Vibration Assignment, B3pw91 Calculation and Conformational Analysis of Antimicrobial 5-Amino -3-(Methylthio)-1-(1,3,4-Thiadiazol -2-Yl)-1H-Pyrazole-4-Carbonitrile.

Medhat Mohamed El-Moselhy, Usama. A. Soliman, H. G. Mohamedbakr, Mohamed S. Thabet, Mahmoud M. Abdelall, Ali M. Hassan

Keywords: Conformational durability, vibrational categorization, NMR profiles, standard coordinate assessment, obstacles to inner rotation, and computational estimations using DFT.

In this study, we conducted infrared spectroscopy measurements on solid 5-amino-3-(methylthio)-1-(1,3,4-thiadiazol-2-yl)-1H-pyrazole-4-carbonitrile (AMTDPC, C7H6N6S2). The spectra were obtained at a resolution of 4 cm?1 and 0.5 cm-1, within the spectrum region of 4000–200 cm-1. Furthermore, the observation of NMR spectra for 1H and 13C has been documented. Nine rotational isomerisms, consisting of nine Cs and one C1 symmetry, are postulated for the AMTDPC molecule due to internal rotation occurring around C–N and/or C–S bonds. The isomers are finally characterized by two conformers (1-2) with energies below 1000 cm-1, as determined through quantum mechanical calculations utilizing RHF and DFT/B3PW91. Based on forecasts, conformer 1, which is the rotamer with the lowest energy and produces real frequencies, is expected to have a stability order of 1 > 2. The spectrum modeling provides complete support for Conformer 1, making it the preferred option based on the recorded infrared (IR), 1H, and 13C spectral data. The chemical shifts at the B3PW91/6-31G level were successfully determined using the Polarizable Continuum Model (PCM) and the Gauge-Invariant Atomic Orbitals (GIAO) technique, regardless of the presence or absence of the solvent. The results of the NMR studies provided indications of both constrained and unconstrained internal rotation of NH2 around C-N bonds. In order to propose a comprehensive and reliable vibrational assignment for each of the foundations of AMTDPC, potential energy distributions and normal coordinate analysis have been employed. Additionally, supplementary investigations were carried out to examine the torsional obstacles encountered during the internal rotation of the NH2, CH3, CH3S, and thiadiazole ring. Based on spectrum measurements that exhibited a high level of concurrence with the anticipated values, it may be concluded that conformer 1 emerged as the isomer with the highest stability. Also there are small differences between the calculated bond distances and the x-ray readings for comprised compounds.

[1]       M. H. Baren, S. A. Ibrahim, M. M. Al-Rooqi, S. A. Ahmed, M. M. El-Gamil, and H. A. Hekal, “A new class of anticancer activity with computational studies for a novel bioactive aminophosphonates based on pyrazole moiety,” Scientific Reports, vol. 13, no. 1, p. 14680, 2023.

[2]       P. Mahesh et al., “Antiproliferative Activity of New Pyrazole-4-sulfonamide Derivatives: Synthesis and Biological Evaluation,” ACS Omega, vol. 8, no. 29, pp. 25698–25709, Jul. 2023, doi: 10.1021/acsomega.2c07539.

[3]       M. Mantzanidou, E. Pontiki, and D. Hadjipavlou-Litina, “Pyrazoles and pyrazolines as anti-inflammatory agents,” Molecules, vol. 26, no. 11, p. 3439, 2021.

[4]       K. R. Jyothikumari, K. N. Rajasekharan, and K. Dhevendran, “Synthesis of Some New Pyrazolo3’, 4-d-pyrimidine Derivatives and their Antibacterial Activity,” Journal of the Indian Chemical Society, vol. 68, no. 10, pp. 578–580, 1991.

[5]       T. A. Mohamed, A. M. Hassan, U. A. Soliman, W. M. Zoghaib, J. Husband, and M. M. Abdelall, “Infrared, Raman and NMR spectra, conformational stability, normal coordinate analysis and B3LYP calculations of 5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbothioamide,” Journal of molecular structure, vol. 985, no. 2–3, pp. 277–291, 2011.

[6]       T. A. Mohamed, A. M. Hassan, U. A. Soliman, W. M. Zoghaib, J. Husband, and M. M. Abdelall, “Infrared, Raman and NMR spectra, conformational stability, normal coordinate analysis and B3LYP calculations of 5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbothioamide,” Journal of molecular structure, vol. 985, no. 2–3, pp. 277–291, 2011.

[7]       V. J. Ram, U. K. Singha, and P. Y. Guru, “Chemotherapeutic agents XI: synthesis of pyrimidines and azolopyrimidines as leishmanicides.,” European Journal of Medicinal Chemistry, vol. 25, no. 6, pp. 533–538, 1990.

