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An assessment of DFT methods for predicting the thermochemistry of ion-molecule reactions of group 14 elements (Si, Ge, Sn)

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Abstract

Experimental mass-spectrometry data on thermochemistry of methide transfer reactions (CH3)3M+ + M'(CH3)4 ↔ M(CH3)4 + (CH3)3M'+ (M, M' = Si, Ge or Sn) and the formation energy of the [(CH3)3Si-CH3-Si(CH3)3]+ complex are used as benchmarks for DFT methods (B3LYP, BMK, M06L, and ωB97XD). G2 and G3 theory methods are also used for the prediction of thermochemical data. BMK, M06L, and ωB97XD methods give the best fit to experimental data (close to chemical accuracy) as well as to G2 and G3 results, while B3LYP demonstrates poor performance. From the first three methods M06L gives the best overall result. Structures and formation energies of intermediate “mixed” [(CH3)3M-CH3- M′(CH3)3] complexes not observed in experiment are predicted. Their structures, better described as M(CH3)4∙[M′(CH3)3]+ complexes, explain their fast decompositions.

Graphical representation of the molecular structureof the intermediates in the methide transfer reactions: (CH3)3M+ + M'(CH3)4 ↔ M(CH3)4 + (CH3)3M'+ (M,M'=Si, Ge, Sn)

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References

  1. Stone JA (1997) Gas-phase association reactions of trimethylsilylium ((CH3)3Si+) with organic bases. Mass Spectrom Rev 16:25–49

    Article  CAS  Google Scholar 

  2. Potzinger P, Lampe FW (1971) Ion-molecule reactions in dimethylsilane, trimethylsilane, and tetramethylsilane. J Phys Chem 75:13–19

    Article  CAS  Google Scholar 

  3. Odiorne TJ, Harvey J, Vouros P (1972) Chemical ionization mass spectrometry using tetramethylsilane. J Phys Chem 76:3217–3220

    Article  CAS  Google Scholar 

  4. Klevan L, Munson B (1974) Gaseous ionic reactions in tetramethylsilane. Int J Mass Spectrom Ion Phys 13:261–268

    Article  CAS  Google Scholar 

  5. Wojtyniak A, Li X, Stone JA (1987) The formation of (CH3)7Si2 + in (CH3)4Si/CH4 mixtures and CH3− exchange reactions between (CH3)4Si, (CH3)4Ge, and (CH3)4Sn studied by high pressure mass spectrometry. Can J Chem 65:2849–2854

    Article  CAS  Google Scholar 

  6. Dávalos JZ, Herrero R, Abboud JLM, Mó O, Yáñez M (2007) How can a carbon atom be covalently bound to five ligands? The case of Si2(CH3)7 +. Angew Chem Int Ed 46:381–385

    Article  Google Scholar 

  7. Xavier LA, Pliego JR Jr, Riveros JM (2003) Ligand exchange ion–molecule reactions of simple silyl and germyl cations. Int J Mass Spectrom 228:551–562

    Article  CAS  Google Scholar 

  8. Fernández I, Uggerud E, Frenking G (2007) Stable pentacoordinate carbocations: structure and bonding. Chem Eur J 13:8620–8626

    Article  Google Scholar 

  9. Jursic BS (1999) Energetic and structural properties of silicon dicarbides calculated with complete basis set and hybrid density functional theory methods. J Mol Struct (Theochem) 458:257–261

    Article  CAS  Google Scholar 

  10. Chandra AK, Nguyen MT (1998) A density functional study of weakly bound hydrogen bonded complexes. Chem Phys 232:299–306

    Article  CAS  Google Scholar 

  11. Rappe AK, Bernstein ER (2000) Ab Initio calculation of nonbonded interactions: are we there yet? J Phys Chem A 104:6117–6128

    Article  CAS  Google Scholar 

  12. Tsuzuki S, Luthi HP (2001) Interaction energies of van der Waals and hydrogen bonded systems calculated using density functional theory: assessing the PW91 model. J Chem Phys 114:3949–3957

    Article  CAS  Google Scholar 

  13. Boese AD, Martin JML (2004) Development of density functionals for thermochemical kinetics. J Chem Phys 121:3405–3416

    Article  CAS  Google Scholar 

  14. Check CE, Gilbert TM (2005) Progressive systematic underestimation of reaction energies by the B3LYP model as the number of C−C bonds increases: why organic chemists should use multiple DFT models for calculations involving polycarbon hydrocarbons. J Org Chem 70:9828–9834

    Article  CAS  Google Scholar 

  15. Paier J, Marsman M, Kresse G (2007) Why does the B3LYP hybrid functional fail for metals? J Chem Phys 127:024103

    Article  Google Scholar 

  16. Neese F, Hansen A, Wennmohs F, Grimme S (2009) Accurate theoretical chemistry with coupled pair models. Acc Chem Res 42:641–648

    Article  CAS  Google Scholar 

  17. Korth M, Grimme S (2009) “Mindless” DFT benchmarking. J Chem Theory Comput 5:993–1003

    Article  CAS  Google Scholar 

  18. Xu X, Alecu IM, Truhlar DG (2011) How well can modern density functionals predict internuclear distances at transition states? J Chem Theory Comput 7:1667–1676

    Article  CAS  Google Scholar 

  19. Kruse H, Goerigk L, Grimme S (2012) Why the standard B3LYP/6-31G* model chemistry should not be used in DFT calculations of molecular thermochemistry: understanding and correcting the problem. J Org Chem 77:10824–10834

