Advertisement

Comprehensive understanding of multiple binding of D-penicillamine with Cu2+-hexa aqua complex: a DFT approach

  • Tamalika Ash
  • Tanay Debnath
  • Avik Ghosh
  • Abhijit Kr. DasEmail author
Original Research
  • 8 Downloads

Abstract

The multiple-ligand-binding of D-penicillamine with [Cu(H2O)6]2+ has been explored computationally using density functional theory (DFT). Because of the implementation of bulk aqueous medium and considering the pH at physiological level, both neutral as well as de-protonated analogues of D-penicillamine are taken into account to study the binding phenomena with Cu2+. In doing so, at first, we have studied the binding of both neutral and de-protonated analogues of two D-penicillamine with Cu2+ in bi-dentate mode by replacing four molecules of H2O (di-amino complex) and afterward, the binding of three D-penicillamine with Cu2+ has been investigated by substituting all six molecules of H2O (tri-amino complex). Apart from bi-dentate binding, the de-protonated form of D-penicillamine can also bind in tri-dentate mode and in that case, all six H2O molecules are substituted during di-amino complex formation. Based on the coordinating modes of the artificial amino acids, for each di- and tri-amino complex, more than one isomer has been detected and the isomers are designated accordingly. By analyzing the optimized geometries, it is noticed that most of the di- and tri-amino complexes are distorted hexa-coordinated in nature and in few cases, they adopt penta-coordinated geometry. To analyze the stability of the complexes, we have determined the binding energy (BE) in both DCM and CDCM mechanisms for each di- and tri-amino complex. Overall, the present study is arranged in such a way so that it can provide a complete understanding about the binding process of the aforementioned artificial amino acid with Cu2+-aqua complex.

Keywords

Artificial amino acid Multiple binding DCM CDCM Binding energy 

Notes

Acknowledgments

TA and TD are thankful to Indian Association for the Cultivation of Science and AG is thankful to UGC for providing them research fellowships.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interest.

Supplementary material

11224_2019_1365_MOESM1_ESM.docx (2.2 mb)
ESM 1 (DOCX 2.18  mb)

