Microsoft Word - Khadka and Joshi _40-52_.doc R C O S T N Publisher: Research Council of Science and Technology, Biratnagar, Nepal p.40 BIBECHANA A Multidisciplinary Journal of Science, Technology and Mathematics ISSN 2091-0762 (print), 2382-5340 (online) Journal homepage: http://nepjol.info/index.php/BIBECHANA Molecular electrostatic potential, HOMO-LUMO and vibrational study of aristolochic acid II using density functional theory Jang Bahadur Khadka 1 , Bhawani Datt Joshi 2* 1Department of Chemistry, Siddhanath Sc. Campus, Mahendranagar, Tribhuvan University, Nepal 2Department of Physics, Siddhanath Sc. Campus, Mahendranagar, Tribhuvan University, Nepal * E-mail: bdjoshi_007@yahoo.com Accepted for publication: December 12, 2014 Abstract Because of their wide applications in human or animal medicine, the natural products have been the subject of investigation. Aristolochic acids (AAs) (Aristolochiaceae), however toxic, are reported for many medicinal uses. In this work, computational study on the molecular properties of AA II is presented using density functional theory (DFT), B3LYP functional along with Hartree-Fock (HF) theory at 6-311++G(d,p) level. A complete vibrational assignment has been done for the observed FT-IR and Raman wavenumbers with the results of quantum chemical calculations. The structure– activity relationship has been interpreted by mapping electrostatic potential surface (MEP). Graphical representation of frontier molecular orbitals with their energy gap has been analyzed theoretically for both the gaseous and solvent environment employing TD-DFT using IEF-PCM model. DOI: http://dx.doi.org/10.3126/bibechana.v12i0.11702 © 2014 RCOST: All rights reserved. Keywords: MEP; HOMO-LUMO; vibrational spectroscopy; DFT. 1. Introduction Medicinal plants play a fundamental role in the world health, since they are sources of several pharmacologically active compounds such as flavonoids and tannins. Many of these molecular structures are similar to those of our molecules and this is the basis for their physiological action [1]. The use of medicinal plants has been an elected practice throughout human history. It is important to point out that the plants, in addition to their therapeutic use in folk medicine, have contributed to the obtention of many drugs which are still in use, such as morphine, the main anesthetic alkaloid in opium, vincristine etc. Aristolochic acids (AAs), found in Aristolochia spp, are structurally related nitrophenanthrene carboxylic acids. Drugs derived from Aristolochia plants have been used as medicine in obstetrics and in the treatment of snake bites [2]. The plant extracts have also been used for the therapy of arthritis, gout, rheumatism, and festering wounds [3,4]. However, aristolochic acid is an established human carcinogen [5,6], increase risk of developing urothelial carcinoma [7-11] in the patients with endemic nephropathy and chronic renal failure with some herbal medicines [12]. Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 41 In this communication, we have presented molecular electrostatic potential surface (MEP), highest occupied molecular orbitals (HOMO)- lowest unoccupied molecular orbital (LUMO), and the vibrational spectra of the molecule aristolochic acid II (AA II) using ab initio Hartree- Fock (HF) and density functional theory (DFT). With the help of specific scaling procedures, the observed vibrational wavenumbers were analyzed and accurately assigned to different normal modes of the molecule; and using PED’s the contributions of the different modes to each wavenumber were determined. 