Skip to main content
SpringerLink
Log in

Molecular modeling of the conformational dynamics of nitroxide derivatives of chitosan in aqueous solution

  • Full Articles
  • Published:
Russian Chemical Bulletin Aims and scope

Abstract

The structures of low-molecular-weight chitosan oligomers and their two nitroxide derivatives were examined using the force field molecular dynamics (MD) and density functional theory calculations with implicit and explicit solvent models. Rotamers of both neutral oligomers and those protonated at amino group were determined and the influence of the chain length and solvent (water) on their stability was studied. Bent conformations of the chitosan chain were found to be the most stable in the gas phase, whereas a linear structure of the polysaccharide is more preferred in water. Conformational transitions between the bent structures can occur only via the linear conformation of chitosan. According to the MD calculations, the nitroxides linked at the amino group do not form intramolecular hydrogen bonds with polar groups of the polysaccharide. The nitroxide substituents enhance the conformational flexibility of chitosan, but the linear conformation of the substituted oligomers remains most populated in water.

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

Similar content being viewed by others

References

  1. I. Younes, M. Rinaudo, Mar. Drugs, 2015, 13, 1133; DOI: https://doi.org/10.3390/md13031133.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. M. Anraku, J. M. Gebicki, D. Iohara, H. Tomida, K. Uekama, T. Maruyama, F. Hirayama, M. Otagiri, Carbohydr. Polym., 2018, 199, 141; DOI: https://doi.org/10.1016/j.carbpol.2018.07.016.

    Article  CAS  PubMed  Google Scholar 

  3. A. S. Berezin, E. A. Lomkova, Yu. A. Skorik, Russ. Chem. Bull., 2012, 61, 781.

    Article  CAS  Google Scholar 

  4. O. V. Melchakova, A. V. Pestov, N. V. Pechishcheva, K. Yu. Shunyaev, Russ. Chem. Bull., 2019, 68, 521.

    Article  CAS  Google Scholar 

  5. W. Wang, Ch. Xue, X. Mao, Int. J. Biol. Macromol., 2020, 164, 4532; DOI: https://doi.org/10.1016/j.ybiomac.2020.09.042.

    Article  CAS  PubMed  Google Scholar 

  6. A. E. Chalykh, T. F. Petrova, V. V. Matveev, V. K. Gerasimov, R. R. Khasbiullin, A. A. Shcherbina, N. A. Abaturova, Russ. Chem. Bull., 2020, 69, 675.

    Article  CAS  Google Scholar 

  7. C. S. Wilcox, Pharmacol. Ther., 2010, 126, 119; DOI: https://doi.org/10.1016/j.pharmthera.2010.01.003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. V. D. Sen’, E. M. Sokolova, N. I. Neshev, A. V. Kulikov, E. M. Pliss, React. Funct. Polym., 2017, 53, 111; DOI: https://doi.org/10.1016/j.reactfunctpolym.2016.12.006.

    Google Scholar 

  9. A. A. Balakina, V. A. Mumyatova, E. M. Pliss, A. A. Terent’ev, V. D. Sen’, Russ. Chem. Bull., 2018, 67, 2135.

    Article  CAS  Google Scholar 

  10. K. Okuyama, K. Noguchi, T. Miyazawa, T. Yui, K. Ogawa, Macromolecules, 1997, 30, 5849; DOI: https://doi.org/10.1021/ma970509n.

    Article  CAS  Google Scholar 

  11. K. Ogawa, T. Yui, K. Okuyama, Int. J. Biol. Macromol., 2004, 34, 1; DOI: https://doi.org/10.1016/j.ybiomac.2003.11.002.

    Article  CAS  PubMed  Google Scholar 

  12. C. Schatz, C. Viton, T. Delair, C. Pichot, A. Domard, Biomacromolecules, 2003, 4, 641; DOI: https://doi.org/10.1021/bm025724c.

    Article  CAS  PubMed  Google Scholar 

  13. G. A. Morris, J. Castile, A. Smith, G. G. Adams, S. E. Harding, Carbohydr. Polym., 2009, 76, 616; DOI: https://doi.org/10.1016/j.carbpol.2008.11.025.

    Article  CAS  Google Scholar 

  14. V. B. Luzhkov, Russ. Chem. Rev., 2017, 86, 211; DOI: https://doi.org/10.1070/RCR4610.

    Article  CAS  Google Scholar 

  15. V. G. Dashevsky, Konformatsionnyi analiz organicheskikh molekul [Conformaional Analysis of Organic Molecules], Khimiya, Moscow, 1982, 272 pp. (in Russian).

    Google Scholar 

  16. I. Braccini, R. P. Grasso, S. Pe’rez, Carbohydr. Res., 1999, 317, 119; DOI: https://doi.org/10.1016/S0008-6215(99)00062-2.

    Article  CAS  PubMed  Google Scholar 

  17. T. Sakajiri, T. Kikuchi, I. Simon, K. Uchida, T. Yamamura, T. Ishii, H. Yajima, J. Mol. Struct.: THEOCHEM, 2006, 764, 133; DOI: https://doi.org/10.1016/j.theochem.2006.02.016.