References

  1. 1.
    Osredkar J, Sustar N (2011) Copper and zinc, biological role and significance of copper/zinc imbalance. J Clinic Toxicol S3:001CrossRefGoogle Scholar
  2. 2.
    Bertini I, Gray HB, Lippard SJ (1994) Valentine, J. S. Bioinorganic Chemistry; University Science Books: Sausalito, CA, pp 1−36Google Scholar
  3. 3.
    Desai V, Kaler SG (2008) Role of copper in human neurological disorders. Am J Clin Nutr 88:855S–858SCrossRefGoogle Scholar
  4. 4.
    Sarkar B (1999) Treatment of Wilson and Menkes diseases. Chem Rev 99:2535–2544CrossRefGoogle Scholar
  5. 5.
    Zhang H, Wang Y, Zhao M, Wu J, Zhang X, Gui L, Zheng M, Li L, Liu J, Peng S (2012) Synthesis and in vivo lead detoxification evaluation of poly-α,β-dl-aspartyl-l-methionine. Chem Res Toxicol 25:471–477CrossRefGoogle Scholar
  6. 6.
    Peisach J, Blumberg WE (1969) A mechanism for the action of penicillamine in the treatment of Wilson’s disease. Mol Pharmacol 5:200–209Google Scholar
  7. 7.
    Kandanapitiye MS, Gunathilake C, Jaroniec M, Huang SD (2015) Biocompatible D-penicillamine conjugated au nanoparticles: targeting intracellular free copper ions for detoxification. J Mater Chem B 3:5553–5559CrossRefGoogle Scholar
  8. 8.
    Scheinberg IH, Sternlieb I, Schilsky M, Stockert RJ (1987) Penicillamine may detoxify copper in Wilson’s disease. Lancet 330:95CrossRefGoogle Scholar
  9. 9.
    Jalilehvand F, Leung BO, Mah V (2009) Cadmium(II) complex formation with cysteine and penicillamine. Inorg Chem 48:5758–5771CrossRefGoogle Scholar
  10. 10.
    Baidya N, Olmstead MM, Mascharak PK (1991) Structure and properties of bis(D-penicillaminato-N,S)nickelate(II) tetrahydrate: a monomeric nickel complex of D-penicillamine, the antidote for nickel toxicity. Inorg Chem 30:3967–3969CrossRefGoogle Scholar
  11. 11.
    Sangvanich T, Morry J, Fox C, Ngamcherdtrakul W, Goodyear S, Castro D, Fryxell GE, Addleman RS, Summers AO, Yantasee W (2014) Novel oral detoxification of mercury, cadmium, and lead with thiol-modified nanoporous silica. ACS Appl Mater Interfaces 6:5483–5493CrossRefGoogle Scholar
  12. 12.
    Belcastro M, Marino T, Russo N, Sicilia E (2204) Structure and coordination modes in the interaction between Cd2+ and 3-mercaptopropionic acid. J Phys Chem A 108:8407–8410CrossRefGoogle Scholar
  13. 13.
    Bagchi S, Mandal D, Ghosh D, Das AK (2013) Interaction between group IIb divalent transition-metal cations and 3-mercaptopropionic acid: a computational and topological perspective. J Phys Chem A 117:1601–1613CrossRefGoogle Scholar
  14. 14.
    Shen H, Chen J, Dai H, Wang L, Hu M, Xia Q (2013) New insights into the sorption and detoxification of chromium(VI) by tetraethylenepentamine functionalized nanosized magnetic polymer adsorbents: mechanism and pH effect. Ind Eng Chem Res 52:12723–12732CrossRefGoogle Scholar
  15. 15.
    Pathak RK, Hinge VK, Mondal M, Rao CP (2011) Triazole-linked-thiophene conjugate of calix[4]arene: its selective recog-nition of Zn2+ and as biomimetic model in supporting the events of the metal detoxification and oxidative stress involving metal-lothionein. J Org Chem 76:10039–10049CrossRefGoogle Scholar
  16. 16.
    Wang GF, Ren XL, Zhao M, Qiu XL, Qi AD (2011) Paraquat detoxification with p-sulfonatocalix-[4]arene by a pharma-cokinetic study. J Agric Food Chem 59:4294–4299CrossRefGoogle Scholar
  17. 17.
    Šponer J, Burda JV, Sabat M, Leszczynski J, Hobza P (1998) Interaction between the guanine−cytosine Watson−Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. J Phys Chem A 102:5951–5957Google Scholar
  18. 18.
    Šponer J, Sabat M, Burda JV, Leszczynski J, Hobza P (1999) Interaction of the adenine−thymine Watson−Crick and adenine−adenine reverse-Hoogsteen DNA base pairs with hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) metal cations: absence of the base pair stabilization by metal-induced polarization effects. J Phys Chem B 103:2528–2534CrossRefGoogle Scholar
  19. 19.
    Rulíšek L, Šponer J (2003) Outer-shell and inner-shell coordination of phosphate group to hydrated metal ions (Mg2+, Cu2+, Zn2+, Cd2+) in the presence and absence of nucleobase. The role of nonelectrostatic effects. J Phys Chem B 107:1913–1923CrossRefGoogle Scholar
  20. 20.
    Rulíšek L, Havlas Z (2003) Theoretical studies of metal ion selectivity. 1. DFT calculations of interaction energies of amino acid side chains with selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+ and Hg2+). J Am Chem Soc 122:10428–10439CrossRefGoogle Scholar
  21. 21.
    Rulíšek L, Havlas Z (2002) Theoretical studies of metal ion selectivity. 2. DFT calculations of complexation energies of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metal-binding sites of metalloproteins. J Phys Chem A 106:3855–3866CrossRefGoogle Scholar
  22. 22.
    Rulíšek L, Havlas Z (2003) Theoretical studies of metal ion selectivity. 3. A theoretical design of the most specific combinations of functional groups representing amino acid side chains for the selected metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+). J Phys Chem B 107:2376–2385CrossRefGoogle Scholar
  23. 23.