2. Methodology 2.1 Experimental Infrared spectra were recorded on a Bruker TENSOR 27 FT-IR spectrometer with a spectral resolution of 4 cm-1 in the region 400-4000 cm-1. KBr pellets of solid samples were prepared from mixtures of KBr and the sample in 200:1 ratio using a hydraulic press. Multi-tasking OPUS software was used for base line corrections. The FT-Raman spectra were recorded on a Perkin-Elmer 2000R spectrometer as powder sealed in a capillary tube in the region 100-3500 cm-1. The 1064 nm line of an Elforlight Model L04-2000S Nd: YAG laser was used as the exciting source with an output power of about 100 mW at the sample position. All spectra were accumulated for 100 scans with a resolution of 4 cm-1. 2.2 Computational Geometry optimization has been performed as the first task of the computational work. The geometric parameters available from the PubChem data base [13] have been used as the basis for the optimization. The molecular structure, vibrational frequencies and energies of the AA II were computed employing the DFT [14] method using Gaussian 09 program [15] package and Becke’s three parameter (local, non-local, Hartree–Fock) hybrid exchange functional with Lee–Yang–Parr correlation functional (B3LYP) [16–18]. The split valence basis set 6-311++G(d,p), augmented by ‘d’ polarization functions on heavy atoms and ‘p’ polarization functions on hydrogen atoms as well as diffuse functions for both hydrogen and heavy atoms were used [19,20]. The IR absorption intensities and absolute Raman intensities were calculated in the same level of theory as used for the optimized geometry. The normal mode analysis was performed and the PED was calculated, employing GAR2PED program [21], along the internal coordinates using localized symmetry. For this purpose, a complete set of 90 internal coordinates were defined using Pulay’s recommendations [22,23]. The vibrational assignments of the normal modes were done on the basis of the band profile, intensity and PED. Gauss-View program [24] was used for graphical presentation of the calculated Raman and IR spectra. To elucidate the differences of first excitation energies and oscillator strengths in gas and solution, the solvent effects were taken into account by means of integral equation formalism polarizable continuum model (IEF-PCM) [25-27]. 3. Results and discussion 3.1 Geometry optimization Geometry optimization has been performed as the first task in the ab initio calculations, using the molecular conformation obtained from PubChem data base [13]. The ground state optimized structure (in gas phase) of the molecule is presented in Fig. 1. The optimized parameters have been used for the other calculations. Some of the calculated bond parameters are listed below in the Table 1. Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 42 Table 1. Some calculated (DFT) bond parameters of AA II. Bond length (Å) Bond Angle (o) Dihedral Angle (o) C23-O4 = 1.2079 C13-C23-O3 = 112.74992 C17-C13-C23-O3 = 35.36312 O4-O6 = 2.87273 C12-C23-O4 = 124.70005 16-C13-C23-O4 = 30.81523 O4-O5 3.17938 C14-N7-O6 = 116.97323 C9-C14-N7-O6 = 34.44447 O6-H32 2.27952 C14-N7-O5 = 117.98883 C16-C14-N7-O5 = 38.83665 O1-H26 2.13096 O6-N7-O5 = 124.87079 C13-C23-O3-H32 = 176.71139 Fig. 1. Opitmized structure of AA II. The equilibrium geometry has been determined by the energy minimization. The energy calculated by DFT (-1121.42720029 Hartree) is lower than the one calculated by HF (-1114.91828124 Hartree) as it should be. Similarly, the dipole moment calculated by DFT (6.6567 Debye) is higher than that calculated by HF (6.4607 Debye). 