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Equilibrium Molecular Structure of 3,3,6-trimethyl-1,5-diazabicyclo[3.1.0]hexane: the joint analysis of the gas-phase electron diffraction data and quantum chemical simulations

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Abstract

The equilibrium structure of the 3,3,6-trimethyl-1,5-diazabicyclo[3.1.0]hexane (TMDABH) molecule was studied for the first time by means of gas-phase electron diffraction (GED) supplemented with quantum chemical calculations. TMDABH exists as a mixture of two conformers of Cs point group symmetry, namely, a chair and a boat. The fractions of these two forms are 74 and 26% respectively, if the reference approximation was obtained at the MP2/aug-cc-PVTZ level, and 81 and 19%, if the reference approximation was generated at the DFT-B3LYP/cc-pVTZ level. The agreement between the theoretical and experimental molecular intensities is characterized by Rf disagreement factors of 5.06 and 6.93%, respectively. Based on the more accurate MP2/aug-cc-PVTZ quantum chemical approximation, the energy difference between the global minimum, which corresponds to the chair conformer of TMDABH, and the local minimum of the boat on the potential energy surface (PES) was found to be 1.39 kcal/mol. Moreover, NMR, IR, and Raman spectroscopic studies were carried out. According to the joint analysis of the data obtained, the most important equilibrium parameters of the chair and boat TMDABH conformers were determined to be as follows (bond lengths in Å, angles in degrees, for boat form in square brackets, Cs symmetry): N1N5 = 1.554(2) [1.520(2)], C2C3 = 1.525(2) [1.539(2)], N1C2C3 = 105.7(14) [108.8(14)], θ = C2-C3-C4/C2-N1-N5-C4 = 37.4(6) [−16.6(6)], φ = N1-C6-N5/C2-N1-N5-C4 = 72.9(3) [73.9(3)]. Comparison of especially NN bond lengths reveals a strong dependence on the bicyclic system conformation.

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All data generated or analyzed during this study are included in this published paper [and its supplementary information files].

References

  1. Gessner KJ, Ball DW (2005) J Mol Struct: THEOCHEM 730:95–103

    Article  CAS  Google Scholar 

  2. Vishnevskiy YV, Schwabedissen J, Rykov AN, Kuznetsov VV, Makhova NN (2015) J Phys Chem A 119:10871–10881

    Article  CAS  Google Scholar 

  3. Shustov GV, Kadorkina GK, Varlamov SV, Kachanov AV, Kostyanovskii RG, Rauk A (1992) J Am Chem Soc 114:1616–1623

    Article  CAS  Google Scholar 

  4. Kamuf M, Trapp O (2011) Chirality 23:113–117

    Article  CAS  Google Scholar 

  5. Paget CJ, Davis CS (1964) J Med Chem 7:626–628

    Article  CAS  Google Scholar 

  6. Baichurina AZ, Semina VI, Garaev RS (1996) Bull Exp Biol Med 121:584–586

    Article  Google Scholar 

  7. Makhova NN, Petukhova VY, Shevtsov AV, Novakovskiy VV, Kuznetsov VV (2013) Agents for treating neurodegenerative disorders, US Pat., WO2013/111117A2

  8. Makhova NN, Petukhova VY, Shevtsov AV, Novakovskiy VV, Kuznetsov VV (2013) Agents for treating neurodegenerative disorders, US Pat., WO2013/111118A2

  9. Makhova NN, Petukhova VY, Shevtsov AV, Novakovskiy VV, Kuznetsov VV (2013) Agents for treating neurodegenerative disorders, US Pat., WO2013.121334A2

  10. Syroeshkina YS, Kuznetsov VV, Lyssenko KA, Makhova NN (2009) Russ Chem Bull 58:366–379

    Article  CAS  Google Scholar 

  11. Kuznetsov VV, Kutepov SA, Makhova NN, Lyssenko KA, Dmitriev DE (2003) Russ Chem Bull Int Ed 52:665–673

    Article  CAS  Google Scholar 

  12. Makhova NN, Petukhova VY, Kuznetsov VV (2008) ARKIVOC, i, 128

  13. Makhova NN, Shevtsov AV, Petukhova VY (2011) Russ Chem Rev 80:1085–1133

    Article  Google Scholar 

  14. Vishnevskiy YV, Vogt N, Vogt J, Rykov AN, Kuznetsov VV, Makhova NN, Vilkov LV (2008) J Phys Chem A 112:5243–5250

    Article  CAS  Google Scholar 

  15. Atavin EG, Golubinsky AV, Popik MV, Kuznetsov VV, Makhova NN, Vilkov LV (2003) J Struct Chem 44:779–783

    Article  CAS  Google Scholar 

  16. Khaikin LS, Ageev GG, Rykov AN, Grikina OE, Shishkov IF, Kochikov IV, Kuznetsov VV, Makhova NN, Bukalov SS, Leites LA (2020) Phys Chem Chem Phys 22:22477–22492

