8) C(1) O(11) 121.3 121.4 C(3) C(2) N(6) 111.3 111.6
N(9) C(1) O(11) 120.8 121.4 C(3) C(2) N(8) 122.5 122.1
C(3) C(2) N(6) 111.5 111.8 N(6) C(2) N(8) 126.2 126.3
C(3) C(2) N(8) 121.7 121.3 C(2) C(3) C(4) 122.7 123.4
N(6) C(2) N(8) 126.7 126.8 C(2) C(3) N(7) 105.3 105.2
C(2) C(3) C(4) 123.2 123.9 C(4) C(3) N(7) 132.0 131.5
C(2) C(3) N(7) 105.2 105.1 C(3) C(4) N(9) 110.1 109.6
C(4) C(3) N(7) 131.5 131.0 C(3) C(4) O(10) 128.0 128.3
C(3) C(4) N(9) 111.6 111.0 N(9) C(4) O(10) 121.9 122.1
C(3) C(4) O(10) 125.8 126.4 N(6) C(5) N(7) 114.2 113.7
N(9) C(4) O(10) 122.7 122.6 N(6) C(5) H(21) 124.0 124.6
N(6) C(5) N(7) 114.2 113.8 N(7) C(5) H(21) 121.9 121.7
N(6) C(5) H(24) 123.9 124.6 C(2) N(6) C(5) 103.9 103.8
N(7) C(5) H(24) 121.8 121.6 C(3) N(7) C(5) 105.3 105.7
C(2) N(6) C(5) 103.8 103.6 C(3) N(7) C(16) 126.8 126.4
C(3) N(7) C(5) 105.2 105.7 C(5) N(7) C(16) 127.9 127.9
C(3) N(7) C(16) 127.1 126.6 C(1) N(8) C(2) 119.1 119.6
C(5) N(7) C(16) 127.7 127.7 C(1) N(8) C(12) 118.5 118.2
C(1) N(8) C(2) 119.3 119.7 C(2) N(8) C(12) 122.5 122.2
C(1) N(8) C(20) 118.3 118.1 C(1) N(9) C(4) 129.4 129.9
C(2) N(8) C(20) 122.4 122.1 C(1) N(9) H(20) 114.3 114.0
C(1) N(9) C(4) 126.3 126.9 C(4) N(9) H(20) 116.4 116.0
C(1) N(9) C(12) 115.2 115.1 N(8) C(12) H(13) 110.0 110.0
C(4) N(9) C(12) 118.5 118.0 N(8) C(12) H(15) 108.0 107.8
N(9) C(12) H(13) 109.9 110.0 H(13) C(12) H(14) 108.6 108.5
N(9) C(12) H(15) 107.8 107.3 H(13) C(12) H(15) 110.2 110.3
H(13) C(12) H(14) 108.6 108.3 N(7) C(16) H(17) 110.1 110.2
H(13) C(12) H(15) 110.3 110.6 N(7) C(16) H(19) 108.5 108.5
N(7) C(16) H(17) 110.1 110.4 H(17) C(16) H(18) 108.9 108.5
N(7) C(16) H(19) 108.5 108.5 H(17) C(16) H(19) 109.7 109.8
H(17) C(16) H(18) 108.8 108.3
H(17) C(16) H(19) 109.7 109.9
N(8) C(20) H(21) 110.1 110.1
N(8) C(20) H(23) 107.9 107.7
H(21) C(20) H(22) 108.7 108.3
H(21) C(20) H(23) 110.0 110.3
 F. Ucun et al. / Spectrochimica Acta Part A 67 (2007) 342–349 345

Table 4
Experimental and calculated vibrational frequencies of xanthine
Symmetry Assignments Experimentala Calculated frequencies (cm−1 )
frequencies
(cm−1 )
IR R HF 6-31 G(d, p) B3LYP 6-31 G(d, p)

