Molecular structure, vibrational spectroscopic studies and natural bond orbital analysis of 7-amino-4-trifluoromethyl coumarin

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1 PRAMANA c Indian Academy of Sciences Vol. 74, No. 5 journal of May 2010 physics pp Molecular structure, vibrational spectroscopic studies and natural bond orbital analysis of 7-amino-4-trifluoromethyl coumarin M K SUBRAMANIAN, P M ANBARASAN and S MANIMEGALAI Department of Physics, Periyar University, Salem , India Corresponding author. anbarasanpm@gmail.com MS received 2 January 2009; revised 22 September 2009; accepted 1 December 2009 Abstract. Quantum mechanical calculations of energies, geometries and vibrational wave numbers of 7-amino-4-trifluoromethyl coumarin (7A4TFMC) were carried out using Hartree Fock (HF) and density functional theory (DFT) using hybrid functional BLYP and B3LYP with 6-31G(d,p) as basis set. The optimized geometrical parameters obtained by HF and DFT calculations are in good agreement with the experimental X-ray data. The best method to reproduce the experimental wave numbers is B3LYP method with the 6-31G(d,p) basis set. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the infrared spectra of 7A4TFMC was also reported. The entropy of the title compound was also performed at HF using the hybrid functional BLYP and B3LYP with 6-31 G(d,p) as basis set levels of theory. Natural bond orbital (NBO) analysis of the title molecule is also carried out. The theoretical spectrogram for FTIR spectra of the title molecule has been constructed. Keywords. Vibrational spectra; ab-initio Hartree Fock; density functional theory; natural bond orbital; 7-amino-4-trifluoromethyl coumarin. PACS Nos Tp; Ae; Ar; Ew 1. Introduction Coumarins are chemicals, found in a large number of natural products. They occur widely as secondary plant metabolites and are known to exhibit numerous interesting biological properties. More than 1800 different natural coumarins have been discovered and described to date. Most of these coumarins are mono- or deoxygenated on the aromatic ring [1]. Recently, more attention has been drawn towards the less common tri- and tetraoxygenated coumarins, which are shown to exhibit very interesting pharmacological properties such as antibacterial activity [2], antiplatelet aggregation [3] and antileukemia activity [4]. Many natural 5,6,7-trioxygenated coumarins have the capacity to induce cell differentiation in human leukemia U-937 cells, which make them potential lead compounds in the search for differentiation 845

2 M K Subramanian, P M Anbarasan and S Manimegalai therapeutics [4]. 7-Amino-4-trifluoromethyl coumarin is used for the preparation of new fluorogenic substrate for cystine, aminopeptidase, chymotrypsin, trypsin and elastase [5]. It is also used in the synthesis of substrates for the fluorometric assay of proteolytic enzymes in biological fluids and as a reference compound in enzyme assay [6]. Synthesis of new fluorogenic substrates derived from 7-amino- 4-trifluoromethyl coumarin are helpful to detect streptococci and euterococci [7]. Some coumarin derivatives are found to have anticancer [8,9], diuretic, analgesic, myorelaxant [10], antifungal [11] and anthelmintic [12] properties. Literature survey reveals that, to the best of our knowledge, the quantum chemical calculations for 7A4TFMC have not been reported so far. Therefore, the present investigation was undertaken to study the vibrational spectra of this molecule completely and to identify various normal modes with greater wave number accuracy. Ab-initio HF and density functional theory (DFT/BLYP and DFT/B3LYP) calculations have been performed to support our wave-number assignment. 2. Computational details The entire calculations were performed at Hartree Fock (HF) and density functional (DFT) levels on a Pentium IV/3.02 GHz personal computer using Gaussian 03W program package [13], invoking gradient geometry optimization [14]. Initial geometry generated from standard geometrical parameters was minimized without any constraint in the potential energy surface at Hartree Fock level, adopting the standard 6-31G(d,p) basis set. This geometry was then re-optimized again at DFT levels, using the same basis set, for better description of polar bonds of NH 2, CF 3 and C=O groups. The optimized structural parameters were used in the vibrational frequency calculations at DFT levels to characterize all stationary points as minima. We have used ab-initio HF and DFT/BLYP and DFT/B3LYP approach for the computation of molecular structure, vibrational frequencies and energies of optimized structures, in the present work. Using GAUSSVIEW program [15] with symmetry considerations along with available related molecules, vibrational frequency assignments were made with a high degree of accuracy. 3. Results and discussion 3.1 Geometric structure 7A4TFMC (C 10 H 6 F 3 NH 2 ) consists of two moieties, the benzene and the pyrone rings, fused together. The crystal structure of 7A4TFMC was reported by Selladurai and Subramanian [16]. The structure is triclinic and the space group is PĪ, with the cell dimension (296 K), a = 5.190(3), b = (4), c = (4) Å, Z = 2. The optimized geometrical parameters of 7A4TFMC calculated by abinitio HF and DFT/B3LYP and DFT/BLYP levels with the 6-31G(d,p) basis sets are listed in table 1 (please see which are in accordance with numbering scheme given in figure Pramana J. Phys., Vol. 74, No. 5, May 2010

