Skip to main content
Log in

Comparison between cluster and supercell approaches: the case of defects in diamond

  • Regular Article
  • Published:
Theoretical Chemistry Accounts Aims and scope Submit manuscript

Abstract

The results produced by the cluster and the supercell approaches, when applied to the study of the vacancy and \(\langle 100\rangle\) split self-interstitial defects in diamond, are critically compared. The same computer code, Crystal, basis set and DFT functional (the hybrid B3LYP) are used. Clusters of increasing size (from 35 to 969 C atoms) are considered, and the results compared to those from a supercell containing \(128\pm 1\) atoms, for which the interaction between defects in different cells can be considered negligible. It is shown that geometry and energy data (atomic relaxation, defect formation energy, relative energy between different spin states) show a very local nature and then converge rapidly with the cluster size. Other properties, frequently used for the characterization of the defects using relatively small clusters (band gaps, impurity energy levels in the gap, Raman spectra), converge slowly and, also at the limit of the very large clusters here considered, still differ from the periodic counterpart.

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

Access this article

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  1. Grimes RW, Catlow CRA, Shluger L (1992) Quantum mechanical cluster calculations in solid state studies. WorldScientific, Singapore

    Book  Google Scholar 

  2. Bagus PS, Pacchioni G, Parmigiani F (1993) Final state effects for the core-level XPS spectra of NIO. Chem Phys Lett 207(4):569–574

    Article  CAS  Google Scholar 

  3. Barandiarán Z, Seijo L (1988) The ab-initio model potential representation of the crystalline environment. Theoretical study of the local distortion on NaCl: Cu+. J Chem Phys 89(9):5739–5746

    Article  Google Scholar 

  4. Li LH, Lowther JE (1996) Lattice relaxation at vacancy aggregates in diamond. Phys Rev B 53:11277–11280

    Article  CAS  Google Scholar 

  5. Mainwood A (1978) Relaxation about the vacancy in diamond. J Phys C Solid State Phys 11(13):2703

    Article  CAS  Google Scholar 

  6. Hyde-Volpe D, Slepetz B, Kertesz M (2010) The [V\(-\)C=C\(-\)V] divacancy and the interstitial defect in diamond: vibrational properties. J Phys Chem C 114(21):9563–9567

    Article  CAS  Google Scholar 

  7. Breuer SJ, Briddon PR (1995) Ab initio investigation of the native defects in diamond and self-diffusion. Phys Rev B 51(11):6984–6994

    Article  CAS  Google Scholar 

  8. Gali A, Maze JR (2013) Ab initio study of the split silicon-vacancy defect in diamond: electronic structure and related properties. Phys Rev B 88(23):235205

    Article  Google Scholar 

  9. Krosnicki M, Kedziorski A, Seijo L, Barandiarán Z (2013) Ab initio theoretical study on the 4f2 and 4f5d electronic manifolds of cubic defects in CaF2: Pr\(^{3+}\). J Phys Chem A 118(2):358–368

    Article  Google Scholar 

  10. Pacchioni G (2003) Ab initio theory of point defects in oxide materials: structure, properties, chemical reactivity. Surf Sci 540:63–75

    Article  Google Scholar 

  11. Boerve KJ, Pettersson LGM (1991) Hydrogen abstraction from methane on a magnesia (001) surface. J Phys Chem 95(19):7401–7405

    Article  CAS  Google Scholar 

  12. Neyman KM, Rösch N (1993) Bonding and vibration of co molecules adsorbed on low-coordinated surface sites of MgO: a LCGTO-LDF cluster investigation. Surf Sci 297(2):223–234

    Article  CAS  Google Scholar 

  13. Sauer J (1992) Modelling of Structure and Reactivity in Zeolites, Edited by Catlow RCA. pp. 183–216. Academic Press:New York

  14. Teunissen EH, Van Duijneveldt FB, Van Santen RA (1992) Interaction of ammonia with a zeolitic proton: ab initio quantum-chemical cluster calculations. J Phys Chem 96(1):366–371

    Article  CAS  Google Scholar 

  15. Ferrari AM, Ugliengo P, Garrone E (1993) Geminal silica hydroxyls as adsorbing sites: an ab-initio study. J Phys Chem 97:2671–2676

