Research Article  Open Access
Hakan Arslan, Aydin Demircan, Gun Binzet, Ilhan Ozer Ilhan, "Vibrational Spectroscopy Investigation Using Ab Initio and Density Functional Theory Analysis on the Structure of tertButyl 3aChloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate", Journal of Chemistry, vol. 2013, Article ID 124659, 13 pages, 2013. https://doi.org/10.1155/2013/124659
Vibrational Spectroscopy Investigation Using Ab Initio and Density Functional Theory Analysis on the Structure of tertButyl 3aChloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate
Abstract
The molecular structure, vibrational frequencies, and infrared intensities of the tertbutyl 3achloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate were calculated by the HF and DFT (BLYP and B3LYP) methods using 631G(d) and 631G(d,p) basis sets. The FT infrared spectrum of the solid sample was measured under standard condition. We obtained two stable conformers for the title compound; however Conformer 1 is approximately 0.2 kcal/mol more stable than the Conformer 2. The comparison of the theoretical and experimental geometry of the title compound shows that the Xray parameters fairly well reproduce the geometry of Conformer 2. Comparison of the observed fundamental vibrational frequencies of the title molecule and calculated results by HF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. The harmonic vibrations computed by the B3LYP/631G(d,p) method are in a good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using VEDA 4 program.
1. Introduction
Epoxides are used as an important intermediate tool in organic synthesis of fine chemicals and pharmaceuticals [1]. Intramolecular DielsAlder (IMDA) reactions and epoxidation of its cycloadduct have also been of great interest in synthetic pathway of natural products, like conduritols [2], zisomeric insect sex pheromone components [3], dihydrophenanthroline derivatives [4], vitamin D total synthesis [5], and so on. We have previously prepared a variety of key precursors to the intramolecular DielsAlder reaction of furan (IMDAF) diene via facile alkylation of furan compounds and its protection. Subsequently IMDAF reaction carried out under thermal condition provided five and sixmembered heterocycles fused to an easily cleavable oxabicycloheptene moiety [6–9].
In this study, tertbutyl 3achloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate, 3, was prepared from 5chloro10oxa3azatricyclo[5.2.1.01,5]dec8en3carboxylic acid tertbutyl ester, 1, using metachloroperbenzoic acid, 2, in dry dichloromethane which was previously recrystallized in dry diethyl ether at 0°C. The product 3 was analyzed by Xray diffractometer [10], ^{1}H and ^{13}C NMR, IR, mass spectrometer, and elemental analysis. The goal of this project is to transferring chlorocycloadduct, 3, to highly substituted tetrahydroisoindole derivative, 4. We are currently researching this stage by opening epoxy bridges on compound 3 (Scheme 1).
The crystal structure of tertbutyl 3achloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate (TBCEIC) has been determined by Xray diffraction [10], however so far no ab initio studies have been made on the conformation and vibrational spectra of the title compound in the gas phase. In the present study, we have synthesized and calculated the vibrational frequencies and geometric parameters of TBCEIC in the ground state to distinguish the fundamentals from the experimental vibrational frequencies and geometric parameters, by using the HartreeFock [11] and density functional using B3LYP [12, 13] and Becke’s exchange functional in combination with the Lee, Yang, and Parr correlation functional methods [13, 14] (BLYP) with the standard 631G(d) and 631G(d,p) basis sets. In continuation of our theoretical studies, in the present work, we checked the relative performance of B3LYP and BLYP methods, as well as of HF for comparison, at the 631G(d) and 631G(d,p) levels taking as a test compound tertbutyl 3achloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate.