3 7-Amino-4-trifluoromethyl coumarin Figure 1. Numbering system adopted in this study for 7-amino-4-trifluoromethyl coumarin (7A4TFMC). From the theoretical values of both the HF and DFT/6-31G(d,p) for 7A4TFMC we find that most of the optimized bond lengths and bond angles are slightly smaller, as well as longer than the experimental (X-ray data) values. This is due to the fact that the theoretical calculations are done on isolated molecule in gaseous phase and experimental results are done on molecule in solid phase. The correlation between the experimental and calculated geometric parameters obtained by several methods are shown in figures 2a 2f (please see In our calculations, HF method correlates well for the bond lengths when compared with other methods (table 1). The largest difference between the experimental and calculated HF bond length is about Å for the title compound. The B3LYP leads to geometric parameters of bond angles which are much closer to experimental data. This pattern was not found for bond length as can be seen from table 1. In the case of B3LYP, the biggest difference between the experimental and calculated values of bond lengths was Å for the title compound. The bond angles provided by B3LYP method are the closest to the experimental values (table 1). When B3LYP method is used, the largest difference is found to be 1.7 for the title compound. As a result, the optimized bond lengths obtained by HF method and bond angles by DFT (B3LYP) method are in good agreement with the experimental values. 3.2 Natural charges The natural atomic charges of 7-amino-4-fluoromethyl coumarin (title molecule) and 7-methyl-4-bromomethyl coumarin calculated by density functional methods using 6-31G(d,p) basis set are compared in table 2 (please see The results show that replacement of NH 2 and CF 3 groups by CH 3 and CH 2 Br groups in 7-amino-4- Pramana J. Phys., Vol. 74, No. 5, May

4 M K Subramanian, P M Anbarasan and S Manimegalai trifluoromethyl coumarin molecule leads to the redistribution of electron density. The σ-electron withdrawing character of Br atom is demonstrated by the increase of electron density on C16, C3 and C12 atoms and decrease of electron density at C9 atom. The C4 atom in 7-amino-4-bromomethyl coumarin is more positive compared to 7A4TFMC. O14 atom in 7A4BMC is more negative than in 7A4TFMC, indicating C4 O14 is more polar in 7A4BMC than in 7A4TFMC. Another interesting aspect is that C11=O14 in 7A4BMC is also more polar than in 7A4TFMC. 3.3 Vibrational assignments It has been reported that the substitution of the CF 3 group in coumarin derivatives reduces the overall symmetry of the molecule. In order to interpret the vibrational spectra of 7A4TFMC it is assumed that all the atoms of the molecule are in the plane of the benzene and pyrone rings, except the two F atoms of CF 3 group, which are positioned symmetrically above and below the pyrone ring plane. It has 22 atoms, with 60 normal modes of fundamental vibrations which span the irreducible representations, 41A +19A. All 60 fundamental vibrations are active in both IR and Raman measurements. The harmonic-vibrational frequencies calculated for 7A4TFMC at HF, BLYP and B3LYP levels using 6-31G(d,p) as basis set along with diffuse and polarization functions are given in table 3 (please see supplement.pdf). The FTIR and FT Raman spectra of 7A4TFMC recorded by Arjunan et al [17] for various modes of vibrations are also presented in table 3. Comparison of the frequencies calculated by ab-initio HF, B3LYP and BLYP levels with experimental values reveals the overestimation of the calculated vibrational modes due to neglect of anharmonicity in real system. Inclusion of electron correlation in density functional theory, to a certain extend, makes the frequency values smaller than the experimental values. Anyway, notwithstanding the level of calculations, it is customary to scale down the calculated harmonic frequencies in order to improve the agreement with the experiment. In our study we have followed three different scaling factors HF/6-31G(d,p): , BLYP/6-31G(d,p): , B3LYP/6-31G(d,p): [18]. The experimental FT IR and FT Raman spectra of 7-amino-4-trifluoromethyl coumarin are shown in figures 3a and 3b (please see The theoretically predicted IR spectra of 7-amino-4-trifluoromethyl coumarin (7A4TFMC) at B3LYP, BLYP and HF level of calculations are shown in figure 4 (please see The scaled vibration, mode nos: 58, 57, 56 and 55, correspond to stretching modes of C2 H, C1 H, C5 H and C12 H units. The vibrations assigned to aromatic as well as pyrone ring C H stretch computed in the range cm 1 by B3LYP method shows good agreement with recorded FT IR spectrum at cm 1. The counterpart of the FT Raman spectrum which also shows the same kind of vibration at cm 1, deviate a little bit with HF method at cm 1. All the aromatic C H stretching bands are found to be weak and this is due to a decrease of the dipole moment caused by the reduction of negative charge on the carbon atom. This reduction occurs because of the electron withdrawal on 848 Pramana J. Phys., Vol. 74, No. 5, May 2010