    Article  CAS  Google Scholar 

  16. Ferrari AM, Huber S, Knözinger H, Neyman KM, Rösch N (1998) FTIR spectroscopic and density functional model cluster studies of methane adsorption on mgo. J Phys Chem B 102(23):4548–4555

    Article  CAS  Google Scholar 

  17. Panas I (1993) Properties of molecular crystals by means of theory. Acta Crystallogr Sec A 49(6):881–889

    Article  Google Scholar 

  18. Ángyán JG, Silvi B (1987) Electrostatic interactions in three-dimensional solids. Self-consistent Madelung potential (SCMP) approach. J Chem Phys 86(12):6957–6966

    Article  Google Scholar 

  19. Ojamäe L, Hermansson K (1992) Water molecules in different crystal surroundings: vibrational O–H frequencies from ab initio calculations. J Chem Phys 96(12):9035–9045

    Article  Google Scholar 

  20. Shashkin SY, Goddard WA III (1986) Optical spectrum and Jahn–Teller splitting of Cu\(^{2+}\) sites in K\(_2\) CuF\(_4\) Based on ab initio studies of (CuF\(_6\))\(^{4-}\) clusters. Phys Rev B 33(2):1353

    Article  CAS  Google Scholar 

  21. Pacchioni G, Sousa C, Illas F, Parmigiani F, Bagus PS (1993) Measures of ionicity of alkaline-earth oxides from the analysis of ab initio cluster wave functions. Phys Rev B 48(16):11573

    Article  CAS  Google Scholar 

  22. Mehdaoui I, Kluner T (2007) Bonding of CO and NO to NiO(100): a strategy for obtaining accurate adsorption energies. J Phys Chem A 111:13233–13237

    Article  CAS  Google Scholar 

  23. Illas F, de PR Moreira I, Bofill JM, Filatov M (2006) Spin symmetry requirements in density functional theory: the proper way to predict magnetic coupling constants in molecules and solids. Theor Chem Acc 116:587–597

    Article  CAS  Google Scholar 

  24. Pacchioni G, Ieranø G (1998) Ab initio theory of optical transitions of point defects in SiO\(_{2}\). Phys Rev B 57:817–832

    Article  Google Scholar 

  25. Nazeeruddin MK, De Angelis F, Fantacci S, Selloni A, Viscardi G, Liska P, Ito S, Takeru B, Grätzel M (1998) Combined experimental and DFT–TDDFT computational study of photoelectrochemical cell ruthenium sensitizers. J Am Chem Soc 127:1683516847

    Google Scholar 

  26. Azpiroz JM, De Angelis F (1998) DFT/TDDFT study of the adsorption of N3 and N719 dyes on ZnO(\(10\overline{1}0\)) surfaces. J Phys Chem A 118:5885–5893

    Google Scholar 

  27. Ihm J, Zunger A, Cohen ML (1979) Momentum-space formalism for the total energy of solids. J Phys C 12(21):4409

    Article  CAS  Google Scholar 

  28. Nichols CS, Van de Walle CG, Pantelides ST (1989) Mechanisms of dopant impurity diffusion in silicon. Phys Rev B 40(8):5484

    Article  CAS  Google Scholar 

  29. De Vita A, Gillan MJ, Lin JS, Payne MC, Štich I, Clarke LJ (1992) Defect energetics in MgO treated by first-principles methods. Phys Rev B 46(20):12964

    Article  Google Scholar 

  30. Freyria-Fava C, Dovesi R, Saunders VR, Leslie M, Roetti C (1993) Ca and Be substitution in bulk MgO: ab initio Hartree–Fock and ionic model supercell calculations. J Phys Condens Matter 5(27):4793

    Article  CAS  Google Scholar 

  31. Giordano L, Del Vitto A, Pacchioni G, Ferrari AM (2000) CO adsorption on Rh, Pd and Ag atoms deposited on the MgO surface: a comparative ab initio study. Solid State Sci 2:161–179

    Article  Google Scholar 

  32. Pacchioni G, Ferrari AM, Bagus P (1995) Cluster and band structure ab initio calculations on the adsorption of CO on acid sites of the TiO\(_{2}\) (110) surface. Surf Sci 350:159–175

