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Synthesis, theoretical and experimental spectroscopic properties, molecular docking, ADMET, and RDG analysis of copper(II) complex of dichloro(1,10-phenanthroline)(1,2,4-triazole-3-carboxcylic acid)

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Abstract

A new dichloro(1,10-phenanthroline)(1,2,4-triazole-3-carboxylic-acid)copper(II) was synthesized, and the most stable optimized structure was determined using the B3LYP/LANL2DZ basis set, followed by FTIR and NMR characterization. The molecular geometric structure analysis and vibrational frequencies of the Cu(II) complex were calculated by using density functional theory calculations in the ground state. Metal-ligand and intra-ligand vibrations were investigated using vibrational analysis, and the obtained computational values were compared with the experimental values. The ProTox-II webserver was utilized for toxicological evaluation of the organism and organ, as well as molecular mechanisms of toxicity evidenced by the median lethal dose (LD50). SwissADME prediction was performed ADMET properties. Reduced density gradient (RDG) analysis is employed to study the weak interactions within the molecule. The nature of the chemical bonds in the [Cu(phen)(TCA)2Cl2] complex is investigated using electron localization function (ELF) analysis. MEPs, HOMO, LUMO, global reactivity descriptors, and Fukui functions are performed to study the chemical reactivity of the compound. Molecular docking studies are performed to predict the antibacterial, antidepressant, and anti-anxiety active site of the complex. Cu(phen)(TCA)2Cl2 was defined and used to evaluate the antibacterial properties of this Cu(II) complex against B. subtilis.

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References

  • Accorsi G, Listorti A, Yoosaf K, Armaroli N (2009) 1, 10-phenanthrolines: versatile building blocks for luminescent molecules, materials and metal complexes. Chem Soc Rev 38:1690–1700

    Article  CAS  PubMed  Google Scholar 

  • Ajayi TJ, Shapi M (2020) Solvent-free mechanochemical synthesis, Hirshfeld surface analysis, crystal structure, spectroscopic characterization and NBO analysis of Bis(ammonium) Bis((4-methoxyphenyl) phosphonodithioato)-nickel (II) dihydrate with DFT studies. J Mol Struct 1202:127254

  • Ako-Nai AK, Abumere G, Akinyoola AL, OT, Kassim OO, (2013) Characterization of bacterial isolates from patients wounds and environmental factors predictive of post-surgical infections at the orthopedic ward in ile-ife. Nigeria East Afr Med J 90(12):380–386

    CAS  PubMed  Google Scholar 

  • Alyar S, Tülin S (2019) Synthesis, spectroscopic characterizations, enzyme inhibition, molecular docking study and DFT calculations of new Schiff bases of sulfa drugs. J Mol Struct 1185:416–424

    Article  CAS  Google Scholar 

  • Amalanathan M, Joe IH, Prabhu SS (2010) Charge transfer interaction and terahertz studies of a nonlinear optical material glutamine picrate: a DFT study. J Phys Chem A 114:13055–13064

    Article  CAS  PubMed  Google Scholar 

  • Anuradha A, Sara Saji R, Varghese MG, Muthu S, Prasana JC (2020) Vibrational spectroscopic, DFT studies and molecular docking on (2R)-2-acetamido-N-benzyl-3-methoxy propanamide as an antineuropathic pain drug. Mater Today

  • Aycan T, Öztürk F, Doruk T, Demir S, Fidan M, Paşaoğlu H (2020) Synthesis, structural, spectral and antimicrobial activity studies of copper-nalidixic acid complex with 1,10-phenanthroline: DFT and molecular docking. Spectrochim Acta Part A Mol Biomol Spect 241:118639

  • Balci M (2005) Basic 1H- and 13C-NMR spectroscopy. Elsevier, Amsterdam. ISBN: 9780444518118

  • Banuppriya G, Sribalan R, Padmini V (2018) Synthesis and characterization of curcumin-sulfonamide hybrids: Biological evaluation and molecular docking studies. J Mol Struct 1155:90–100

    Article  CAS  Google Scholar 

  • Belkhir-Talbi D, Makhloufi-Chebli M, Terrachet-Bouaziz S, Hikem-Oukacha D, Ghemmit N, Ismaili L, Silva AMS, Hamdi M (2019) Synthesis, characterization, theoretical studies, ADMET and drug-Likeness analysis: electrochemical and biological activities of metal complexes of 3-(2-hydroxybenzoyl)-2H-chromen-2-one. J Mol Struct 1179:495–505

