Quantum Computational, Structural Characterization, Hirshfeld Surface, Electronic Properties and Molecular Docking Studies on N-(2,3,5,6-Tetra­Fluoropyridin-4-yl) Formamide

Document Type : Research Article

Author

Department of Medical Services and Techniques, Vocational School of Health Services, Igdır University, Iğdır, TURKEY

Abstract

In this study, the structural, spectroscopic, and electronic properties of N-(2,3,5,6-Tetrafluoropyridin-4-yl) formamide compound were investigated theoretically using the DFT/B3LYP method and 6-311++G(d,p) basis set. The obtained results were compared with geometric structure and 1H-NMR data known in the literature and were seen to be compatible. Characters of intermolecular interactions were explained by Hirshfeld surface analysis and molecular electrostatic potential map analysis. Electronic properties of the N-(2,3,5,6-Tetra­fluoropyridin-4-yl) formamide compound were calculated considering frontier molecular orbital analysis. ADME study, conducted according to Lipinski's five criteria, revealed drug similarity properties of the N-(2,3,5,6-Tetrafluoropyridin-4-yl) formamide compound. In the last part of this study, the effect of nucleophilic substitution reactions on biochemical interactions between the perfluorinated compound and target protein was tested by molecular docking method using the Carbonic Anhydrase I (4WR7) enzyme.

