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Theoretical investigation of anion perfluorocubane

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Abstract

Context

In this work, we did a theoretical exploration of C8F8 (Ib) and its anion radical analogue (IIb) in this work. By investigating the thermochemistry of electron capture, we find that the free energy associated with the conversion of C8H8 (Ia) into its anion radical analogue IIa is of the order of + 92.83 kcal.mol-1, while the conversion of Ib into IIb is − 6.42 kcal.mol-1. Therefore, species IIb is thermodynamically more stable than its neutral analogue. Natural bond orbitals (NBO) analyses revealed that compound Ib exhibits a relative electronic stability as a function of intramolecular delocalisations of the type \({\sigma }_{C-C}\to {\sigma }_{C-F}^{*}\) of the order of 2.70 kcal.mol-1. Similar delocalizations for Ia are energetically lower (1.45 kcal.mol-1). Topological analyses of compounds Ib and IIb indicate that the addition of an electron to Ib enhances the covalency of the C-C bond, as can be seen by the reduction in the ellipticity of the C-C bond. The opposite is observed for Ia, whose addition of the electron (leading to IIa) reduces the covalency of the C-C bond. By comparing the free and packaged forms of the species, it is found that, in the crystalline form, the system will present greater relative stability due to the dispersive interactions involved, as evidenced by non-covalent interactions (NCI) analysis. Finally, it was possible to verify that the manifestation of the current density with a lower paratropic and less antiaromatic character in Ib and IIb point to C8F8 as a strong candidate for electron capture.

Methods

Geometry optimization calculations were carried out, for all monomer structures using the hybrid functional B3LYP-D3 and the 6-31+G(d,p) basis set. To determine the formation thermochemistry of the ions, electronic energy corrections was performed using the DLPNO-CCSD(T)/aug-cc-pVTZ/C method. Starting from the optimised forms, shielding, nuclear magnetic resonance (NMR) spectra employing gauge-independent atomic orbital (GIAO), and NBO calculations were performed for these monomers, using the PBE0 functional and the pCSseg-2 atomic basis set. The magnetochemical analysis of ring currents was performed using the GIMIC formalism. For the topological analysis, it was applied the combination DLPNO-CCSD(T)/aug-cc-pVTZ/C, previously used for correcting the electronic energy.

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References

  1. Hopf H, Von Eggers Doering W (2000) Classics in hydrocarbon chemistry: syntheses, concepts, perspectives. Wiley

    Google Scholar 

  2. Biegasiewicz KF, Griffiths JR, Savage GP et al (2015) Cubane: 50 years later. Chem Rev 115:6719–6745. https://doi.org/10.1021/cr500523x

    Article  CAS  PubMed  Google Scholar 

  3. Eaton PE, Cole TW (1964) Cubane. J Am Chem Soc 86:3157–3158. https://doi.org/10.1021/ja01069a041

    Article  CAS  Google Scholar 

  4. Fleischer EB (1964) X-ray structure determination of cubane. J Am Chem Soc 86:3889–3890. https://doi.org/10.1021/ja01072a069

    Article  CAS  Google Scholar 

  5. Voloshin YZ, Kostromina NA, Krämer RK (2002) Clathrochelates: synthesis, structure and properties. Elsevier Science

    Google Scholar 

  6. Kato T, Yamabe T (2003) Electron–phonon interactions in charged cubic fluorocarbon cluster, (CF)8. J Chem Phys 120:1006–1016. https://doi.org/10.1063/1.1631931

    Article  CAS  Google Scholar 

  7. Sugiyama M, Akiyama M, Yonezawa Y et al (2022) Electron in a cube: synthesis and characterization of perfluorocubane as an electron acceptor. Science 377:756–759. https://doi.org/10.1126/science.abq0516

    Article  CAS  PubMed  Google Scholar 

  8. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098–3100. https://doi.org/10.1103/PhysRevA.38.3098

