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Current Organic Chemistry

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ISSN (Print): 1385-2728
ISSN (Online): 1875-5348

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Letter Article

NMR and FT-IR Investigation Study and Topological Analysis of Various Conformations of 2,5-dimethyl-2,5-dihydroxyl-1,4-dithian using Density Functional Theory Method

Author(s): Elmira Danaie, Shiva Masoudi* and Nasrin Masnabadi

Volume 27, Issue 13, 2023

Published on: 04 October, 2023

Page: [1123 - 1131] Pages: 9

DOI: 10.2174/1385272827666230911115837

Price: $65

Abstract

1,4-dithian-2,5-dihydroxyl is the major source for the synthesis of sulfur-containing heterocyclic compounds such as thiophene and 1,3-thiazole derivatives, which these compounds are widely used in pharmaceuticals and agricultural industries. Sulfur-containing heterocycles, such as 2-aminothiophene, thiazolidine, oxothiazolidine, and thiazoles, can be comprehensively synthesized from dimerization of the derivatives of 1,4-dithian-2,5-dihydroxyl. FT-IR and NMR spectra of axial and equatorial conformations of 2,5-dimethyl-2,5-dihydroxyl-1,4-dithian compound were investigated by density functional theory (DFT) using B3LYP/6-311++G** and M06-2X/aug-ccpVDZ computational methods. The topological properties of the electron charge density were calculated by the quantum theory of atoms in molecules (QTAIM) and non-covalent interactions/ reduced electron density gradient (NCI-RDG) theoretical methods. The obtained results of the analyses were also discussed in more detail. The results showed that the steric interactions are more prominent than the van der Waals interactions, and in both conformations, steric interactions are included in the middle of the 1,4-dithian ring and there is hydrogen bonding between hydroxyl groups and 1,4-dithian ring structure heteroatoms in the axial conformation while this interaction is not observed in the case of equatorial conformation. The presence of these interactions was confirmed using NBO analysis.