2. Results and Discussion
2.1. Conformational Stability
We performed full geometry optimization of the title compound. To establish the most stable conformation as the initial point for further calculations, the molecule was submitted to a rigorous conformation analysis around all bonds having free rotation. This study was performed with the software Spartan 06 [15, 16]. The structure of the title compound has two conformations which are shown in Figure 1. For comparison, the total energy and the relative energies of both conformer of the title compound are given in Table 1. Energetics show that Conformer 1 is the most stable. But comparison of the theoretical and experimental geometry of the title compound shows that the Xray parameters fairly well reproduce the geometry of Conformer 2. Therefore, we will focus on this particular form (Conformer 2) of the title compound in this paper.

(a)
(b)
2.2. Molecular Geometry
The optimized structure parameters of the title compound calculated by ab initio and DFT method listed in Table 2 are in accordance with atom numbering scheme given in Figure 2(a). The crystal and molecular structure of the title compound have been reported previously [10]. The geometric structure is monoclinic, the space group P2_{1}/c, with the cell dimensions: Å, Å, Å, , and Å^{3} (Figure 2(b)). The structure parameters obtained by Xray singlecrystal diffraction method are given in Table 2. Also, Table 2 compares the calculated geometric parameters with the experimental data.
 
^{
a}The atom numbering scheme of the molecular structure is given in Figure 2(a). ^{ b}r: correlation coefficient between optimized and experimental geometrical parameters. ^{ c}From [10]. 
(a)
(b)
Based on this comparison, the bond lengths and angles calculated for the title compound show good agreement with experiment. However, according to our calculations, the optimized both bond lengths and bond angles obtained by DFT methods show the best agreement with the experimental values. The large difference between experimental and calculated DFT/B3LYP631G(d,p) bond length and bond angle is 0.065 Å and 1.65 °, respectively.
2.3. Vibrational Assignments
Table 3 lists the wavenumbers of the bands observed in the FTIR spectra of the tertbutyl 3achloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate. The theoretical frequencies and infrared intensities calculated by HF, BLYP, and B3LYP methods of the title compound are gathered in Table 3. The last column of Table 3 shows the detailed vibrational assignment obtained from the calculated potential energy distribution (PED).
 
^{
a}Harmonic frequencies (in cm^{−1}) and IR intensities (km/mol). ^{ b}ν: stretching; : inplane bending; : outofplane bending; : torsion; sym: symmetric; asym: asymmetric; R1: C19O12C21C20C25; R2: C19O12C21C16C24; R3: C16C21C18N13C22. PED less than 10% are not shown. 
Comparison of the frequencies calculated at HF, BLYP, and B3LYP 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 extent makes the frequency values lower in comparison with the HartreeFock frequency data [17–20]. Reductions in the computed harmonic vibrations, though basis set sensitives are only marginal as observed in the DFT values using 631G(d) and 631G(d,p). Any way notwithstanding the level of calculations, it is customary to scale down the calculated harmonic frequencies in order to improve the agreement with the experiment [17–20]. Therefore, the scaling factor values of 0.8953/0.8992, 0.9614/0.9614, and 0.9945/1.0072 for HF, B3LYP, and BLYP (631G (d)/631G(d,p)), respectively, are used in our study [17, 21–25]. Experimental fundamentals are in better agreement with the scaled fundamentals which are found to have a good correlation for DFT/B3LYP/631G(d,p) () than HF method. The calculated frequencies (scaled) do not differ so much from the experimental ones that the maximum difference between two spectra is not more than 27 cm^{−1} for DFT/B3LYP/631G(d,p) method. Also, the average absolute error of the calculated frequencies was found less than 0.86% for DFT/B3LYP/631G(d,p) method.
A general better performance of B3LYP and BLYP versus HF can be quantitatively characterized by using the mean deviation, mean absolute deviation, average absolute error, root mean square values, and coefficients of correlation () between the calculated and observed vibration frequencies and given in Table 3. All these values were calculated in this study by the PAVF 1.0 program [26] according to Scott and Radom [21]. The root mean square (RMS) values were obtained in this study using the following expression [21]: The values for both DFT methods were greater than 0.9998, whereas for HF it was 0.9997. These values are very close to those reported in the literature [27–33]. These results indicate that the B3LYP calculations approximate the observed fundamental frequencies much be better than the HF results. The small difference between experimental and calculated vibrational modes is observed. It must be due to the fact that hydrogen bond vibrations present in crystal lead to strong perturbation of the infrared frequencies (and intensities) of many other modes. Also, we state that the experimental results belong to solid phase and theoretical calculations belong to gaseous phase [17, 19, 20, 23–25, 30–34].