    Article  CAS  Google Scholar 

  • Bencini A, Lippolis V (2010) 1, 10-Phenanthroline: a versatile building block for the construction of ligands for various purposes. Coord Chem Rev 254:2096–2180

    Article  CAS  Google Scholar 

  • Bergamo A, Dyson PJ, Sava G (2018) The mechanism of tumor cell death by metal based anticancer drugs is not only a matter of DNA interactions. Coord Chem Rev 360:17–33

    Article  CAS  Google Scholar 

  • Chandraleka S, Ramya K, Chandramohan G, Dhanasekaran D, Priyadharshini A, Panneerselvam A (2014) Antimicrobial mechanism of copper (II) 1,10-phenanthroline and 2,20 -bipyridyl complex on bacterial and fungal pathogens. J Saudi Chem Soc 18:953–962

    Article  Google Scholar 

  • Chen X-B, Chen B, Li Y-Z, You X-Z (2007) Remarkable solvent effects in the hydro- and solvothermal synthesis of copper-1,10-phenanthroline complexes. Appl Organometal Chem 21:777–781

    Article  CAS  Google Scholar 

  • Clemente L, Dragovic D, Milocco C, Fontana F (2016) Report of a rare case of sepsis caused by Bacillus pumilus in an immunocompetent child with the involvement of soft tissues cellulitis. Microbiologia Medica 31:118–119

    Article  Google Scholar 

  • DeLano WL (2002) Pymol: an open-source molecular graphics tool. CCP4 Newslett Prot Crystallogr 40:82–92

  • Dennington R, Keith T, Millam J (2009) GaussView version 5. Semichem Inc., Shawnee Mission, KS

    Google Scholar 

  • Dhiman P, Malik N, Sobarzo-Sánchez E, Uriarte E, Khatkar A (2019) Quercetin and related chromenone derivatives as monoamine oxidase inhibitors: targeting neurological and mental disorders. Molecules 24:418–436

    Article  PubMed Central  Google Scholar 

  • Dunaj-Jurco M, Ondrejovic G, Melnik M, Garaj J (1988) Mixed-valence copper(I)-copper(II) compounds: analysis and classification of crystallographic data. Coord Chem Rev 83:1–28

    Article  CAS  Google Scholar 

  • Erdogdu Y, Başköse ÜC, Sağlam S (2019) Conformational, structural, electronic, and vibrational investigations on 5-methyl-4-(2-thiazolylazo)resorcinol by FT-IR, FT–Raman, NMR, and DFT. Chem Pap 73:1879–1891

    Article  CAS  Google Scholar 

  • Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian, Inc., Wallingford CT

  • Hammuda HH, Kortz U, Bhattacharya S, Demirdjian S, Haririd E, Isbere S, Sang E, Choi ES, Mirtamizdoustg B, Mrouehh M, Daher CF (2020) Structure, DFT studies, magnetism and biological activity of bis[(µ-azido)-chloro-(1,10-phenanthroline)-copper(II)] complex. Inorg Chim Acta 506:119533

  • Henkel G, Weissgräber S, Buse G, Soulimane T, Steffens GCM, Nolting H-F (1995) The active sites of the native cytochrome-c oxidase from bovine heart mitochondria: EXAFS-spectroscopic characterization of a novel homobinuclear copper center (CuA) and of the heterobinuclear Fea3-CuB center. Angew Chem Int Edn Engl 34:1488–1492

    Article  CAS  Google Scholar 

  • Houser RP, Young VG, Tolman WB (1996) A thiolate-bridged, fully delocalized mixed-valence dicopper (I, II) complex that models the Cu A biological electron-transfer site. J Am Chem Soc 118:2101–2102

    Article  CAS  Google Scholar 

  • Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38

    Article  CAS  PubMed  Google Scholar 

  • Jeon HJ, Yi SC, Oh SG (2003) Preparation and antibacterial effects of AgSiO2 thin films by sol-gel method. Biomaterials 24:4921–4928

    Article  CAS  PubMed  Google Scholar 

  • Kargar H, Behjatmanesh-Ardakani R, Torabi V, Kashani M, Chavoshpour-Natanzi Z, Kazemi Z, Mirkhani V, Sahraei A, Nawaz Tahir M, Ashfaq M, Munawar KS (2021a) Synthesis, characterization, crystal structures, DFT, TD-DFT, molecular docking and DNA binding studies of novel copper(II) and zinc(II) complexes bearing halogenated bidentate N,O-donor Schiff base ligands. Polyhedron 195:114988

