Skip to main content
SpringerLink
Log in

Probability of reaction pathways of amine with epoxides in the reagent ratio of 1:1 and 1:2

  • Original Research
  • Published:
Structural Chemistry Aims and scope Submit manuscript

Abstract

The algorithm for generating and estimating the probability of possible reaction pathways for multichannel bimolecular interactions was used to predict the reaction products in the reagent ratio of 1:1 and 1:2. Here, we have considered the possible reaction pathways of the reaction of amine (1S,2S,4S)-bicyclo[2.2.1]hept-5-en-2-ylmethanamine (1) with epoxides 2-((cyclohexyloxy)methyl)oxirane (2), 2-(phenoxymethyl)oxirane (3), N-(oxiran-2-ylmethyl)-N-phenylbenzenesulfonamide (8) in order to explain experimental observed data, which indicate differences in the reactivity of glycidyl ethers and glycidylsulfonamide with framework amines. Based on the proposed algorithm (Borysenko et al. 2021), we have investigated the reaction in the reagent ratio of 1:1 and 1:2. Calculated values of activation barriers indicate a low probability of formation of interaction products of amine (1) with epoxide (8) with a (1:2) reagent ratio due to steric hindrances in the reaction center.

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

Scheme 1
Scheme 2
Fig. 1
Fig. 2
Scheme 3
Fig. 3
Fig. 4

Similar content being viewed by others

Availability of data and material

Additional data (Cartesian Coordinates and Gibbs free energies of TS conformations from the M062X/6-31G(d) calculation) are available as Supplementary Information.

Code availability

Not applicable.

References

  1. Borysenko I, Sviatenko L, Okovytyy S, Leszczynski J (2021) Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Epoxide ring opening reaction. Struct Chem 32:581–589. https://doi.org/10.1007/s11224-020-01663-0

    Article  CAS  Google Scholar 

  2. Bergmeier S (2000) The synthesis of vicinal amino alcohols. Tetrahedron 56(17):2561–2576

    Article  CAS  Google Scholar 

  3. Cristau H-J, Pirat J-L, Drag M, Kafarski P (2000) Regio- and stereoselective synthesis of 2-amino-1-hydroxy-2-aryl ethylphosphonic esters. Tetrahedron Lett 41:9781–9785

    Article  CAS  Google Scholar 

  4. Kasyan L, Okovytyy S, Kasyan A (2004) reactions of alicyclic epoxy compounds with nitrogen-containing nucleophiles Russ. J Org Chem 40:1–34

    CAS  Google Scholar 

  5. Kasyan L, Palchikov V (2010) Cage-like amino alcohols. Synthesis, reactions, and application. Russ J Org Chem 46:1–42

    Article  CAS  Google Scholar 

  6. Sayer J, Chadha A, Agarwal S, Yeh H, Yagi H, Jerina D (1991) Covalent nucleoside adducts of benzo[a]pyrene 7,8-diol 9,10-epoxides: structural reinvestigation and characterization of a novel adenosine adduct on the ribose moiety. J Org Chem 56:20–29

    Article  CAS  Google Scholar 

  7. Scharfenberg M, Hilf J, Frey H (2018) Functional polycarbonates from carbon dioxide and tailored epoxide monomers: degradable materials and their application potential. Adv Func Mater 28(10):1704302. https://doi.org/10.1002/adfm.201704302

    Article  CAS  Google Scholar 

  8. Wang R, Schuman T (2013) Vegetable oil-derived epoxy monomers and polymer blends: a comparative study with review. Express Polym Lett 7(3):272–292. https://doi.org/10.3144/expresspolymlett.2013.25

    Article  CAS  Google Scholar 

  9. Ma S, Liu X, Fan L, Jiang Y, Cao L, Tang Z, Zhu J (2013) Synthesis and properties of a bio-based epoxy resin with high epoxy value and low viscosity. Chemsuschem 7(2):555–562. https://doi.org/10.1002/cssc.201300749

    Article  CAS  Google Scholar 

  10. Mangold C, Obermeier B, Wurm F, Frey H (2011) From an epoxide monomer toolkit to functional PEG copolymers with adjustable LCST behavior. Macromol Rapid Commun 32(23):1930–1934. https://doi.org/10.1002/marc.201100489

    Article  CAS  PubMed  Google Scholar 

  11. Huang K, Liu Z, Zhang J, Li S, Li M, Xia J, Zhou Y (2014) Epoxy monomers derived from tung oil fatty acids and its regulable thermosets cured in two synergistic ways. Biomacromol 15(3):837–843. https://doi.org/10.1021/bm4018929