[8]       R. K. Robins, “Potential Purine Antagonists. I. Synthesis of Some 4,6-Substituted Pyrazolo [3,4-d] pyrimidines 1,” J. Am. Chem. Soc., vol. 78, no. 4, pp. 784–790, Feb. 1956, doi: 10.1021/ja01585a023.

[9]       A.-R. Farghaly, S. A. Ahmed, K. S. Ismail, D. Ibrahim, N. Amri, and S. Elgogary, “Synthesis, antitumor activity, antimicrobial evaluation and molecular docking studies of some hydrazone, 1, 3, 4-oxadiazole, 1, 2, 4-triazole and pyrazole derivatives bearing nicotinoyl moiety,” Results in Chemistry, vol. 7, p. 101474, 2024.

[10]     P. Rzepecki, M. Wehner, O. Molt, R. Zadmard, K. Harms, and T. Schrader, “Aminopyrazole Oligomers for β-SheetStabilization of Peptides,” Synthesis, no. 12, pp. 1815–1826, 2003, doi: 10.1055/s-2003-41031.

[11]     O. Ebenezer, M. Shapi, and J. A. Tuszynski, “A review of the recent development in the synthesis and biological evaluations of pyrazole derivatives,” Biomedicines, vol. 10, no. 5, p. 1124, 2022.

[12]     W. Abisha, D. A. Dhas, S. Balachandran, and I. H. Joe, “Synthesis, Structural, and Quantum Chemical Spectroscopic, Hydrogen Bonding, and Molecular Docking Investigation of Antifungal Compound Pyrazole-Pyrazolium Picrate,” Polycyclic Aromatic Compounds, vol. 43, no. 9, pp. 8455–8481, Oct. 2023, doi: 10.1080/10406638.2022.2149571.

[13]     K. Karrouchi et al., “Synthesis, X-ray structure, vibrational spectroscopy, DFT, biological evaluation and molecular docking studies of (E)-N’-(4-(dimethylamino) benzylidene)-5-methyl-1H-pyrazole-3-carbohydrazide,” Journal of Molecular Structure, vol. 1219, p. 128541, 2020.

[14]     P. Rejnhardt and M. Daszkiewicz, “Crystal structure and vibrational spectra of salts of 1H-pyrazole-1-carboxamidine and its protonation route,” Struct Chem, vol. 32, no. 2, pp. 539–551, Apr. 2021, doi: 10.1007/s11224-020-01671-0.

[15]     A. D. Becke, “Density-functional exchange-energy approximation with correct asymptotic behavior,” Phys. Rev. A, vol. 38, no. 6, pp. 3098–3100, Sep. 1988, doi: 10.1103/PhysRevA.38.3098.

[16]     A. D. Becke, “Density-functional thermochemistry. I. The effect of the exchange-only gradient correction,” The Journal of chemical physics, vol. 96, no. 3, pp. 2155–2160, 1992.

[17]     M. J. Frisch et al., “Uranyl extraction by N, N-dialkylamide ligands studied by static and dynamic DFT simulations,” Gaussian, vol. 9, p. 227, 2009.

[18]     C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B, vol. 37, no. 2, pp. 785–789, Jan. 1988, doi: 10.1103/PhysRevB.37.785.

[19]     Chr. Møller and M. S. Plesset, “Note on an Approximation Treatment for Many-Electron Systems,” Phys. Rev., vol. 46, no. 7, pp. 618–622, Oct. 1934, doi: 10.1103/PhysRev.46.618.

[20]     J. R. Durig, G. A. Guirgis, C. Zheng, and T. A. Mohamed, “Spectra and structure of silicon-containing compounds.: Part XXXVIII: Infrared and Raman spectra, vibrational assignment, conformational stability, and ab initio calculations of vinyldifluorosilane,” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 59, no. 9, pp. 2099–2114, 2003.

[21]     H. Lampert, W. Mikenda, and A. Karpfen, “Molecular Geometries and Vibrational Spectra of Phenol, Benzaldehyde, and Salicylaldehyde: Experimental versus Quantum Chemical Data,” J. Phys. Chem. A, vol. 101, no. 12, pp. 2254–2263, Mar. 1997, doi: 10.1021/jp962933g.

[22]     A. Nasser, M. A. Migahed, N. M. EL Basiony, H. M. Abd-El-Bary, and T. A. Mohamed, “Raman and Infrared Spectral Analysis, Normal Coordinate Analysis, DFT calculations of Novel Schiff Base Containing di-imine moieties,” Egyptian Journal of Chemistry, vol. 66, no. 9, pp. 271–291, 2023.