    Article  Google Scholar 

  33. Hellstrom M, Spangberg D, Hermansson K (2015) Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: the case of Cu on ZnO (10–10). J Comput Chem 36:2394–2405

    Article  Google Scholar 

  34. Persson P, Lundqvist MJ (2005) Calculated structural and electronic interactions of the ruthenium dye N3 with a titanium dioxide nanocrystal. J Phys Chem 109:11918–11924

    Article  CAS  Google Scholar 

  35. Civalleri B, Ugliengo P, Garrone E (1999) Cagelike clusters as models for the isolated hydroxyls of silica: ab-initio B3-LYP calculations of the interaction with ammonia. Langmuir 15:5829–5835

    Article  CAS  Google Scholar 

  36. Ferrari AM, Neyman KM, Mayer M, Staufer M, Gates BC, Rösch N (1999) Faujasite-supported Ir\(_{4}\) clusters: a density functional model study of metal-zeolite interactions. J Phys Chem B 479:5311–5319

    Article  Google Scholar 

  37. Ferrari AM, Soave R, D’Ercole A, Pisani C, Giamello E, Pacchioni G (2001) Theoretical characterization of charge-transfer reactions between N\(_{2}\) and O\(_{2}\) molecules and paramagnetic oxygen vacancies on the MgO surface. Surf Sci 479:83–97

    Article  Google Scholar 

  38. Ferrari AM, Pacchioni G (1996) Size and shape dependence of the electrostatic potential in cluster models of the MgO (100) surface. Int J Quantum Chem 58:241–250

    Article  CAS  Google Scholar 

  39. Baima J, Zelferino A, Olivero P, Erba A, Dovesi R (2016) Raman spectroscopic features of the neutral vacancy in diamond from ab initio quantum-mechanical calculations. Phys Chem Chem Phys 18(3):1961–1968

    Article  CAS  Google Scholar 

  40. Zelferino A, Salustro S, Baima J, Lacivita V, Orlando R, Dovesi R (2016) The electronic states of the neutral vacancy in diamond; a quantum mechanical approach. Theor Chem Acc 135(3):1–11

    Article  CAS  Google Scholar 

  41. Salustro S, Erba A, Zicovich-Wilson CM, Nöel Y, Maschio L, Dovesi R (2016) Infrared and Raman spectroscopic features of the self-interstitial defect in diamond from exact-exchange hybrid DFT calculations. Phys Chem Chem Phys 18(31):21288–21295

    Article  CAS  Google Scholar 

  42. Orlando R, Dovesi R, Azavant P, Harrison NM, Saunders VR (1994) A super-cell approach for the study of localized defects in solids: carbon substitution in bulk silicon. J Phys Cond Matter 6(41):8573

    Article  CAS  Google Scholar 

  43. Dovesi R, Orlando R, Erba A, Zicovich-Wilson CM, Civalleri B, Casassa S, Maschio L, Ferrabone M, De La Pierre M, D’Arco P, Noël Y, Causà M, Rérat M, Kirtman B (2014) CRYSTAL14: a program for the ab initio investigation of crystalline solids. Int J Quantum Chem 114:1287

    Article  CAS  Google Scholar 

  44. Dovesi R, Saunders VR, Roetti C, Orlando R, Zicovich-Wilson CM, Pascale F, Civalleri B, Doll K, Harrison NM, Bush IJ, D’Arco Ph, Llunell M (2013) CRYSTAL 2014 user’s manual. University of Torino, Torino

    Google Scholar 

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

    Article  CAS  Google Scholar 

  46. 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 

  47. Binkley JS, Pople JA, Hehre WJ (1980) Self-consistent molecular orbital methods. 21. Small split-valence basis sets for first-row elements. J Am Chem Soc 102(3):939–947

    Article  CAS  Google Scholar 

  48. Hehre WJ, Stewart RF, Pople JA (1969) Self-consistent molecular-orbital methods. I. Use of Gaussian expansions of Slater-type atomic orbitals. J Chem Phys 51(6):2657–2664

    Article  CAS  Google Scholar 

  49. Dovesi R, Pisani C, Roetti C, Saunders VR (1983) Treatment of Coulomb interactions in Hartree–Fock calculations of periodic systems. Phys Rev B 28:5781–5792