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[1]
Okutsu, R.; Suzuki, Y.; Ando, S.; Ueda, M. Poly (thioether sulfone) with high refractive index and high Abbe’s number. Macromolecules, 2008, 41(16), 6165-6168.
[http://dx.doi.org/10.1021/ma800797p]
[2]
Suzuki, Y.; Higashihara, T.; Ando, S.; Ueda, M. Synthesis and characterization of high refractive index and high Abbe’s number poly (thioether sulfone)s based on tricyclo [5.2. 1.02, 6] decane moiety. Macromolecules, 2012, 45(8), 3402-3408.
[http://dx.doi.org/10.1021/ma300379w]
[3]
Suzuki, Y.; Higashihara, T.; Ando, S.; Ueda, M. Synthesis of high refractive index poly(thioether sulfone)s with high Abbe’s number derived from 2,5-Bis(sulfanylmethyl)-1,4-dithiane. Polym. J., 2009, 41(10), 860-865.
[http://dx.doi.org/10.1295/polymj.PJ2009124]
[4]
Yue, T.J.; Wang, L.Y.; Ren, W.M. The synthesis of degradable sulfur-containing polymers: Precise control of structure and stereochemistry. Polym. Chem., 2021, 12(46), 6650-6666.
[http://dx.doi.org/10.1039/D1PY01065D]
[5]
Liu, J.; Ueda, M. High refractive index polymers: Fundamental research and practical applications. J. Mater. Chem., 2009, 19(47), 8907-8919.
[http://dx.doi.org/10.1039/b909690f]
[6]
Kalpana, B.; Nanthini, R. Synthesis, characterization and in vitro antimicrobial, antioxidant and anticancer activity of random copolyester using 1,4-dithiane-2,5-diol. Asian J. Chem., 2019, 31(10), 2341-2344.
[http://dx.doi.org/10.14233/ajchem.2019.21997]
[7]
Fu, M.C.; Ueda, M.; Ando, S.; Higashihara, T. Development of novel triazine-based poly(phenylene sulfide)s with high refractive index and low birefringence. ACS Omega, 2020, 5(10), 5134-5141.
[http://dx.doi.org/10.1021/acsomega.9b04152] [PMID: 32201800]
[8]
Kobayashi, S.; Morijiri, H. Polymerizable composition containing novel cyclic sulfur compound and resin obtained by curing the polymerizable composition. . WO Patent 2003074588A1,, 2006.
[9]
Wayton, G.B.; Trefonas, P.; Coley, S.; Kurihara, T. Coating compositions for use with an overcoated photoresist. EP 2275490A1, 2007.
[10]
Zamberlan, F.; Fantinati, A.; Trapella, C. 1,4-Dithiane-2,5-diol: An attractive platform for the synthesis of sulfur-containing functionalized heterocycles. Eur. J. Org. Chem., 2018, 2018(25), 3248-3264.
[http://dx.doi.org/10.1002/ejoc.201701785]
[11]
Benetti, S.; De Risi, C.; Pollini, G.P.; Zanirato, V. Synthetic routes to chiral nonracemic and racemic dihydro- and tetrahydrothiophenes. Chem. Rev., 2012, 112(4), 2129-2163.
[http://dx.doi.org/10.1021/cr200298b] [PMID: 22277095]
[12]
Tranberg, C.E.; Zickgraf, A.; Giunta, B.N.; Luetjens, H.; Figler, H.; Murphree, L.J.; Falke, R.; Fleischer, H.; Linden, J.; Scammells, P.J.; Olsson, R.A. 2-Amino-3-aroyl-4,5-alkylthiophenes: Agonist allosteric enhancers at human A(1) adenosine receptors. J. Med. Chem., 2002, 45(2), 382-389.
[http://dx.doi.org/10.1021/jm010081p] [PMID: 11784142]
[13]
Takahashi, H.; Miwa, K.; Igarashi, T.; Kobayashi, Y. Conformational studies of mercaptoacetaldehyde and mercaptoacetone by 1H-NMR, Raman and infrared spectroscopy. Spectrochim. Acta A, 1982, 38(7), 759-765.
[http://dx.doi.org/10.1016/0584-8539(82)80064-0]
[14]
Saji, R.S.; Prasana, J.C.; Muthu, S.; George, J. Experimental and theoretical spectroscopic (FT-IR, FT-Raman, UV-VIS) analysis, natural bonding orbitals and molecular docking studies on 2-bromo-6-methoxynaphthalene: A potential anti-cancer drug. Heliyon, 2021, 7(6), e07213.
