A Comparative Study of DFT/B3LYP/6-31G(d,p), RM062X/6-31G(d,p), B3LYP/6-311++G(d,p) and HSEH1PBE/6-31G(d,p) Methods Applied to Molecular Geometry and Electronic properties of Cs-C60Cl6 Molecule

Year 2021, Volume 11, Issue 2, 456 - 473, 31.12.2021

Ebru KARAKAŞ SARIKAYA Ömer DERELİ Semiha BAHÇELİ

https://doi.org/10.37094/adyujsci.938050

Abstract

In this study, four different levels, B3LYP/6-31G(d,p), RM062X/6-31G(d,p), B3LYP/6-311++G(d,p) and HSEH1PBE/6-31G(d,p) of the DFT quantum chemical calculation method have been applied to the molecular structure of the Cs-C60Cl6 molecule as a halogenated fullerene. Additionally, the molecular structure of pure C60 fullerene was presented as complementary and supportive work. Furthermore, the simulated FT-IR, Raman and UV-Vis (in cyclohexane solvent) spectra, HOMO-LUMO analysis, the molecular electrostatic potential (MEP) map, the 13C NMR chemical shift values in both gas phase and tetrachloromethane with deuterated chloroform solvent and the thermodynamics properties at the mentioned levels of the Cs-C60Cl6 molecule were reported. Fullerene has many physical and electrochemical properties, which can be utilized in several medical fields. Especially, it can fit inside the hydrophobic cavity of HIV proteases, restricting the get into substrates to the catalytic site of the enzyme. Hence, it is utilizable as an antioxidant and radical scavenger.

Keywords

Fullerenes, Cs-C60-Cl6, DFT, HOMO-LUMO analysis, The 13C NMR chemical shifts, MEP

Cs-C60Cl6 Molekülünün Moleküler Geometri ve Elektronik Özelliklerine Uygulanan Metot ve Baz Seti, DFT/B3LYP/6-31G(d,p), RM062X/6-31G(d,p), B3LYP/6-311++ G(d,p) ve HSEH1PBE/6-31G(d,p), Yöntemlerinin Karşılaştırmalı İncelemesi

Abstract

Bu çalışmada, DFT kuantum kimyasal hesaplama yönteminin, B3LYP/6-31G(d,p), RM062X/6-31G(d,p), B3LYP/6-311++G(d,p) ve HSEH1PBE/6-31G(d,p) olmak üzere dört farklı düzeyinde, halojenleşmiş bir fulleren olan Cs-C60Cl6 molekülünün moleküler yapısına uygulanmıştır. Ek olarak, saf C60 fullerenin molekül yapısı, tamamlayıcı ve destekleyici bir çalışma olarak sunulmuştur. Ayrıca, simüle edilmiş FT-IR, Raman ve UV-Vis (sikloheksan çözücüsünde) spektrumları, HOMO-LUMO analizi, moleküler elektrostatik potansiyel (MEP) haritası, döteryumlanmış kloroform çözücü ile hem gaz fazında hem de tetraklorometanda 13C NMR kimyasal kayma değerleri ve Cs-C60Cl6 molekülünün belirtilen düzeylerdeki termodinamik özellikleri rapor edilmiştir. Fuleren, çeşitli tıbbi alanlarda kullanılabilecek birçok fiziksel ve elektrokimyasal özelliğe sahiptir. Özellikle, HIV proteazlarının hidrofobik boşluğunun içine sığabilir ve substratlara enzimin katalitik bölgesine girmesini kısıtlayabilir. Bu nedenle, bir antioksidan ve radikal temizleyici olarak kullanılabilir.

Keywords

Fulleren; Cs-C60Cl6; DFT; HOMO-LUMO analizi; 13C NMR kimyasal kayma; MEP.