[23]     A. Asensio, N. Kobko, and J. J. Dannenberg, “Cooperative Hydrogen-Bonding in Adenine−Thymine and Guanine−Cytosine Base Pairs. Density Functional Theory and Møller−Plesset Molecular Orbital Study,” J. Phys. Chem. A, vol. 107, no. 33, pp. 6441–6443, Aug. 2003, doi: 10.1021/jp0344646.

[24]     D. B. Chesnut and C. G. Phung, “Nuclear magnetic resonance chemical shifts using optimized geometries,” The Journal of chemical physics, vol. 91, no. 10, pp. 6238–6245, 1989.

[25]     V. Chiş, “Molecular and vibrational structure of 2, 4-dinitrophenol: FT-IR, FT-Raman and quantum chemical calculations,” Chemical physics, vol. 300, no. 1–3, pp. 1–11, 2004.

[26]     P. K. Chowdhury, “Infrared depletion spectroscopy of the hydrogen-bonded aniline-diethylamine (C6H5-NH2 center dot center dot center dot NHC4H10) complex produced in supersonic jet,” Journal of Physical Chemistry A, vol. 107, no. 30, pp. 5692–5696, 2003.

[27]     R. Ditchfield, “Self-consistent perturbation theory of diamagnetism: I. A gauge-invariant LCAO method for N.M.R. chemical shifts,” Molecular Physics, vol. 27, no. 4, pp. 789–807, Apr. 1974, doi: 10.1080/00268977400100711.

[28]     H.-G. Korth, M. I. De Heer, and P. Mulder, “A DFT Study on Intramolecular Hydrogen Bonding in 2-Substituted Phenols: Conformations, Enthalpies, and Correlation with Solute Parameters,” J. Phys. Chem. A, vol. 106, no. 37, pp. 8779–8789, Sep. 2002, doi: 10.1021/jp025713d.

[29]     T. Kupka, G. Pasterna, P. Lodowski, and W. Szeja, “GIAO-DFT prediction of accurate NMR parameters in selected glucose derivatives,” Magn. Reson. Chem., vol. 37, no. 6, pp. 421–426, Jun. 1999, doi: 10.1002/(SICI)1097-458X(199906)37:6<421::AID-MRC479>3.0.CO;2-W.

[30]     T. Kupka, M. Kol̵aski, G. Pasterna, and K. Ruud, “Towards more reliable prediction of formaldehyde multinuclear NMR parameters and harmonic vibrations in the gas phase and solution,” Journal of Molecular Structure: THEOCHEM, vol. 467, no. 1, pp. 63–78, 1999.

[31]     V. G. Malkin, O. L. Malkina, M. E. Casida, and D. R. Salahub, “Nuclear Magnetic Resonance Shielding Tensors Calculated with a Sum-over-States Density Functional Perturbation Theory,” J. Am. Chem. Soc., vol. 116, no. 13, pp. 5898–5908, Jun. 1994, doi: 10.1021/ja00092a046.

[32]     W. J. Hehre, “Ab initio molecular orbital theory,” Acc. Chem. Res., vol. 9, no. 11, pp. 399–406, Nov. 1976, doi: 10.1021/ar50107a003.

[33]     T. A. Mohamed, U. A. Soliman, A. I. Hanafy, and A. M. Hassan, “Conformational stability, barriers to internal rotation of 2-aminothiophenol (d0 and d3): A combined vibrational and theoretical approach,” Journal of Molecular Structure: THEOCHEM, vol. 865, no. 1–3, pp. 14–24, 2008.

[34]     T. A. Mohamed, I. A. Shabaan, W. M. Zoghaib, J. Husband, R. S. Farag, and A. E.-N. M. Alajhaz, “Tautomerism, normal coordinate analysis, vibrational assignments, calculated IR, Raman and NMR spectra of adenine,” Journal of Molecular Structure, vol. 938, no. 1–3, pp. 263–276, 2009.

[35]     U. A. Soliman, A. M. Hassan, and T. A. Mohamed, “Conformational stability, vibrational assignmenents, barriers to internal rotations and ab initio calculations of 2-aminophenol (d0 and d3),” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 68, no. 3, pp. 688–700, 2007.

[36]     S. M. Hassan, H. A. Emam, and M. M. Abdelall, “Heteroaromatization with Ketene Dithioacetals: Part II. Synthesis of Some Novel 5-Aminopyrazole-3-Carbonitrile, 3-Carboxamide and Pyrazolo [3, 4-d] Pyrimidin-4-One Derivatives as Antimicrobial Agents,” Phosphorus, Sulfur, and Silicon and the Related Elements, vol. 175, no. 1, pp. 109–127, 2001.

[37]     P. Pulay, “Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules: I. Theory,” Molecular Physics, vol. 17, no. 2, pp. 197–204, 1969.

[38]     J. Zukerman-Schpector, E. J. Barreiro, and A. C. C. Freitas, “Structures of pyrazole derivatives. III. 5-Amino-4-cyano-1-phenylpyrazole,” Acta Crystallographica Section C: Crystal Structure Communications, vol. 50, no. 12, pp. 2095–2096, 1994.