[http://dx.doi.org/10.1016/j.heliyon.2021.e07213] [PMID: 34169166]
[15]
Jayabharathi, J.; Thanikachalam, V.; Srinivasan, N.; Venkatesh Perumal, M.; Jayamoorthy, K. Physicochemical studies of molecular hyperpolarizability of imidazole derivatives. Spectrochim. Acta A Mol. Biomol. Spectrosc., 2011, 79(1), 137-147.
[http://dx.doi.org/10.1016/j.saa.2011.02.024] [PMID: 21414837]
[16]
Jayabharathi, J.; Thanikachalam, V.; Jayamoorthy, K.; Perumal, M.V. A physiochemical study of excited state intramolecular proton transfer process. Spectrochim. Acta A Mol. Biomol. Spectrosc., 2011, 79(1), 6-16.
[http://dx.doi.org/10.1016/j.saa.2010.12.027] [PMID: 21398171]
[17]
Jayabharathi, J.; Thanikachalam, V.; Venkatesh Perumal, M.; Srinivasan, N. A physiochemical study of azo dyes: DFT based ESIPT process. Spectrochim. Acta A Mol. Biomol. Spectrosc., 2011, 83(1), 200-206.
[http://dx.doi.org/10.1016/j.saa.2011.08.017] [PMID: 21903457]
[18]
Sebastian, S.; Sylvestre, S.; Jayabharathi, J.; Ayyapan, S.; Amalanathan, M.; Oudayakumar, K.; Herman, I.A. Study on conformational stability, molecular structure, vibrational spectra, NBO, TD-DFT, HOMO and LUMO analysis of 3,5-dinitrosalicylic acid by DFT techniques. Spectrochim. Acta A Mol. Biomol. Spectrosc., 2015, 136(Pt B), 1107-1118.
[http://dx.doi.org/10.1016/j.saa.2014.09.135] [PMID: 25459508]
[19]
Subramanian, N.; Sundaraganesan, N.; Jayabharathi, J. Molecular structure, spectroscopic (FT-IR, FT-Raman, NMR, UV) studies and first-order molecular hyperpolarizabilities of 1,2-bis(3-methoxy-4-hydroxybenzylidene)hydrazine by density functional method. Spectrochim. Acta A Mol. Biomol. Spectrosc., 2010, 76(2), 259-269.
[http://dx.doi.org/10.1016/j.saa.2010.03.033] [PMID: 20413344]
[20]
Civcir, P.Ü.; Kurtay, G.; Sarıkavak, K. Experimental and theoretical investigation of new furan and thiophene derivatives containing oxazole, isoxazole, or isothiazole subunits. Struct. Chem., 2017, 28(3), 773-790.
[http://dx.doi.org/10.1007/s11224-016-0863-1]
[21]
Becke, A.D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A Gen. Phys., 1988, 38(6), 3098-3100.
[http://dx.doi.org/10.1103/PhysRevA.38.3098] [PMID: 9900728]
[22]
Guan, Y.; Shree Sowndarya, S.V.; Gallegos, L.C.; St John, P.C.; Paton, R.S. Real-time prediction of 1H and 13C chemical shifts with DFT accuracy using a 3D graph neural network. Chem. Sci. , 2021, 12(36), 12012-12026.
[http://dx.doi.org/10.1039/D1SC03343C] [PMID: 34667567]
[23]
Jain, R.; Bally, T.; Rablen, P.R. Calculating accurate proton chemical shifts of organic molecules with density functional methods and modest basis sets. J. Org. Chem., 2009, 74(11), 4017-4023.
[http://dx.doi.org/10.1021/jo900482q] [PMID: 19435298]
[24]
Danaie, E.; Masoudi, S.; Masnabadi, N. A computational study of the conformational behavior of 2,5-dimethyl-1,4-dithiane-2,5-diol and analogous S and Se: DFT and NBO study. Lett. Org. Chem., 2020, 17(10), 749-759.
[http://dx.doi.org/10.2174/1570178617666200129144750]
[25]
Fukui, K. Role of frontier orbitals in chemical reactions. Science, 1982, 218(4574), 747-754.
[http://dx.doi.org/10.1126/science.218.4574.747] [PMID: 17771019]
[26]