Keywords

Main Subjects

References

[1] Griswold W.R., Toney M.D., Role of the Pyridine Nitrogen in Pyridoxal 5′-Phosphate Catalysis: Activity of Three Classes of PLP Enzymes Reconstituted with Deazapyridoxal 5′-Phosphate, J. Am. Chem. Soc., 133(37): 14823-14830 (2011).
[2] Han H., Kovtonyuk V.N., Gatilov Y.V., Andreev R.V., Directed Synthesis of Isomeric Polyfluorinated Dinitrotetraoxacalixarenes and Bicyclooxacalixarenes, J. Fluorine Chem., 261: 110022 (2022).
[3] Ishchenko R.A., Kargapolova I.Y., Orlova N.А., Shelkovnikov V.V., Maksimov A.М., Ryazanov N.D., Berezhnaya V.N., Chernonosov A.А., Polyfluorinated Triphenyl-4, 5-Dihydro-1H-Pyrazoles with Dendroid Arylsulfanyl Moieties as Donor Blocks in Donor-Acceptor Chromophores, J. Fluorine Chem., 248: 109841 (2021).
[4] Cao T., Zhou Y., Wang H., Qiao R., Zhang X., Liu L., Tong Z., Preparation of Polyfluorinated Azobenzene/Niobate Composite as Electrochemical Sensor for Detection of Ascorbic Acid and Dopamine, Microchem. J., 179: 107422 (2022).
[5] Ranjbar-Karimi R., Poorfreidoni A., Masoodi H.R., Survey Reactivity of Some N-aryl Formamides with Pentafluoropyridine, J. Fluorine Chem., 180: 222-226 (2015).
[6] Shi J., Lou Z., Yang M., Zhang Y., Liu H., Meng Y., Theoretical Characterization of Formamide on the Inner Surface of Montmorillonite, Surf. Sci., 624: 37-43 (2014).
[7] Bommuraj V., Chen Y., Birenboim M., Barel S., Shimshoni J.A., Concentration-and Time-Dependent Toxicity of Commonly Encountered Pesticides and Pesticide Mixtures to Honeybees (Apis Mellifera L.), Chemosphere, 266: 128974 (2021).
[8] CARTER B.G., Chamberlain K., Wain R., Investigations on Fungicides: XV. The Fungitoxicity and Systemic Antifungal Activity of N‐(2, 2, 2‐Trichloro‐1‐Methoxyethyl) Formamide and Related Compounds, Ann. Appl. Biol., 75(1): 49-55 (1973).
[9] Alla K., Vijayakumar V., Sarveswari S., Synthesis
and in Vitro Antimicrobial Evaluation of New Quinolone Based 2-Arylamino Pyrimidines, Polycyclic Aromat. Compd.: 1-22 (2022).
[10] Ibrahiem E.H.I., Nigam V.N., Brailovsky C.A., Madarnas P., Elhilali M., Orthotopic Implantation of Primary N-[4-(5-Nitro-2-Furyl)-2-Thiazolyl] Formamide-Induced Bladder Cancer in Bladder Submucosa: An Animal Model for Bladder Cancer study, Cancer Res., 43(2): 617-622 (1983).
[11] Ilies M.A., Vullo D., Pastorek J., Scozzafava A., Ilies M., Caproiu M.T., Pastorekova S., Supuran C.T., Carbonic Anhydrase Inhibitors. inhibition of Tumor-Associated Isozyme IX by Halogenosulfanilamide and Halogenophenylaminobenzolamide Derivatives, J. Med. Chem., 46(11): 2187-2196 (2003).
[12] Winum J.-Y., Dogné J.-M., Casini A., de Leval X., Montero J.-L., Scozzafava A., Vullo D., Innocenti A., Supuran C.T., Carbonic Anhydrase Inhibitors: Synthesis and Inhibition of Cytosolic/Membrane-Associated Carbonic Anhydrase Isozymes I, II, and IX with Sulfonamides Incorporating Hydrazino Moieties, J. Med. Chem., 48(6): 2121-2125 (2005).
[13] Krishnamurthy V.M., Bohall B.R., Kim C.Y., Moustakas D.T., Christianson D.W., Whitesides G.M., Thermodynamic Parameters for the Association of Fluorinated Benzenesulfonamides with Bovine Carbonic Anhydrase II, Chemistry–An Asian Journal, 2(1): 94-105 (2007).
[14] Samanta P.N., Das K.K., Prediction of Binding Modes and Affinities of 4-Substituted-2, 3, 5, 6-Tetrafluorobenzenesulfonamide Inhibitors to the Carbonic Anhydrase Receptor by Docking and ONIOM Calculations, J. Mol. Graphics Modell., 63: 38-48 (2016).
[15] Shchegol'kov E., Shchur I., Burgart Y.V., Saloutin V., Trefilova A., Ljushina G., Solodnikov S.Y., Markova L., Maslova V., Krasnykh O., Polyfluorinated Salicylic Acid Derivatives as Analogs of Known Drugs: Synthesis, Molecular Docking and Biological Evaluation, Bioorg. Med. Chem., 25(1): 91-99 (2017).
[16] Harris J.D., Coon C.M., Doherty M.E., McHugh E.A., Warner M.C., Walters C.L., Orahood O.M., Loesch A.E., Hatfield D.C., Sitko J.C., Engineering and Characterization of Dehalogenase Enzymes from Delftia Acidovorans in Bioremediation of Perfluorinated Compounds, Synth. Syst. Biotechnol., 7(2): 671-676 (2022).