Finally, we calculated the optimal scaling factors, which are crucial for IR spectral predictions, using the PAVF 1.0 program [26]. Without accounting for different vibrations, only singleuniform scaling factors were calculated. The values obtained are 0.8974/0.9024, 0.9587/0.9612, and 0.9891/0.9906 for the HF, B3LYP, and BLYP (631G(d)/631G(d,p)) methods, respectively. They are very close to those recommended by Scott and Radom [21] for the same levels of theory and increase in the same order of the HF, B3LYP and BLYP methods. Thus, for future IR spectral predictions for unknown derivatives of the title compound, one can recommend scaling factors of 0.897/0.902, 0.959/0.961, and 0.989/0.991 for the HF, B3LYP, and BLYP (631G(d)/631G(d,p)) methods, respectively.
The IR bands at 3082, 3067, and 3010 cm^{−1} in FTIR spectrum of the title compound have been designated to νCH stretching fundamentals of C20, C25, and C19 atoms, respectively [23, 35, 36]. The wavenumbers corresponding to the aliphatic νCH stretching are listed in Table 3. All the calculated values in each method are overestimated, as well known in theoretical quantum mechanic assignment concerning hydrocarbons. After we applied the scale factor both calculated in this research and given by Scott and Radom [21] for all the methods, we observed a good concordance between the experimental and the calculated values. The vibrational spectra show six bands in the aliphatic νCH stretching region and evident overlap between the different C–H stretching modes. The asymmetric and the symmetric νC–H stretching bands for –CH_{2}– group are listed in Table 3. These assignments were also supported by the literature [20, 23, 35, 37]. The inplane and outofplane bending vibrations of C–H group have also been identified for the title compound and they are presented in Table 3.
The carbonyl stretching vibrations are found in the region 1780–1700 cm^{−1} [38, 39]. The sharp intense band in IR spectrum at 1686 cm^{−1} can be assigned to the carbonyl group νC=O stretching vibration.
The vibrational modes concerning the bond angle bending (–CH_{2}–), scissoring, wagging, twisting, and rocking are well defined in all the calculations. As seen from Table 3, the bands observed at 1460, 1451, and 1431 cm^{−1} in FTIR spectrum correspond to scissoring deformation of –C(18)H_{2}–, –C(22)H_{2}– and –C(24)H_{2}– group in the title compound, respectively [37, 40]. The theoretically computed values of scissoring deformation vibration modes show a good agreement with the experimental values. The wagging, twisting, and rocking vibrational modes are distributed in a wide range [36, 37, 40, 41]. Twisting and wagging vibrational modes of the –CH_{2}– groups were assigned in the range of 1350–1163 cm^{−1}. The above result is in close agreement with the literature values [36, 37, 40–42]. These vibrational modes are described in the tables by mean of the general symbol δCH_{2}. The rocking –CH_{2}– is assigned in the wavenumber range of 1109–852 cm^{−1}, and the wavenumber shift of these bands is due to the atom nature in which the –CH_{2}– group is bonded. The –CH_{2}– rocking vibrational modes are generally intensive bands which can be appreciating the vibrational coupling with other vibrational modes [36, 37]. These bands are assigned using calculated potential energy distribution.
For the assignments of CH_{3} group frequencies, 15 fundamental vibrations can be associated to CH_{3} groups. Nine stretching, three umbrella, and three rocking vibration modes are designated the motion of the methyl group. The CH_{3} asymmetric and symmetric stretching frequencies are established at 3067, 3010, 3003, and 2923 cm^{−1} in infrared spectrum. The three methyl hydrogen deformation modes are also well established in the spectrum. We have observed the methyl deformation mode at 1474, 1451, 1431, and 1409 cm^{−1} in the infrared spectrum.