IR intensity R activity IR intensity R activity

(km/mol) (Å4 /amu) (km/mol) (Å4 /amu)

A ν(NH) 3133 3137 3369 157 62 3373 103 93

A ν(NH) 3002 3010 3349 146 67 3364 103 91
A ν(NH) 2875 2875 3322 116 62 3335 80 85
A ν(CH) 2825 2797 2956 2 99 3012 1 122
A ν(C O) + δ(NH) 1700 1685 1720 785 20 1689 655 13
A ν(C O) + δ(NH) 1658 1600 1704 1100 42 1662 639 48
A ν(C C) + δ(NH) + δ(CH) 1567 1560 1555 134 28 1506 66 27
A νring (imidazole) + νring (pyrimidine) 1507 160 14 1477 123 14
+ δ(NH) + δ(CH)
A δ(NH) + δ(CH) + νring (imidazole) 1400 8 5 1367 26 9
A δ(NH) + δ(CH) + νring (imidazole) 1380 148 54 1348 42 31
A νring (pyrimidine) + δ(NH) 1334 1335 1347 241 6 1313 171 17
A δ(NH) 1258 1268 1334 2 6 1285 ∼0 8
A νring (imidazole) + νring (pyrimidine) 1220 1212 1259 26 59 1232 27 40
+ δ(NH)
A δ(NH) + δ(CH) 1215 1212 1210 24 8 1194 29 6
A ν(CN) + δ(NH) 1205 1220 1203 18 16 1179 9 15
A ν(CN) + δ(NH) + δ(CH) 1152 1160 1132 101 3 1115 52 4
A ν(CN) + δ(NH) 1120 1132 1067 83 3 1044 76 1
A δ(NH) + δ(CH) 1032 1040 1047 4 6 1022 3 11
A ν(CN) + δ(NH) 958 964 929 14 2 911 12 1
A δring (imidazole) 895 919 898 1 8 885 ∼0 7
A γ(CN) 853 843 882 3 ∼0 780 6 1
A δring (imidazole) + δring (pyrimidine) 765 766 795 8 1 773 9 1
A γ ring (pyrimidine) 735 138 1 691 ∼0 1
A γ ring (pyrimidine) + γ ring (imidazole) 722 711 722 17 2 681 60 ∼0
A γ ring (pyrimidine) + γ ring (imidazole) 660 658 687 22 ∼0 659 41 1
A ρr (pyrimidine) + δ(C O) 645 19 1 632 12 1
A γ(NH) + w(CH) + w(NH) 613 622 610 31 ∼0 606 21 1
A γ(NH) + w(CH) + w(NH) 587 61 3 583 58 ∼0
A Breathing (xanthine) 538 547 584 2 13 577 1 22
A γ(NH) + w(CH) 489 250 1 496 168 2
A τ ring (xanthine) 498 487 487 29 1 484 15 3
A γ(NH) + w(CH) 479 ∼0 2 477 25 2
A δ(pyrimidine) 428 411 441 14 3 437 12 4
A ρr (C O) 359 10 2 347 6 2
A γ ring (pyrimidine) + γ ring (imidazole) 310 ∼0 1 305 1 1
A ρr (imidazole) + ␳r (C O) 273 27 1 269 23 1
A γ ring (pyrimidine) + wring (imidazole) 175 174 ∼0 ∼0 172 ∼0 ∼0
A ρr (imidazole) out of 143 5 1 143 4 ∼0
plane + w(C O) + w(NH)
A w(imidazole) + w(C O) 107 1 ∼0 106 1 ∼0
+ γ ring (pyrimidine)

ν: stretching; δ: bending; γ: out of plane bending; ρr : rocking; w: wagging; τ: torsion.

a Taken from Ref. [2].