3.2 Molecular electrostatic potential Molecular electrostatic potential surface is a good tool for assessing the reactive sites towards positively or negatively charged reactants to explain hydrogen bonding and structure-activity of the molecule; however, the molecular charge distribution remains unperturbed through the external test charge [28]. By quantum chemical calculations it is observed that there is a strong correlation between the dipole moment, electro-negativity, and partial charges with electrostatic potential [29]. It provides a visual method to understand the relative polarity of a molecule through mapping total density surface on electrostatic potential energy surface, which depict the size, shape, charge density, and site of chemical reactivity of the molecules. Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 43 . Fig. 2. (a & b) MEP (molecular electrostatic potential) (c) ESP (electrostatic potential), and (d) ED (Electron density) mapped on the isodensity surface from -5.5982 e-2 to +5.5982 e-2. The MEP plots of AA II, shown in the Fig. 2, was based on the calculations performed with B3LYP/6-311++G(d,p) level of theory visualized with Gauss view program 5.0 [30]. In this molecule, regions near the oxygen atoms of methyl group are most negative (red regions) due the concentrated electron density. The regions near the hydrogen atoms of the same group are the most positive regions (blue regions) which correspond to the repulsion of proton by low electron density. The ED (electron density) plots of the investigated molecule show uniform charge distribution. However, yellowish blob from the ESP (electrostatic potential), in the Fig 2(c), reflects that the negative ESP is localized more over the oxygen atoms and the positive ESP is localized on the rest of the molecule. This result is expected, because ESP correlates with electro negativity and partial charges. 3.3 Frontier molecular orbitals and electronic absorption The electronic transition corresponds from HOMO (characterizes of electron giving) to the LUMO (characterizes of electron accepting) orbital. Both the frontier molecular orbitals (FMOs), highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are the main orbitals taking part in chemical reaction. The electron delocalization between these orbitals is a principal factor in determining the easiness of a chemical reaction and the stereo-selective path, irrespective of intra and intermolecular processes. The energy gap between the HOMO and LUMO molecular orbitals characterizes the chemical reactivity and kinetic stability along with spectroscopic properties [31]. The electronic transitions of high oscillatory strength (f) along with their absorption wavelength (λmax) and excitation energies (eV), obtained from the time dependent DFT (TD-DFT) calculation employing 6-31G(d,p) level of theory [32,33], have been listed in the Table 2. Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 44 The negative values of all the FMO energies indicate the stability of the title molecule. The calculation in the gas phase shows that the bands at 389.22, 269.69, 208.29 and 206.13 nm originate due to H→L, H-1→L+1, H-4→L+2 and H-7→L+1 transitions, respectively. However, the electronic transitions between these FMOs occur with some different values of λ and the oscillatory strengths. This discripancy is due to the solvent effect on the molecular orbitals. The HOMO-LUMO plot is shown below in the Fig. 3. Fig. 3. HOMO-LUMO plot of AA II in the gas phase. 3.4 Vibrational wavenumbers The total number of atoms in AA II molecule is 32 and gives 90 (3N-6; N- the number of atoms) normal modes of vibrations. All the fundamental modes of vibrations are both FT-IR and Raman active. As DFT calculation yields Raman scattering amplitude but not the Raman intensities, so the Raman scattering amplitudes can be predicted for each wavenumber using a relation [34,35]; j jj j j S c h kT hc                               − −       −       = Ω∂ ∂ νπν νν πσ 2 4 044 8 exp1 45 2 where Sj and υj are the calculated scattering activities and the predicted wavenumbers, respectively, of the jth normal mode, υ0 is the Raman excitation wavenumber and h, c and k are the universal constants. Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 45 Table 2. Electronic transitions, absorption wavelength λmax (nm), excitation energy (eV), oscillator strengths (f), frontier orbital energies (eV) and dipole moment (Debye). Excited states Gas phase Solvent phase Transition types Transition states λmax E (eV) Oscilator strength (f) Transition states λmax E (eV) Oscilator strength (f) 1 H→L 389.22 3.1855 0.0538 H→L 428.20 2.8955 0.0559 π→π * 2 H-1→L 337.82 3.6701 0.0028 H-1→L 355.67 3.4859 0.0046 π→π * 3 H-2→L 331.52 3.7399 0.0104 H→L+1 340.88 3.6372 0.1354 π→π * 4 H→L+1 325.78 3.8058 0.0939 H-2→L 321.46 3.8569 0.1008 π→π * 5 H→L+2 304.96 4.0656 0.0894 H→L+2 318.42 3.8937 0.0732 π→π * 6 H-1→L+1 269.69 4.5973 0.1155 H-1→L+1 281.14 4.4101 0.0905 π→π * 7 H-3→L+1 261.71 4.7374 0.1583 H-1→L+1 275.03 4.5081 0.1723 π→π * 8 H-1→L+1 252.87 4.9031 0.1294 H-2→L+1 265.17 4.6756 0.0637 π→π * 9 H→L+3 245.47 5.0509 0.0615 H-1→L+2 259.49 4.7780 0.2527 π→π * 10 H-4→L+1 237.32 5.2244 0.1899 H-1→L+2 242.99 5.1024 0.3188 π→π * 11 H→L+5 222.51 5.5721 0.1024 H→L+4 229.71 5.3974 0.0620 π→π * 12 H-8→L 217.15 5.7097 0.0719 H-4→L+1 221.30 5.6025 0.2128 σ→π * 13 H-4→L+2 208.21 5.9548 0.2432 H-1→L+3 215.89 5.7429 0.2100 σ →π * 14 H-7→L+1 206.13 6.0149 0.2034 H-3→L+2 212.62 5.8313 0.057 σ →π * 15 H-8→L+1 200.22 6.1923 0.0838 H-2→L+3 201.04 6.1672 0.1219 σ→π * EHOMO (eV) ELUMO (eV) ∆E (eV) µ (D) Gas - 5.90364486 - 2.44626063 3.45738423 6.9762 Ethanol - 5.90359044 - 2.44103631 3.46255413 8.1606 The calculated Raman and IR intensities were used to convolute each predicted vibrational mode with a Lorentzian line shape (FWHM = 8 cm-1) to produce simulated spectra. Since, the DFT and HF vibrational wavenumbers are known to be higher than the experimental wavenumbers due to neglect of anharmonicity effects, they were scaled down by the wavenumber linear scaling procedure (WLS) [υobs = (1.0087–0.0000163 υcalc) υcalc cm-1] of Yoshida et al. [36]. Comparison of the wavenumbers, calculated with the HF and DFT method with experimental values, reveals that the DFT method shows very good agreement with experimental observation than the HF due to inclusion of electron correlation, approximate treatment of basis set deficiencies and for the anharmonicity. The detailed comparison of observed and scaled wavenumbers along with the potential energy distribution is presented in Table 3. The comparison of observed and calculated FT-IR and Raman spectra of AA II molecule is presented in Figs. 4 and 5, respectively. The description of vibrational assignments of the 4 rings and the functional groups has been given below: 3.4.1 O-H vibrations In this molecule, there is one hydroxyl group (O-H) attached at the ring R2 through carbonyl. The hydroxyl group vibrations are the most sensitive to the environment, so the hydrogen bonded species show pronounced variation in the observables of a spectral band, such as band intensity and shape, frequency position of band maxima. The free hydroxyl group absorbs strongly in the region 3600– 3550 cm-1, whereas the existence of hydrogen bond can Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 46 lower the O-H stretching wavenumber to the 3550–3200 cm-1 region with an increase in IR intensity and breadth [37]. In our study, the O-H stretching is calculated at 3566/3875 cm-1 in scaled DFT/HF and match with very weak band at 3477 cm-1 in the IR spectrum, which indicates the group involvement in intermolecular hydrogen bonding. The O-H deformation is calculated at 1164/1245 cm-1 in the DFT/HF and assigned to the observed peaks at 1149/1148 cm-1 in the IR/Raman spectra. 