The C–C stretching vibrations in cyclic alkanes appeared as weak bands, so these vibrations are of little importance for structural study [43]. The IR bands appearing at 1360, 1247, 1222, 1211, 1180, 1163, 1128, 1109 1089, 1045, 993, 947, and 928 cm^{−1} were assigned to νCC vibrations coupled with the δCCH for the title compound. So, in our study, the C–C stretching vibrations are observed as mediumintensity bands. These results were confirmed by Gunasekaran et al. [44].
The identification of CN vibrations is a difficult task, since the mixing of vibrations is possible in CN stretching vibration frequencies region. However, with the help of both the animation option of Gaussian programs and theoretical calculations (VEDA 4), the CN vibrations are identified and assigned in this study. The IR bands appearing at 1409, 1282 and 1211 cm^{−1} are assigned to νCN vibrations. These results agree with Sundaraganesan et al. [45].
Epoxide group could be identified via its characteristic C–O stretching bands which gives two different absorption bands in the fingerprint region around ~800–950 and ~1250 cm^{−1}, respectively [46, 47]. There is also a third band in the range 750–850 cm^{−1}. The IR bands appearing at 1180, 993, and 883 cm^{−1} are assigned to C–O stretching vibrations. These results agree with Evtushenko et al. [47]. The difference between observed and literature values is coming from the effects of the aromatic rings.
The νC–Cl stretching vibrations give generally strong bands in the region of 710–505 cm^{−1}. The band observed at 685 cm^{−1} in FTIR spectrum has been assigned to νC–Cl stretching vibration in the present investigation [37].
2.4. Other Molecular Properties
Several calculated thermodynamic parameters are presented in Table 4. The total energies and the changes in the total entropy of the title compound at room temperature at different methods also presented.

3. Experimental
Dichloromethane (DCM) was distilled from calcium hydride. Reactions were monitored by thin layer chromatography (TLC) using precoated silica plates (Macherey Nagel sil G UV254). Compounds were visualized using ultraviolet fluorescence, alkaline potassium permanganate solution, or acidic cerium (IV) sulphate solution. Column chromatography was carried out using Macharey Nagel Kieselgel 60 (230–240 mesh).
3.1. Instrumentation
Melting points were determined using an Electrothermal9300 Digital Melting Points Apparatus (Electrothermal Inc., Essex, UK). The ^{1}H and ^{13}C NMR spectra were recorded on a BrukerAvance DPX400 spectrometer at the TÜBİTAK Analytical Laboratory (Ankara, Turkey). The chemical shifts are quoted in ppm, as δ values downfield of tetramethylsilane (TMS) or relative to the residual solvent resonance. Electron ionisation mass spectra (EI, 70 eV) were obtained on a Perkin Elmer Clarus 500 mass spectrometer. Elemental analysis was carried on LECO CHNS 932, TÜBİTAK Analytical Laboratory (Ankara, Turkey). The roomtemperatureattenuated total reflection Fourier transform infrared (FTIR ATR) spectrum of the tertbutyl 3achloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate was recorded using Varian FTS1000 FTIR spectrometer with Diamond/ZnSe prism (4000–525 cm^{−1}; number of scans: 250; resolution: 1 cm^{−1}) in the solid (Figure 3).