    Article  CAS  Google Scholar 

  17. Shevtsov AV, Kuznetsov VV, Kislukhin AA, Petukhova VYu, Strelenko YuA, Makhova NN (2006) J Heterocycl Chem 43:881–888

  18. Chagarovskiy AO, Vasin VS, Kuznetsov VV, Ivanova OA, Rybakov VB, Shumsky AN, Makhova NN, Trushkov IV (2018) Angew Chem Int Ed 57:10338–10342

    Article  CAS  Google Scholar 

  19. Chagarovskiy AO, Kuznetsov VV, Ivanova OA, Goloveshkin AS, Levina II, Makhova NN, Trushkov IV (2019) Eur J Org Chem 2019:5475–5485

  20. Pitzer K, Donath WE (1959) J Am Chem Soc 81:3213–3218

    Article  CAS  Google Scholar 

  21. Romers C, Altona C, Buys HR, Havinga E (1969) Top Stereochem 4:39–97

    CAS  Google Scholar 

  22. Fuchs B (1978) Top Stereochem 10:1–94

    CAS  Google Scholar 

  23. Greenberg A, Liebman JF (1978) Strained Organic Molecules. Academic Press, New York

    Google Scholar 

  24. Zhang X, Senay L et al (2017) In Eng Chem Res 56:2883–2888

    Article  CAS  Google Scholar 

  25. Kuznetsov VV, Kachala VV, Makhova NN (2018) Mendeleev Commun 28:497–500

    Article  CAS  Google Scholar 

  26. Kochikov IV, Kovtun DM, Tarasov YI (2008) A new software for processing the radial symmetric diffractograms, in Numerical methods and programming. Section 2, Programming (Vychislitel’nye Metody i Programmirovanie) 9:12–18

  27. Kochikov IV, Tarasov YuI, Ivanov AA (2007) J Struct Chem 48:558–563

    Article  CAS  Google Scholar 

  28. Ross AW, Fink M, Hilderbrandt RL (1999) In: Wilson AJC (ed) International tables for X-ray crystallography, Vol. 4. Kluwer, Dordrecht

  29. Tavard C, Nicolas D, Rouault M (1967) J Chem Phys 64:540–554

    CAS  Google Scholar 

  30. Spiridonov VP (1997) in Advances in molecular structure research, ed. Hargittai I and Hargittai M, JAI. Greenwich 3:53–81

    CAS  Google Scholar 

  31. Spiridonov VP, Vogt N, Vogt J (2001) Struct Chem 12:349–376

    Article  CAS  Google Scholar 

  32. Ischenko AA, Girichev GV, Tarasov YI (2013) Electron diffraction: Structure and dynamics of free molecules and condensed state of substance. Fizmatlit, Moscow (in Russian)

  33. Ischenko AA (2018) Structure and dynamics of free molecules and condensed matter. Fizmatlit, Moscow (in Russian)

  34. Kochikov IV, Tarasov YI, Kuramshina GM, Spiridonov VP, Yagola AG, Strand TG (1998) J Mol Struct 445:243–258

    Article  CAS  Google Scholar 

  35. Kochikov IV, Tarasov YI, Spiridonov VP, Kuramshina GM, Yagola AG, Saakjan AS, Popik MV, Samdal S (1999) J Mol Struct 485–486:421–443

    Article  Google Scholar 

  36. Kochikov IV, Tarasov YI, Vogt N, Spiridonov VP (2002) J Mol Struct 607:163–174

    Article  CAS  Google Scholar 

  37. Dakkouri M, Kochikov IV, Tarasov YI, Vogt N, Vogt J, Bitschenauer R (2002) J Mol Struct 607:195–206

    Article  CAS  Google Scholar 

  38. Kochikov IV, Tarasov YI (2003) Struct Chem 14:227–238

    Article  CAS  Google Scholar 

  39. Kovtun DM, Kochikov IV, Tarasov YI (2015) J Phys Chem A 119:1657–1665

    Article  CAS  Google Scholar 

  40. Khaikin LS, Kochikov IV, Grikina OE, Tikhonov DS, Baskir EG (2015) Struct Chem 26:1651–1687

    Article  CAS  Google Scholar 

  41. Khaikin LS, Vogt N, Rykov AN, Grikina OE, Vogt J, Kochikov IV, Ageeva ES, Shishkov IF (2018) Mendeleev Commun 28:236–238

