Conformational Study and Vibrational Spectroscopic (FT-IR

ANALYTICAL SCIENCES JANUARY 2017, VOL. 33 99

Introduction

Borreverine (N-methyl-2-[(4aS)-2,4a,10,10aα-tetrahydro-1,1,3,13-tetramethyl-1H,5H-4bβ,9bβ-(iminoethano)indeno[1,2-b]indol-10α-yl]-1H-indole-3-(ethan-1-amine)) is one of the most well-known and important antimalarial natural products extracted from Borreria verticillata.1 Borreria verticillata (belongs to Rubiaceae family) is a traditional herb having immense potential as a therapeutic drug. It has also been isolated from Flindersia fournieri,2 which belongs to Rutaceae family. Pousset et al. were the first to isolate borreverine along with isoborreverine and dimethylisoborreverine.3 It was found that borreverine have a selective antiplasmodial activity that is different from that of chloroquine.4 Thus, borreverine seems to be a wonderful alternative as an antimalarial drug. In the present work, the borreverine derivative obtained two steps before the synthesis of borreverine was taken for investigation.5 The novel chemical structure and vitally important biological activity of these alkaloids made it attractive for further investigation. In our previous report,5 the synthesis of the borreverine derivative discussed in this work namely, ethyl 10-(3-(2-((ethoxycarbonyl)-amino) ethyl)-1-(phenylsulfonyl)-1H-indol-2-yl)-1,1,3-trimethyl-5-(phenyl sulfonyl)-2,4a,10,10a-tetrahydro-1H,5H-4b,9b-

(epiminoethano)indeno[1,2-b]indole-13-carboxylate (abbreviated as BD thereafter), was already discussed along with the crystal structure. In a continuation of our work, here we are interested in dealing with a conformational analysis of BD along with a vibrational spectroscopic investigation of the compound.

Vibrational spectroscopy is a wonderful tool for the analysis of molecular structure, conformation and intra-/intermolecular interactions of complex molecules.6–10 Here, we report on concise Fourier transform Raman (FT-Raman) and Fourier transform infrared (FT-IR) spectroscopic studies of the title molecule. Density functional theory (DFT) has become a beneficial tool to study the vibrational spectra of the complex molecules.8–10 A detailed conformational analysis was conducted in order to predict the most stable conformer along with all possible conformations of the title molecule. In order to investigate the possible conformers, a one-dimensional potential energy scan of the title molecule was performed using the DFT and B3LYP/6-31G(d,p) level of theory. The predicted most stable conformer and initial crystallographic structure are taken into further investigation. The optimized structure, intensity, and wavenumber of the vibrational bands of both conformers were obtained by DFT employing the B3LYP level of theory and using the 6-31G(d,p) basis set. The molecular electrostatic potential (MEP) surface was plotted in order to illustrate the reactive sites of the molecule. Natural bond orbital (NBO) analysis was also performed to study the stability and intramolecular charge transfer (ICT) within the molecule. Vibrational assignments of some selective modes were made

2017 © The Japan Society for Analytical Chemistry

† To whom correspondence should be addressed.E-mail: [email protected]; [email protected]

Conformational Study and Vibrational Spectroscopic (FT-IR and FT-Raman) Analysis of an Alkaloid–Borreverine Derivative

Swapnil SINGH,* Harshita SINGH,* T. KARTHICK,* Poonam TANDON,*† Dattatraya H. DETHE,** and Rohan D. ERANDE**

*Department of Physics, University of Lucknow, Lucknow 226007, India **Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India

In the present work, structural and spectroscopic investigations were carried out on a borreverine derivative. Borreverine is a class of alkaloid as well a natural antimalarial drug extracted from Borreria verticillata. With the aim of finding possible conformers, a detailed conformational analysis of a borreverine derivative was conducted utilizing density functional theory employing the B3LYP/6-31G(d,p) method. The crystallographic geometry was used for full geometry optimization, followed by a conformational analysis. The conformational investigation predicted the most stable conformer (conformer I), which was further compared with the initial crystallographic geometry (conformer V). The geometry optimization, vibrational frequency, and intensity of these two conformers (I and V) were calculated in the ground state using density functional theory with the B3LYP functional and 6-31G(d,p) basis set. The spectroscopic investigation was conducted using Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) techniques. Tentative vibrational assignments of some selective modes were presented utilizing the observed FT-IR, FT-Raman, and calculated spectra. The scaled and observed wavenumbers were found to be in good agreement. The molecular electrostatic potential was computed and plotted so as to elucidate the reactive sites of the molecule. Natural bond orbital studies were performed to investigate the intramolecular charge transfer that results in molecular stability.