3.2. Synthesis of tertbutyl 3achloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate
To a solution of metachloroperbenzoic acid (mCPBA) (120 mg, 0.66 mmol), which had previously been purified and recrystallized from dry diethyl ether, in dichloromethane (10 mL), cooled to 0 °C, was added dropwise a solution of tertbutyl 7achloro1,6,7,7atetrahydro3a,6epoxyisoindole2carboxylate (0.66 mmol) in dichloromethane (10 mL) over a period of 3 min (Scheme 1). The reaction mixture was stirred at room temperature for 4 h and then diluted with cold 4% sodium bicarbonate solution (4 mL). The organic layer was separated, washed with water ( mL), and concentrated in vacuum. The residue was subjected to flash column chromatography. As white crystal (110 mg, 56%). M.p.: 137–139 °C, TLC, (hexane: ethyl acetate (7 : 3)): Rf: 0.26. ^{1}H NMR (400 MHz CDCl_{3}) δ: 4.63 (d, 1H, H4, ), 4.01–3.73 (m, 4H, H7, H8), 3.75 (d, 1H, H3, , AB ), 3.52 (d, 1H, H2, , AB ), 2.52 (dd, 1H, H5, , , AB), 1.90 (d, 1H, H5, , AB), 1.45 (s, 9H, H11, H12, H13). ^{13}C NMR (75 MHz CDCl_{3}) δ: 154.0 (C9, q), 91.1 (C1, q), 80.2 (C10, q), 77.2 (C4), 75.3 (C6, q), 60.5 (C2), 49.1 (C7), 48.3 (C8), 45.3 (C5), 42.1 (C3), 28.4 (C11, C12, C13). GCMS (m/z): 288 [M^{+}, %100], 252 [M^{+}–(Cl), %55], 213 [M^{+}–(OtBu), % 45] 167 [M^{+}–(C8H9N), %85]. Elemental analysis (%) for C_{13}H_{18}ClNO_{4}: theoretical (experimental) C, 54.26 (54.03); H, 6.31 (6.15); N, 4.87 (4.71).
3.3. Calculations Details
The conformation analysis study was performed by Spartan 06 program package [15, 16]. All the other calculations were performed with the Gaussian 03W program package on a double xeon/3.2 GHz processor with 8 GB Ram [48]. The molecular structure of the title compound, in the ground state, is optimized by using HF, BLYP and B3LYP methods with the standard 631G(d) and 631G(d,p) basis sets. The vibrational frequencies were also calculated with these methods. The frequency values computed at these levels contain known systematic errors [27–29, 49–53]. Therefore, we have used the scaling factor for HF, B3LYP, and BLYP methods [17, 21–25]. We have also calculated optimal scaling factors for all investigated methods. We have also calculated optimal scaling factors for all investigated methods. The assignment of the calculated wavenumbers is aided by the animation option of GaussView 3.0 graphical interface for gaussian programs, which gives a visual presentation of the shape of the vibrational modes [52]. Furthermore, theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using VEDA 4 program [54].
4. Conclusions
The frequency assignment for the tertbutyl 3achloroperhydro2,6aepoxyoxireno[e]isoindole5carboxylate has been done for the first time from the FTIR spectrum recorded. The conformation stability, equilibrium geometries, and harmonic frequencies of the title compound were determined and analyzed both at HF and DFT level of theories utilizing 631G(d) and 631G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Any discrepancy noted between the observed and the calculated frequencies may be due to the fact that the calculations have been actually done on a single molecule in the gaseous state contrary to the experimental values recorded in the presence of intermolecular interactions. The IR spectrum of the title compound was interpreted in terms of the potential energy distribution (PED) analysis. Optimal uniform scaling factors were calculated for the title compound. Taking into account small variations of the scaling factors for the derivatives of the title compound, for future IR spectral predictions for unknown compounds of this class, one can recommend scaling factors of 0.897/0.902, 0.959/0.961, and 0.989/0.991 for HF, B3LYP, and BLYP (631G(d)/631G(d,p)), respectively.
Acknowledgments
The authors are grateful to TÜBİTAK, The Scientific and Research Council of Turkey (Project no. 107T831), and Mersin University Research Fund (Project no. BAP.ECZ.F.TB.(HA).20061) for financial support of this work.
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Copyright © 2013 Hakan Arslan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.