References

• [[1] Kroto, H.W., Heath, J.R., O’Brien, S.C., Curl, R.F. Smalley, R.E., C60:Buckminsterfullerene, Nature, 318(6042), 162-163, 1985.
• [2] Ward, J., ed., The artifacts of R. buckminster fuller: A comprehensive collection of his designs and drawings in four volumes, New York: Garland, 1984.
• [3] Krätschmer, W., Fostiropoulos, K., Huffman, D.R., The infrared and ultraviolet absorption spectra of laboratory-produced carbon dust: evidence for the presence of the C60 molecule, Chemical Physics Letters, 170(2-3), 167-170, 1990.
• [4] Kroto, H.W., Allaf, A.W., Balm, S.P., C60:Buckminsterfullerene, Chemical Reviews, 91(6), 1213-1235, 1991.
• [5] Lin, T., Zhang, W.D., Huang, J., He, C.A., DFT study of the amination of fullerenes and carbon nanotubes: reactivity and curvature, The Journal of Physical Chemistry B, 109(28), 13755-13760, 2005.
• [6] Yang, C.C., Shen, J.Y., Well-defined sensing property of ZnO: Al relative humidity sensor with selected buffer layer, Vacuum, 118, 118-124, 2015.
• [7] Nalwa, H.S., ed. Handbook of advanced electronic and photonic materials and devices, ten-volume set, Academic Press, 1 ed., United States, 2000.
• [8] Omacrsawa, E., Perspectives of fullerene nanotechnology, Kluwer Academic Publisher, Dordrecht-Boston-London, 2002.
• [9] Bianco A., Da Ros T., Langa. F., Nierengarten J.F., Biological applications of fullerenes, in fullerenes principles and applications, Royal Society of Chemistry, 10, 301-328, 2008.
• [10] Hudhomme P., Cousseau, J., Langa. F., Nierengarten J.F., Plastic solar cells using fullerene derivatives in the photoactive layer, in fullerenes principles and applications, Royal Society of Chemistry, 8, 221-265, 2008.
• [11] So, H.Y., Wilkins, C.L., First observation of carbon aggregate ions >C600+ by laser desorption Fourier transform mass spectrometry, The Journal of Physical Chemistry, 93(4), 1184-1187, 1989.
• [12] Rubin, Y., Kahr, M., Knobler, C.B., Diederich, F., Wilkins, C.L., The higher oxides of carbon C8nO2n (n= 3-5): synthesis, characterization, and X-ray crystal structure. Formation of cyclo [n] carbon ions Cn+ (n= 18, 24), Cn- (n= 18, 24, 30), and higher carbon ions including C60+ in laser desorption Fourier transform mass spectrometric experiments, Journal of the American Chemical Society, 113(2), 495-500, 1991.
• [13] Makurin, Y.N., Sofronov, A.A., Gusev, A.I., Ivanovsky, A.L., Electronic structure and chemical stabilization of C28 fullerene, Chemical Physics, 270(2), 293-308, 2001.
• [14] Lin, M., Chiu, Y.N., Lai, S.T., Xiao, J., Fu, M., Theoretical study of metallofullerenes M@C32, Journal of Molecular Structure: Theochem, 422(1-3), 57-67, 1998.
• [15] Guo, T., Smalley, R.E., Scuseria, G.E., Ab initio theoretical predictions of C28, C28H4, C28F4, (Ti@C28)H4, and M@C28 (M= Mg, Al, Si, S, Ca, Sc, Ti, Ge, Zr, and Sn), The Journal of Chemical Physics, 99(1), 352-359, 1993.
• [16] Kadish, K.M., Ruoff, R.S., Fullerenes: chemistry, physics, and technology, John Wiley & Sons, Newyork, 2000.
• [17] Prinzbach, H., Weiler, A., Landenberger, P., Wahl, F., Wörth, J., Scott, L.T., Issendorff, B.V., Gas-phase production and photoelectron spectroscopy of the smallest fullerene, C20, Nature, 407(6800), 60-63, 2000.
