Skip to main content
SpringerLink
Log in

Coordination numbers in hydrated Cu(II) ions

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

The potential energy surface of [Cu(H2O)n]2+ clusters with n = 12, 16, and 18 was explored by using a modified version of the simulated annealing method. Such exploration was carried out by using the PM7 semiempirical method to obtain around 100,000 isomers, which provide candidates to be optimized with PBE0-D3, M06-2X, and BHLYP exchange-correlation functionals coupled with the 6–311++G** basis set. These methods based on the Kohn-Sham approach delivered isomers with coordination numbers of 4, 5, and 6. The analysis used to obtain coordination numbers was based on geometrical parameters and the quantum theory of atoms in molecules (QTAIM) approach. Our methodology found only one isomer with fourfold coordination and its probabilities to appear in these clusters are quite small for high temperatures. The procedure used in this article predicts important populations of fivefold and sixfold coordination clusters, in fact, the fivefold coordination dominates for PBE0-D3 and BHLYP methods, although the sixfold coordination starts to be important when the number of water molecules is increased. The nature of axial and equatorial contacts is discussed in the context of the QTAIM and the noncovalent interaction index (NCI), which gives a clear classification of such orientations. Also, these methods suggest a partial covalent interaction between the Cu2+ and water molecules in both positions; equatorial and axial.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Jones CJ, Thornback J (2007) Medicinal applications of coordination chemistry. Royal Society of Chemistry, Cambridge

    Google Scholar 

  2. Strausak D, Mercer JF, Dieter HH, Stremmel W, Multhaup G (2001) Copper in disorders with neurological symptoms: Alzheimer’s, Menkes, and Wilson diseases. Brain Res Bull 55:175–185

    Article  CAS  PubMed  Google Scholar 

  3. Mercer SW, Wang J, Burke R (2017) In vivo modeling of the pathogenic effect of copper transporter mutations that cause Menkes and Wilson diseases, motor neuropathy, and susceptibility to Alzheimer’s disease. J Bio Chem 292:4113–4122

    Article  CAS  Google Scholar 

  4. Bowron DT, Amboage M, Boada R, Freeman A, Hayamab S, Díaz-Moreno S (2013) The hydration structure of Cu2+: more tetrahedral than octahedral? RSC Adv 3:17803–17812

    Article  CAS  Google Scholar 

  5. Frank P, Benfatto M, Szilagyi RK, D’Angelo P, Della Longa S, Hodgson KO (2005) The solution structure of [cu(aq)]2+ and its implications for rack-induced bonding in blue copper protein active sites. Inorg Chem 44:1922–1933

    Article  CAS  PubMed  Google Scholar 

  6. Garcia J, Benfatto M, Natoli C, Bianconi A, Fontaine A, Tolentino H (1989) The quantitative Jahn-teller distortion of the Cu2+ site in aqueous solution by xanes spectroscopy. Chem Phys 132:295–302

    Article  CAS  Google Scholar 

  7. Galván-García EA, Agacino-Valdés E, Franco-Pérez M, Gómez-Balderas R (2017) [Cu(H2O)n]2+(n=1-6) complexes in solution phase: a DFT hierarchical study. Theor Chem Accounts 136:29

    Article  CAS  Google Scholar 

  8. Schwenk CF, Rode BM (2004) Influence of electron correlation effects on the solvation of Cu2+. J Am Chem Soc 126:12786–12787

    Article  CAS  PubMed  Google Scholar 

  9. Amira S, Spångberg D, Hermansson K (2005) Distorted five-fold coordination of Cu2+ (aq) from a car-parrinello molecular dynamics simulation. Phys Chem Chem Phys 7:2874–2880

    Article  CAS  PubMed  Google Scholar 

  10. Pasquarello A, Petri I, Salmon PS, Parisel O, Car R, Tóth É, Powell DH, Fischer HE, Helm L, Merbach AE (2001) First solvation shell of the Cu (II) aqua ion: evidence fivefold coordination. Science 291:856–859

    Article  CAS  PubMed  Google Scholar 

  11. Li X, Tu Y, Tian H, Ågren H (2010) Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures. J Chem Phys 132:104505

    Article  CAS  PubMed  Google Scholar 

  12. Bryantsev VS, Diallo MS, Van Duin AC, Goddard IIIWA (2008) Hydratation of copper (II): new insights from density functional theory and the COSMO solvatation model. J Phys Chem A 112:9104–9112