[17] Etsè K.S., Etsè K.D., Zaragoza G., Mouithys-Mickalad A., Structural Description, IR, TGA, Antiradical, HRP Activity Inhibition and Molecular Docking Exploration of N-Cyclohexyl-N-Tosylformamide, J. Mol. Struct., 1269: 133731 (2022).
[18] Newell B.D., McMillen C.D., Lee J.P., N-(2, 3, 5, 6-Tetrafluoropyridin-4-yl) Formamide, IUCrData, 7(8): x220804 (2022).
[19] Cartwright M.W., Parks E.L., Pattison G., Slater R., Sandford G., Wilson I., Yufit D.S., Howard J.A., Christopher J.A., Miller D.D., Annelation of Perfluorinated Heteroaromatic Systems by 1, 3-Dicarbonyl Derivatives, Tetrahedron, 66(17): 3222-3227 (2010).
[20] Panova M.A., Shcherbakov K.V., Burgart Y.V., Saloutin V.I., Selective Nucleophilic Aromatic Substitution of 2-(Polyfluorophenyl)-4H-Chromen-4-Ones with Pyrazole, J. Fluorine Chem., 263: 110034 (2022).
[21] Shabalin A.Y., Adonin N.Y., Bardin V.V., Taran O.P., Ayusheev A.B., Parmon V.N., Synthesis of Potassium 4-(1-Azol-1-yl)-2, 3, 5, 6-Tetrafluorophenyltrifluoroborates from K [C6F5BF3] and Alkali Metal Azol-1-Ides. The Dramatic Distinction in Nucleophilicity of Alkali Metal Azol-1-Ides and Dialkylamides, J. Fluorine Chem., 156: 290-297 (2013).
[22] Morgan P.J., Saunders G.C., Macgregor S.A.,
Marr A.C., Licence P., Nucleophilic Fluorination Catalyzed by a Cyclometallated Rhodium Complex, Organometallics, 41(7): 883-891 (2022).
[23] Barim E., Akman F., Synthesis, Characterization and Spectroscopic Investigation of N-(2-Acetylbenzofuran-3-yl) Acrylamide Monomer: Molecular Structure, HOMO–LUMO Study, TD-DFT and MEP Analysis, J. Mol. Struct., 1195: 506-513 (2019).
[24] Akman F., Kaçal M.R., Akman F., Soylu M.S., Determination of Effective Atomic Numbers and Electron Densities from Mass Attenuation Coefficients for Some Selected Complexes Containing Lanthanides, Can. J. Phys., 95(10): 1005-1011 (2017).
[25] SenthilKannan K., Sivaramakrishnan V., Kalaipoonguzhali V., Chinnadurai M., Kannan S., Electronic Transport, HOMO–LUMO and Computational Studies of CuS Monowire for Nano Device Fabrication by DFT Approach, Mater. Today: Proc., 33: 2746-2749 (2020).
[26] Mumit M.A., Pal T.K., Alam M.A., Islam M.A.-A.-A.-A., Paul S., Sheikh M.C., DFT Studies on Vibrational and Electronic Spectra, HOMO–LUMO, MEP, HOMA, NBO and Molecular Docking Analysis of Benzyl-3-N-(2, 4, 5-Trimethoxyphenylmethylene) Hydrazinecarbodithioate, J. Mol. Struct., 1220: 128715 (2020).
[27] Khan B.A., Ashfaq M., Muhammad S., Munawar K.S., Tahir M.N., Al-Sehemi A.G., Alarfaji S.S., Exploring Highly Functionalized Tetrahydropyridine as a Dual Inhibitor of Monoamine Oxidase A and B: Synthesis, Structural Analysis, Single Crystal XRD, Supramolecular Assembly Exploration by Hirshfeld Surface Analysis, and Computational Studies, ACS Omega, 7(33): 29452-29464 (2022).
[28] Yu Z., Kang L., Zhao W., Wu S., Ding L., Zheng F., Liu J., Li J., Identification of Novel Umami Peptides from Myosin via Homology Modeling and Molecular Docking, Food chemistry, 344: 128728 (2021).
[29] Yu Z., Ji H., Shen J., Kan R., Zhao W., Li J., Ding L., Liu J., Identification and Molecular Docking Study of fish Roe-Derived Peptides as Potent BACE 1, AChE, and BChE Inhibitors, Food Funct., 11(7): 6643-6651 (2020).
[30] 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., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Vreven T., Montgomery J.A., Peralta Jr. J.E., Ogliaro F., Bearpark M., Heyd J.J., Brothers E., Kudin K.N., Staroverov V.N., Kobayashi R., Normand J., Raghavachari K., Rendell A., Burant J.C., Iyengar S.S., Tomasi J., Cossi M., Rega N., Millam J.M., Klene M., Knox J.E., Cross J.B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Martin R.L., Morokuma K., Zakrzewski V.G., Voth G.A., Salvador P., Dannenberg J.J., Dapprich S., Daniels A.D., Farkas O., Foresman J.B., Ortiz J.V., Cioslowski J., Fox D.J., Gaussian, Inc, Wallingford CT, 121: 150-166 (2009).