[39]     P. Prusiner, M. Sundaralingam, T. Ito, and T. Sakurai, “The crystal and molecular structure of 3-amino-4, 5-dicyano-1-methylpyrazole,” Acta Crystallographica Section B: Structural Crystallography and Crystal Chemistry, vol. 32, no. 3, pp. 853–856, 1976.

[40]     J. Zukerman-Schpector, E. E. Castellano, G. Oliva, A. C. Massabni, and A. D. Pinto, “Hydrogen bonding in the crystal structures of the adducts between 1-phenyl-3, 5-dimethylpyrazole with oxalic and perchloric acids,” Canadian Journal of Chemistry, vol. 62, no. 4, pp. 725–728, 1984.

[41]     A. van Bondi, “van der Waals volumes and radii,” The Journal of physical chemistry, vol. 68, no. 3, pp. 441–451, 1964.

[42]     J. E. Huheey, E. A. Keiter, R. L. Keiter, and O. K. Medhi, Inorganic chemistry: principles of structure and reactivity. Pearson Education India, 2006.

[43]     H. Lampert, W. Mikenda, and A. Karpfen, “Molecular geometries and vibrational spectra of phenol, benzaldehyde, and salicylaldehyde: experimental versus quantum chemical data,” The Journal of Physical Chemistry A, vol. 101, no. 12, pp. 2254–2263, 1997.

[44]     T. A. Mohamed, G. A. Guirgis, Y. E. Nashed, and J. R. Durig, “Spectra and structure of silicon containing compounds: Part XXXIV. Raman and infrared spectra, vibrational assignment, barriers to internal rotation, and ab initio calculations of 1-chloroethylsilane,” Vibrational spectroscopy, vol. 30, no. 2, pp. 111–120, 2002.

[45]     T. Kupka, G. Pasterna, P. Lodowski, and W. Szeja, “GIAO-DFT prediction of accurate NMR parameters in selected glucose derivatives,” Magn. Reson. Chem., vol. 37, no. 6, pp. 421–426, Jun. 1999, doi: 10.1002/(SICI)1097-458X(199906)37:6<421::AID-MRC479>3.0.CO;2-W.

[46]     V. Barone, M. Cossi, and J. Tomasi, “A new definition of cavities for the computation of solvation free energies by the polarizable continuum model,” The Journal of chemical physics, vol. 107, no. 8, pp. 3210–3221, 1997.

[47]     J. Tomasi and M. Persico, “Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent,” Chemical Reviews, vol. 94, no. 7, pp. 2027–2094, 1994.

[48]     L. J. Bellamy and R. L. Williams, “The NH stretching frequencies of primary amines,” Spectrochimica Acta, vol. 9, no. 4, pp. 341–345, 1957.

[49]     J. Swaminathan, M. Ramalingam, and N. Sundaraganesan, “Molecular structure and vibrational spectra of 3-amino-5-hydroxypyrazole by density functional method,” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 71, no. 5, pp. 1776–1782, 2009.

[50]     T. A. Mohamed, “Structural parameters, barriers to internal rotation, normal coordinate analysis and quantum mechanics calculations of 1, 1, 1-trimethyldisilane,” Journal of Molecular Structure: THEOCHEM, vol. 635, no. 1–3, pp. 161–172, 2003.

[51]     T. A. Mohamed and M. M. Abo Aly, “Vibrational analysis, conformational stability, force constants, barriers to internal rotations, RHF, MP2 and DFT calculations of trans, trans-2, 4-hexadiene,” Journal of Raman Spectroscopy, vol. 35, no. 10, pp. 869–878, 2004.

[52]     T. A. Mohamed and R. S. Farag, “Raman spectrum, conformational stability, barriers to internal rotations and DFT calculations of 1, 1, 1-trifluoro-propane-2-thione with double-internal-symmetric rotor,” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 62, no. 4–5, pp. 800–807, 2005.

[53]     J. R. Durig, G. A. Guirgis, and S. Bell, “Torsional spectrum and ab initio calculations for propene,” The Journal of Physical Chemistry, vol. 93, no. 9, pp. 3487–3491, 1989.

[54]     J. R. Durig, W. J. Natter, and P. Groner, “Analysis of torsional spectra of molecules with two internal C 3 V rotors. IX. The torsional potential functions of isobutene-d and-d 6,” The Journal of Chemical Physics, vol. 67, no. 11, pp. 4948–4951, 1977.

[55]     R. t Schwendeman and G. D. Jacobs, “Molecular structure of ethyl chloride,” The Journal of Chemical Physics, vol. 36, no. 5, pp. 1245–1250, 1962.