Spectroscopic (FT-Raman, FT-IR, UV-Vis, and NMR) and Theoretical Analysis of 1-Methylindole: Structural Characterization, Non-Covalent Interactions, and Electronic Properties

Öz

The structural and spectroscopic characterization of 1-Methylindole (1MI) by favors of FT-Raman (4000–200 cm−1), FT- IR (4000–400 cm−1), UV-Vis, and 1H and 13C NMR techniques is presented. The experimental observations were enlightened by density functional theory (DFT) calculations at the B3LYP/6-311G(d,p) level of theory. Geometrical structure of the molecule was obtained, and bond order analysis was performed based on the optimized structure. Non-Covalent Interactions (NCIs) were analyzed by using the Reduced Density Gradient (RDG) with energy density descriptors to visualize the limiting regions of these interactions. Furthermore, molecular charge distribution and isosurface mappings with local extrema were obtained and the critical regions on the molecular surface were visualized. The vibrational spectra were calculated, and the normal modes were assigned based on total energy distribution (TED) calculations. The electronic properties of 1MI were explored experimentally through UV-Vis spectroscopy and analyzed in detail via Atoms in Molecules (AIMs) methodology. Total and partial density of state (TDOS and PDOS) and overlap population density of state (OPDOS) diagrams were calculated and fractional contributions of nonpolar methyl group and aromatic indole to frontier molecular orbitals were obtained through this methodology. Theoretical NMR chemical shifts were assigned based on DFT calculations that use the gauge-invariant atomic orbital (GIAO) method. Inclusion of solvents effect in NMR calculations produces twice less dispersive data and better fitting results to experimental observations. Non-linear optical properties: polarizability, anisotropy of polarizability, and first hyperpolarizability of the molecule were also computed to explore the potential of 1MI as nonlinear spectroscopy agent.

Anahtar Kelimeler

• 1-methylindole
• DFT
• UV
• IR and Raman
• NMR
• Non-Covalent Interactions
• Orbital Fragmentation

Kaynakça

1. [1]. Casapullo, A., Bifulco, G., Bruno, I., Riccio, R. New bisindole alkaloids of the topsentin and hamacanthin classes from the Mediterranean marine sponge Rhaphisia lacazei, 2000. Journal of Natural Products; 63: 447–451.
2. [2]. Garbe, T.R., Kobayashi, M., Shimizu, N., Takesue, N., Ozawa, M., Yukawa, H. Indolyl Carboxylic Acids by Condensation of Indoles with α-Keto Acids, 2000. Journal of Natural Products; 63: 596–598.
3. [3]. Vicente, R. Recent advances in indole syntheses: New routes for a classic target., 2011. Organic & Biomolecular Chemistry; 9: 6469–6480.
4. [4]. Bao, B., Sun, Q., Yao, X., Hong, J., Lee, C.O., Sim, C.J., Im, K.S., Jung, J.H. Cytotoxic bisindole alkaloids from a marine sponge Spongosorites sp., 2005. Journal of Natural Products; 68: 711–715.
5. [5]. Powell, B.J. 5,6-Dihydroxyindole-2-carboxylic acid: A first principles density functional study, 2005. Chemical Physics Letters; 402: 111–115.
6. [6]. Powell, B.J., Baruah, T., Bernstein, N., Brake, K., McKenzie, R.H., Meredith, P., Pederson, M.R. A first-principles density-functional calculation of the electronic and vibrational structure of the key melanin monomers, 2004. Journal of Chemical Physics; 120: 8608–8615.
7. [7]. Zhang, M.-Z., Mulholland, N., Beattie, D., Irwin, D., Gu, Y.-C., Chen, Q., Yang, G.-F., Clough, J. Synthesis and antifungal activity of 3-(1,3,4-oxadiazol-5-yl)-indoles and 3-(1,3,4-oxadiazol-5-yl)methyl-indoles, 2013. European Journal of Medicinal Chemistry; 63: 22–32.
8. [8]. Xu, H., Wang, Q., Yang, W.-B. Antifungal activities of some indole derivatives., n.d. Zeitschrift Fur Naturforschung. Teil C: Biochemie, Biophysik, Biologie, Virologie; 65: 437–439.