for xanthine are also given in Table 1. Taking into account that
the molecular geometry in the vapour phase may be different
from in the solid phase, owing to extended hydrogen bonding
and stacking interactions there is reasonable agreement between
the calculated and experimental geometric parameters. The dif-
ferences are also attributed to that the experimental data taken
X-ray crystallographic analysis have been obtained the averaged
geometries of the structures of Cu(xanthine)2 (NO3 )2 ·2H2 O,
Cu(xanthine)2 Cl2 ·2H2 O and Zn(xanthine)·2Cl2 [7]. The largest
differences of the calculated geometries from the experimental
ones are 0.035 Å (HF), 0.032 Å (B3LYP) for the bond lengths
and 1.9◦ (HF), 2.2◦ (B3LYP) for the bond angles.
3.3. Vibrational frequencies
The resulting vibrational frequencies for the optimised
geometries, and the proposed vibrational assignments are given
in Tables 4–6. In the tables are also given IR intensities and
346 F. Ucun et al. / Spectrochimica Acta Part A 67 (2007) 342–349

Table 5
Experimental and calculated vibrational frequencies of caffeine
Symmetry Assignments Experimentala Calculated frequencies (cm−1 )
frequencies
(cm−1 )
IR R HF 6-31 G(d, p) B3LYP 6-31 G(d, p)

IR intensity R activity IR intensity R activity

(km/mol) (Å4 /amu) (km/mol) (Å4 /amu)

A ν(CH) 3049 3 90 3364 1 110

A ν(CH3 )asym 3000 1 34 3102 1 32
A ν(CH3 )asym 2980 4 41 3093 1 36
A ν(CH3 )asym 2954 2963 2951 12 57 3071 7 63
A ν(CH3 )asym 2957b 2947 14 65 3058 7 61
A ν(CH3 )asym 2944 23 68 3050 15 77
A ν(CH3 )asym 2940 20 70 3046 12 77
A ν(CH3 )sym 2882 36 127 2985 28 163
A ν(CH3 )sym 2876 37 128 2982 15 207
A ν(CH3 )sym 2872 41 105 2981 46 67
A ν(C O) 1700 1700 1746 467 30 1739 332 36
A ν(C O) 1660 1656 1705 1066 22 1701 705 28
A ν(C C) + δ(HCN) 1600 1600 1607 212 36 1591 98 36
A δ(HCN) + νring (imidazole) 1548 1550 1551 194 9 1543 140 4
+ νring (pyrimidine)
A δ(HCN) + δ(CH3 ) 1470b 1487 117 19 1491 37 12