    Article  CAS  PubMed  Google Scholar 

  13. Rios-Font R, Sodupe M, Rodríguez-Santiago L, Taylor PR (2010) The role of exact exchange in the description of Cu2+((H2O)n (n= 1− 6)) complexes by means of DFT methods. J Phys Chem A 114:10857–10863

    Article  CAS  PubMed  Google Scholar 

  14. Salmon P, Howells W, Mills R (1987) The dynamics of water molecules in ionic solution. II. Quasi-elastic neutron scattering and tracer diffusion studies of the proton and ion dynamics in concentrated Ni2+, Cu2+ and Nd3+ aqueous solutions. J Phys C Solid State Phys 20:5727

    Article  CAS  Google Scholar 

  15. Powell DH, Helm L, Merbach AE (1991) 17O nuclear magnetic resonance in aqueous solutions of Cu2+: the combined effect of Jahn-teller inversion and solvent exchange on relaxation rates. J Chem Phys 95:9258–9265

    Article  CAS  Google Scholar 

  16. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Sci 220:671–680

    Article  CAS  Google Scholar 

  17. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953). J Chem Phys 21:1087–1092

    Article  CAS  Google Scholar 

  18. Aarts E, Laarhoven H (1987) Simulated annealing: theory and applications. Springer, New York

    Google Scholar 

  19. Kohn W, Sham LJ (1965) Self-consistent equations including exchange and correlation effects. Phys Rev 140:A1133

    Article  Google Scholar 

  20. Bader RFW (1990) Atoms in molecules: a quantum theory. Oxford University, New York

    Google Scholar 

  21. Johnson ER, Keinan S, Mori-Sanchez P, Contreras-Garcia J, Cohen AJ, Yang W (2010) Revealing non-covalent interactions. J Am Chem Soc 132:6498–6506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Contreras-García J, Johnson ER, Keinan S, Chaudret R, Piquemal JP, Beratan DN, Yang W (2011) NCIPLOT: a program for plotting noncovalent interaction regions. J Chem Theory Comput 7:625–632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Pérez JF, Hadad C, Restrepo A (2008) Structural studies of the water tetramer. Int J Quantum Chem 108:1653–1659

    Article  CAS  Google Scholar 

  24. Pérez JF, Florez E, Hadad CZ, Fuentealba P, Restrepo A (2008) Stochastic search of the quantum conformational space of small lithium and bimetallic lithium-sodium clusters. J Phys Chem A 112:5749–5755

    Article  CAS  PubMed  Google Scholar 

  25. Stewart JJ (2013) Optimization of parameters for semi-empirical methods vi: more modifications to the nddo approximations and re-optimization of parameters. J Mol Model 19:1–32

    Article  CAS  PubMed  Google Scholar 

  26. Stewart JJP (2008) MOPAC2009, Stewart computational chemistry, Colorado Springs, CO. Available at OpenMOPAC. net. Accessed 13 May 2016

  27. Zhao Y, Truhlar DG (2006) A new local density functional for main group thermochemistry, transition metal bonding, thermochemical kinetics, and non-covalent interactions. J Chem Phys 125:194101

    Article  CAS  PubMed  Google Scholar 

  28. Zhao Y, Truhlar DG (2011) Applications and validations of the Minnesota density functionals. Chem Phys Lett 502:1–13

    Article  CAS  Google Scholar 

  29. Rassolov VA, Pople JA, Ratner MA, Windus TL (1998) 6-31g* basis set for atoms K through Zn. J Chem Phys 109:1223–1229

    Article  CAS  Google Scholar 

  30. Francl MM, Pietro WJ, Hehre WJ, Binkley JS, Gordon MS, DeFrees DJ, Pople JA (1982) Self-consistent molecular orbital methods. XXIII. A polarization-type basis set for second-row elements. J Chem Phys 77:3654–3665

    Article  CAS  Google Scholar 

  31. Hariharan PC, Pople JA (1973) The influence of polarization functions on molecular orbital hydrogenation energies. Theor Chim Acta 28:213–222

    Article  CAS  Google Scholar 

  32. Adamo C, Barone V (1999) Toward reliable density functional methods without adjustable parameters: the PBE0 model. J Chem Phys 110:6158–6170

    Article  CAS  Google Scholar 

  33. Andersson MP, Uvdal P (2005) New scale factors for harmonic vibrational frequencies using the b3lyp density functional method with the triple-ζ basis set 6-311+g(d, p). J Phys Chem A 109:2937–2941