3.4.2 C=O vibrations Most of the characteristic features of the carboxylic group are observed usually 1750–1600 cm-1 region [38]. C=O bonds being highly polar show intense peak in the IR and weak peak the Raman spectra. The C=O stretching vibration is calculated at 1749 cm-1, which match with the observed strong peak at 1687 cm-1 in the IR and weak peak at 1740 cm-1 in the Raman spectra, respectively. The wagging, deformation and rocking of C=O are calculated at 800/889, 665/721 and 431/464 cm-1 in the DFT/HF showing good agreements with the observed wavenumbers at 791/797, 650/672 and 420/430 cm-1 in the IR/Raman spectra. Table 3. Observed and calculated FT-IR and Raman wavenumbers (cm-1) of AA II. Un- scaled DFT Scaled Observed PED % DFT HF IR Raman 3765 3566 3875 3477 - υ(OH)(100) 3250 3106 3269 3097 3096 R4[υ(CH)](98) 3229 3087 3233 3078 3083 R2[υ(CH)](99) 3204 3065 3223 - 3072 R3[υ(CH)](99) 3192 3054 3199 3020 3042 R4[υ(CH)](99) 3177 3040 3184 3018 3032 R4[υ(CH)](99) 3169 3032 3175 3016 3028 R4[υ(CH)](99) 3131 2998 3160 2999 2997 R1[υa(CH2)](99) 3012 2890 3061 2852 2880 R1[υs(CH2)](100) 1785 1749 1933 1687 1740 υ(C=O)(77)+R2[υ(C13C23)](6) 1660 1630 1804 1685 1624 R3[υ(CC)(40)+δa(10)+δin(CH)(5)]+R2[υ(CC)](9)+R1[υ(CC)](7) 1648 1618 1761 1626 1609 R4[υ(CC)(51)+δa(8)+δin(CH)(12)] 1630 1600 1755 1595 1593 R2[υ(CC)(26)+δa(6)]+R1[υ(CC)](21)+R4[υ(CC)](12)+R3[υ(CC)](7) 1620 1591 1740 1593 1591 R2[υ(CC)(46)+δ’a(9)+δin(CH)(6)]+R1[δ’ring](6)+R3[υ(CC)](5) 1589 1562 1734 1539 1543 υa(NO2)(78)+ρ(NO2)(6) 1569 1543 1678 1525 1541 R4[υ(CC)(30)+δin(CH)(10)]+R3[υ(CC)](22)+R2[υ(CC)](6) 1539 1514 1648 1523 1508 R1[δ(CH2)](77) 1529 1504 1630 1506 1507 R4[δin(CH)(23)+υ(CC)(5)]+R3[υ(CC)](23+R1[δ(CH2)](17) 1480 1458 1603 1452 1451 R4[δin(CH)(31)+υ(CC)(16)]+R3[υ(CC)(8)+δtrig](7)]+R2[υ(CC)](14) 1473 1450 1581 1450 1449 R2[υ(CC)(20)+δin(CH)(7)]+R4[δin(CH)](15)+υ(CC)(8)]+R3[υ(CC)](15)+ R1[υ(CO)](7) 1436 1415 1569 1417 1406 R1[ω(CH2)](42)+R3[υ(CC)](11)+δin(CH)(5)]+R2[δtrig](8) 1422 1401 1543 - 1391 R1[ω(CH2)](30)+R3[υ(CC)(16)+δin(CH)(11)]+R4[δin(CH)](10) 1400 1380 1516 1373 1372 R2[υ(CC)(33)+υ(C13C23)(12)]+R1[υ(CO)](14) 1377 1358 1502 1350 1350 R2[υ(CC)(21)+δin(C13C23)(6)]+R3[υ(CC)](25) 1371 1353 1473 1348 1348 υs(NO2)(57)+δ(NO2)(14)+R3[υ(CN)](12) 1360 1342 1416 1347 R4[υ(CC)](44)+R3[υ(CC)](11)+R3[δin(CH)](9) 1350 1332 1387 1331 1331 R2[υ(CC)](37)+R1[υ(CC)](10)+R3[υ(CC)](8)+δ(CHO)(5) 1321 1304 1376 - - R4[δin(CH)](17)+υ(CC)(5)]+R3[υ(CC)](11)+δtrig(6)]+δ(CHO)(14)+R2[υ(CC)](8) 1287 1271 1344 1273 1271 R4[δin(CH)(19)+υ(CC)(10)]+R2[υ(CC)(16)+δin(CH)(9)]+R3[υ(CC)(11)+δtrig(5)] 1269 1253 1328 1348 1246 R4[υ(CC)(14)+δtrig)(10)+δin(CH)(9)]+R3[υ(CC)](27)+R1[υ(CO)](8) 1231 1217 1322 - 1213 R1[γ(CH2)(9)+υ(CO)(9)]+R3[δin(CH)](17)+R2[δtrig(9)+δin(CH)(7)]+R4[υ(CC)](9)+δ(CHO)(5) 1220 1206 1302 1205 1194 R1[γ(CH2)](77) 1202 1189 1282 1171 1173 R2[δin(CH)(29)+υ(CC)(13)]+R3[δin(CH)(12)+υ(CC)(10)]+R4[δin(CH)](7) 1195 1182 1266 1169 1171 R4[δin(CH)(49)+υ(CC)(8)]+δ(CHO)(8)+R2[δin(CH)](6) 1177 1165 1244 1149 1148 δ(OH)(20)+υ(CO)(18)+R4[δin(CH)](14)+R2[υ(C13C23)](7) 1160 1148 1234 1147 1142 R4[δin(CH)(30)+υ(CC)(17)]+R3[δtrig](9)+R4[δtrig)](7) 1146 1134 1223 1126 1115 R1[ρ(CH2)](85) 1122 1111 1175 1080 1113 υ(CO)(20)+R2[δtrig](18)+R1[υ(CO)](17)+δ(CHO)(5) 1076 1067 1171 1066 1067 R1[υ(CO)](33)+R3[υ(CN)(7)+δtrig(5)]+R4[δtrig)](7) 1065 1056 1149 1065 1065 R4[υ(CC)(52)+δin(CH)(9)]+R1[υ(CO)](16) 1053 1044 1109 1043 1040 