• [18] Priimagi, A., Cavallo, G., Metrangolo, P., Resnati, G., The halogen bond in the design of functional supramolecular materials: recent advances, Accounts of Chemical Research, 46(11), 2686-2695, 2013.
• [19] Popov A.A., Senyavin V.M., and Granovsky A.A., Vibrational spectra of chloro- and bromofullerenes, Fullerenes, Nanotubes, And Carbon Nanostructures, Marcel Dekker, 12, 305–310, 2004.
• [20] Troshin, P.A., Lyubovskaya, R.N., Ioffe, I.N., Shustova, N.B., Kemnitz, E., Troyanov, S.I., Synthesis and structure of the highly chlorinated [60]Fullerene C60Cl30 with a drum‐shaped carbon cage, Angewandte Chemie International Edition, 44(2), 234-237, 2005.
• [21] Kuvychko, I.V., Streletskii, A.V., Popov, A.A., Kotsiris, S.G., Drewello, T., Strauss, S.H., Boltalina, O.V., Seven‐minute synthesis of pure Cs‐C60Cl6 from [60] Fullerene and iodine monochloride: First IR, Raman, and Mass spectra of 99 mol% C60Cl6, Chemistry A European Journal, 11(18), 5426-5436, 2005.
• [22] Yan, Q.B., Zheng, Q.R., Su, G., Theoretical study on the structures, properties and spectroscopies of fullerene derivatives C66X4 (X= H, F, Cl), Carbon, 45(9), 1821-1827, 2007.
• [23] Troyanov, S.I., Boltalina, O.V., Kouvytchko, I.V., Troshin, P.A., Kemnitz, E., Hitchcock, P.B., Taylor, R., Molecular and crystal structure of the adducts of C60F18 with aromatic hydrocarbons, Fullerenes, Nanotubes And Carbon Nanostructures, 10(3), 243-259, 2002.
• [24] Adjizian, J.J., Vlandas, A., Rio, J., Charlier, J.C., Ewels, C.P., Ab initio infrared vibrational modes for neutral and charged small fullerenes (C20, C24, C26, C28, C30 and C60), Philosophical Transactions Of The Royal Society A: Mathematical, Physical And Engineering Sciences, 374(2076), 20150323, 2016.
• [25] Yang, T., Zhao, X., Nagase, S., Di-lanthanide encapsulated into large fullerene C100: a DFT survey, Physical Chemistry Chemical Physics, 13(11), 5034-5037, 2011.
• [26] Carter, E.A., Rossky, P.J., Computational and theoretical chemistry, Accounts of Chemical Research, 39(2), 71-72, 2006.
• [27] Bauernschmitt, R., Ahlrichs, R., Hennrich, F.H., Kappes, M.M., Experiment versus time dependent density functional theory prediction of fullerene electronic absorption, Journal of the American Chemical Society, 120(20), 5052-5059, 1998.
• [28] Schettino, V., Pagliai, M., Cardini, G., The infrared and Raman spectra of fullerene C70. DFT calculations and correlation with C60, The Journal of Physical Chemistry A, 106(9), 1815-1823, 2002.
• [29] Jensen, F. Introduction to computational chemistry, John Wiley & Sons, Newyork, 664p., 3 ed., 1974.
• [30] Pulay, P., Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules: I. Theory, Molecular Physics, 17(2), 197-204, 1969.
• [31] Perdew, J.P., “Electronic Structure of Solids”, in Proceeding of the 21st Annual International Symposium, p11, 1991.
• [32] Perdew, J. P., Wang, Y., Pair-distribution function and its coupling-constant average for the spin-polarized electron gas, Physical Review B, 46(20), 12947, 1992.
• [33] Becke, A.D., A new mixing of Hartree–Fock and local density‐functional theories, The Journal of Chemical Physics, 98(2), 1372-1377, 1993.
• [34] Lee, C., Yang, W., Parr, R.G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Physical Review B, 37(2), 785, 1988.