5 7-Amino-4-trifluoromethyl coumarin the carbon atom by the substituent due to the decrease of inductive effect, which in turn is caused by the increase in chain length of the substitutent [19]. The FT IR bands at 1637, 1597, 1455, 1415, 1365 and 1351 cm 1 in 7A4TFMC are due to C C stretching in benzene as well as in pyrone ring. The same vibration occurs in FT Raman spectrum at 1663, 1630, 1617, 1454, 1413 and 1361 cm 1. In our present study the medium and weak bands observed in the FT IR and FT Raman spectra at 1272 and 1274 cm 1 are assigned to C CF 3 stretching vibration for 7A4TFMC. The theoretically scaled value at 1258/1253 cm 1 (mode no. 44) by B3LYP/BLYP method shows excellent agreement with the recorded experimental data. The CF 3 rocking mode is observed at 255 cm 1 in FT Raman spectra. The calculated results by the B3LYP method at 241 cm 1 is in excellent agreement with experimental observations. The mode with the lowest magnitude is the torsion mode of CH 3 group and it lies beyond the investigated region. The NH 2 stretching vibrations show the characteristic frequency shift caused by the halogen substituent. In our title molecule 7A4TFMC, the very strong bands observed at 3453 and 3366 cm 1 in FT IR and FT Raman spectra are assigned to NH 2 asymmetric and symmetric stretching vibrations. The FT Raman and FT IR bands observed at 710, 747 and 529, 746 cm 1 in 7A4TFMC have been assigned to C C C in-plane bending vibration. 4. Other molecular properties Entropy of the title compound is presented in table 4 (please see ias.ac.in/pramana/v74/p845/supplement.pdf). Scale factors have been recommended [20] for an accurate prediction in determining the zero-point vibration energies (ZPVE) and the entropy, S vib (T ). The variations in the ZPVE s seem to be insignificant. The total energies and the change in the total entropy of 7A4TMC at room temperature in different methods are also presented. 5. Conclusion We have carried out ab-initio HF and density functional theory calculations on the structure and vibrational spectrum of 7A4TFMC. The equilibrium geometry of 7A4TFMC has been obtained as HF, BLYP and B3LYP levels of theory using the 6-31G(d,p) basis set. HF method has performed better than DFT method for both the bond lengths and bond angles. The vibrational frequencies and NBO analysis by B3LYP method agree satisfactorily with experimental results. On the basis of agreement between the calculated and experimental results, assignments of all the fundamental vibrational modes of 7A4TFMC were examined and proposed in this investigation. Therefore, assignments made at higher level of theory with lower basis set with only reasonable deviations from the experimental values, seems to be correct. This study demonstrates that a scaled DFT/B3LYP calculation is a powerful tool to understand the vibrational spectra of large-sized molecule. Pramana J. Phys., Vol. 74, No. 5, May

6 References M K Subramanian, P M Anbarasan and S Manimegalai [1] R D H Murray, Prog. Chem. Org. Nat. Prod. 83, 673 (2002) [2] O Kayser and H Kolodziej, Z. Naturforsch 54c, 169 (1999) [3] T-S Wu, Z-J Tsang, P-L Wu, F-W Lin, C-Y Li, C-M Teng and K-H Lee, Bioorg. Med. Chem. 9, 77 (2001) [4] M Eugenia Riveiro, C Shayo, F Monczor, N Fernandez, A Baldi, N De Kimpe, J Rossi, S Debenedetti and C Davio, Cancer Lett. 210, 179 (2004) [5] Y Kanaoka, T Takahashi, T Nakayama, T Ueno and T Sekine, Chem. Pharm. Bull. (Tokyo) 30, 1485 (1982) [6] M Zimmermann, Anal. Biochem. 70, 258 (1976) [7] A Agban, M Ounanian, C Luu-Duc and D Monget, Ann. Pharm. Fr. 48, 326 (1990) [8] R V Nair, E P Fischer, S H Safe, C Courtez, R G Harvey and J DiGiovanni, Carcinogenesis 25, 65 (1991) [9] X Sang, X Shipping and L Lanmin, Chem. Abstr. 133, (2000) [10] L Bonsignore, G Loy, D Seci and A Calignano, Eur. J. Med. Chem. 28, 517 (1993) [11] S Shah and R U H Mehta, J. Indian Chem. Soc. 64, 708 (1987) [12] M F Clothier and L Byunghyun, Chem. Abstr. 117, 787 (1992) [13] M J Frisch et al, Gaussian 03, Revision B.03, Gaussian Inc., Wallingford, CT (2004) [14] H B Schlegel, J. Comput. Chem. 3, 214 (1982) [15] A Frisch, A B Nielsen and A J Holder, GAUSSIANVIEW Users Manual, Gaussian Inc., Pittsburgh, PA (2000) [16] S Selladurai and K Subramanian, Acta Crystallogr. C48, 281 (1992) [17] V Arjunan, N Puviarasan, S Mohan and P Murugasen, Spectrochim. Acta A67, 1290 (2007) [18] A P Scott and L Radom, J. Phys. Chem. 100, (1996) [19] N Sundaraganesan, H Saleem and S Mohan, Spectrochim. Acta A59, 2511 (2003) [20] M Alcolea Palafox, Int. J. Quant. Chem. 77, 661 (2000) 850 Pramana J. Phys., Vol. 74, No. 5, May 2010