R1[υ(CO)](32)]+R4[υ(CC)](10)+R2[υ(CC)](9)+R3[υ(CN)](8) 1005 997 1107 999 1001 R4[oop(CH)(86)+puck(11)] 987 980 1104 982 980 R1[υ(CO)](25)+R2[δ’a(10)+υ(C13C23)(7)+δtrig(5)]+R3[δtrig(14)+υ(CN)(7)]+R4[δtrig)](11) 980 973 1084 962 9961 R4[oop(CH)](89)+R4[τ’a](5) 952 946 1065 943 947 R1[υ(CO)](68)+R1[δ’ring](8) 933 927 1043 920 928 R3[oop(CH)](63)+ puck(12)+oop(CN)(7)] 925 919 1011 903 915 R4[δtrig)](30)+R1[ν(CO)](14)+R3[υ(CN)](8)+δ(NO2)(7)+R2[δa](6) 905 899 997 901 897 R2[oop(CH)(73)+oop(C13C23)(6)+puck(7)+τa(6)] 881 876 970 877 872 R4[oop(CH)(81)+puck(5)] 870 865 934 856 862 R3[υ(CC)(23)+δ’a(6)]+R4[υ(CC)](10)+δtrig)(5)]+R1[υ(CO)(10)+υ(CC)(5)]+R2[δa](8) 846 842 915 841 839 δ(NO2)(30)+R3[υ(CC)(6)+δa(5)]+R2[υ(C13C23)](9)+R4[δtrig)](8) 804 800 889 791 797 ω(C=O)(30)+R2[oop(15)+δin)(6)](C13C23)(6)+puck(5)]+R1[δring](6 790 787 880 789 780 R3[puck](16)+R2[puck(14)+oop(C13C23)(11)]+R1[δring](12)+ω(C=O)(7) 787 784 860 777 778 R3[oop(CN)(15)+puck(15)]+ω(NO2)(15)+R4[oop(CH)](15)+R2[puck](13) 775 772 856 766 770 R4[puck](37)+R3[puck](22)+ω(NO2)(7)+R2[τa](5) 766 763 840 754 756 R4[oop(CH)](51)+R3[puck(11)+oop(CN)(7)]+R2[puck](7) 751 748 818 729 745 R1[δ’ring(31)+δring(24)]+R1[υ(CO)](7) 735 733 806 727 726 R2[puck(24)+τa(8)]+R4[puck](16)+R3[δ’a](6) 721 719 784 714 - R2[puck](36)+R4[puck](6)+R1[δ’ring](5) 702 700 765 700 702 R2[τ’a(10)+oop(C13C23)(7)+δin(C13C23)(7)+ω(NO2)(7) 687 685 750 675 683 R2[τ’a](25)+R3[oop(CN)(9)+puck(7)]+τ(C8C9)(9)+R1[τ](5) 667 665 721 650 672 R4[δa)](32)+δ[(C=O)](22) 623 622 672 621 619 R4[δ’a)(30)+δa)(8)]+δ(C=O)](16)+R2[δa](8) 617 616 662 619 618 τ(O3C23)(23)+R2[oop(C13C23)(17)+τa(6)+puck(5)]+R3[puck(7) 609 608 659 607 600 R4[puck](12)+R4[δ’a)](12)+δa(8)]+R2[τa](11)+R3[puck](10) 584 583 628 592 589 τ(O3C23)(16)+R3[δa(11)+oop(CN)(5)]+R2[τ’a](11)+τ(C10C12)(5) 543 543 587 550 537 R2[τ’a(20)+τa(10)]+R3[oop(CN)(11)+puck(11)]+R4[τ’a](12) 536 536 580 530 531 R2[τ’a(10)+δ’a(9)+puck(5)+R3[δa](10)+ρ(NO2)(9)+τ(C8C9)(7)+τ(C10C12)(6)+ρ(C=O)(6) 512 512 557 507 504 R2[τa(24)+oop(C13C23)(9)]+R3[oop(CN)](11)+R4[τa(10)+τ’a(8)] 450 450 493 447 447 R4[τ’a(24)+τa(18)]+R2[τa](16)+τ(C10C12)(11)+τ(C11C15)(6) 431 431 464 420 430 R2[δ’a(13)+τa(9)]+R3[oop(CN)(6)+δ’a(6)]+ρ(C=O)(10)+τ(C11C15)(7)+R2[puck](7) 401 402 436 - 402 R3[δa](14)+ρ(NO2)(13)+R4[τ’a](13)+R2[δa](10)+τ(C11C15)(5) 375 376 409 - 378 R2[τ’a(15)+δ’a(10)]+τ(C11C15)(14)+R4[τ’a](13)+ρ(N=O)(8) 353 354 376 - 346 R2[δa(15)+δ’a(14)+υ(CC)(7)]+R3[δ’a(25)+δa(5)]+R1[υ(CO)](5) 339 340 366 - 344 R3[υ(CN)(21)+υ(CC)(13)+δ’a(11)]+R2[υ(CC)(10)+υ(C13C23)(7)]+δ[(C=O)](5) 328 329 361 - - R2[oop(C13C23)(13)+τ’a(9)+τa(8)]+τ(C8C9)(12)+R1[τ](11+τ(C11C15)(9)+R2[puck](5) +ρ[(C=O)](5) 302 303 330 - 308 τ(C11C15)(33)+R2[τa(6)+τ’a(6)]+R4[τa](9)+R1[τ’](7)+R3[puck](6) 274 275 299 - 288 τ(C11C15)(13)+R3[δa](9)+τ(C8C9)(6)+R4[τ’a](8) 257 259 283 - 255 R3[oop(CN)](30)+R4[τ’a](16)+R2[τa](11)+τ(C8C9)(5) 203 204 222 - 201 R2[τ’a(16)+oop(C13C23)(8)]+R3[δin(CN)](15)+R1[τ](13)+τ(C10C12)(12)+R4[τa](7) 198 199 213 - 199 R2[δin(C13C23)(17)+oop(C13C23)(7)+τ’a(6)]+R1[τ](11) 185 186 204 - - R2[oop(C13C23)(17)+τ’a(15)]+τ(C10C12)(14)+R4[τa](9)+R1[τ](6)+R3[oop(CN)](5) +τ(C11C15)(5) 173 174 188 - - R2[δin(C13C23)(19)+τ’a(7)]+R3[δin(CN)](17)+τ(C10C12)(13)+R4[τa](7)+R1[τ’](5) 154 155 164 - 151 R1[τ’(50)+τ(27)] 109 109 124 - - τ(NC)(37)+R2[δin(C13C23)(14)+τ’a(5)]+R3[δin(CN)](9) 100 101 111 - - R2[τ’a(25)+τa(12)]+τ(C11C15)(13)+R1[τ](10)+τ(NC)(9)+τ(C10C12)(8) 92 93 100 - 85 R2[oop(C13C23)](19)+τ(C8C9)(16)+R3[oop(CN)](14)+R1[τ’](12)+τ(C10C12)(9)+R1[τ](7) 80 81 90 - 83 τ(NC)(31)+τ(C13C23)(30)+R2[τa(11)+τ’a(5)]+τ(C10C12)(8) 69 69 76 - - R2[τ’a(39)+τa(10)]+τ(C13C23)(12)+τ(C8C9)(10)+τ(C10C12)(8)+R4[τa](8) 38 38 41 - 41 R2[τa(27)+τ’a(11)]+τ(C13C23)(20)+τ(C8C9)(20)+τ(NC)(7) Proposed assignments and potential energy distribution (PED) for vibrational normal modes. Types of vibration: ν, stretching; δ, deformation (bending), scissoring; oop, out-of-plane bending; ω, wagging; γ, twisting; ρ, rocking; τ, torsion. aPotential energy distribution (contribution ≥ 5). 