Keywords Conformational study, FT-IR, FT-Raman, NBO, MEP

(Received September 10, 2016; Accepted October 19, 2016; Published January 10, 2017)

100 ANALYTICAL SCIENCES JANUARY 2017, VOL. 33

with the aid of calculated vibrational wavenumbers. Furthermore, the calculated results were applied to simulate infrared and Raman spectra of the title compound, which show good agreement with the observed spectra. To the best of our knowledge, this is the first time that a structural and conformational study of the title compound has been done by combining a quantum chemical approach and vibration spectroscopy.

Experimental

The FT-IR spectrum was recorded on a Bruker TENSOR 27 FT-IR spectrometer using a KBr pellet technique in the region of 4000 – 400 cm–1. KBr pellets of solid samples were prepared from mixtures of KBr and the sample in a 200:1 ratio using a hydraulic pressure machine. The spectral resolution of this instrument was 4 cm–1. The FT-Raman spectrum of the sample was recorded on a Bruker multiRAM Raman spectrometer at 1064 nm using an Nd-YAG laser as the excitation wavelength in the region 3400 – 100 cm–1; the spectral resolution of the instrument was 4 cm–1. The samples were measured in the hemispheric bore of an aluminum sample holder. The typical spectrum was acquired with 512 scans and a laser power of 500 mW at the sample location.

Computational Details

Density functional theory was used for all theoretical calculations by adopting a Gaussian 09 program11 employing B3LYP theory12–14 and the 6-31G(d,p) basis set. All of the calculations (viz., conformational analysis, structural parameters, vibrational wavenumber, infrared and Raman intensities of the title compound) were carried out using the same level of theory. In

order to investigate the most stable conformer, one-dimensional potential energy scans were performed using the same theory. On account of such a huge molecule, the normal-mode analysis, and the vibrational assignment was prepared only for some selective bands. Raman and infrared spectra were simulated using a pure Lorentzian band profile (FWHM = 8 cm–1) as well as indigenously developed software. Visualizations of the normal-mode vibrations and graphical representations of the calculated Raman and IR spectra were made using Gaussview 0515 and the Chemcraft16 program. The isoelectronic molecular electrostatic potential (MEP) surface was plotted using the Gaussview 05 program. NBO calculations were performed by using the same Gaussian 09 package at the B3LYP/6-31G(d,p) level of theory.

Results and Discussion

Conformational studies and geometry optimizationThe chemical structure of borreverine is presented in Fig. 1

for a structural comparison with the borreverine derivative. The crystallographic structure were used for initial geometry optimization using DFT and the B3LYP/6-31G(d,p) method, as shown in Fig. 2. In order to find all possible conformations, a one-dimensional PES scan was performed along all of the fourteen dihedral angles, f1 – f14, as mentioned in Fig. 2 using

Fig. 1　Chemical structure of borreverine. Fig. 2　Optimized structure of crystallographic input file of BD.

Fig. 3　One-dimensional potential energy scans along the dihedral angles f1 – f14.


the same level of theory. The scans were performed by varying the torsion angles at a step of 10° in the range of 0 – 360° rotation around the bond. The scan plots for all 14 dihedral angles are presented in Fig. 3. PES revealed that 26 conformers were identified at the minima of the scan graphs; out of them, six may possibly exist at room temperature, since their energy difference with the lowest energy conformer is less than ~2.48 kJ mol–1 (see Table S1, Supporting Information). The lowest energy (9130404.68139 kJ mol–1) conformation was obtained along the scan f10 and named as conformer I, as shown in Fig. 4. On the basis of the energy, the initial optimized geometrical crystallographic structure is named as conformer V. Furthermore, conformers I and V are under investigation, and the geometrical parameters and frequency calculations are computed using the same level of theory.

