Journal of Molecular Structure (Theochem) 668 (2004) 93–99

www.elsevier.com/locate/theochem

Theoretical study of ofloxacin: geometrical parameters

and vibrational wavenumbers
S. Sagdinca, S. Bayarib,*
a
Department of Physics, Faculty of Art and Science, University of Kocaeli, Kocaeli, Turkey
b
Department of Physics, Faculty of Education, University of Hacettepe, Beytepe, Ankara 06532, Turkey
Received 16 July 2003; accepted 13 October 2003

Abstract
Molecular modeling of ofloxacin was performed using MM þ molecular mechanics, AM1, PM3, MNDO, MINDO3, ZINDO/1, TNDO
semi-empirical methods, as well as Model Builder. The calculated geometries have been compared to the corresponding X-ray structure of
ofloxacin perclorate. The FT-IR spectrum of ofloxacin was recorded. The assignments are based on the concept of group frequencies, band
intensities and taking into account the results of the semi-empirical vibrational analysis.
q 2004 Elsevier B.V. All rights reserved.
Keywords: Ofloxacin; FT-IR; Molecular mechanics; Semi-empirical; Calculations

1. Introduction Our aim is to compare the calculated and experimental

geometric data of ofloxacin and to determine which method
[(Oflo); (^ )-9-Fluoro-2,3-dihydro-3-methyl-10-(4- give the best agreement between the experimental and the
methyl-1-piperazinyl)-7-oxo-7H-pyrido [1,2,3-de]-1,4 ben- calculated data. We performed molecular modeling of
zoxazine-6-carboxylic acid)] is a synthetic broad spectrum ofloxacin molecule, using both molecular mechanics and
antimicrobial agent that displays activity against a large semi-empirical methods, supplied with HyperChem pack-
spectrum of Gram-positive and Gram-negative bacteria [1, age [9]. The geometric parameters obtained without any
2]. The crystal structure of ofloxacin [3,4] and its complexes constrains by the MM þ molecular mechanics, semi-
[5,6] have been very limited studied. In our previous paper empirical AM1, PM3, MINDO/3, MNDO, ZINDO/1,
[7], elemental analysis, Fourier transform infrared spec- TNDO methods, as well as the Model Builder tool, have
troscopy, X-ray powder diffraction patterns, 1H NMR been compared with the X-ray data reported in Refs. [3,4].
spectra were used to investigate the effect of alkaline In this paper, we have also carried out semi-empirical
earth metal cations [Mg(II), Ca(II) or Ba(II)] and transition calculations using AM1, PM3, MNDO, and MINDO3
metal ions [Co(II), Ni(II) or Zn(II)] with ofloxacin. methods to simulate infrared spectrum of ofloxacin. To the
Molecular modeling of the ofloxacin-lipid bilayer best of our knowledge, this is the first time that normal
interaction and the drug-divalent cation complex formation vibrational modes are assigned for ofloxacin. In order to
(Caþ2 and Mgþ2) was reported by Fresta et al. [8]. In that understand the environmental effects on the frequencies and
study, in order to understand of interaction mechanism, intensities of compounds infrared bands, the detailed assign-
ment of all vibrational bands of the ligand itself is necessary.
ofloxacin structure calculated by optimization procedure
employing molecular mechanics, semi-empirical and ab
initio methods. They used experimental data from the
2. Experimental
crystallographic result [Cambridge Structural Database:
CSD code: SOYBEN [4]] of ofloxacin.
2.1. Infrared spectra
* Corresponding author. Tel.: þ90-312-297-8606; fax: þ 90-312-299-
2083. Ofloxacin was kindly supplied by Prof. S. Patir, Depart-
E-mail address: [email protected] (S. Bayari). ment of Chemistry Education, Hacettepe University,
0166-1280/$ - see front matter q 2004 Elsevier B.V. All rights reserved.
doi:10.1016/S0166-1280(03)00878-9
94 S. Sagdinc, S. Bayari / Journal of Molecular Structure (Theochem) 668 (2004) 93–99

Ankara, Turkey. The FTIR spectrum were using Shimadzu energy state with no configuration interaction. Before the IR
FTIR 8201PC and Mattson 1000 spectrometer with the KBr simulations, in all semi-empirical calculations, full geome-
and nujol mull technique, in the region 4000 –400 cm21 try optimization was performed with Polak –Ribiere algor-
which was calibrated by polystyrene. There is not any ithm [13] until a RMS gradient less than
decomposition of the sample due to effect of potassium 0.001 kcal (Å mol)21. The assignment of the calculated
bromide. wave numbers is aided by the animation option of the same
program, which gives a visual presentation of the shape of
2.2. Method of calculations the vibrational modes.