  • Kargar H, Behjatmanesh-Ardakani R, Torabi V, Sarvian A, Kazemi Z, Chavoshpour-Natanzi Z, Mirkhani V, Sahraei A, Tahir MN, Ashfaq M (2021b) Novel copper(II) and zinc(II) complexes of halogenated bidentate N,O-donor Schiff base ligands: Synthesis, characterization, crystal structures, DNA binding, molecular docking, DFT and TD-DFT computational studies. Inorg Chim Acta 14:120004

  • Kargar H, Aghaei-Meybodi F , Behjatmanesh-Ardakani R, Reza Elahifard M, Torabi V, Fallah-Mehrjardi M, Nawaz Tahir M, Ashfaq M, Munawar KS (2021c) Synthesis, crystal structure, theoretical calculation, spectroscopic and antibacterial activity studies of copper(II) complexes bearing bidentate schiff base ligands derived from 4-aminoantipyrine: influence of substitutions on antibacterial activity. J Mol Struct 1230:129908

  • Khodja IA, Boulebd H (2021) Synthesis, biological evaluation, theoretical investigations, docking study and ADME parameters of some 1,4-bisphenylhydrazone derivatives as potent antioxidant agents and acetylcholinesterase inhibitors. Mol Divers 25:279–290

    Article  Google Scholar 

  • Lappalainen P, Saraste M (1994) The binuclear CuA center of cytochrome oxidase. Biochim Biophys Acta 1187:222–225

    Article  CAS  Google Scholar 

  • Liu J-n, Chen Z-r, Yuan S-f (2005) Study on the prediction of visible absorption maxima of azobenzene compounds. J Zhejiang Univ Sci B 6:584–589

    Article  PubMed  PubMed Central  Google Scholar 

  • Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunction analyzer. J Comput Chem 33:580–592

    Article  PubMed  Google Scholar 

  • Luman CR, Castellano FN (2003) Phenanthroline Ligands Compr Coord Chem II:25–39

    Google Scholar 

  • Machura B, Wolff M, Jaworska M, Lodowski P, Benoist E, Carrayon C, Saffon N, Kruszynski R, Mazurak Z (2011) Rhenium(I) carbonyl complex of 4,7-diphenyl 1,10-phenanthrolineeSpectroscopic properties, X-ray structure, theoretical studies of ground and excited electronic states. J Organomet Chem 696:3068–3075

    Article  CAS  Google Scholar 

  • Malmatrom BG, Aasa R (1993) The nature of the Cu Acenter in cytochrome coxidase. FEBS Lett 325:49–52

    Article  Google Scholar 

  • Mi H, Xiao G, Chen X (2015) Theoretical evaluation of corrosion inhibition performance of three antipyrine compounds. Comp Theor Chem 1072:7–14

    Article  CAS  Google Scholar 

  • Mondal S, Mandal SM, Mondal TK, Sinha C (2015) Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure. Spectrochim Acta A Mol Biomol Spectrosc 150:268–279

    Article  CAS  PubMed  Google Scholar 

  • Morell C, Grand A, Toro-Labbe A (2005) New dual descriptor for chemical reactivity. J Phys Chem 109:205–212

    Article  CAS  Google Scholar 

  • Morris GM, Goodwill DS, Halliday RS, Huey R, Hart W, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comp Chem 19:1639–1662

    Article  CAS  Google Scholar 

  • Noureddine O, Gatfaoui S, Brandan SA, Sagaama A, Marouani H, Issaoui N (2020) Experimental and DFT studies on the molecular structure, spectroscopic properties, and molecular docking of 4-phenylpiperazine-1-ium dihydrogen phosphate. J Mol Struct 207:127762

  • Onawumi OOE, Adeoye IO, Adekunle FAO (2013) Synthesis, characterization and microbial studies of [bis(1,10-phenanthroline) (ethylenediamine) copper(II)] diperchlorate and its bromide analogue. Open J Inorg Chem 3:26–33

    Article  CAS  Google Scholar 

  • Osmialowski B, Kolehmainen E, Gawinecki E (2001) GIAO/DFT calculated chemical shifts of tautomeric species. 2-Phenacylpyridines and (Z)-2-(2-hydroxy-2-phenylvinyl)pyridines. Magn Res Chem 39:334–340

    Article  CAS  Google Scholar 

  • Pirhadi S, Ghasemi JB (2012) Pharmacophore identification, molecular docking, virtual screening, and in silico ADME studies of non-nucleoside reverse transcriptase inhibitors. Mol Inf 31:856–866

    Article  CAS  Google Scholar 

  • Pophristic V, Goodman L, Guchhait N (1997) Role of lone-pairs in internal rotation barriers. J Phys Chem 101:4290–4297