    Article  CAS  Google Scholar 

  9. Grimme S (2011) Density functional theory with London dispersion corrections. WIREs Comput Mol Sci 1:211–228. https://doi.org/10.1002/wcms.30

    Article  CAS  Google Scholar 

  10. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652. https://doi.org/10.1063/1.464913

    Article  CAS  Google Scholar 

  11. 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. https://doi.org/10.1103/PhysRevB.37.785

    Article  CAS  Google Scholar 

  12. Hariharan PC, Pople JA (1973) The influence of polarization functions on molecular orbital hydrogenation energies. Theor Chim Acta 28:213–222. https://doi.org/10.1007/BF00533485

    Article  CAS  Google Scholar 

  13. Hehre WJ, Ditchfield R, Pople JA (1972) Self—consistent molecular orbital methods. XII. Further extensions of Gaussian—type basis sets for use in molecular orbital studies of organic molecules. J Chem Phys 56:2257–2261. https://doi.org/10.1063/1.1677527

    Article  CAS  Google Scholar 

  14. Riplinger C, Neese F (2013) An efficient and near linear scaling pair natural orbital based local coupled cluster method. J Chem Phys 138:34106. https://doi.org/10.1063/1.4773581

    Article  CAS  Google Scholar 

  15. Riplinger C, Sandhoefer B, Hansen A, Neese F (2013) Natural triple excitations in local coupled cluster calculations with pair natural orbitals. J Chem Phys 139:134101. https://doi.org/10.1063/1.4821834

    Article  CAS  PubMed  Google Scholar 

  16. Liakos DG, Sparta M, Kesharwani MK et al (2015) Exploring the accuracy limits of local pair natural orbital coupled-cluster theory. J Chem Theory Comput 11:1525–1539. https://doi.org/10.1021/ct501129s

    Article  CAS  PubMed  Google Scholar 

  17. Liakos DG, Neese F (2015) Is It possible to obtain coupled cluster quality energies at near density functional theory cost? Domain-based local pair natural orbital coupled cluster vs modern density functional theory. J Chem Theory Comput 11:4054–4063. https://doi.org/10.1021/acs.jctc.5b00359

    Article  CAS  PubMed  Google Scholar 

  18. Dunning TH (1989) Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J Chem Phys 90:1007–1023. https://doi.org/10.1063/1.456153

    Article  CAS  Google Scholar 

  19. Kendall RA, Dunning TH, Harrison RJ (1992) Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J Chem Phys 96:6796–6806. https://doi.org/10.1063/1.462569

    Article  CAS  Google Scholar 

  20. Weigend F, Köhn A, Hättig C (2002) Efficient use of the correlation consistent basis sets in resolution of the identity MP2 calculations. J Chem Phys 116:3175–3183. https://doi.org/10.1063/1.1445115

    Article  CAS  Google Scholar 

  21. Sandler I, Chen J, Taylor M et al (2021) Accuracy of DLPNO-CCSD(T): effect of basis set and system size. J Phys Chem A 125:1553–1563. https://doi.org/10.1021/acs.jpca.0c11270

    Article  CAS  PubMed  Google Scholar 

  22. Jensen F (2015) Segmented contracted basis sets optimized for nuclear magnetic shielding. J Chem Theory Comput 11:132–138. https://doi.org/10.1021/ct5009526

    Article  CAS  PubMed  Google Scholar 

  23. Jusélius J, Sundholm D (1999) Ab initio determination of the induced ring current in aromatic molecules. Phys Chem Chem Phys 1:3429–3435. https://doi.org/10.1039/A903847G

    Article  Google Scholar 

  24. Cossío FP (2021) 1 - Aromaticity in molecules and transition structures: from atomic and molecular orbitals to simple ring current models. In: Fernandez I (ed) Aromaticity. Elsevier, pp 1–41