Gunasekaran, S.; Balaji, R.A.; Kumaresan, S.; Anand, G.; Srinivasan, S. Experimental and theoretical investigations of spectroscopic properties of N-acetyl-5-methoxytryptamine. Can. J. Anal. Sci. Spectrosc., 2008, 53(4), 149-162.
[27]
Pathak, S.K.; Srivastava, R.; Sachan, A.K.; Prasad, O.; Sinha, L.; Asiri, A.M.; Karabacak, M. Experimental (FT-IR, FT-Raman, UV and NMR) and quantum chemical studies on molecular structure, spectroscopic analysis, NLO, NBO and reactivity descriptors of 3,5-Difluoroaniline. Spectrochim. Acta A Mol. Biomol. Spectrosc., 2015, 135, 283-295.
[http://dx.doi.org/10.1016/j.saa.2014.06.149] [PMID: 25078461]
[28]
Ferro-Costas, D.; Vila, A.; Mosquera, R.A. Anomeric effect in halogenated methanols: A quantum theory of atoms in molecules study. J. Phys. Chem. A, 2013, 117(7), 1641-1650.
[http://dx.doi.org/10.1021/jp310534x] [PMID: 23350752]
[29]
Tamafo Fouegue, A.D.; Nono, J.H.; Nkungli, N.K.; Ghogomu, J.N. A theoretical study of the structural and electronic properties of some titanocenes using DFT, TD-DFT, and QTAIM. Struct. Chem., 2021, 32(1), 353-366.
[http://dx.doi.org/10.1007/s11224-020-01630-9]
[30]
Bavafa, S.; Nowroozi, A.; Ebrahimi, A. Quantum chemical study of the nature of interactions between the boraphosphinine and alumaphosphinine with some of the mono- and divalent cations: Cation-πor cation-lone pair? Struct. Chem., 2019, 30(5), 1887-1898.
[http://dx.doi.org/10.1007/s11224-019-01320-1]
[31]
Persch, E.; Dumele, O.; Diederich, F. Molecular recognition in chemical and biological systems. Angew. Chem. Int. Ed., 2015, 54(11), 3290-3327.
[http://dx.doi.org/10.1002/anie.201408487] [PMID: 25630692]
[32]
Ben-Naim, A. The role of hydrogen bonds in protein folding and protein association. J. Phys. Chem., 1991, 95(3), 1437-1444.
[http://dx.doi.org/10.1021/j100156a074]
[33]
Watson, J.D.; Crick, F.H.C. Molecular structure of nucleic acids; A structure for deoxyribose nucleic acid. Nature, 1953, 171(4356), 737-738.
[http://dx.doi.org/10.1038/171737a0] [PMID: 13054692]
[34]
Mignon, P.; Loverix, S.; Steyaert, J.; Geerlings, P. Influence of the - Interaction on the hydrogen bonding capacity of stacked DNA/RNA bases. Nucleic Acids Res., 2005, 33(6), 1779-1789.
[http://dx.doi.org/10.1093/nar/gki317] [PMID: 15788750]
[35]
Ma, J.C.; Dougherty, D.A. The cation-πinteraction. Chem. Rev., 1997, 97(5), 1303-1324.
[http://dx.doi.org/10.1021/cr9603744] [PMID: 11851453]
[36]
Motherwell, W.B.; Moreno, R.B.; Pavlakos, I.; Arendorf, J.R.T.; Arif, T.; Tizzard, G.J.; Coles, S.J.; Aliev, A.E. Noncovalent interactions of πsystems with sulfur: The atomic chameleon of molecular recognition. Angew. Chem. Int. Ed., 2018, 57(5), 1193-1198.
[http://dx.doi.org/10.1002/anie.201708485] [PMID: 29194884]
[37]
Hohenstein, E.G.; Sherrill, C.D. Wavefunction methods for noncovalent interactions. Wiley Interdiscip. Rev. Comput. Mol. Sci., 2012, 2(2), 304-326.
[http://dx.doi.org/10.1002/wcms.84]
[38]
Kitaura, K.; Morokuma, K. A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation. Int. J. Quantum Chem., 1976, 10(2), 325-340.
[http://dx.doi.org/10.1002/qua.560100211]
[39]
Blanco, M.A.; Martín Pendás, A.; Francisco, E. Interacting quantum atoms: A correlated energy decomposition scheme based on the quantum theory of atoms in molecules. J. Chem. Theory Comput., 2005, 1(6), 1096-1109.
[http://dx.doi.org/10.1021/ct0501093] [PMID: 26631653]