9. [9]. Da Silva, J.F.M., Garden, S.J., Pinto, A.C. The Chemistry of Isatins: A Review from 1975 to 1999, 2001. Journal of the Brazilian Chemical Society; 12: 273–324.
10. [10]. Maj, J., Kołodziejczyk, K., Rogóz, Z., Skuza, G. Roxindole, a potential antidepressant. I. Effect on the dopamine system, 1996. Journal of Neural Transmission; 103: 627–641.
11. [11]. i Chen, Scott K. Spear, J.G.H. and R.D.R. Polyethylene glycol and solutions of polyethylene glycol as green reaction media, 2005. Green Chemistry; 7: 64.
12. [12]. Smith, T.R., Sunshine, A., Stark, S.R., Littlefield, D.E., Spruill, S.E., Alexander, W.J. Sumatriptan and Naproxen Sodium for the Acute Treatment of Migraine, 2005. Headache: The Journal of Head and Face Pain; 45: 983–991.
13. [13]. Budovská, M., Pilátová, M., Varinská, L., Mojžiš, J., Mezencev, R. The synthesis and anticancer activity of analogs of the indole phytoalexins brassinin, 1-methoxyspirobrassinol methyl ether and cyclobrassinin, 2013. Bioorganic & Medicinal Chemistry; 21: 6623–6633.
14. [14]. Qin, X., Cui, X. Methyl-indole inhibits pancreatic cancer cell viability by down-regulating ZFX expression, 2020. 3 Biotech; 10: 187.
15. [15]. Billaud, D., Maarouf, E.B., Hannecart, E. Chemical oxidation and polymerization of indole, 1995. Synthetic Metals; 69: 571–572.
16. [16]. Holze, R., Hamann, C.H. Electrosynthetic aspects of anodic reactions of anilines and indoles, 1991. Tetrahedron; 47: 737–746.
17. [17]. Prakash, P.C.P.; R. Electrochemical Synthesis of Polyindole and Its Evaluation for Rechargeable Battery Applications, 1998. Journal of The Electrochemical Society; 145: 999–1003.
18. [18]. Tourillon, G., Garnier, F. New electrochemically generated organic conducting polymers, 1982. Journal of Electroanalytical Chemistry and Interfacial Electrochemistry; 135: 173–178.
19. [19]. Roychowdhury, P., Basak, B.S. The crystal structure of indole, 1975. Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry; 31: 1559–1563.
20. [20]. Catalán, J., de Paz, J.G. The molecular geometry of indole, 1997. Journal of Molecular Structure: THEOCHEM; 401: 189–192.
21. [21]. Lin, J.L., Tzeng, W.B. Mass analyzed threshold ionization spectroscopy of 1-methylindole cation, 2003. Chemical Physics Letters; 377: 620–626.
22. [22]. Karaca, C., Bardak, F., Kose, E., Atac, A. A comprehensive study on the effect of substitution position and solvent effect on absorption and emission characteristics of n-methylindoles via linear response and State-Specific formalisms, 2024. Journal of Photochemistry and Photobiology A: Chemistry; 450: 115469.
23. [23]. Mourik, T. Van, Price, S.L., Clary, D.C. Ab initio calculations on indole–water, 1-methylindole–water and indole–(water)2, 2000. Chemical Physics Letters; 331: 253–261.
24. [24]. Muñoz, M. a., Carmona, C., Balón, M. FTIR and fluorescence studies on the ground and excited state hydrogen-bonding interactions between 1-methylindole and water in water–triethylamine mixtures, 2007. Chemical Physics; 335: 43–48.
25. [25]. Muñoz, M.A., Galán, M., Carmona, C., Balón, M. Hydrogen-bonding interactions between 1-methylindole and alcohols, 2005. Chemical Physics Letters; 401: 109–114.
26. [26]. Mons, M., Dimicoli, I., Tardivel, B., Piuzzi, F., Brenner, V., Millié, P. Site Dependence of the Binding Energy of Water to Indole: Microscopic Approach to the Side Chain Hydration of Tryptophan, 1999. The Journal of Physical Chemistry A; 103: 9958–9965.
27. [27]. Karaca, C., Bardak, F., Kose, E., Atac, A. A comprehensive study on the effect of substitution position and solvent effect on absorption and emission characteristics of n-methylindoles via linear response and State-Specific formalisms, 2024. Journal of Photochemistry and Photobiology A: Chemistry; 450: 115469.
28. [28]. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K.......................... (Gaussian, Inc., Wallingford CT, ). Gaussian 16 Revision A.03, 2016.