    Google Scholar 

  25. Kupka T (2021) Theory and computation of nuclear shielding. The Royal Society of Chemistry

    Book  Google Scholar 

  26. London F (1937) Théorie quantique des courants interatomiques dans les combinaisons aromatiques. J Phys le Radium 8:397–409. https://doi.org/10.1051/jphysrad:01937008010039700

    Article  CAS  Google Scholar 

  27. McWeeny R (1962) Perturbation theory for the Fock-Dirac density matrix. Phys Rev 126:1028–1034. https://doi.org/10.1103/PhysRev.126.1028

    Article  Google Scholar 

  28. Ditchfield R (1974) Self-consistent perturbation theory of diamagnetism. Mol Phys 27:789–807. https://doi.org/10.1080/00268977400100711

    Article  CAS  Google Scholar 

  29. 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 112:8251–8260. https://doi.org/10.1021/ja00179a005

    Article  CAS  Google Scholar 

  30. Cheeseman JR, Trucks GW, Keith TA, Frisch MJ (1996) A comparison of models for calculating nuclear magnetic resonance shielding tensors. J Chem Phys 104:5497–5509. https://doi.org/10.1063/1.471789

    Article  CAS  Google Scholar 

  31. Ruud K, Helgaker T, Bak KL et al (1993) Hartree-Fock limit magnetizabilities from London orbitals. J Chem Phys 99:3847–3859. https://doi.org/10.1063/1.466131

    Article  CAS  Google Scholar 

  32. Carpenter JE, Weinhold F (1988) Analysis of the geometry of the hydroxymethyl radical by the “different hybrids for different spins” natural bond orbital procedure. J Mol Struct THEOCHEM 169:41–62. https://doi.org/10.1016/0166-1280(88)80248-3

    Article  Google Scholar 

  33. Foster JP, Weinhold F (1980) Natural hybrid orbitals. J Am Chem Soc 102:7211–7218. https://doi.org/10.1021/ja00544a007

    Article  CAS  Google Scholar 

  34. Reed AE, Weinhold F (1983) Natural bond orbital analysis of near-Hartree–Fock water dimer. J Chem Phys 78:4066–4073. https://doi.org/10.1063/1.445134

    Article  CAS  Google Scholar 

  35. Reed AE, Weinstock RB, Weinhold F (1985) Natural population analysis. J Chem Phys 83:735–746. https://doi.org/10.1063/1.449486

    Article  CAS  Google Scholar 

  36. Reed AE, Weinhold F (1985) Natural localized molecular orbitals. J Chem Phys 83:1736–1740. https://doi.org/10.1063/1.449360

    Article  CAS  Google Scholar 

  37. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88:899–926. https://doi.org/10.1021/cr00088a005

    Article  CAS  Google Scholar 

  38. Naaman R, Vager Z (1988) The structure of small molecules and ions. Springer, US, Boston, MA

    Book  Google Scholar 

  39. Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865–3868. https://doi.org/10.1103/PhysRevLett.77.3865

    Article  CAS  PubMed  Google Scholar 

  40. Perdew JP, Burke K, Ernzerhof M (1997) Generalized Gradient approximation made simple. Phys Rev Lett 78:1396–1396. https://doi.org/10.1103/PhysRevLett.78.1396

    Article  CAS  Google Scholar 

  41. Rauhalahti M, Taubert S, Sundholm D, Liégeois V (2017) Calculations of current densities for neutral and doubly charged persubstituted benzenes using effective core potentials. Phys Chem Chem Phys 19:7124–7131. https://doi.org/10.1039/C7CP00194K

    Article  CAS  PubMed  Google Scholar 

  42. Sundholm D, Fliegl H, Berger RJF (2016) Calculations of magnetically induced current densities: theory and applications. Wiley Interdiscip Rev Comput Mol Sci 6:639–678. https://doi.org/10.1002/wcms.1270