• [35] Burke, K., Perdew, J.P., Wang, Y., Derivation of a Generalized Gradient Approximation: The PW91 Density Functional, Electronic Density Functional Theory, Springer, Boston, MA., 81-111, 1998.
• [36] Zhao, Y., Pu, J., Lynch, B. J., Truhlar, D.G., Tests of second-generation and third-generation density functionals for thermochemical kinetics, Physical Chemistry Chemical Physics, 6(4), 673-676, 2004.
• [37] Heyd, J., Scuseria, G.E., Ernzerhof, M., Hybrid functionals based on a screened Coulomb potential, The Journal of Chemical Physics, 118(18), 8207-8215, 2006.
• [38] Wolinski, K., Hinton, J.F., Pulay, P., Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations, Journal of the American Chemical Society, 112(23), 8251-8260, 1990.
• [39] Avcı, D., Dede, B., Bahceli, S., Varkal, D., Spectroscopic and quantum chemical calculation study on 2–ethoxythiazole molecule, Journal of Molecular Structure, 1138, 110-117, 2017.
• [40] Heyd, J., Scuseria, G.E., Ernzerhof, M., Hybrid functionals based on a screened Coulomb potential, The Journal of Chemical Physics, 118(18), 8207-8215, 2003.
• [41] Zhao, Y., Truhlar, D.G., Comparative DFT study of van der Waals complexes: Rare-Gas Dimers, Alkaline-Earth Dimers, Zinc Dimer, And Zinc-Rare-Gas Dimers, The Journal of Physical Chemistry A, 110(15), 5121-5129, 2006.
• [42] Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., ... Fox, D.J., Gaussian 09, Gaussian, Inc., Wallingford CT, 2009.
• [43] Dennington, R., Keith, T., Millam, J., GaussView Version 5. Semichem Inc., Shawnee Mission, Kans, 2009.
• [44] Foresman, J.B., Frisch., E., Exploring chemistry with electronic structure methods, Gaussian Inc., Pittsburgh, Pa., USA, 1993.
• [45] London, F. Théorie quantique des courants interatomiques dans les combinaisons aromatiques, Journal de Physique et le Radium, 8(10), 397-409, 1937.
• [46] Bauernschmitt, R., Ahlrichs, R., Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory, Chemical Physics Letters, 256(4-5), 454-464, 1996.
• [47] Jamorski, C., Casida, M.E., Salahub, D.R., Dynamic polarizabilities and excitation spectra from a molecular implementation of time‐dependent density‐functional response theory: N2 as a case study, The Journal of Chemical Physics, 104(13), 5134-5147, 1996.
• [48] Birkett, P.R., Hitchcock, P.B., Kroto, H.W., Taylor, R., Walton, D.R., Preparation and characterization of C60Br6 and C60Br8, Nature, 357(6378), 479-481, 1992.
• [49] Birkett, P.R., Avent, A.G., Darwish, A.D., Kroto, H.W., Taylor, R., Walton, D.R., Holey fullerenes! a bis-lactone derivative of [70 fullerene with an eleven-atom orifice, Journal of the Chemical Society, Chemical Communications, 18, 1869-1870, 1995.
• [50] Politzer, P., Murray, J.S., Clark, T., Halogen bonding and other σ-hole interactions: a perspective, Physical Chemistry Chemical Physics, 15(27), 11178-11189, 2013.
• [51] Troyanov, S.I., Troshin, P.A., Boltalina, O.V., Kemnitz, E., Bromination of [60]Fullerene. II. Crystal and molecular structure of [60]Fullerene bromides, C60Br6, C60Br8, and C60Br24, Fullerenes, Nanotubes and Carbon Nanostructures, 11(1), 61-77, 2003.