A δ(CH3 ) 1466b 1461 35 13 1476 20 22
A δ(CH3 ) 1459 12 8 1472 17 17
A γ(CH3 ) 1451 7 15 1461 8 17
A δ(CH3 ) 1448 160 12 1455 155 11
A γ(CH3 ) 1443 6 16 1455 8 16
A δ(CH3 ) 1431 36 3 1443 12 20
A γ(CH3 ) 1431 7 19 1428 25 1
A δ(CH3 ) 1415 33 13 1417 31 22
A δ(CH3 ) 1403b 1410 43 9 1406 35 9
A δ(CH3 ) + νring (imidazole) 1380 155 7 1386 21 4
A δ(HCN) + νring (imidazole) + δ(CH3 ) 1360b 1365 123 56 1353 62 53
A νring (imidazole) + νring (pyrimidine) 1326 1331 1330 34 26 1331 56 19
A νring (pyrimidine) 1285 1288 1282 33 33 1273 34 29
A ν(CN) + ρr (CH3 ) 1251b 1249 12 4 1240 29 10
A δ(CH) 1237 1241 1223 130 8 1229 60 7
A δ(CH) + ρr (CH3 ) 1210 1215 1205 19 3 1209 14 1
A δ(CH) + ρr (CH3 ) 1188 1189 1171 13 3 1179 12 3
A ρr (CH3 ) out of plane 1130 1131 1124 2 3 1126 ∼0 3
A ρr (CH3 ) out of plane 1120 2 3 1124 ∼0 2
A ρr (CH3 ) out of plane 1117 1 2 1119 ∼0 2
A ρr (CH3 ) + ρr (CH) 1071 1080 1064 9 6 1061 2 6
A ρr (CH3 ) 1049 ∼0 4 1058 2 6
A ρr (CH3 ) + ρr (CH) 1025 1020 1024 76 2 1015 62 3
A ν(N CH3 ) + δring (imidazole) + ρr (CH3 ) 973 975 956 20 5 967 32 2
A γ(CH) 923 925 909 5 ∼0 921 1 3
A ρr (CH3 ) + ν(N CH3 ) + δ(C O) 862 850 908 7 7 810 9 ∼0
A ρr (pyrimidine) + δ(C O) 800 800 790 2 2 791 1 4
A γ(NC O) 766 64 ∼0 734 17 8
A γ ring (pyrimidine) + γ ring (imidazole) 743 745 745 17 2 724 6 1
A τ(caffeine) 724 24 7 716 25 ∼0
A γ ring (pyrimidine) + γ ring (imidazole) 700 700 703 ∼0 ∼0 678 ∼0 ∼0
A δring (pyrimidine) + ρr (imidazole) 642 645 626 1 2 629 1 5
A γ ring (imidazole) 611 613 595 20 2 598 13 2
A Breathing(caffeine) 550 556 531 1 16 540 1 21
A τ(caffeine) 481 488 468 27 2 470 22 4
A δring (pyrimidine) 450 444 427 13 2 433 13 3
A ρr (C O) 420 394 400 30 ∼0 397 15 ∼0
A ρr (CH3 ) + ρr (C O) 382 16 2 383 14 2
A ρr (CH3 ) 346 9 ∼0 347 ∼0 1
A γ ring (pyrimidine) + γ ring (imidazole) 346 ∼0 1 344 9 ∼0
A ρr (CH3 ) 288 2 ∼0 287 2 ∼0
A γ(N CH3 ) 266 ∼0 ∼0 269 ∼0 ∼0
 F. Ucun et al. / Spectrochimica Acta Part A 67 (2007) 342–349 347