29. [29]. Perdew, J.P., Wang, Y. Accurate and simple analytic representation of the electron-gas correlation energy, 1992. Physical Review B; 45: 13244–13249.
30. [30]. Lee, C., Yang, W., Parr, R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, 1988. Physical Review B; 37: 785–789.
31. [31]. Becke, A.D. Density-functional thermochemistry.III. The role of exact exchange, 1993. The Journal of Chemical Physics; 98: 5648–5652.
32. [32]. Sundaraganesan, N., Ilakiamani, S., Saleem, H., Wojciechowski, P.M., Michalska, D. FT-Raman and FT-IR spectra, vibrational assignments and density functional studies of 5-bromo-2-nitropyridine., 2005. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy; 61: 2995–3001.
33. [33]. Baker, J., Jarzecki, A.A., Pulay, P. Direct scaling of primitive valence force constants: An alternative approach to scaled quantum mechanical force fields, 1998. Journal of Physical Chemistry A; 102: 1412–1424.
34. [34]. Dennington, R., Keith, T.A., Millam, J.M. GaussView Version 6, 2016.
35. [35]. O’Boyle, N.M., Tenderholt, A.L., Langner, K.M. Software News and Updates cclib : A Library for Package-Independent Computational Chemistry Algorithms, 2008. Journal of Computational Chemistry; 29: 839–845.
36. [36]. Bader, R. Atoms in Molecules: A Quantum Theory, Oxford University Press, Oxford (UK), 1994.
37. [37]. Mayer, I. Improved definition of bond orders for correlated wave functions, 2012. Chemical Physics Letters; 544: 83–86.
38. [38]. Mayer, I. Bond order and valence indices: A personal account, 2007. Journal of Computational Chemistry; 28: 204–221.
39. [39]. Lu, T., Chen, F. Quantitative analysis of molecular surface based on improved Marching Tetrahedra algorithm, 2012. Journal of Molecular Graphics and Modelling; 38: 314–323.
40. [40]. Lu, T., Chen, F. Multiwfn: A multifunctional wavefunction analyzer, 2012. Journal of Computational Chemistry; 33: 580–592.
41. [41]. Karaca, C., Atac, A., Karabacak, M. Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid, 2015. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 136: 295–305.
42. [42]. Gorelsky, S.I. Complexes with a single metal-metal bond as a sensitive probe of quality of exchange-correlation functionals, 2012. Journal of Chemical Theory and Computation; 8: 908–914.
43. [43]. Johnson, E.R., Keinan, S., Mori-Sánchez, P., Contreras-García, J., Cohen, A.J., Yang, W. Revealing noncovalent interactions., 2010. Journal of the American Chemical Society; 132: 6498–506.
44. [44]. Runge, E., Gross, E.K.U. Density-Functional Theory for Time-Dependent Systems, 1984. Physical Review Letters; 52: 997–1000.
45. [45]. Humphrey, W., Dalke, A., Schulten, K. VMD: Visual molecular dynamics, 1996. Journal of Molecular Graphics; 14: 33–38.
46. [46]. Atac, A., Karaca, C., Gunnaz, S., Karabacak, M. Vibrational (FT-IR and FT-Raman), electronic (UV–Vis), NMR (1H and 13C) spectra and reactivity analyses of 4,5-dimethyl-o-phenylenediamine, 2014. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 130: 516–525.
47. [47]. Socrates, G. Infrared and Raman Characteristic Group Frequencies: Tables and Charts, John Wiley & Sons Ltd., West Sussex, England, 2001.
48. [48]. Collier, W., Klots, T.. Heteroatom derivatives of indene. Part 1. Vibrational frequencies and a refined scaled overlay of the AM1 force field of indole, benzofuran benzothiophene, benzoxazole and benzothiazole, 1995. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 51: 1255–1272.
49. [49]. Klots, T., Collier, W.. Heteroatom derivatives of indene Part 3. Vibrational spectra of benzoxazole, benzofuran, and indole, 1995. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 51: 1291–1316.
50. [50]. Silverstein, R.M., Webster, F.X., Kiemle, D.J. Spectrometric identification of organic compounds, John Wiley & Sons, 2005.