The optimized structural parameters, such as the bond length, bond angle and dihedral angle of the conformers I and V, are presented in Table S2 (Supporting Information) in accordance with the atom numbering scheme given in Fig. 2. The molecule consists of four phenyl rings (R1, R6, R7, R9), three pyrrole rings (R2, R5, R8), a single five-membered ring (R3) and a six-membered ring (R4). The two rings R1 and R2 as well R8 and R9 are basically coplanar, as evident from the dihedral angles (N12–C69–C68–C76 (~179°) and C93–C92–C91–C90 (~ –178°)),

respectively. However, rings R3, R4, R5, and R6 are not in a plane with each other. Rings R7 and R8 as well the rings R2 and R6 are bridging with the SO2 group. Furthermore, to compare the molecular structures of both conformers, the overlapped structures are shown in Fig. 5. It can be clearly seen from Fig. 5 that conformers I and V are exactly overlapped with each other, except for the orientation of ring R6 and the C23=O4 group. It is worth mentioning that from Table S2 and Fig. 5, the ring R6 of conformer I is tilted by an angle ~28° with conformer V, and that the C23=O4 group is facing ~180° opposite to conformer V.

Vibrational assignmentsOn account of such a huge molecule, a vibrational assignment

of all the normal modes is not possible to collect from the force field-based simulations. Hence, tentative assignments of selective vibrational modes were made and are discussed on the basis of the normal coordinate analysis, relative intensities, energies and line shape. The spectral analysis of the observed FT-IR and FT-Raman spectra and theoretically predicted spectra of both the conformations V and I are shown in Figs. 6 and 7, respectively. Since the molecule possesses C1 point group symmetry, most of the vibrational modes are expected to be active in both the IR and Raman spectra. All of the vibrational

Fig. 4　Optimized structure of the most stable conformer I of BD.Fig. 5　Comparison of the optimized structures of conformer I (green) with conformer V (red) of BD.

Fig. 6　Combine observed and calculated (scaled) infrared spectrum of BD, at room temperature in the higher region (3700 – 2800 cm–1) and a lower region (1800 – 400 cm–1).


bands have been assigned carefully by comparing previous reports of similar kind of molecules.6–10 The calculated scaled and unscaled wavenumbers of both the conformers and the corresponding observed peaks are tabulated in Table 1.

In the present study, the NH stretching vibrations were observed only in the infrared spectrum with a broad peak at 3357 cm–1 and calculated at 3452/3459 cm–1 in conformers I/V, respectively. The lower shift in the wavenumber and broadening in peak confirms the presence of dimerization through intermolecular (N–H···O) hydrogen bonding.17–19 The ring CH stretching vibrations are found in the range of 3100 – 3060 cm–1. CH stretching vibration of ring R9 was observed at 3069 cm–1 in both the infrared and Raman spectra. The presence of various CH3/CH2 groups in the molecule results in overlapping of the peaks; hence, it is very difficult to prepare an exact assignment of this region. The asymmetric and symmetric stretching vibrations of the CH3 and CH2 groups were found in the region 3054 – 2895 cm–1. The asymmetric stretching vibrations of C16H3 were observed at 2973 cm–1 in IR, while the corresponding peak was not observed in the Raman spectra. The asymmetric stretching vibrations of C64H3 are observed at 2956/2971 cm–1 in IR/Raman spectra, respectively. The symmetric stretching vibrations of C64H3 are observed at 2896/2878 cm–1 in IR/Raman spectra, respectively. The symmetric stretching vibrations of C52H2 are observed at 2860 cm–1 only in the FT-IR spectrum. The calculated and experimental peaks for CH stretching vibrations of both the CH3 and CH2 groups are in good agreement with each other.

In the lower wavenumber region, the peaks at 1700 and 1702 cm–1 were observed in IR and Raman spectra, respectively, which correspond to C=O stretching. The observed lower shift in the carbonyl group suggest the formation of a C=O···H type network with the neighboring moiety, and confirmed the presence of intermolecular H-bonding.18–20 The CC stretching vibrations of ring R4 is observed at 1638 and 1646 cm–1 in IR and Raman spectra, respectively. CH in-plane bending vibrations are observed in a wide range from 1515 to 1093 cm–1. CH in-plane bending of ring R1 is observed at 1477 cm–1 in the FT-IR spectrum and the calculated peak at 1460/1461 cm–1 in conformers I/V, respectively. The scissoring of C108H2 is observed at 1448/1453 cm–1 in FT-IR/FT-Raman spectra, respectively. The peak observed at 1350/1382 cm–1 in the IR/Raman spectra is respectively assigned to C20H2 wagging. The stretching of S2O2 is observed at 1091 cm–1 in FT-IR, while it is not active in the Raman spectra. The stretching vibrations between the carbon atoms in the linear chain ν(C108C111) are

observed at 1030 and 1029 cm–1 in the infrared and Raman spectra, respectively. The ring CH out-of-plane bending is found within the range of 1093 – 937 cm–1. The peak observed at 915 cm–1 in both FT-IR and FT-Raman spectra corresponds to the out-of-plane bending of ring R7. A close agreement was found between the scaled and observed wavenumbers as well as the intensities of the observed infrared and Raman bands.