3.4.3 C-NO2 vibrations There is one nitro (NO2) group connected with the ring R3 as a functional group in this molecule. Generally, the asymmetric NO2 stretching modes are expected in the interval 1600-1500 cm-1 and symmetric stretching modes in the interval 1400–1300 cm-1 in the IR absorption bands [39]. In this study, the asymmetric N=O vibration is calculated at 1562/1734 cm-1 in the DFT/HF, which matches well with a weak band at 1539 cm-1 in the IR and the medium intensity band at 1534 cm-1 in the Raman spectrum. Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 48 cm-1 in the Raman spectrum. The symmetric N=O vibration is calculated at 1353/1473 cm-1 in the DFT/HF, which is observed with the weak intensity at 1348 cm-1 in the IR spectrum and the strong peak at 1348 cm-1 in the Raman spectrum. This mode is mixed with NO2 deformation and C-N stretching vibration of the ring. The deformation (or scissoring) of NO2 vibration is calculated at 842/915 cm-1 in the DFT/HF and observed at 841/839 cm-1 in the IR/Raman spectra. The NO2 wagging vibration is calculated at 784/860 in DFT/HF, which is observed at 777 cm-1 in the IR spectrum and 778 cm-1 in the Raman spectrum. The mixed rocking mode vibration of NO2 is calculated at 536/580 cm-1 in DFT/HF. Fig. 4. Observed and calculated FT-IR spectra between the ranges 400-3600 cm -1 . 3.4.4 Ring R1 vibrations There is one CH2 moiety in this five membered planer ring. Basically, one can expect six fundamental modes associated with each CH2 group vibrations namely: symmetric, asymmetric stretch, deformation and rocking modes which belong to polarized in-plane vibrations. In addition to that, CH2 wagging and twisting modes would be expected to be depolarized out-of-plane symmetry species. The asymmetric CH2 stretching vibrations are generally observed in the range 3000–2900 cm-1, while the symmetric stretch appears in the region 2900–2800 cm-1 [40,41]. In this study, the pure CH2 asymmetric stretching vibration is calculated at 2998/3160 cm-1 in the DFT/HF, which is observed at 2999 cm-1 in the IR spectrum and 2995 cm-1 in the Raman spectrum. Symmetric stretching vibrarion of this group is calculated at 2830/3061 cm-1 in the DFT/HF and assigned at 2852 cm-1 in the IR and 2880 cm-1 in the Raman spectra, respectively. The CH2 deformation calculated at 1514/1648 cm-1 in the DFT/HF is observed with good agreements with strong band at 1523 cm-1 in the IR and with weak band at 1508 cm-1 in the Raman spectra, respectively. The mixed CH2 wagging vibration is calculated at 1415/1569 cm-1 in the DFT/HF, which is assigned at 1417 cm-1 in the IR spectrum and at 1406 cm-1 in the Raman spectrum. The pure CH2 rocking mode is calculated at 1134/1223 cm-1 in the DFT/HF. This mode is observed at 1126 cm-1 in the IR and at 1115 cm-1 in the Raman spectra, respectively. The twisting vibration of CH2 is calculated at 1206/1302 cm-1 in the DFT/HF. Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 49 3.4.5 Ring R2 vibrations An aromatic six membered ring R2 lying between R1 and R3 have a methine (CH) and a carboxyl (COOH) moiety as functional groups. The characteristic region for the identification of C-H stretching in the heteroaromatic structures is 3100–3000 cm-1 [42,43]. In this study, the C-H stretching vibration is calculated at 3087/3233 cm-1 in the DFT/HF as a pure mode. The observed IR/Raman peaks are at 3038/3083 cm-1. The mixed in-plane deformation is calculated at 1189 in DFT and at 1282 cm-1 in HF, respectively. The observed wavenumbers of this mode are 1171 cm-1 in the IR spectrum and at 1173 cm-1 in the Raman spectrum. The C-H out-of-plane deformation is calculated at 899/997 cm-1 in the DFT/HF, which is observed at the peaks 901 cm-1 in the IR and at 897 cm-1 in the Raman spectra, respectively. Fig. 5. Observed and calculated FT-Raman spectra between the range 0-3700 cm -1 . 