Table 5 (Continued )
Symmetry Assignments Experimentala Calculated frequencies (cm−1 )
frequencies
(cm−1 )
IR R HF 6-31 G(d, p) B3LYP 6-31 G(d, p)

IR intensity R activity IR intensity R activity

(km/mol) (Å4 /amu) (km/mol) (Å4 /amu)

A γ ring (pyrimidine) + γ ring (imidazole) 225 204 1 1 211 1 ∼0

A ρr (CH3 ) 200 10 ∼0 203 9 ∼0
A ρr (CH3 ) + w(imidazole) 156 4 1 154 6 1
A w(CH3 ) 119 13 ∼0 124 7 ∼0
A ρr (CH3 ) out of plane 116 ∼0 ∼0 109 ∼0 ∼0
A ρr (CH3 ) out of plane 94 ∼0 ∼0 90 1 ∼0
A w(CH3 ) 86 1 1 84 ∼0 1
A ρr (CH3 ) out of plane 80 2 1 65 ∼0 ∼0
A ρr (CH3 ) out of plane 62 ∼0 ∼0 32 1 ∼0

ν: stretching; δ: bending; γ: out of plane bending; ρr : rocking; w: wagging; τ: torsion.

a Taken from Ref. [2].
b Ref. [6].

Table 6
Experimental and calculated vibrational frequencies of theobromine
Symmetry Assignments Experimentala Calculated frequencies (cm−1 )
frequencies
(cm−1 )
IR R HF 6-31 G(d, p) B3LYP 6-31 G(d, p)

IR intensity R activity IR intensity R activity

(km/mol) (Å4 /amu) (km/mol) (Å4 /amu)

A ν(NH) 3114 3119 3325 113 68 3407 77 94

A ν(CH) 3027 3007 2947 3 86 3066 1 104
A ν(CH3 )asym 2882 3 38 2998 1 33
A ν(CH3 )asym 2851 13 63 2976 7 64
A ν(CH3 )asym 2849 11 58 2965 6 60
A ν(CH3 )asym 2841 21 75 2952 13 82
A ν(CH3 )sym 2779 37 136 2891 22 168
A ν(CH3 )sym 2774 38 112 2889 36 125
A ν(C O) 1691 1689 1697 586 32 1699 540 11
A ν(C O) + δ(NH) 1667 1660 1690 1162 20 1686 663 43
A ν(C C) + δ(NH) 1592 1600 1543 265 35 1533 130 38
A νring (imidazole) + νring (pyrimidine) 1548 1561 1497 149 10 1494 118 5
+ δ(NH)
A δ(CH3 ) + δ(NH) 1434 77 20 1445 28 12
A δ(CH3 ) 1412 24 14 1430 19 23
A δ(CH3 ) 1397 154 4 1410 7 16
A γ(CH3 ) 1394 6 15 1408 154 4
A γ(CH3 ) 1383 7 19 1399 9 20
A δ(CH3 ) 1378 11 3 1381 9 5
A δ(CH3 ) 1366 48 16 1373 32 22
A δ(NH) + δ(CH3 ) 1338 43 6 1346 46 9
A δ(CH3 ) + δ(NH) + δ(CH) 1334 1340 1335 111 13 1317 39 13
A νring (imidazole) + δ(NH) + δ(CH) 1316 136 54 1307 26 38
A νring (imidazole) + νring (pyrimidine) 1224 1231 1263 22 23 1274 34 16
+ δ(NH)
A νring (imidazole) + νring (pyrimidine) 1204 1210 1236 16 25 1235 31 35
A ρr (CH3 ) + δ(CH) 1173 1183 1178 157 8 1185 92 5
A ρr (CH3 ) + δ(CH) 1140 1144 1115 23 2 1160 10 3
A ρr (CH3 ) + ρr (NH) 1106 1 3 1113 4 1
A ρr (CH3 ) out of plane 1082 2 3 1091 ∼0 3
A ρr (CH3 ) out of plane 1079 1 2 1084 ∼ 2
A ρr (CH3 ) + ν(NC) + δ(NH) 1072 1065 1075 56 5 1070 45 8
A ρr (CH3 ) + ρr (CH) 1041 1046 1013 15 3 1020 13 3
A ρr (CH3 ) + δ(imidazole) 941 952 987 4 5 995 5 3
348 F. Ucun et al. / Spectrochimica Acta Part A 67 (2007) 342–349

Table 6 (Continued )
Symmetry Assignments Experimentala Calculated frequencies (cm−1 )
frequencies
(cm−1 )
IR R HF 6-31 G(d, p) B3LYP 6-31 G(d, p)
IR intensity R activity IR intensity R activity
(km/mol) (Å4 /amu) (km/mol) (Å4 /amu)