    Article  CAS  PubMed  Google Scholar 

  34. Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected density functional theory. J Comput Chem 32:1456–1465

    Article  CAS  PubMed  Google Scholar 

  35. Valiev M, Bylaska EJ, Govind N, Kowalski K, Straatsma TP, van Dam HJJ, Wang D, Nieplocha J, Apra E, Windus TL, de Jong WA (2010) NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations. Comput Phys Commun 181:1477–1489

    Article  CAS  Google Scholar 

  36. 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 M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Keith T, 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 (2013) Gaussian 09, Revision D.01. Gaussian Inc, Wallingford

    Google Scholar 

  37. Benfatto M, D’ Angelo P, Della Longa S, Pavel N (2002) Evidence of distorted fivefold coordination of the Cu2+ aqua ion from an x-ray absorption spectroscopy quantitative analysis. Phys Rev B 65:174205

  38. Becke AD (1993) A new mixing of Hartree–Fock and local density-functional theories. J Chem Phys 98:1372–1377

    Article  CAS  Google Scholar 

  39. Hernández-Esparza R, Mejía-Chica SM, Zapata-Escobar AD, Guevara-García A, Martínez-Melchor A, Hernández-Pérez JM, Vargas R, Garza J (2014) Grid based algorithm to search critical points, in the electron density, accelerated by graphics processing units. J Comp Chem 35:2272–2278

    Article  CAS  Google Scholar 

  40. Kumar PSV, Raghavendra V, Subramanian V (2016) Bader’s theory of atoms in molecules (AIM) and its applications to chemical bonding. J Chem Sci 128:1527–1536

    Article  CAS  Google Scholar 

  41. 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 120:3467–3478

    Article  CAS  PubMed  Google Scholar 

  42. Bryantsev VS, Diallo MS, Goddard IIIWA (2009) Computational study of copper (II) complexation and hydrolysis in aqueous solutions using mixed cluster/continuum models. J Phys Chem A 113:9559–9567

    Article  CAS  PubMed  Google Scholar 

  43. Duncombe BJ, Duale K, Buchanan-Smith A, Stace AJ (2007) The solvation of Cu2+ with gas-phase clusters of water and ammonia. J Phys Chem A 111:5158–5165

    Article  CAS  PubMed  Google Scholar 

  44. Berces A, Nukada T, Margl P, Ziegler T (1999) Solvation of Cu2+ in water and ammonia. Insight from static and dynamical density functional theory. J Phys Chem A 103:9693–9701

    Article  CAS  Google Scholar 

  45. Persson I (2010) Hydrated metal ions in aqueous solution: how regular are their structures? Pure Appl Chem 82:1901–1917

    Article  CAS  Google Scholar 

  46. Noyes RM (1962) Thermodynamics of ion hydration as a measure of effective dielectric properties of water. J Am Chem Soc 84:513–522

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank the facilities provided by the Laboratorio de Supercómputo y Visualización en Paralelo at the Universidad Autónoma Metropolitana-Iztapalapa. A. Monjaraz-Rodríguez and M. Rodriguez-Bautista thank CONACYT, México, for the scholarships 286378 and 283261, respectively.

This article was written to recognize the contributions of Professor Pratim Kumar Chattaraj to Density Functional Theory and celebrate his 60th anniversary.

Author information

Authors and Affiliations

  1. Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, A.P. 55-534, C. P. 09340, Ciudad de México, Mexico

    Alejandra Monjaraz-Rodríguez, Mariano Rodriguez-Bautista, Jorge Garza, Rafael A. Zubillaga & Rubicelia Vargas

Authors
  1. Alejandra Monjaraz-Rodríguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mariano Rodriguez-Bautista
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jorge Garza
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Rafael A. Zubillaga
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rubicelia Vargas
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rubicelia Vargas.

Additional information

This paper belongs to Topical Collection International Conference on Systems and Processes in Physics, Chemistry and Biology (ICSPPCB-2018) in honor of Professor Pratim K. Chattaraj on his sixtieth birthday

Electronic supplementary material

ESM 1

(PDF 2734 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Monjaraz-Rodríguez, A., Rodriguez-Bautista, M., Garza, J. et al. Coordination numbers in hydrated Cu(II) ions. J Mol Model 24, 187 (2018). https://doi.org/10.1007/s00894-018-3725-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-018-3725-5

Keywords

Search

Navigation