    Article  CAS  Google Scholar 

  43. Semenov VA, Krivdin LB (2020) DFT computational schemes for 1H and 13C NMR chemical shifts of natural products, exemplified by strychnine. Magn Reson Chem 58:56–64. https://doi.org/10.1002/mrc.4922

    Article  CAS  PubMed  Google Scholar 

  44. Liang J, Wang Z, Li J et al (2023) Efficient calculation of NMR shielding constants using composite method approximations and locally dense basis sets. J Chem Theory Comput 19(2):514–523. https://doi.org/10.1021/acs.jctc.2c00933

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Fouda AEA, Besley NA (2017) Assessment of basis sets for density functional theory-based calculations of core-electron spectroscopies. Theor Chem Acc 137:6. https://doi.org/10.1007/s00214-017-2181-0

    Article  CAS  Google Scholar 

  46. Semenov VA, Krivdin LB (2022) Computational NMR of natural products. Russ Chem Rev 91:RCR5027. https://doi.org/10.1070/RCR5027

  47. Bader RFW (1991) A quantum theory of molecular structure and Its appllcatlons. Chem Rev 91:893–928

    Article  CAS  Google Scholar 

  48. Bader RFW (1994) Atoms in molecules: a quantum theory. Clarendon Press

    Google Scholar 

  49. Contreras-García J, Yang W, Johnson ER (2011) Analysis of hydrogen-bond interaction potentials from the electron density: Integration of noncovalent interaction regions. J Phys Chem A 115(45):12983–12990. https://doi.org/10.1021/jp204278k

    Article  CAS  PubMed  Google Scholar 

  50. Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunction analyzer. J Comput Chem 33:580–592. https://doi.org/10.1002/jcc.22885

    Article  CAS  PubMed  Google Scholar 

  51. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38

    Article  CAS  PubMed  Google Scholar 

  52. Keith TA (2019) AIMAll (Version 19.10.12), TK Gristmill Software, Overland Park KS. aim.tkgristmill.com

  53. Frisch MJ, Trucks GW, Schlegel HB et al (2013) Gaussian 09

  54. Cremer D, Kraka E (1984) A description of the chemical bond in terms of local properties of electron density and energy. Croat Chem Acta 57:1259–1281

    Google Scholar 

  55. Castro TS, Martins GF, de Alcântara Morais SF, Ferreira DAC (2023) Aromaticity of Cope and Claisen rearrangements. Theor Chem Acc 142:40. https://doi.org/10.1007/s00214-023-02975-0

    Article  CAS  Google Scholar 

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Acknowledgements

G. F. M. and T. S. C. are grateful to the CAPES for PhD scholarship. D. A. C. F. is grateful to the PET/IQ-UnB/SESu/MEC for the tutor fellowship. We would like to thank the editorial board of JMM, especially the editor Prof Dr Itamar Borges Jr. for improving the final version of the manuscript.

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Authors and Affiliations

  1. Instituto de Química, Laboratório de Dinâmica e Reatividade Molecular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília-DF, CEP, 70910-900, Brazil

    Guilherme Ferreira Martins, Thiago Sampaio Castro & Daví Alexsandro Cardoso Ferreira

  2. Instituto Federal do Tocantins-Campus Gurupi, Gurupi, TO, CEP, 77410-470, Brazil

    Thiago Sampaio Castro

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  1. Guilherme Ferreira Martins
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  2. Thiago Sampaio Castro
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Contributions

G.F.M conceived the study performed and carried out the interpretation of the theoretical data. T.S.C. assisted in the execution and interpretation of the NCI and GIMIC calculations. D.A.C.F conceived the work performed and calculated the GIMIC properties, topology, thermochemistry, and NCI. The authors contributed equally to the study.

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Correspondence to Daví Alexsandro Cardoso Ferreira.

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Martins, G.F., Castro, T.S. & Ferreira, D.A.C. Theoretical investigation of anion perfluorocubane. J Mol Model 29, 319 (2023). https://doi.org/10.1007/s00894-023-05725-y

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