A ρr (CH3 ) + ρr (NH) + δ(imidazole) 889 895 887 7 7 892 8 5

A γ(CH) 865 860 879 5 ∼0 787 9 ∼0
A γ ring (pyrimidine) 752 782 740 111 ∼0 739 8 5
A δring (pyrimidine) + δring (imidazole) 733 740 732 12 3 706 ∼0 1
+ ν(N CH3 )
A γ ring (pyrimidine) + γ ring (imidazole) 723 15 2 697 52 ∼0
A γ ring (pyrimidine) + γ ring (imidazole) 687 13 ∼0 687 13 4
A τ(theobromine) + ρr (pyrimidine) 684 681 685 21 4 669 21 1
+ δ(C O)
A δring (pyrimidine) + ν(N CH3 ) 617 626 634 7 2 643 7 2
+ ρr (CH)
A γ(NH) 601 90 1 608 66 2
A γ ring (imidazole) + γ(NH) 573 2 3 577 1 3
A Breathing(theobromine) 508 515 560 11 13 572 6 20
A δring (pyrimidine) + ρr (imidazole) 456 465 478 16 5 480 14 7
A δring (pyrimidine) 423 415 415 27 2 420 22 3
A ρr (C O) + ρr (imidazole) 376 374 7 1 376 3 2
A ρr (C O) + ρr (CH3 ) 349 19 2 347 14 3
A γ ring (pyrimidine) + γ ring (imidazole) 335 ∼0 1 337 ∼0 1
A ρr (CH3 ) 284 2 ∼0 284 2 ∼0
A γ ring (pyrimidine) + γ ring (imidazole) 209 4 ∼0 215 3 ∼0
A ρr (CH3 ) 195 12 ∼0 198 11 ∼0
A γ ring (pyrimidine) + γ ring (imidazole) 184 3 1 186 2 ∼0
ρr ρr (CH3 ) out of plane + w(imidazole) 141 3 ∼0 141 5 ∼0
A w(CH3 ) 106 4 ∼0 106 2 ∼0
A w(CH3 ) 91 ∼0 ∼0 91 ∼0 ∼0
ρr ρr (CH3 ) out of plane 74 2 ∼0 38 ∼0 1
ρr ρr CH3 ) out of plane 40 ∼0 ∼0 19 1 ∼0

ν: stretching; δ: bending; γ: out of plane bending; ρr : rocking; w: wagging; τ: torsion.

a Taken from Ref. [2].

Raman activities. All the calculated vibration values are scaled. root mean standard (RMS) deviations between the experimental
Since there is an obvious intensity different between two near and calculated vibrational frequency values, defined by
supreme peaks and other peaks in the spectra the used scale fac- 
tors have been obtained by the ratio of the frequency values of  (wcal − wexp )2
i i
the strongest peaks in the experimental and calculated spectra. RMS(wi ) = ,
N
These frequencies in the experimental spectra are 1700 cm−1
exp
due to the mode of ν(C O) + δ(NH) for xanthine and, 1700 and i and wi
where wcal are the calculated and experimental fre-
1691 cm−1 due to the modes of ν(C O) for caffeine and theo- quencies of mode i, respectively and N denotes the number of
bromine, respectively, and those in the calculated spectra are the modes, RMS deviations for our scales are lower than those for
non-scaled frequency values of the modes having maximum IR reference’s scales (Table 8). This indicates that our scales are
intensity in the tables. All the used scale factors are presented in more reasonable for all the title molecules.
Table 7. They are very close to the scale factors (0.8992 for HF
and 0.9614 for B3LYP) at the same level of theory given in Ref. Table 8
[15]. If we compare our and reference’s scales by means of the The root mean standard (RMS) deviations between experimental and calculated
frequencies
Table 7 Molecule RMS deviations (%)
Used scale factors for all the title molecules
HF 6-31 G(d, p) B3LYP 6-31 G(d, p)
Molecule Calculated [6-31 G(d, p)] Our scales Ref.’s scale Our scales Ref.’s scale
HF B3LYP (0.8992) (0.9614)