3.4.6 Ring R3 vibrations The six membered ring R3 has a CH and one NO2 moiety. The C-H stretching vibration is calculated at 3065/3223 cm-1 in the DFT/HF and observed at 3072 cm-1 in the Raman spectrum. The C-H in- plane deformation is calculated at 1217/1322 cm-1 in DFT/HF and observed at the very weak band in Raman spectrum. The out-of-plane deformation is calculated at 927/1043 cm-1 in the DFT/HF, which is observed in the bands at 920 cm-1 in the IR and at 928 cm-1 in the Raman spectrum, respectively. The mixed C-C ring stretching vibrations are calculated below 772/856 cm-1 in the DFT/HF calculations. The highly mixed C-N stretching vibrations are calculated below 1380 cm-1 in DFT with low contributions. The DFT calculation yields C-N out-of plane deformations below 950 cm-1 as mixed modes and with low contributions. Similarly, the C-N and in-plane deformations are calculated below 500 cm-1. Khadka and Joshi / BIBECHANA 12 (2015) 40-52: p. 50 3.4.7 Ring R4 vibrations Ring R4 is also a phenyl ring having four methine moieties and connected with the other ring R3 as shown in the Fig. 1. The C-H stretching vibrations are calculated as the pure modes in the ranges 3106-3032 in the DFT and 3269-3175 cm-1 in the HF, respectively. The mixed C-H in-plane deformations are calculated at 1504, 1528, 1271, 1182 and 1148 cm-1 in the DFT, which have good agreements with the observed IR and Raman bands. Similarly, these wavenumbers are calculated at 1630, 1603, 1344, 1266 and 1264 cm-1 in the HF method. The C-H out-of-plane deformations are calculated below 1000 cm-1 in the DFT. These mixed modes of vibration are calculated below 1110 cm-1 in the HF. In the DFT, the C-C ring stretching vibrations are calculated at 1618 and 1543 cm-1, which match with the strong peak at 1626, 1525 cm-1 in the IR spectrum and with the weak peaks at 1609, 1541 cm-1 in the Raman spectrum. The trigonal deformation, puckering, asymmetric deformation and asymmetric torsion of this ring are calculated at 919, 772, 622 and 450 cm-1 in the DFT method. 4 Conclusion In the present study, the frequency assignments of the normal modes of AA II using the spectroscopic intuition as well as the quantum chemical calculations were performed. The comparison of the results of experimental and theoretical study has given a full description of the geometry, vibrational wavenumbers and electronic properties of this molecule. The scaled wavenumbers obtained using DFT/HF methods for AA II, showed good correlation with the observed Raman and FT-IR spectra. Any discrepancies noted between the observed and the calculated wavenumbers was observed due to the fact that the calculations have been actually performed on single (or isolated) molecule in the gaseous state. By mapping molecular electrostatic potential surface (MEP) on the electron density isosurface helps in assessing information regarding the size, shape, charge density distribution and sites of chemical reactivity of the title molecule. Our studies have shown that the DFT calculations are qualitative tools for assigning overall understanding of the electronic, structural and vibrational properties of the natural products. 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