51. [51]. Kalsi, P.S. Spectroscopy of Organic Compounds, Wiley Eastern Limited, New Delhi, 1995.
52. [52]. Jeyavijayan, S., Arivazhagan, M. Study of density functional theory and vibrational spectra of hypoxanthine, 2010. Indian Journal of Pure and Applied Physics; 48: 869–874.
53. [53]. Sundaraganesan, N., Joshua, B.D. Vibrational spectra and fundamental structural assignments from HF and DFT calculations of methyl benzoate., 2007. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy; 68: 771–7.
54. [54]. Ramalingam, S., Jayaprakash, a, Mohan, S., Karabacak, M. Vibrational investigation on FT-IR and FT-Raman spectra, IR intensity, Raman activity, peak resemblance, ideal estimation, standard deviation of computed frequencies analyses and electronic structure on 3-methyl-1,2-butadiene using HF and DFT (LSDA/B3LYP/, 2011. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy; 82: 79–90.
55. [55]. Kose, E., Atac, A., Bardak, F. The structural and spectroscopic investigation of 2-chloro-3-methylquinoline by DFT method and UV–Vis, NMR and vibrational spectral techniques combined with molecular docking analysis, 2018. Journal of Molecular Structure; 1163: 147–160.
56. [56]. Silverstein, Robert M., Bassler, G. Clayton, Morrill, T.C. Spectrometric Identification of Organic Compounds, Wiley, New York, 1981.
57. [57]. Varsányi, G., Kovner, M.A., Láng, L. Assignments for Vibrational Spectra of 700 Benzene Derivatives, 1973.
58. [58]. Guillaumont, D., Nakamura, S. Calculation of the absorption wavelength of dyes using time-dependent density-functional theory (TD-DFT), 2000. Dyes and Pigments; 46: 85–92.
59. [59]. Bardak, F., Karaca, C., Bilgili, S., Atac, A., Mavis, T., Asiri, A.M., Karabacak, M., Kose, E. Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT., 2016. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 165: 33–46.
60. [60]. Hoffman, R. Solids and surfaces: a chemist’s view of bonding in extended structures, 1988.
61. [61]. Hughbanks, T., Hoffmann, R. Chains of trans-edge-sharing molybdenum octahedra: metal-metal bonding in extended systems, 1983. Journal of the American Chemical Society; 105: 3528–3537.
62. [62]. Małecki, J.G. Synthesis, crystal, molecular and electronic structures of thiocyanate ruthenium complexes with pyridine and its derivatives as ligands, 2010. Polyhedron; 29: 1973–1979.
63. [63]. Chen, M., Waghmare, U. V., Friend, C.M., Kaxiras, E. A density functional study of clean and hydrogen-covered α-MoO3(010): Electronic structure and surface relaxation, 1998. The Journal of Chemical Physics; 109: 6854–6860.
64. [64]. Babur Saş, E., Kurt, M., Can, M., Okur, S., İçli, S., Demiç, S. Structural investigation of a self-assembled monolayer material 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid for organic light-emitting devices, 2014. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 133: 307–317.
65. [65]. Fukui, K. Role of frontier orbitals in chemical reactions., 1982. Science (New York, N.Y.); 218: 747–754.
66. [66]. Jayavarthanan, T., Sundaraganesan, N., Karabacak, M., Cinar, M., Kurt, M. Vibrational spectra, UV and NMR, first order hyperpolarizability and HOMO-LUMO analysis of 2-amino-4-chloro-6-methylpyrimidine, 2012. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy; 97: 811–824.
67. [67]. Wolinski, K., Hinton, J.F., Pulay, P. Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations, 1990. Journal of the American Chemical Society; 112: 8251–8260.
68. [68]. Sajan, D., Devi, T.U., Safakath, K., Philip, R., Němec, I., Karabacak, M. Ultrafast optical nonlinearity, electronic absorption, vibrational spectra and solvent effect studies of ninhydrin, 2013. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy; 109: 331–343.
69. [69]. Cho, M., Fleming, G.R., Mukamel, S. Nonlinear response functions for birefringence and dichroism measurements in condensed phases, 1993. The Journal of Chemical Physics; 98: 5314–5326.