    Article  CAS  Google Scholar 

  12. Ng F, Couture G, Philippe C, Boutevin B, Caillol S (2017) Bio-based aromatic epoxy monomers for thermoset materials. Molecules 22(1):149. https://doi.org/10.3390/molecules22010149

    Article  CAS  PubMed Central  Google Scholar 

  13. Stadler B, Tin S, Kux A, Grauke R, Koy C, Tiemersma-Wegman T, de Vries J (2020) Co-oligomers of renewable and “inert” 2-MeTHF and propylene oxide for use in bio-based adhesives. ACS Sustain Chem Eng 8(35):13467–13480. https://doi.org/10.1021/acssuschemeng.0c04450

    Article  CAS  Google Scholar 

  14. Cerit A, Marti M, Soydal U, Kocaman S, Ahmetli G (2016) Effect of modification with various epoxide compounds on mechanical, thermal, and coating properties of epoxy resin. Int J Polym Sci 7:1–13. https://doi.org/10.1155/2016/4968365

    Article  CAS  Google Scholar 

  15. Kasyan L, Pridma S, Palchikov V, Karat L, Turov A, Isayev O (2010) Reaction of bicyclo[2.2.1]hept-5-ene-endo-2-ylmethylamine and nitrophenyl glycidyl ethers. J Phys Org Chem 24(8):705–713. https://doi.org/10.1002/poc.1815

    Article  CAS  Google Scholar 

  16. Palchikov V, Svyatenko L, Plakhotnii I, Kas’yan L (2013) Experimental and theoretical study of the reaction between bicyclo[2.2.1]hept-5-en-endo-2-ylmethylamine and 2-[(2-allylphenoxy)methyl]oxirane. Zh Org Khim 49:704–708

    Google Scholar 

  17. Ohno K, Maeda S (2004) A scaled hypersphere search method for the topography of reaction pathways on the potential energy surface. Chem Phys Lett 384:277–282

    Article  CAS  Google Scholar 

  18. Maeda S, Ohno K (2005) Global mapping of equilibrium and transition structures on potential energy surfaces by the scaled hypersphere search method: applications to ab initio surfaces of formaldehyde and propyne molecules. J Phys Chem A 109:5742–5753

    Article  CAS  PubMed  Google Scholar 

  19. Ohno K, Maeda S (2006) Global reaction route mapping on potential energy surfaces of formaldehyde, formic acid, and their metal-substituted analogues. J Phys Chem A 110:8933–8941

    Article  CAS  PubMed  Google Scholar 

  20. Maeda S, Ohno K, Morokuma K (2013) Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods. Phys Chem 15:3683–3701

    CAS  Google Scholar 

  21. Maeda S, Morokuma K (2010) Communications: a systematic method for locating transition structures of A + B = X type reactions. J Chem Phys 132:241102

    Article  PubMed  Google Scholar 

  22. Maeda S, Morokuma K (2011) Finding reaction pathways of type A + B = X: toward systematic prediction of reaction mechanisms. J Chem Theory Comput 7:2335–2345

    Article  CAS  PubMed  Google Scholar 

  23. Maeda S, Abe E, Hatanaka M, Taketsugu T, Morokuma K (2012) Exploring potential energy surfaces of large systems with artificial force induced reaction method in combination with ONIOM and Microiteration. J Chem Theory Comput 8:5058–5063

    Article  CAS  PubMed  Google Scholar 

  24. Maeda S, Harabuchi Y, Takagi M, Taketsugu T, Morokuma K (2016) Artificial force induced reaction (AFIR) method for exploring quantum chemical potential energy surfaces. Chem Rec 16:2232–2248

    Article  CAS  PubMed  Google Scholar 

  25. Maeda S, Harabuchi Y, Takagi M, Saita K, Suzuki K, Ichino T, Sumiya Y, Sugiyama K, Ono Y (2017) Implementation and performance of the artificial force induced reaction method in the GRRM17 program. J Comput Chem 39:233–250

    Article  PubMed  PubMed Central  Google Scholar 

  26. Martínez-Núñez E (2015) An automated transition state search using classical trajectories initialized at multiple minima. Phys Chem 17:14912–14921

    Google Scholar 

  27. Martínez-Núñez E (2015) An automated method to find transition states using chemical dynamics simulations. J Comput Chem 36:222–234

