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DFT investigation and molecular docking studies on dinuclear metal carbonyls containing pyridyl ligands with alkyne unit

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Abstract

CO-releasing (CORM) complexes ([(CO)4LW]2(μ-DPB) (L = CO, PMe3, P(OMe)3, PPh3 and P(OPh)3) were optimized using various methods and basis sets. The most suitable level according to the correlation between the calculated and experimental structural parameters was found at B3LYP/LANL2DZ/6-31G(d)level for [(CO)4LW]2(μ-DPB) [L = CO, PPh3, P(OPh)3]. [(CO)4LW]2(μ-DPB) (L = PMe3, P(OMe)3) are hypothetical complexes which have been not synthesized yet. Experimental IR, NMR and UV–Vis spectra for [(CO)4LW]2(μ-DPB) [L = CO, PPh3, P(OPh)3] were compared with the calculated values. At the same time, IR, 1H-NMR chemical shift values and UV–Vis spectra were estimated for the hypothetical complexes. Polarizability (α) and first hyperpolarizability (β0) values were calculated for nonlinear optical properties (NLO). To investigate the therapeutic effects of complexes such as CO-releasing reagents, the target protein was identified as the empty coordination domain in the data bank and the soluble sGC and hemoglobin coordination code was determined as PDB ID:2O0G and molecular docking was performed between target protein and mentioned complexes. The calculated structural parameters, stretching frequencies, 1H-NMR chemical shift values and UV–Vis spectra for [(CO)4LW]2(μ-DPB) [L = CO, PPh3, P(OPh)3] complexes were found to be in agreement with the experimental values. When the [(CO)4LW]2(μ-DPB) (L = PMe3, P(OMe)3) complexes are synthesized, it is considered that there will be a good fit between the experimental results and the calculated values. All complexes can be used as optical material according to their polarizability (α) and first hyperpolarizability (β0) values. In addition, the binding energy of the [(CO)5W]2(μ-DPB), [(CO)4PMe3W]2(μ-DPB), [(CO)4P(OMe)3W]2(μ-DPB), [(CO)4PPh3W]2(μ-DPB) and [(CO)4P(OPh)3W]2(μ-DPB) complexes to the target protein was calculated to be − 385.18, − 423.89, − 496.95, − 479.73 and − 538.31 kcal/mol, respectively.

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References

  • Acar N, Şener S (2018) Computational studies of metal carbonyl complexes of 3 [4-ethyl (phenly) imino][indoline-2-one] and 3 [4-butyl (phenly) imino][indoline-2-one]. J Mol Model 24(7):170

    Article  CAS  PubMed  Google Scholar 

  • Bagno A, Rastrelli F, Saielli G (2006) Toward the complete prediction of the 1H and 13C NMR spectra of complex organic molecules by DFT methods: application to natural substances. Chem A Eur J 12(21):5514–5525

    Article  CAS  Google Scholar 

  • Bandarra D, Lopes M, Lopes T, Almeida J, Saraiva MS, Vasconcellos-Dias M, Meireles M (2010) Mo (II) complexes: a new family of cytotoxic agents? J Inorg Biochem 104(11):1171–1177

    Article  CAS  PubMed  Google Scholar 

  • Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98(7):5648–5652

    Article  CAS  Google Scholar 

  • Bianco G, Forli S, Goodsell DS, Olson AJ (2016) Covalent docking using autodock: two-point attractor and flexible side chain methods. Protein Sci 25(1):295–301

    Article  CAS  PubMed  Google Scholar 

  • Casida ME (1995) Time-dependent density functional response theory for molecules. In: Recent advances in density functional methods (Part I), pp 155–192

  • Collman JP (1975) Disodium tetracarbonylferrate, a transition metal analog of a Grignard reagent. Acc Chem Res 8(10):342–347

    Article  CAS  Google Scholar 

  • Datta P, Mukhopadhyay AP, Manna P, Tiekink ER, Sil PC, Sinha C (2011) Structure, photophysics, electrochemistry, DFT calculation, and in vitro antioxidant activity of coumarin Schiff base complexes of Group 6 metal carbonyls. J Inorg Biochem 105(4):577–588