    Article  CAS  Google Scholar 

  20. Grimme S (2006) Seemingly simple stereoelectronic effects in alkane isomers and the implications for Kohn–Sham density functional theory. Angew Chem Int Ed 45:4460–4464

    Article  CAS  Google Scholar 

  21. Grimme S (2011) Density functional theory with London dispersion corrections. WIREs Comput Mol Sci 1:211–228

    Article  CAS  Google Scholar 

  22. Amin EA, Truhlar DG (2008) Zn coordination chemistry: development of benchmark suites for geometries, dipole moments, and bond dissociation energies and their use to test and validate density functionals and molecular orbital theory. J Chem Theory Comput 4:75–85

    Article  CAS  Google Scholar 

  23. Zhao Y, Truhlar DG (2009) Benchmark energetic data in a model system for grubbs II metathesis catalysis and their use for the development, assessment, and validation of electronic structure methods. J Chem Theory Comput 5:324–333

    Article  CAS  Google Scholar 

  24. Zhao Y, Ng HT, Hanson E (2009) Benchmark data for noncovalent interactions in HCOOH···Benzene complexes and their use for validation of density functionals. J Chem Theory Comput 5:2726–2733

    Article  CAS  Google Scholar 

  25. Zhang Y, Ma N, Wang W (2012) Assessment of the performance of the M05-class and M06-class functionals for the structure and geometry of the hydrogen-bonded and halogen-bonded complexes. J Theo Comput Chem 11:1165–1173

    Article  CAS  Google Scholar 

  26. Liu Y, Zhao J, Li F, Chen Z (2013) Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods. J Comput Chem 34:121–131

    Article  Google Scholar 

  27. Hohenstein EG, Chill ST, Sherrill GD (2008) Assessment of the performance of the M05-2X and M06-2X exchange-correlation functionals for noncovalent interactions in biomolecules. J Chem Theory Comput 4:1996–2000

    Article  CAS  Google Scholar 

  28. Leang SS, Zahariev F, Gordona MS (2012) Benchmarking the performance of time-dependent density functional methods. J Chem Phys 136:104101

    Article  Google Scholar 

  29. Grimme S, Steinmetz M, Korth M (2007) How to compute isomerization energies of organic molecules with quantum chemical methods. J Org Chem 72:2118–2126

    Article  CAS  Google Scholar 

  30. Quintal MM, Karton A, Iron MA, Boese AD, Martin JML (2006) Benchmark study of DFT functionals for late-transition-metal reactions. J Phys Chem A 110:709–716

    Article  CAS  Google Scholar 

  31. Izgorodina EI, Coote ML, Radom L (2005) Trends in R−X bond dissociation energies (R = Me, Et, i-Pr, t-Bu; X = H, CH3, OCH3, OH, F): a surprising shortcoming of density functional theory. J Phys Chem A 109:7558–7566

    Article  CAS  Google Scholar 

  32. Zheng W-R, Fu Y, Guo Q-X (2008) G3//BMK and its application to calculation of bond dissociation enthalpies. J Chem Theory Comput 4:1324–1333

    Article  CAS  Google Scholar 

  33. Wang Y-G (2009) Examination of DFT and TDDFT methods II. J Phys Chem A 113:10873–10879

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  35. 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 37:785–789

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  37. Chai J-D, Head-Gordon M (2008) Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections. Phys Chem Chem Phys 10:6615–6620

    Article  CAS  Google Scholar 

  38. Woon DE, Dunning TH (1993) Gaussian basis sets for use in correlated molecular calculations III. The atoms aluminum through argon. J Chem Phys 98:1358–1371

    Article  CAS  Google Scholar 

  39. 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 82:270–283

    Article  CAS  Google Scholar 

  40. Hay PJ, Wadt WR (1985) Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi. J Chem Phys 82:284–298

    Article  Google Scholar 

  41. 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 82:299–310

    Article  CAS  Google Scholar 

  42. Curtiss LA, Raghavachari K, Trucks GW, Pople JA (1991) Gaussian-2 theory for molecular energies of first- and second-row compounds. J Chem Phys 94:7221–7230

    Article  CAS  Google Scholar 

  43. Curtiss LA, Raghavachari K, Redfern PC, Rassolov V, Pople JA (1998) Gaussian-3 (G3) theory for molecules containing first and second-row atoms. J Chem Phys 109:7764–7776

    Article  CAS  Google Scholar 

  44. Frisch MJ et al. (2009) Gaussian 09, Revision B.01, Gaussian Inc., Wallingford

  45. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88:899–926

    Article  CAS  Google Scholar 

  46. Glendening ED, Reed AE, Carpenter JE, Weinhold F (1988) NBO v3.1, Madison

  47. Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry, Radiochemistry Laboratory, St. Petersburg State University, St. Petersburg, 199034, Russia

    Igor S. Ignatyev

  2. Department of Physical and Analytical Chemistry, University of Jaén, Campus “Las Lagunillas”, 23071, Jaén, Spain

    Manuel Montejo & Juan Jesús López González

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  1. Igor S. Ignatyev
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  2. Manuel Montejo
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  3. Juan Jesús López González
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Correspondence to Juan Jesús López González.

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Ignatyev, I.S., Montejo, M. & López González, J.J. An assessment of DFT methods for predicting the thermochemistry of ion-molecule reactions of group 14 elements (Si, Ge, Sn). J Mol Model 19, 5439–5444 (2013). https://doi.org/10.1007/s00894-013-2038-y

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  • DOI: https://doi.org/10.1007/s00894-013-2038-y

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