Molecular electrostatic potentialThe MEP is an important tool for investigating the active

binding sites of the isolated molecule.21–25 The MEP is useful as an indicator of the reactive sites of a molecule that predicts the possibility of interactions with reactants.26 The color-mapped surface generated from the cube files indicates the sites that are suitable for electrophilic and nucleophilic attack. The red color represents the region of the most negative electrostatic potential, blue represents the region of the most positive electrostatic

Fig. 7　Combine observed and calculated (scaled) Raman spectrum of BD, at room temperature in the higher region (3700 – 2800 cm–1) and a lower region (1800 – 100 cm–1).

Table 1　Observed and calculated vibrational wavenumbers (in cm–1) of conformers I and V of BD

Unscaled

ScaledFT-IR

FT-Raman

Vibrational assignmentaCon-

former ICon-

former V

3598 3452 3459 33573207 3083 3083 3069 3069 R9[CH]3136 3013 3015 2973 νa(C16H3) + νa(C20H2)3117 2991 2997 2956 2971 νa(C64H3)3046 2928 2929 2928 2934 νs(C56H3) + νs(C60H3)3022 2904 2906 2896 2878 νs(C64H3)3011 2895 2895 2860 νs(C52H2)1791 1719 1721 1700 1702 ν(C23=O)1741 1675 1674 1638 1646 R4[ν(CC)]1562 1501 1501 1516 δin(N13H)1520 1460 1461 1477 R1[δin(CH)]1498 1440 1440 1448 1453 δsci(C108H2)1389 1332 1335 1350 1382 ω(C20H2) + δ(C16H3)1364 1312 1311 1341 R7[ν(CC) + δin(CH)]1134 1095 1091 1091 ν(S2O2)1052 1015 1012 1030 1029 ν(C108C111)1013 974 974 997 R7[δtri] 947 910 910 915 915 R7[δoop(CH)]

a. Proposed assignment for vibrational normal modes.Types of vibrations: ν, stretching; δ, deformation (bending); oop, out-of-plane bending; ω, wagging; tri, trigonal; in, in-plane.


potential, and green represents the region of zero potential. Such mapped electrostatic potential surfaces have been plotted for both conformers I and V using GaussView 05 software. The MEP maps of both conformers look similar, and are presented in Figs. 8a and 8b. To find the electrophilic and nucleophilic sites precisely, the electrostatic point charges and potential values on each atom with respect to the other have been predicted; the most electrophilic and nucleophiles are depicted in Table 2.

MEP shows that the negative potential is localized more over the oxygen atoms O4, O6 of the carbonyl group, illustrated as a reddish blob, while O5, O7, O8, and O9 atoms exhibit less electronegative potentials and reflected as a yellowish blob. From Table 2, it is clearly seen that N13 is the most electrophilic site in the molecule, followed by O4, O6, and O10. Since N13 is surrounded by many electropositive atoms of carbon, it does not seem to be an electrophile in Figs. 8a and 8b.

The positive charge is localized on rings R6 and R7, which is shown as a bluish blob. The derived electrostatic point charges show that the carbon atoms of the carbonyl group, such as C107 and C23, are the most nucleophile species in the molecule. From these results, one can easily understand the reactive behavior of the molecule. The oxygen atoms of the carbonyl group exert the most negative potential, and are major active electrophilic centers, whereas the whole molecule seems to exert almost neutral electrostatic potential (green color). The

positive regions (blue) are considered to be possible sites for nucleophilic attack. These reactive sites predict the possible interaction sites for reactants.