A Pentium II computer with a 350 MHz processor and

64MB RAM was utilized to run all calculations. Semi- 3. Results and discussion
empirical PM3, AM1, ZINDO/1, MNDO, MNDO/3 and
TNDO calculations [9] in the gas phase were performed by
using HyperChem Version 7.0 demo Program [10]. 3.1. Geometrical parameters
Preoptimization was performed by applying the molecu-
lar-mechanics [11] method using MM þ force field [12]. Fig. 1(a) shows the molecular structure of ofloxacin
The lowest energy conformation obtained by the perchlorate. The benzoxazine ring of molecule is almost
molecular mechanics (MM þ ) method was further opti- planar, though the C13 atom slightly deviates from this
mized at semi-empirical methods and its fundamental mean plane. The methyl group in oxazine ring is axially
vibrations were calculations. All semi-empirical calcu- oriented from the ring. The piperazine ring exists in the
lations carried out at the RHF level for the singlet lowest chair form, and the methyl group is equatorially oriented.

Fig. 1. (a) Molecular structure of ofloxacin perchlorate (CSD code: SOYBEN). (b) PM3 calculated structure of ofloxacin.
 S. Sagdinc, S. Bayari / Journal of Molecular Structure (Theochem) 668 (2004) 93–99 95

The initial geometry for input to the semi-empirical the optimized structures, the O(4) –C(13) bond length is
calculation was obtained by means of the MM þ molecular found to range from 1.333 to 1.388 Å as compared to the
mechanic program. According to the geometry optimiz- observed value of 1.556 Å in the structure of SOYBEN. The
ation, proposed molecular structure of ofloxacin using PM3 ionized bond lengths of C –H of piperazine and benzoxazine
method is shown in Fig. 1(b). rings are calculated to range from 1.09 to 1.124 and from
When optimized using the MM þ force field, the 1.09 to 1.116 as compared to the observed values of 1.422
ofloxacin structure is found to have an energy of and 1.440, respectively. If the aforementioned bond lengths
35.517 kcal mol 21 with a RMS gradient of 0.098 are omitted, ZINDO/1 provides the best results (correlation
kcal21mol21Ang. The energy values from semi-empirical coefficient of CC ¼ 0.979 in terms of bond lengths,
calculations using the PM3, ZINDO/1, AM1, MNDO, then their quality decreases in the order PM3
MINDO3, TNDO routine are 2 4874.516 with a gradient (CC ¼ 0.972), TNDO (CC ¼ 0.97), AM1 CC ¼ 0.965,
0.016, 2 14332.79 with a gradient of 0.094, 2 4845.675 MNDO (CC ¼ 0.965), Model Builder (CC ¼ 0.961),
with a gradient 0.098, 2 4859.059 with a gradient of 0.009, MM þ (CC ¼ 0.953) and MINDO/3 (CC ¼ 0.953),
2 4877.545 with a gradient of 0.094, 2 14861.706 with a respectively. According to PM3 and ZINDO/1 geometries,
gradient of 0.094, respectively. bond angles give satisfactory result (correlation coefficient
In Fig. 2, we plotted the all calculated bond lengths and of 0.916 and 0.914, respectively). Since correlation
angles versus the experimental ones (ofloxacin crystal coefficients are below 0.9 (the best is CC ¼ 0.873 for
structure as in the Cambridge Structural Database file (CSD AM1), the others methods are not consistent with bond
code: SOYBEN) [4]. It is clear that the value of correlation angles of SOYBEN. Regarding the torsion angles, it is
coefficients are affected by the points corresponding to difficult to find an appropriate numerical criterion (such as
bond lengths of O(4) – C(13) and C –H of ofloxacin: For correlation coefficient employed above) to estimate

Fig. 2. Graphic correlation between the bond lengths and angles in ofloxacin, obtained by computer modeling and their experimental counterparts. CC,
correlation coefficient.
96 S. Sagdinc, S. Bayari / Journal of Molecular Structure (Theochem) 668 (2004) 93–99