• [52] Fedurco, M., Olmstead, M.M., Fawcett, W.R., Single-crystal X-ray structure of C60•6SbPh3. A well-ordered structure of C60 and a new fullerene solvent, Inorganic Chemistry, 34(1), 390-392, 1995.
• [53] Birkett, P.R., Avent, A.G., Darwish, A.D., Kroto, H.W., Taylor, R., Walton, D.R.M, Preparation and 13C NMR spectroscopic characterisation of C60Cl6, Journal of the Chemical Society, Chemical Communications, 15, 1230-1232, 1993.
• [54] Kuvychko, I.V., Streletskii, A.V., Shustova, N.B., Seppelt, K., Drewello, T., Popov, A.A., Boltalina, O.V., Soluble Chlorofullerenes C60Cl2,4,6,8,10. Synthesis, purification, compositional analysis, stability, and experimental/theoretical structure elucidation, including the X-ray structure of C1-C60Cl10, Journal of the American Chemical Society, 132(18), 6443-6462, 2010.
• [55] Süleymanoğlu, N., Ustabaş, R., Alpaslan, Y.B., Eyduran, F., İskeleli, N.O., Experimental and theoretical investigation of the molecular and electronic structure of 3-ethoxy-4-isopropylaminocyclobut-3-ene-1,2-dione, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 96, 35-41, 2012.
• [56] Popov, A.A., Kareev, I.E., Shustova, N.B., Stukalin, E.B., Lebedkin, S.F., Seppelt, K., Dunsch, L., Electrochemical, spectroscopic, and DFT study of C60(CF3)n frontier orbitals (n= 2− 18): the link between double bonds in pentagons and reduction potentials, Journal of the American Chemical Society, 129(37), 11551-11568, 2007.
• [57] Pearson, R.G., Absolute electronegativity and hardness correlated with molecular orbital theory, Proceedings of the National Academy of Sciences, 83(22), 8440-8441, 1986.
• [58] Lee, C.K., Kim, Y.H. Spectroscopic studies of conjugated uracil derivatives, Bulletin of the Korean Chemical Society, 12(2), 207-210, 1991.
• [59] Fukui, K., Role of frontier orbitals in chemical reactions, Science, 218(4574), 747-754, 1982.
• [60] Chtita, S., Ghamali, M., Larif, M., Adad, A., Hmammouchi, R., Bouachrine, M., Lakhlifi, T., Prediction of biological activity of imidazo [1,2-a] pyrazine derivatives by combining DFT and QSAR results, International Journal of Innovative Research in Science, Engineering and Technology, 2(11), 7951-7962, 2013.
• [61] Murray, J.S., Sen K. eds., Molecular electrostatic potentials concepts and applications, Elsevier Science BV, Amsterdam, The Netherlands, 1996.
• [62] Pîrnău, A., Chiş, V., Oniga, O., Leopold, N., Szabo, L., Baias, M.,nCozar, O., Vibrational and DFT study of 5-(3-pyridyl-methylidene)-thiazolidine-2-thione-4-one, Vibrational spectroscopy, 48(2), 289-296, 2008.
• [63] Sarıkaya, E.K., Bahçeli, S., Varkal, D., Dereli, Ö., FT-IR, micro-Raman and UV–vis spectroscopic and quantum chemical calculation studies on the 6-chloro-4-hydroxy-3-phenyl pyridazine compound, Journal of Molecular Structure, 1141, 44-52, 2017.
• [64] Yilmaz, M., Aydin, B., Dogan, O., Dereli, O., Molecular structure and spectral investigations of 3,5-Di-tert-butyl-o-benzoquinone, Journal of Molecular Structure, 1128, 345-354, 2017.
• [65] Fankam, J.B., Ejuh, G.W., Tchangnwa N.F., Ndjaka, J.M.B., Theoretical investigation of the molecular structure, vibrational spectra, thermodynamic and nonlinear optical properties of 4,5-dibromo-2,7dinitro-fluorescein, Optical and Quantum Electronics, 52, 1-23, 2020.