    Article  CAS  Google Scholar 

  42. Khaikin LS, Vogt N, Rykov AN, Grikina OE, Demaison J, Vogt J, Kochikov IV, Shishova YD, Ageeva ES, Shishkov IF (2018) Russ J Phys Chem A 92:1970–1974

    Article  CAS  Google Scholar 

  43. Yagola AG, Kochikov IV, Kuramshina GM, Pentin YA (1999) Inverse problems of vibrational spectroscopy. VSP BV, Utrecht

    Book  Google Scholar 

  44. Fogarasi G, Pulay P (1985) In: Durig JR (ed) Vibrational spectra and structure, Vol. 14, Chap. 3. Elsevier, Amsterdam, pp 125–219

  45. Pulay P, Fogarasi G, Pang F, Boggs JE (1979) J Am Chem Soc 101:2550–2560

    Article  CAS  Google Scholar 

  46. Pulay P, Fogarasi G, Pongor G, Boggs JE, Vargha A (1983) J Am Chem Soc 105:7037–7047

    Article  CAS  Google Scholar 

  47. Hamilton W (1965) Acta Cryst 18:502–510

    Article  CAS  Google Scholar 

  48. Kuznetsov VV, Marochkin II, Goloveshkin AS, Makhova NN, Shishkov IF (2017) Struct Chem 28:1211–1221

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We respectfully dedicate this paper to the memory of our esteemed late colleague, Dr. Leonid S. Khaikin of Lomonosov Moscow State University, a research leader in the field of GED and its combined application with spectroscopy and quantum chemical calculations for the structural analysis. His long-term study of nitrogen-containing organic molecular structures together with his wife Olga E. Grikina strongly contributed to the development of an extended molecular structure database. His will to overcome obstacles inspired his colleagues to model oneself on him and hand on the torch of structural chemistry in the future.

Funding

This work was supported by the Russian Foundation for Basic Research (Projects Nos. 20–03-00747 and 19–33-90274).

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Authors and Affiliations

  1. Chemistry Department, M. V. Lomonosov Moscow State University, 1 Leninsky Gory, 119991, Moscow, Russia

    Georgiy G. Ageev, Anatoliy N. Rykov, Olga E. Grikina & Igor F. Shishkov

  2. Scientifically Research Calculating Center, M. V. Lomonosov Moscow State University, 1 Leninsky Gory, 119991, Moscow, Russia

    Igor V. Kochikov

  3. N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp, 119991, Moscow, Russia

    Vladimir V. Kuznetsov & Nina N. Makhova

  4. A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova Str, 119991, Moscow, Russia

    Sergei S. Bukalov

Authors
  1. Georgiy G. Ageev
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  2. Anatoliy N. Rykov
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  3. Olga E. Grikina
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  4. Igor F. Shishkov
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  5. Igor V. Kochikov
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  6. Vladimir V. Kuznetsov
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  7. Nina N. Makhova
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  8. Sergei S. Bukalov
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Contributions

The corresponding author carried out a full description of quantum chemical calculations, structural analysis, provided the discussion of the results, and formulated a conclusion. A.N. Rykov carried out a gas-phase electron diffraction experiment. I.F. Shishkov was directly involved in the description and discussion. The introduction and the section devoted to the analysis of NMR spectra were written by V.V. Kuznetsov and N.N. Makhova, who also synthesized 3,3,6-trimethyl-1,5-diazabicyclo[3.1.0]hexane. Quantum chemical calculations using the Gaussian package and structural analysis with the use of Symm/Disp/Large/Eldiff software package were carried out by O.E. Grikina and I.V Kochikov. S.S. Bukalov was responsible for the NMR, IR, and Raman spectroscopic measurements.

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Correspondence to Georgiy G. Ageev.

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Nina N. Makhova passed away during submission of this manuscript.

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Ageev, G.G., Rykov, A.N., Grikina, O.E. et al. Equilibrium Molecular Structure of 3,3,6-trimethyl-1,5-diazabicyclo[3.1.0]hexane: the joint analysis of the gas-phase electron diffraction data and quantum chemical simulations. Struct Chem 33, 113–122 (2022). https://doi.org/10.1007/s11224-021-01828-5

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