Fig. 2 (continued )

the predictions directly (e.g. torsion angle C4 – C3 – C1 –O1 experimental spectra could not be identified in the simulated
for PM3 is 2 120.2218, for SOYBEN is 177.988). However, counterparts, and, therefore, have been omitted.
as can be seen from Fig. 2, the points are most grouped The infrared spectra can be divided into four spectral
along the diagonal for the MM þ and AM1 geometry. regions where different kinds of normal modes exhibit their
activity. In the spectral range over 2800 cm21, O –H and C –
3.2. Infrared spectra H stretches occur. The C– C and COOH group stretching
vibrations occur in the range of 1800– 1500 cm21. In the
To our best knowledge, no vibrational data have been 1500– 1350 cm21 range, – CH3, –CH2 in plane deformation
reported for ofloxacin. In previous studies [7], we have and mixed modes of C – C and O – H stretches are observed.
described the synthesis and spectral characterization of Below 1350 cm21 down to 400 cm21 several characteristic
divalent cation complexes of ofloxacin. We report in present in plane deformations d(C– H), out-of-plane g(C– H), in-
paper, the detailed vibrational analysis of ofloxacin. plane and out-of-plane (CCC) and (COOH) deformations
The observed and calculated frequencies in the infrared take place.
spectra of ofloxacin, their approximate intensities and The most prominent characteristic group vibrations of
probable assignments are given in Table 1. The fundamental ofloxacin are readily identified in solid and in nujol mull
vibrational modes were calculated on the basis of semi- spectra. Carboxylic group is best characterized by the OH
empirical calculations (PM3, AM1, MNDO and MINDO/3). stretch, the n(CyO) stretch, n(C – O) stretch and OH
Because of both molecular asymmetry and large size of deformation. The band in the region 3400– 3430 cm21 is
the system, many vibrations are difficult to describe, in assigned to O – H stretching vibration. The observed
particular those involving the coupled movement of several frequency for O – H stretch vibration of ofloxacin is
parts of groups. Some vibrations identified in the solid phase 3428 cm21. The in-plane bending band is found from
 S. Sagdinc, S. Bayari / Journal of Molecular Structure (Theochem) 668 (2004) 93–99 97

Table 1
Observed and calculated frequencies (cm21), calculated IR intensities (km/mol), and probable assignment of normal modes for ofloxacin

Assignment Ofloxacin PM3 I AM1 I MNDO I MINDO/3 I

n(OH) 3428w 3855 19 3419 75 3971 40 3939 2

n(CH) 3071vw 3205 25 3156 44 3394 11 3528 3
n(CH) 3043m 3183 4 3092 33 3370 4 3381 71
na(CH3) 2983w 3178 3068 4 3350 1 3464 40
n(CH3) 2968w 3133 3065 3 3276 3 3487 70
na(CH2) 2936m 3080 16 3050 4 3266 5 3323 149
na(CH3) 2921w 3078 3024 3238 8 3461 35
ns(CH3) 2895w 3060 3211 25 3458 45
ns(CH3) 2867vw 2945 2994 2 3383 86
n(CH2)ring 2955 2980 3204 16 3308 270
ns(CH2) 2834w 2932 3187 4 3275 111
n(CH) of N –CH3 2786m 2850 2974 4 3200 2 3234 53
n(CyO)c 1714vs 1971 187 2049 187 2107 174 1927 414
n(CyO)r 1622vs 1937 192 2032 142 2092 150 1903 245
nring 1788 221 1787 34 1796 27 1690 7
nring 1758 35 1780 347 1776 126
n(CC) þ n(CF) 1550m 1685 78 1684 156
n(CC) 1618 32 1647 25 1719 213 1649 359
nring 1523vs 1571 108 1604 108 1715 100 1591 96
ds(CH2) þ n(CC) 1468vs 1544 91 1501 94
d(CH3) þ nring 1460vs 1516 16 1533 13 1458 61
d(N –CH3) 1407m 1514 11 1531 85 1423 45
n(C–O) þ d(OH) 1397m 1504 93 1465 13 1409 67
d(C–CH3) þ n(CC) 1371m 1396 2 1407 193
n(CC) þ t (CH2) 1350m 1361 4 1512 45 1396 55
n(CN) 1463 10 1508 31 1378 20
Ring 1345 62 1483 5 1368 4
n(C–OH) 1325vw 1344 61 1442 89 1454 41
CH3 1431 16 1441 2
w(CH2)r 1336 1411 11 1436 25 1348 18
w(CH2) þ d(CH) 1306s 1324 23 1404 1418 20
n(C–F) þ n(COOH) 1289s 1316 35 1413 57
n(CC) 1254w 1315 2
nring 1285 10 1383
Ring þ n(C–O) 1241m 1260 5 1361 42 1410 17
CH2 twist 1225vw 1277 3 1347 1343 63
d(OH) þ n(C–O) 1199m 1242 38 1291
d(CH) 1163vw 1231 10 1341 4 1367 13 1297 42
d(CH) 1146vs 1197 1338 4 1366 12 1288 68
d(CH) þ ring 1132m 1136 6 1284 4 1365 12 1277 28
n(C–N) þ CH3 þ CH2 1117m 1120 5 1189 5 1199 11 1254 22
d(CH) 1094mw 1103 2 1180 2 1193 15 1248 8
Skeletal 1072w 1091 3 1140 16 1178 24 1235
d(CH) þ ring 1056s 1076 1119 3 1150 7 1180 4
dring 1011m 1064 1103 4 1075 3 1139 26
g(CH) 980m 999 3 954 3 994 3 1108 2
g(CH) þ r(CH2) 956m 964 5 953 2 989 2 1106 12
ring 891w 929 2 948 6 915 2 1024 20
g(CyO)c 877m 906 3 838 40 826 4 896 8
Skeletal þ CH2 rock 850mw 864 1 824 1 808 4 849 10
d(CyO)r þ n(C –O) 827mw 824 23 776 2 781 3 733 38
g(CH) 804vs 813 25 728 6 762 4 692 10
d(COOH) 782m 776 2 726 3 692 10 633 24
gring 766vw 687 716 610 1
g(CH) 745mw 735 957 594 14
CH2 rock þ g(CH) 710m 709 9 677 6 676 3
g(O –CyO) þ g(OH) 669m 640 5 665 11 647 29 572 32
dring 631vw 560 17 534 2
dring 597vw 603 8 641 3 523 3
d(CyO)r þ d(C –O)c 568mw 560 17 616 13 550 4
d(CF) þ dring 548vw 532 1 582 2 530 6
(continued on next page)
98 S. Sagdinc, S. Bayari / Journal of Molecular Structure (Theochem) 668 (2004) 93–99