    Marino T, Toscano M, Russo N, Grand A (2006) Structural and electronic characterization of the complexes obtained by the interaction between bare and hydrated first-row transition-metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+) and glycine. J Phys Chem B 110:24666–24673CrossRefGoogle Scholar
  24. 24.
    Marino T, Russo N, Toscano M (2001) Potential energy surfaces for the gas-phase interaction between α-alanine and alkali metal ions (Li+, Na+, K+). a density functional study. Inorg Chem 40:6439–6443CrossRefGoogle Scholar
  25. 25.
    Hoyau S, Ohanessian G (1997) Absolute affinities of α-amino acids for cu+ in the gas phase. A theoretical study. J Am Chem Soc 119:2016–2024CrossRefGoogle Scholar
  26. 26.
    Bertrán J, Rodríguez-Santiago L, Sodupe M (1999) The different nature of bonding in Cu+-glycine and Cu2+-glycine. J Phys Chem B 103:2310–2317CrossRefGoogle Scholar
  27. 27.
    Spezia R, Tournois G, Cartailler T, Tortajada J, Jeanvoine Y (2006) Co2+ binding cysteine and selenocysteine: a DFT study. J Phys Chem A 110:9727–9735CrossRefGoogle Scholar
  28. 28.
    Leung BO, Jalilehvand F, Mah V, Parvez M, Wu Q (2013) Silver(I) complex formation with cysteine, penicillamine, and glutathione. Inorg Chem 52:4593–4602CrossRefGoogle Scholar
  29. 29.
    Ash T, Debnath T, Banu T, Das AK (2016) Exploration of binding interactions of Cu2+ with D-penicillamine and its O- and se- analogues in both gas and aqueous phases: a theoretical approach. J Phys Chem B 120:3467–3478CrossRefGoogle Scholar
  30. 30.
    Pesonen H, Aksela R, Laasonen K (2010) Density functional complexation study of metal ions with cysteine. J Phys Chem A 114:466–473CrossRefGoogle Scholar
  31. 31.
    Sisombath NS, Jalilehvand F, Schell AC, Wu Q (2014) Lead(II) binding to the chelating agent D-penicillamine in aqueous solution. Inorg Chem 53:12459–12468CrossRefGoogle Scholar
  32. 32.
    Jalilehvand F, Sisombath NS, Schell AC, Facey GA (2015) Lead(II) complex formation with L-cysteine in aqueous solution. Inorg Chem 54:2160–2170CrossRefGoogle Scholar
  33. 33.
    Martínez A, Vargas R, Galano A (2018) How to identify promising metal scavengers? D-penicillamine with copper as a study case. Int J Quantum Chem 118:e25457CrossRefGoogle Scholar
  34. 34.
    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 Jr JA, Peralta JE, Ogliaro F, Bearpark MJ, Heyd J, Brothers EN, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, 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 Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2013) Gaussian 09, Revision D.01, Gaussian, Inc., Wallingford, CT, USAGoogle Scholar
  35. 35.
    Zhao Y, Truhlar D (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, non-covalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other Functionals. Theor Chem Accounts 120:215CrossRefGoogle Scholar
  36. 36.
    Zhao Y, Truhlar D (2006) A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. J Chem Phys 125:194101–194118Google Scholar
  37. 37.
    Hay PJ, Wadt WR (1985) Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. J Chem Phys 82:270–283CrossRefGoogle Scholar
  38. 38.
    Hay PJ, Wadt WR (1985) Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals. J Chem Phys 82:299–310CrossRefGoogle Scholar
  39. 39.
    Hay PJ, Wadt WR (1985) Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi. J Chem Phys 82:284–298CrossRefGoogle Scholar
  40. 40.
    Klamt A, Schuurmann G (1993) COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans 2(2):799–805CrossRefGoogle Scholar
  41. 41.
    Galano A (2016) Computational-aided design of melatonin analogues with outstanding multifunctional antioxidant capacity. RSC Adv 6:22951–22963CrossRefGoogle Scholar
  42. 42.
    Francisco-Marquez M, Aguilar-Fernandez M, Galano A (2016) Anthranilic acid as a secondary antioxidant: Implications to the inhibition of .OH production and the associated oxidative stress Comput. Theor. Chem. 2016 1077:18–24
  43. 43.
    Alvarez-Diduk R (2015) Galano a (2015) adrenaline and noradrenaline: protectors against oxidative stress or molecular targets? J Phys Chem B 119:3479–3491CrossRefGoogle Scholar
  44. 44.
    Leon-Carmona JR, Galano A (2012) Free radical scavenging activity of caffeine’s metabolites. Int J Quantum Chem 112:3472–3478CrossRefGoogle Scholar
  45. 45.
    Galano A, Medina ME, Tan DX, Reiter RJ (2015) Melatonin and its metabolites as copper chelating agents and their role in inhibiting oxidative stress: a physicochemical analysis. J Pineal Res 58:107–116CrossRefGoogle Scholar
  46. 46.
    Alvarez-Diduk R, Galano A, Tan DX, Reiter RJ (2015) N-Acetylserotonin and 6-hydroxymelatonin against oxidative stress: implications for the overall protection exerted by melatonin. J Phys Chem B 119:8535–8543CrossRefGoogle Scholar
  47. 47.
    Camaioni M, Schwerdtfeger CA (2005) Comment on “accurate experimental values for the free energies of hydration of H+, OH, and H3O+”. J Phys Chem A 109:10795–10797CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Tamalika Ash
    • 1
  • Tanay Debnath
    • 1
  • Avik Ghosh
    • 1
  • Abhijit Kr. Das
    • 1
    Email author
  1. 1.School of Mathematical and Computational SciencesIndian Association for the Cultivation of ScienceKolkataIndia

Personalised recommendations