[31] Wolff S., Grimwood D., McKinnon J., Turner M., Jayatilaka D., Spackman M., “Crystal Explorer, In, University of Western Australia Crawley”, Australia, 2021.
[32] Daina A., Michielin O., Zoete V., SwissADME:
A Free Web Tool to Evaluate Pharmacokinetics, Drug-Likeness and Medicinal Chemistry Friendliness of Small Molecules, Sci. Rep., 7(1): 1-13 (2017).
[33] Trott O., Olson A.J., AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading, J. Comput. Chem., 31(2): 455-461 (2010).
[34] Systèmes D., Free Download: BIOVIA Discovery Studio Visualizer-Dassault Systèmes, in, 2020.
[35] Sheldrick G.M., A Short History of SHELX, Acta Crystallogr., Sect. A: Found. Crystallogr., 64(1): 112-122 (2008).
[36] Parr R.G., Szentpály L.v., Liu S., Electrophilicity Index, J. Am. Chem. Soc., 121(9): 1922-1924 (1999).
[37] Fukui K., Role of Frontier Orbitals in Chemical Reactions, Science, 218(4574): 747-754 (1982).
[38] Samsonowicz M., Regulska E., Kowczyk-Sadowy M., Butarewicz A., Lewandowski W., The Study on Molecular Structure and Microbiological Activity of Alkali Metal 3-Hydroxyphenylycetates, J. Mol. Struct., 1146: 755-765 (2017).
[39] Samsonowicz M., Regulska E., Świsłocka R., Butarewicz A., Molecular Structure and Microbiological Activity of Alkali Metal 3, 4-Dihydroxyphenylacetates, J. Saudi Chem. Soc., 22(8): 896-907 (2018).
[40] Merza M.M., Hussein F.M., AL-ani R.R., Physical Properties and Biological Activity of Methyldopa Drug Carrier Cellulose Derivatives. Theoretical Study, Egypt. J. Chem., 64(8): 4081-4090 (2021).
[41] Yadav B., Yadav R.K., Srivastav G., Yadav R., Experimental Raman, FTIR and UV-Vis Spectra, DFT Studies of Molecular Structures and Barrier Heights, Thermodynamic Functions and Bioactivity of Kaempferol, J. Mol. Struct., 1258: 132637 (2022).
[42] Bendjeddou A., Abbaz T., Gouasmia A., Villemin D., Molecular Structure, HOMO-LUMO, MEP and Fukui Function Analysis of Some TTF-Donor Substituted Molecules Using DFT (B3LYP) Calculations, Int. Res. J. Pure Appl. Chem., 12(1): 1-9 (2016).
[43] O'boyle N.M., Tenderholt A.L., Langner K.M., Cclib: A Library for Package‐Independent Computational Chemistry Algorithms, J. Comput. Chem., 29(5): 839-845 (2008).
[44] Spackman M.A., Jayatilaka D., Hirshfeld Surface Analysis, Cryst. Eng. Comm., 11(1): 19-32 (2009).
[45] Madni M., Ahmed M.N., Abbasi G., Hameed S., Ibrahim M.A., Tahir M.N., Ashfaq M., Gil D.M., Gomila R.M., Frontera A., Synthesis and X‐ray Characterization of 4, 5‐Dihydropyrazolyl‐Thiazoles Bearing a Coumarin Moiety: On the Importance
of Antiparallel π‐Stacking, Chemistry Select, 7(36): e202202287 (2022).
[46] Ashfaq M., Ali A., Tahir M.N., Khalid M., Assiri M.A., Imran M., Munawar K.S., Habiba U., Synthetic Approach to Achieve Halo Imine Units: Solid-State Assembly, DFT Based Electronic and Non Linear Optical Behavior, Chem. Phys. Lett., 803: 139843 (2022).
[47] Ali A., Ashfaq M., Din Z.U., Ibrahim M., Khalid M., Assiri M.A., Riaz A., Tahir M.N., Rodrigues-Filho E., Imran M., Synthesis, Structural, and Intriguing Electronic Properties of Symmetrical Bis-Aryl-α, β-Unsaturated Ketone Derivatives, ACS Omega:  (2022).
[48] Akoka S., Remaud G.S., NMR-Based Isotopic and Isotopomic Analysis, Prog. Nucl. Magn. Reson. Spectrosc., 120: 1-24 (2020).
[49] Lipinski C.A., Lead-and Drug-Like Compounds: The Rule-of-Five Revolution, Drug Discovery Today: Technol., 1(4): 337-341 (2004).
[50] Zubrienė A., Smirnovienė J., Smirnov A., Morkūnaitė V., Michailovienė V., Jachno J., Juozapaitienė V., Norvaišas P., Manakova E., Gražulis S., Intrinsic Thermodynamics of 4-Substituted-2, 3, 5, 6-Tetrafluorobenzenesulfonamide Binding to Carbonic Anhydrases by Isothermal Titration Calorimetry, Biophys. Chem., 205: 51-65 (2015).
Iranian Journal of Chemistry and Chemical Engineering
Volume 42, Issue 8 - Serial Number 130
August 2023
Pages 2438-2450

Files

Share

How to cite

Statistics