    Article  CAS  Google Scholar 

  50. Causà M, Dovesi R, Orlando R, Pisani C, Saunders VR (1988) Treatment of the exchange interactions in Hartree–Fock LCAO calculations of periodic systems. J Phys Chem 92:909–913

    Article  Google Scholar 

  51. Pascale F, Zicovich-Wilson CM, Gejo F Lòpez, Civalleri B, Orlando R, Dovesi R (2004) The calculation of the vibrational frequencies of the crystalline compounds and its implementation in the CRYSTAL code. J Comput Chem 25(6):888–897

    Article  CAS  Google Scholar 

  52. Zicovich-Wilson CM, Pascale F, Roetti C, Saunders VR, Orlando R, Dovesi R (2004) Calculation of the vibration frequencies of \(\alpha\)-quartz: the effect of Hamiltonian and basis set. J Comput Chem 25(15):1873–1881

    Article  CAS  Google Scholar 

  53. Erba A, Ferrabone M, Orlando R, Dovesi R (2013) Accurate dynamical structure factors from ab initio lattice dynamics: the case of crystalline silicon. J Comput Chem 34:346–354

    Article  CAS  Google Scholar 

  54. Carteret C, De La Pierre M, Dossot M, Pascale F, Erba A, Dovesi R (2013) The vibrational spectrum of CaCO\(_3\) aragonite: a combined experimental and quantum-mechanical investigation. J Chem Phys 138(1):014201

    Article  Google Scholar 

  55. Baima J, Ferrabone M, Orlando R, Erba A, Dovesi R (2016) Thermodynamics and phonon dispersion of pyrope and grossular silicate garnets from ab initio simulations. Phys Chem Miner 43:137–149

    Article  CAS  Google Scholar 

  56. Maschio L, Kirtman B, Orlando R, Rérat M (2012) Ab initio analytical infrared intensities for periodic systems through a coupled perturbed Hartree–Fock/Kohn–Sham method. J Chem Phys 137(20):204113

    Article  Google Scholar 

  57. Maschio L, Kirtman B, Rérat M, Orlando R, Dovesi R (2013) Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree–Fock/Kohn–Sham method in an atomic orbital basis. II. Validation and comparison with experiments. J Chem Phys 139(16):164102

    Article  Google Scholar 

  58. Maschio L, Kirtman B, Rérat M, Orlando R, Dovesi R (2013) Comment on “Ab initio analytical infrared intensities for periodic systems through a coupled perturbed Hartree–Fock/Kohn–Sham method” [J. Chem. Phys. 137, 204113 (2012)]. J Chem Phys 139:167101

    Article  Google Scholar 

  59. Ferrero M, Rérat M, Orlando R, Dovesi R (2008) The calculation of static polarizabilities of periodic compounds. The implementation in the crystal code for 1d, 2d and 3d systems. J Comput Chem 29:1450–1459

    Article  CAS  Google Scholar 

  60. Ferrero M, Rérat M, Orlando R, Dovesi R (2008) Coupled perturbed Hartree–Fock for periodic systems: The role of symmetry and related computational aspects. J Chem Phys 128:014110

    Article  Google Scholar 

  61. Pauling L (1932) The nature of the chemical bond. IV. The energy of single bonds and the relative electronegativity of atoms. J Am Chem Soc 54:3570–3582

    Article  CAS  Google Scholar 

  62. Battiato A, Bernardi E, Picollo F, Bosia F, Lorusso M, Ugues D, Zelferino A, Damin A, Baima J, Pugno NM, Ambrosio EP, Olivero P (2016) Softening the ultra-stiff: controlled variation of Young’s modulus in single-crystal diamond. Acta Mater 116:95–103

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Anna Maria Ferrari.

Additional information

Published as part of the special collection of articles derived from the 10th Congress on Electronic Structure: Principles and Applications (ESPA-2016).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Salustro, S., Ferrari, A.M., Orlando, R. et al. Comparison between cluster and supercell approaches: the case of defects in diamond. Theor Chem Acc 136, 42 (2017). https://doi.org/10.1007/s00214-017-2071-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00214-017-2071-5

Keywords

Navigation