Natural bond orbitalsNBO analysis has been performed for both conformers I and

V using the DFT method with the B3LYP/6-31G(d,p) level of theory, and are tabulated in Tables S3 and S4 (Supporting Information), respectively. The NBO analysis enables us to understand the hybridization, charge transfer, covalency effects and intramolecular and conjugative interactions. Additionally, it provides a better understanding of the charge delocalization between the occupied, Lewis-type (bond or lone pair) NBO orbitals and unoccupied (antibonding) non-Lewis NBO orbitals. In the present study, the lone-pair orbitals, antibonding orbitals and the interacting stabilization energy between them have been analyzed using second-order micro-disturbance theory. The higher value of the hyperconjugative interaction energy E(2) results in a more intensive interaction between the electron donors to the electron acceptors.27–29

The most important interactions between the lone-pair orbitals and the antibonding orbitals result in stabilization of the molecule. The lone-pair of twelve atoms is actively involved in the strong interaction with high stabilizing energy. Among them, the strongest interaction has been derived from lone-pair orbital (LP1) of N11→π*(O4–C23) and (LP2) of O3→π*(O4–C23), leading to stabilization with energy of 268.55/285.85 and 177.91/187.87 kJmol–1 in conformers I/V, respectively. The presence of oxygen (O) atoms and nitrogen atoms (N) in the molecule increase the charge conjugation, resulting in molecular stabilization. The detailed significant results derived from other interactions are depicted in Tables S3 and S4.

Another important intramolecular hyperconjugative interaction was formed by the orbital overlap between π(C–C)→π*(C–C), in rings R1, R6, R7 and R9, which results in ICT (intramolecular charge transfer) causing stabilization of the system within ~80 – 92 kJ mol–1, and further stabilizes into π*(C–C)→π*(C–C) with enormous energy of ~664 – 995 kJ mol–1. These interactions are observed as an increase in the electron density (ED) in the C–C antibonding orbital, which weakens the respective bonds. The electron density of the conjugated bond of the benzene ring (~1.6e) clearly demonstrates strong delocalization. These charge transfers are responsible for the structure activity of the system.

Table 2　Electrostatic point charges and potential values on most electrophiles and nucleophiles of conformers I and V of BD

Atoms

Conformer I Conformer V

Point charges (e)

V(r) (arb. unit)

Point charges (e)

V(r) (arb. unit)

Electrophiles N13 –0.62976 –18.3467 –0.63623 –18.344 O4 –0.57903 –22.3479 –0.53687 –22.3489 O6 –0.52894 –22.3676 –0.52882 –22.3647 O10 –0.48708 –22.3219 –0.48213 –22.3186Nucleophiles C107 0.816203 –14.6149 0.812274 –14.6122 C23 0.785043 –14.5934 0.671488 –14.5942 S1 0.719483 –58.9251 0.697307 –58.9241 S2 0.703547 –58.9345 0.743399 –58.9299

Fig. 8　Molecular electrostatic potential mapped on the isodensity surface in the range from (a) –6.019e-2 (red) to +6.019e-2 (blue) for conformer I (b) –5.790e-2 (red) to +5.790e-2 (blue) for conformer V of BD.


Conclusions

In continuation of our previous work on the borerverine derivative, conformational analysis is carried out along with vibrational analysis using density functional theory. The reported crystallographic structure is further optimized using DFT by employing the B3LYP/6-31G(d,p) method, followed by conformational analysis. The lowest-energy conformer (I) and the optimized crystallographic structure (V) have been carefully investigated. The geometrical parameters of these two conformers were analyzed, showing the difference in the orientation of the ring R6 and C23=O4 group.

We have proceeded with these two conformers, and a spectroscopic investigation was made using FT-IR and FT-Raman techniques. On account of the huge molecule, a tentative assignment is prepared for the analysis of vibrational modes. A good agreement was found between the wavenumbers and the intensities of the observed and simulated spectra. The involvement of intermolecular H-bonding has also been confirmed in the NH and C=O groups. MEP was plotted and has predicted the charge density distribution as well the reactive sites of the molecule. The NBO investigation revealed delocalization of the π and lone-paired electrons of the phenyl ring and nitrogen/oxygen atoms, respectively. O4 and O6 have the most intensive interaction between the Lewis acceptor and Lewis donor, which result in the stability of the molecule.

Acknowledgements

S. S. and T. K. are thankful for the support from the UGC under BSR meritorious and D. S. Kothari fellowship scheme, respectively.

Supporting Information

The relative energy of all the conformers are tabulated in Table S1, geometrical parameters of conformers I and V are tabulated as Table S2, the natural bond analysis for both conformers I and V are presented in Tables S3 and S4, respectively. This material is available free of charge on the Web at http://www.jsac.or.jp/analsci/.

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Conformational Study and Vibrational Spectroscopic (FT-IR