Table 1 (continued)
Assignment Ofloxacin PM3 I AM1 I MNDO I MINDO/3 I

g(OH) 492mw 501 13 532 24 472 41 518 44

g(CCC) 474vw 482 28 465 5
g(CCC) 452w 453 7 491 9 458 2 476 4
g(CCC) 434vw 426 3 439 415 4 439 5
g(CyO)r 415ms 411 4 415 440 5 433 5
(CF) þ (CyO)r þ (CN) 398 4 415 4 355 5
CN 384 4
(CyO)r þ (CyO)c þ ring 356 354 362 1 332 3
CH3 þ (C –O)r 328 351
(CyO)r þ (CyO)c þ CH 310 322 305
OH þ (CF) þ (CyO)r 289 320 294
(CyO)c þ (C –O) þ CF 283 321 2 295 4 293
(CF) þ (CyO)r 298 2 292 2 200
(C– O)r 232 224 217 2

Vibrational modes: n, stretching; d, in-plane deformation; g, out-of-plane deformation. Superscript: s, symmetric; a, antisymmetric; c, carboxlate; r, ring
carbonyl; t, twist; w, wagging; s, strong; m, medium; w, weak; vw, very weak.

1440 to 1395 cm21. In the IR spectrum of ofloxacin, this observed bands in the IR spectra of molecules are assigned
band is found at 1397 cm21. The corresponding calculated and given in Table 1. Table 1 also gives calculated
band is not pure and contains n(C – O) modes. The band frequencies of ofloxacin below 400 cm21.
observed at 1241 cm21 is assigned to the C –O stretching. For the comparative purpose, the simulated PM3 and
As seen from Table 1, the calculations show that the C –O experimental IR spectra of ofloxacin are given in Fig. 3(a)
vibration is not pure and contain ring planar mode. This and (b), respectively, as representative illustration.
band also appears in the same region as C – H bending Scaling the simulated spectra should not be neglected. In
vibrations of methyl group [14]. According to the semi- the present case, the possibility of scaling (i.e. for the whole
empirical calculations the band at 1371 cm21 is assigned to spectral range considered) can be estimated by plotting the
the in-plane bending mode of methyl group and C –C calculated versus experimental wave numbers and analyz-
stretching mode of ring. The C –O stretch of carboxylic ing slopes of the trend lines (Figures are not shown). As it
acids appears between 1320 and 1210 cm21. could be expected, the average (for the whole spectral range
In the IR spectrum of ofloxacin, the very strong band considered) scaling factors (sf) obtained are not equal for
observed at 1714 cm21 is assigned to pure CyO stretching four methods: the highest one, 0.9958, has been found for
mode of carboxylic group. In previously study [7], the bands PM3, then 0.997 for MINDO/3, 0.9933 for MNDO and
at 1397, 1199 and 669 cm21 were absent in the IR spectra of 0.988 AM1.
complexes. These bands attributed to the carboxylic group. When the computed vibrational frequencies from semi-
The band observed at 1622 cm21 is assigned to pure CyO
empirical calculations were compared with the experimen-
stretching mode of ring carbonyl group.
tally observed values, it was found that there was a much
The bands in the 2800 – 3000 cm21 region are due to CH
stretch modes of the ethyl and methyl group. If to
summarize to frequency ranges for n(C– H) vibrations for
the ofloxacin under study (calculated 3068 – 2980 for AM1,
3178 – 2932 cm21 for PM3, 3350 – 3187 cm21 for MNDO,