    Article  CAS  Google Scholar 

  • Ramakrishnan S, Palaniandavar M (2005) Mixed-ligand copper(II) complexes of dipicolylamine and 1,10-phenanthrolines: the role of diimines in the interaction of the complexes with DNA. J Chem Sci 117:179–186

    Article  CAS  Google Scholar 

  • Reiher M, Brehm G, Schneider S (2004) Assignment of vibrational spectra of 1,10-phenanthroline by comparison with frequencies and Raman intensities from density functional calculations. J Phys Chem A 108:734–742

    Article  CAS  Google Scholar 

  • Robertazzi A, Vittorio Vargiu A, Magistrato A, Ruggerone P, Carloni P, de Hoog P, Reedijk J (2009) Copper-1,10-phenanthroline complexes binding to DNA: structural predictions from molecular simulations. J Phys Chem B 113:10881–10890

    Article  CAS  PubMed  Google Scholar 

  • RSCB PDB Protein Data Bank (2021) https://www.rcsb.org/. Accessed 01 October 2021

  • Saha SK, Ghosh P, Hens A, Murmu NC, Banerjee P (2015) Density functional theory and molecular dynamics simulation study on corrosion inhibition performance of mild steel by mercapto-quinoline Schiff base corrosion inhibitor. Phys E Low-Dimens Syst Nanostruct 66:332–341

    Article  CAS  Google Scholar 

  • Saleh G, Gatti C, Lo Presti L (2012) Non-covalent interaction via the reduced density gradient: independent atom model vs experimental multipolar electron densities. Comp Theo Chem 998:148–163

    Article  CAS  Google Scholar 

  • Sayin K, Karakaş D, Kariper SE, Sayin TA (2018) Computational study of some fluoroquinolones: structural, spectral and docking investigations. J Mol Struct 1156:172–181

    Article  CAS  Google Scholar 

  • Schilt A, Taylor RC (1959) Infra-Red spectra of 1:10-Phenanthroline metal complexes in the rock salt region below 2000 cm-1. J Inorg Nucl Chem 9:211–221

    Article  CAS  Google Scholar 

  • Singha K, Bala I, Kataria R (2020) Crystal structure, Hirshfeld surface and DFT based NBO, NLO, ECT and MEP of benzothiazole based hydrazine. Chem Phys 538:110873

  • Son S-Y, Ma J, Kondou Y, Yoshimura M, Yamashita E, Tsukihara T (2008) Structure of human monoamine oxidase A at 2.2-Å resolution: the control of opening the entry for substrates/inhibitors. PNAS 105:5739–5744

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sondi I, Salopek-Sondi B (2004) Silver nanoparticles as antimicrobial agent: a case study on E. coli as a model for Gram-negative bacteria. J Colloid Interface Sci 275:177–182

    Article  CAS  PubMed  Google Scholar 

  • Tapiero H, Townsend DM, Tew KD (2003) Trace elements in human physiology and pathology. Copper Biomed Pharmacother 57:386–398

    Article  CAS  PubMed  Google Scholar 

  • Weinhold F (2005) Chemistry: a new twist on molecular shape. Nature 411:539–541

    Article  Google Scholar 

  • Yurdakul Ş, Tanrıbuyurdu S (2012) FT-IR, FT-Raman, vibrational assignments, and density functional studies of 1,2,4-triazole-3-carboxylic acid, and its tautomers, dimers. Struct Chem 23:433–440

    Article  CAS  Google Scholar 

  • Zhu J, Yin X-H, Feng Y, Zhang S-S, Zhao K, Lin C-W (2008) Chlorido(1,10-phenanthroline)(1H-1,2,4- triazole-3-carboxylato)copper(II). Acta Cryst E64: m71

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Acknowledgements

The authors are thankful to Belgin ERDEM (Kırşehir Ahi Evran University) for the antibacterial activity part of the manuscript.

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Material preparation, data collection, and analysis were performed by SC, SB, and ŞY. The software and formal analysis was performed by SC. Writing—review and editing of the manuscript was done by SC, SB, and ŞY. All authors commented on previous versions of the manuscript. All authors contributed to the study conception and design and approved the final manuscript.

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Correspondence to Sibel Celik.

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Celik, S., Badoğlu, S. & Yurdakul, S. Synthesis, theoretical and experimental spectroscopic properties, molecular docking, ADMET, and RDG analysis of copper(II) complex of dichloro(1,10-phenanthroline)(1,2,4-triazole-3-carboxcylic acid). Chem. Pap. 76, 4099–4114 (2022). https://doi.org/10.1007/s11696-022-02158-4

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