    Article  PubMed  Google Scholar 

  28. Ferro-Costas D, Martínez-Núñez E, Rodríguez-Otero J, Cabaleiro-Lago E, Estévez CM, Fernández B, Fernández-Ramos A, Vázquez SA (2018) Influence of multiple conformations and paths on rate constants and product branching ratios. Thermal decomposition of 1-propanol radicals. J Phys Chem A 122:4790–4800

    Article  CAS  PubMed  Google Scholar 

  29. Varela JA, Vazquez SA, Martinez-Nunez E (2017) An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis. Chem Sci 8:3843–3851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Dewyer AL, Zimmerman PM (2017) Finding reaction mechanisms, intuitive or otherwise. Org Biomol Chem 15:501–504

    Article  CAS  PubMed  Google Scholar 

  31. Ludwig JR, Phan S, McAtee CC, Zimmerman PM, Devery JJ, Schindler CS (2017) Mechanistic investigations of the iron(III)-catalyzed carbonyl-olefin metathesis. J Am Chem Soc 139:10832–10842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Dewyer AL, Zimmerman PM (2017) Simulated mechanism for palladium-catalyzed, directed γ-arylation of piperidine. ACS Catal 7:5466–5477

    Article  CAS  Google Scholar 

  33. Yang M, Zou J, Wang G, Li S (2017) Automatic reaction pathway search via combined molecular dynamics and coordinate driving method. J Phys Chem A 121:1351–1361

    Article  CAS  PubMed  Google Scholar 

  34. PCModel V 9.0 (2004) Molecular modeling software for Windows operating system Apple Macintosh OS Linux and Unix. Serena Software Box 3076 Bloomington, IN 47402–3076 (812)-333–0823

  35. Gajewski JJ, Gilbert KE, McKelvey J (1990) MMX: an enhanced version of MM2. In: Liotta D (ed) Advances in Molecular Modeling, vol. 2. JAI Press, Greenwich, CT, p 65

  36. Stewart JJP (2013) Optimization of parameters for semi-empirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters. J Molec Modeling 19:1–32

    Article  CAS  Google Scholar 

  37. MOPAC2016, Stewart JJP (2016) Stewart computational chemistry, Colorado Springs, CO, USA. http://OpenMOPAC.net

  38. Zhao Y, Truhlar DG (2006) Comparative DFT study of van der Waals complexes: rare-gas dimers, alkaline-earth dimers, zinc dimer, and zinc-rare-gas dimers. J Phys Chem 110:5121–5129

    Article  CAS  Google Scholar 

  39. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson GA, Nakatsuji H, Li X, Caricato M, Marenich AV, Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd JJ, Brothers EN, Kudin KN, Staroverov VN, Keith TA, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, Morokuma K, Farkas O, Foresman JB, Fox DJ (2016) Gaussian 16, Revision C.01. Gaussian Inc, Wallingford CT

    Google Scholar 

  40. Fukui K (1981) The path of chemical-reactions – the IRC approach. Acc Chem Res 14:363–368. https://doi.org/10.1021/ar00072a001

    Article  CAS  Google Scholar 

  41. Hratchian HP, Schlegel HB (2005) Theory and applications of computational chemistry: the first 40 years. In: Dykstra CE, Frenking G, Kim KS, Scuseria G (eds), Elsevier, Amsterdam, pp 195–249

  42. Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute electron density and a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B 113:6378–6396

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

The computation time was provided by the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562 and XSEDE award allocation Number TG-DMR110088. This study was supported by the Ministry of Education and Science of Ukraine (grant 0119U100724).

Author information

Authors and Affiliations

  1. Department of Physical, Organic and Inorganic Chemistry, Oles Honchar Dnipro National University, Dnipro, 49010, Ukraine

    Iryna O. Borysenko & Sergiy I. Okovytyy

  2. Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, 39217, USA

    Jerzy Leszczynski

Authors
  1. Iryna O. Borysenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sergiy I. Okovytyy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jerzy Leszczynski
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

All authors contributed to the study conception and design. Material preparation, data collection, computer simulation were performed by Iryna O. Borysenko. Analysis of the obtained data was performed by Iryna O. Borysenko, Sergiy I. Okovytyy and Jerzy Leszczynski. The first draft of the manuscript was written by Iryna O. Borysenko and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Sergiy I. Okovytyy.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Below is the link to the electronic supplementary material.

Supplementary file1 (RTF 158 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Borysenko, I.O., Okovytyy, S.I. & Leszczynski, J. Probability of reaction pathways of amine with epoxides in the reagent ratio of 1:1 and 1:2. Struct Chem 33, 2115–2125 (2022). https://doi.org/10.1007/s11224-022-01979-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11224-022-01979-z

Keywords

Search

Navigation