    Article  CAS  PubMed  Google Scholar 

  • Dennington R, Keith T, Millam J (2009) Gauss View 5.0. Gaussian Inc., Wallingford

    Google Scholar 

  • Erkan KS, Sayin K, Karakaş D (2017) Theoretical study on the antitumor properties of Ru (II) complexes containing 2-pyridyl, 2-pyridine-4-carboxylic acid ligands. J Mol Struct 1149:473–486

    Article  CAS  Google Scholar 

  • Farah S, Korichi H, Zendaoui SM, Saillard JY, Zouchoune B (2009) The coordination of azepine to transition-metal complexes: a DFT analysis. Inorg Chim Acta 362(10):3541–3546

    Article  CAS  Google Scholar 

  • Farrer NJ, Sadler PJ (2008) Photochemotherapy: targeted activation of metal anticancer complexes. Aust J Chem 61(9):669–674

    Article  CAS  Google Scholar 

  • Feil R, Kemp-Harper B (2006) cGMP signalling: from bench to bedside: conference on cGMP generators, effectors and therapeutic implications. EMBO Rep 7(2):149–153

    Article  CAS  PubMed  Google Scholar 

  • Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA et al (2009) Gaussian09, R.A, vol 121. Gaussian Inc., Wallingford, pp 150–166

    Google Scholar 

  • Furchgott RF, Jothianandan D (1991) Endothelium-dependent and-independent vasodilation involving cyclic GMP: relaxation induced by nitric oxide, carbon monoxide and light. J Vasc Res 28(1–3):52–61

    Article  CAS  Google Scholar 

  • Glans L, Taylor D, de Kock C, Smith PJ, Haukka M, Moss JR, Nordlander E (2011) Synthesis, characterization and antimalarial activity of new chromium arene–quinoline half sandwich complexes. J Inorg Biochem 105(7):985–990

    Article  CAS  PubMed  Google Scholar 

  • Hetrick EM, Schoenfisch MH (2009) Analytical chemistry of nitric oxide. Annu Rev Anal Chem 2:409–433

    Article  CAS  Google Scholar 

  • Ingi T, Cheng J, Ronnett GV (1996) Carbon monoxide: an endogenous modulator of the nitric oxide–cyclic GMP signaling system. Neuron 16(4):835–842

    Article  CAS  PubMed  Google Scholar 

  • Johnson TR, Mann BE, Clark JE, Foresti R, Green CJ, Motterlini R (2003) Metal carbonyls: a new class of pharmaceuticals? Angew Chem Int Ed 42(32):3722–3729

    Article  CAS  Google Scholar 

  • Judd DA, Nettles JH, Nevins N, Snyder JP, Liotta DC, Tang J, Hill CL (2001) Polyoxometalate HIV-1 protease inhibitors. A new mode of protease inhibition. J Am Chem Soc 123(5):886–897

    Article  CAS  PubMed  Google Scholar 

  • Kanis DR, Ratner MA, Marks TJ (1994) Design and construction of molecular assemblies with large second-order optical nonlinearities. Quantum chemical aspects. Chem Rev 94(1):195–242

    Article  CAS  Google Scholar 

  • Karakaş D, Kariper SE (2014) Theoretical investigation on the vibrational and electronic spectra of three isomeric forms of dicobalt octacarbonyl. J Mol Struct 1062:77–81

    Article  CAS  Google Scholar 

  • Kharitonov VG, Sharma VS, Pilz RB, Magde D, Koesling D (1995) Basis of guanylate cyclase activation by carbon monoxide. Proc Natl Acad Sci 92(7):2568–2571

    Article  CAS  PubMed  Google Scholar 

  • Kimmich BF, Fagan PJ, Hauptman E, Marshall WJ, Bullock RM (2005) Molybdenum carbonyl complexes in the solvent-free catalytic hydrogenation of ketones. Organometallics 24(25):6220–6229