3464 – 3275 cm21 for MINDO/3 versus experimental
2983 – 2834 cm21), one can say that PM3 method gives
best results for this vibration. In fact, the assignment of the
vibrations of –CH2 is very difficult because of the presence
of the – CH3 group. For a methyl group, the – CH3
deformation is found around 1460 cm21. The – CH2 group
also gives rise to a band near 1465 cm21 due to the
scissoring vibrations. The bands observed at around
1468 cm21 is assigned as –CH2 scissoring and the bands
observed at around 1460 cm21 is assigned to the CH3
scissoring deformation on the basis of calculation. These
bands are not pure: they interact with the ring modes. The
strong band observed at 1289 cm21 is assigned to the C – F Fig. 3. Comparison of the IR spectra of ofloxacin. (a) Calculated IR
stretching mode which is not pure (Table 1). The other spectrum with PM3 method. (b) The experimental IR spectrum.
 S. Sagdinc, S. Bayari / Journal of Molecular Structure (Theochem) 668 (2004) 93–99 99

better agreement in the case of PM3 (CC ¼ 0.99792) than in References

the case of the others. Then follow MINDO/3
(CC ¼ 0.99663), MNDO (CC ¼ 0.9966), and AM1 [1] V. Aleixandre, G. Herrera, A. Urios, M. Blanco, Antimicrob. Agents
(CC ¼ 0.99397). Chemother. 35 (1991) 20.
[2] D.T.W. Chu, P.B. Fernandes, in: B. Testa (Ed.), Advances in Drug
Research, vol. 21, Academic Press, London, 1991, pp. 39–144.
4. Conclusion [3] A. Yoshida, R. Moroi, Anal. Sci. 7 (1991) 351 CSD code: SOYBEN.
[4] CONQUEST, version 1.3; CSD (Cambridge Structural Database)
version 5.22, October 2001 (code: SOYBEN).
The optimized structure of ofloxacin is very similar to that [5] B. Macias, M.V. Villa, M. Sastre, A. Castineras, J. Borras, J. Pharm.
in the crystal. ZINDO/1 gives the best results for the bond Sci. 91 (2002) 2416.
lengths while PM3 and ZINDO/1 geometries give satisfac- [6] B. Macias, M.V. Villa, I. Rubio, A. Castineras, J. Borras, J. Inorg.
tory result for bond angles. The gas phase frequencies of Biochem. 84 (2001) 163.
ofloxacin are not available, and hence the assignment is [7] S. Sagdinc, Ph. D Thesis, 2003. S.SagdincS.BayarıJ. Mol. Struct.2003
in press.
being made using the vibrational spectra of solid ofloxacin.
[8] M. Fresta, S. Guccione, A.R. Beccari, P.M. Furneri, G. Puglisi,
We have, however attempted to assign the calculated Bioorg. Med. Chem. 10 (2002) 3871.
frequencies to the corresponding observed values based on [9] F. Jensen, Introduction to Computational Chemistry, Wiley, England,
the concept of group frequencies and intensity profiles. 1999.
[10] HyperChem 7.0 Demo Release for windows, HyperCube Inc., USA,
2002.
[11] U. Burkert, N.L. Allinger, Molecular mechanics, ACS Monograph
Acknowledgements
(1982) 177.
[12] N.L. Allinger, J. Am. Chem. Soc. 99 (1977) 8127.
The authors gratefully acknowledge Professor Süleyman [13] P.C. Yates, J. Mol. Struct. (Theochem) 231 (1991) 201.
Patır for providing the ofloxacin. This work was supported [14] P.G. Roeges, A. Guide, A Guide to the Complete Interpretation of
by Hacettepe University Research Fund. No: 0201704001. Infrared Spectra of Organic Structures, Wiley, Canada, 1994.