[40]
Chafaa, F.; Nacereddine, A.K.; Djerourou, A. A combined topological ELF, NCI and QTAIM study of mechanism and hydrogen bond controlling the selectivity of the IMDC reaction of nitrone-alkene obtained from m-allyloxybenzaldehyde. Lett. Org. Chem., 2020, 17(4), 260-267.
[http://dx.doi.org/10.2174/1570178616666190401202143]
[41]
Li, E.; Zhang, J.; Wang, J.; Gao, F.; Yang, Z.; Meng, Q.; Zhang, Q.; Li, N.; Huang, M.; Spengler, G.; Molnar, J.; Wang, Q. Prevention of VP-16 resistance by a disiloxane, SILA409: Effects of SILA409 on the expression of GRP78 in NCI-H446 human small cell lung cancer cells. Lett. Drug Des. Discov., 2011, 8(8), 691-697.
[http://dx.doi.org/10.2174/157018011796575971]
[42]
Domingo, L.R.; Acharjee, N. Molecular electron density theory: A new theoretical outlook on organic chemistry. Front. Comput. Chem., 2020, 5, 174-227.
[http://dx.doi.org/10.2174/9789811457791120050007]
[43]
Lee, C.; Yang, W.; Parr, R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B Condens. Matter, 1988, 37(2), 785-789.
[http://dx.doi.org/10.1103/PhysRevB.37.785] [PMID: 9944570]
[44]
Zhao, Y.; Truhlar, D.G. The M06 suite of density functionals for main group thermochemistry, kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06 functionals and twelve other functionals. Theor. Chem. Acc., 2008, 120, 215-241.
[http://dx.doi.org/10.1007/s00214-007-0310-x]
[45]
Valero, R.; Gomes, J.R.B.; Truhlar, D.G.; Illas, F. Good performance of the M06 family of hybrid meta generalized gradient approximation density functionals on a difficult case: CO adsorption on MgO(001). J. Chem. Phys., 2008, 129(12), 124710-124717.
[http://dx.doi.org/10.1063/1.2982923] [PMID: 19045051]
[46]
Hajji, M.; Mtiraoui, H.; Amiri, N.; Msaddek, M.; Guerfel, T. Crystallographic and first‐principles density functional theorystudy on the structure, noncovalent interactions, and chemical reactivity of 1, 5‐ benzodiazepin‐2‐ones derivatives. Int. J. Quantum Chem., 2019, 119(3), 119e26000.
[http://dx.doi.org/10.1002/qua.26000]
[47]
Espinosa, E.; Molins, E.; Lecomte, C. Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities. Chem. Phys. Lett., 1998, 285(3-4), 170-173.
[http://dx.doi.org/10.1016/S0009-2614(98)00036-0]
[48]
Laplaza, R.; Peccati, F.; Boto, R.A.; Quan, C.; Carbone, A.; Piquemal, J.P.; Maday, Y. Contreras-García, J. NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient. WIREs Rev. Comput. Mol. Sci., 2021, 11(2), e1497.
[http://dx.doi.org/10.1002/wcms.1497]
[49]
Xu, H.; Li, L.; Fan, G.; Chu, X. DFT study of nanotubes as the drug delivery vehicles of Efavirenz. Comput. Theor. Chem., 2018, 1131, 57-68.
[http://dx.doi.org/10.1016/j.comptc.2018.03.032]
[50]
Noureddine, O.; Issaoui, N.; Medimagh, M.; Al-Dossary, O.; Marouani, H. Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: Molecular docking and DFT calculations. J. King Saud Univ. Sci., 2021, 33(2), 101334.
[http://dx.doi.org/10.1016/j.jksus.2020.101334] [PMID: 33432258]
[51]
Glendening, E.D.; Badenhoop, J.K.; Reed, A.E.; Carpenter, J.E.; Bohmann, J.A.; Morales, C.M.; Weinhold, F. Theoretical Chemistry Institute; NBO 5.0; University of Wisconsin: Madison, 2001.
[52]
Hehre, W.J.; Radom, L.; Schleyer, P.V.R.; Pople, J.A. Ab initio molecular orbital theory; Wiley: New York, 1986.

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