    Article  CAS  Google Scholar 

  • Kubeil M, Vernooij RR, Kubeil C, Wood BR, Graham B, Stephan H, Spiccia L (2017) Studies of carbon monoxide release from ruthenium(II) bipyridine carbonyl complexes upon UV-light exposure. Inorg Chem 56(10):5941–5952

    Article  CAS  Google Scholar 

  • Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37(2):785

    Article  CAS  Google Scholar 

  • Lin JT, Sun SS, Wu JJ, Lee L, Lin KJ, Huang YF (1995) Dinuclear metal carbonyls bridged by pyridyl ligands incorporating an alkyne entity. Inorg Chem 34(9):2323–2333

    Article  CAS  Google Scholar 

  • Maines MD, Kappas A (1977) Enzymic oxidation of cobalt protoporphyrin IX: observations on the mechanism of heme oxygenase action. Biochemistry 16(3):419–423

    Article  CAS  PubMed  Google Scholar 

  • Mann BE (2010) Carbon monoxide: an essential signalling molecule. In: Jaouen G, Metzler-Nolte N (eds) Medicinal organometallic chemistry. Springer, Berlin, pp 247–285

    Chapter  Google Scholar 

  • Mann BE, Motterlini R (2007) CO and NO in medicine. Chem Commun 41:4197–4208

    Article  CAS  Google Scholar 

  • Motterlini R, Otterbein LE (2010) The therapeutic potential of carbon monoxide. Nat Rev Drug Discov 9(9):728

    Article  CAS  PubMed  Google Scholar 

  • Motterlini R, Mann BE, Johnson TR, Clark JE, Foresti R, Green CJ (2003) Bioactivity and pharmacological actions of carbon monoxide-releasing molecules. Curr Pharm Des 9(30):2525–2539

    Article  CAS  Google Scholar 

  • Motterlini R, Mann BE, Foresti R (2005) Therapeutic applications of carbon monoxide-releasing molecules. Expert Opin Investig Drugs 14(11):1305–1318

    Article  CAS  PubMed  Google Scholar 

  • Santos-Martins D, Forli S, Ramos MJ, Olson AJ (2014) AutoDock4Zn: an improved AutoDock force field for small-molecule docking to zinc metalloproteins. J Chem Inf Model 54(8):2371–2379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sayin K, Karakaş D, Karakuş N, Sayin TA, Zaim Z, Kariper SE (2015) Spectroscopic investigation, FMOs and NLO analyses of Zn(II) and Ni(II) phenanthroline complexes: a DFT approach. Polyhedron 90:139–146

    Article  CAS  Google Scholar 

  • Sayin K, Kariper SE, Taştan M, Sayin TA, Karakaş D (2019) Investigations of structural, spectral, electronic and biological properties of N-heterocyclic carbene Ag(I) and Pd(II) complexes. J Mol Struct 1176:478–487

    Article  CAS  Google Scholar 

  • Sun SS, Lees AJ (2002) Transition metal based supramolecular systems: synthesis, photophysics, photochemistry and their potential applications as luminescent anion chemosensors. Coord Chem Rev 230(1–2):171–192

    Article  CAS  Google Scholar 

  • Tenhunen R, Marver HS, Schmid R (1969) The enzymatic conversion of hemoglobin to bilirubin. Trans Assoc Am Physicians 82:363

    CAS  PubMed  Google Scholar 

  • Utz J, Ullrich V (1991) Carbon monoxide relaxes ileal smooth muscle through activation of guanylate cyclase. Biochem Pharmacol 41(8):1195–1201

    Article  CAS  PubMed  Google Scholar 

  • Wolinski K, Hinton JF, Pulay P (1990) Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. J Am Chem Soc 112(23):8251–8260

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was made possible by TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure).

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Erkan, S., Karakaş, D. DFT investigation and molecular docking studies on dinuclear metal carbonyls containing pyridyl ligands with alkyne unit. Chem. Pap. 73, 2387–2398 (2019). https://doi.org/10.1007/s11696-019-00784-z

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  • DOI: https://doi.org/10.1007/s11696-019-00784-z

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