Xanthine 0.86 0.92 Xanthine 1.26 1.89 1.33 1.89

Caffeine 0.89 0.97 Caffeine 0.18 0.24 0.32 0.29
Theobromine 0.86 0.94 Theobromine 0.52 0.94 0.68 0.89
 F. Ucun et al. / Spectrochimica Acta Part A 67 (2007) 342–349
As seen from Tables 4–6, the experimental and calculated
vibration frequencies are good agreement with each other except
only than the frequencies of the N H stretching modes in the
highest frequency regions of the spectra. These frequencies are
slightly bigger than their corresponding experimental data. The
vibrational modes due to the N H stretching of primary aliphatic
amines are generally observed between 3250 and 3450 cm−1 .
The calculated results are in this region. The differences may be
explained by the fact that the electronic correlation affects since
polarization functions were not included in the calculations. But,
on this occasion, from the values of RMS in Table 8 we can state
that HF gives more close results to the experimental ones than
B3LYP, for all the molecules.
The proposed vibrational assignments are given in the second
column of Tables 4–6. They are made by inspection of each of
the vibrational mode at HF level. Therefore, at DFT level some
assignments can correspond to its previous vibrational frequency
value. The symmetry species of all the vibrations are written in
the first column of the tables. As we said before, for all the
molecules the vibrations of the A species are in plane and those
of the A species are out of plane. This is indeed what we have
observed as numerically by means of the visual inspection of all
the vibrations.
4. Summary and conclusion
The optimised structure parameters, vibrational frequencies
and corresponding vibrational assignments of xanthine and its
methyl derivatives caffeine and theobromine are theoretically
examined using ab initio HF and B3LYP methods at 6-31G(d,
p) basis set level. The comparison of the experimental and
calculated results shows well agreement with each other. It is
concluded that the scaled HF method gives better results than
the scaled B3LYP method. The scale factors obtained the ratio
of the frequency values of the strongest peaks in the calculated
and experimental spectra seem to cause the gained vibrations
well agreement with the experimental data. Theoretical infrared
intensities and Raman activities are reported.
349
References
[1] K. Oettl, G. Reibnegger, Biochim. Biophys. Acta 1430 (1999) 387.
[2] S. Gunasekaran, G. Sankari, S. Ponnusamy, Spectrochim. Acta A 61 (2005)
117.
[3] B. Kesimli, A. Topacli, C. Topacli, J. Mol. Struct. 645 (2003) 199.
[4] M. de Matas, H.G.M. Edwards, E.E. Lawson, L. Shields, P. York, J. Mol.
Struct. 440 (1998) 97.
[5] P. Derollez, N.T. Correia, F. Danede, F. Capet, F. Affouard, J. Lefebvre, M.
Descamps, Acta Crystallogr. B 61 (2005) 329.
[6] H.G.M. Edwards, D.W. Farwell, L.F.C. de Oliveira, J.-M. Alia, M. le
Hyaric, M.V. de Ameida, Anal. Chim. Acta 532 (2005) 177.
[7] M. Nonella, G. Hanggi, E. Dubler, J. Mol. Struct. (Theochem.) 279 (1993)
173.
[8] P. Cysewski, D. Jeziorek, J. Mol. Struct. (Theochem.) 430 (1998)
219.
[9] M. Fernandez-Quejo, M. de la Fuente, R. Navarro, J. Mol. Struct. 744–747
(2005) 749.
[10] M.O. Platonov, S.P. Samijlenko, O.O. Sudakov, I.V. Kondratyuk, D.M.
Hovorun, Spectrochim. Acta A 62 (2005) 112.
[11] P.J.A. Ribeiro-Claro, A.M. Amado, Spectrochim. Acta A 61 (2005)
2796.
[12] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R.
Cheeseman, J.A. Montgomery Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M.
Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scal-
mani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota,
R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H.
Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, C. Adamo,
J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R.
Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth,
P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels,
M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B.
Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B.
Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin,
D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Chal-
lacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez,
J.A. Pople, GAUSSIAN 03, Revision C.02, Gaussian Inc., Pittsburgh, PA,
2003.
[13] A. Frish, A.B. Nielsen, A.J. Holder, Gauss View User Manual, Gaussian
Inc., Pittsburg, PA, 2001.
[14] E.B. Wilson, J.C. Decius, P.C. Cross, Molecular Vibrations, Dover Pub.
Inc., New York, 1980.
[15] D.C. Young, Computional Chemistry: A Pratical Guide for Applying Tech-
niques to Real-World Problems (Electronics), John Wiley & Sons, Inc.,
New York, 2001.