    Article  CAS  Google Scholar 

  18. E. F. Franca, R. D. Lins, L. C. G. Freitas, T. P. Straatsma, J. Chem. Theor. Comput., 2008, 4, 2141; DOI: https://doi.org/10.1021/ct8002964.

    Article  CAS  Google Scholar 

  19. S. Skovstrup, S. G. Hansen, T. Skrydstrup, B. Schiøtt, Biomacromolecules, 2010, 11, 3196; DOI: https://doi.org/10.1021/bm100736w.

    Article  CAS  PubMed  Google Scholar 

  20. E. L. Kossovich, I. V. Kirillova, L. Yu. Kossovich, R. A. Safonov, D. V. Ukrainskiy, S. A. Apshtein, J. Mol. Modell., 2014, 20, 2452; DOI: https://doi.org/10.1007/s00894-014-2452-9.

    Article  CAS  Google Scholar 

  21. S. V. Shilova, K. A. Romanova, Yu. G. Galyametdinov, A. Ya. Tret’yakova, V. P. Barabanov, Russ. J. Phys. Chem. A, 2016, 90, 1181; DOI: https://doi.org/10.1134/S003602441606025X.

    Article  CAS  Google Scholar 

  22. S. M. Dadou, M. I. El-Barghouthi, S. K. Alabdallah, A. A. Badwan, M. D. Antonijevic, B. Z. Chowdhry, Mar. Drugs, 2017, 15, 298; DOI: https://doi.org/10.3390/md15100298.

    Article  PubMed Central  CAS  Google Scholar 

  23. C. Esteban, I. Donati, S. Pantano, M. Villegas, J. Benegas, S. Paoletti, Biopolymers, 2018, 109, e23221; DOI: https://doi.org/10.1002/bip.23221.

    Article  PubMed  CAS  Google Scholar 

  24. V. B. Krapivin, V. D. Sen’, V. B. Luzhkov, Chem. Phys., 2019, 522, 214; DOI: https://doi.org/10.1016/j.chemphys.2019.02.021.

    Article  CAS  Google Scholar 

  25. C. Lee, W. Yang, R. G. Parr, Phys. Rev. B, 1988, 37, 785; DOI: https://doi.org/10.1103/PhysRevB.37.785.

    Article  CAS  Google Scholar 

  26. A. D. Becke, J. Chem. Phys., 1993, 98, 5648; DOI: https://doi.org/10.1063/1.464913.

    Article  CAS  Google Scholar 

  27. E. Cancès, B. Menucci, J. Tomasi, J. Chem. Phys., 1997, 107, 3032; DOI: https://doi.org/10.1063/1.474659.

    Article  Google Scholar 

  28. A. V. Marenich, C. J. Cramer, D. G. Truhlar, J. Phys. Chem. B, 2009, 113, 6378; DOI: https://doi.org/10.1021/jp810292n.

    Article  CAS  PubMed  Google Scholar 

  29. Y. Zhao, N. E. Schultz, D. G. Truhlar, J. Chem. Theor. Comput., 2006, 2, 364; DOI: https://doi.org/10.1021/ct0502763.

    Article  CAS  Google Scholar 

  30. V. B. Krapivin, A. S. Mendkovich, V. D. Sen, V. B. Luzhkov, Mendeleev Commun., 2019, 29, 77; DOI: https://doi.org/10.1016/j.mencom.2019.01.026.

    Article  CAS  Google Scholar 

  31. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, K. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09, Revision D.01. Gaussian, Inc., Wallingford CT, 2010.

    Google Scholar 

  32. R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, K. Schulten, J. Comput. Phys., 1999, 151, 283; DOI: https://doi.org/10.1006/jcph.1999.6201.

    Article  Google Scholar 

  33. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph., 1996, 14, 33; DOI: https://doi.org/10.1016/0263-7855(96)00018-5.

    Article  CAS  PubMed  Google Scholar 

  34. D. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, J. A. Onufriev, C. Simmerling, B. Wang, R. J. Woods, J. Comput. Chem., 2005, 26, 1668; DOI: https://doi.org/10.1002/jcc.20290.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. K. N. Kirschner, A. B. Yongye, S. M. Tschampel, J. González-Outeiriño, C. R. Daniels, B. L. Foley, R. J. Woods, J. Comput. Chem., 2008, 29, 622; DOI: https://doi.org/10.1002/jcc.20820.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. W. C. Still, A. Tempczyk, R. C. Hawley, T. Hendrickson, J. Am. Chem. Soc., 1990, 112, 6127; DOI: https://doi.org/10.1021/ja00172a038.

    Article  CAS  Google Scholar 

  37. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys., 1983, 79, 926; DOI: https://doi.org/10.1063/1.445869.

    Article  CAS  Google Scholar 

  38. V. B. Luzhkov, Russ. J. Phys. Chem. A, 2020, 94, 908; DOI: https://doi.org/10.31857/S0044453720050155.

    Article  CAS  Google Scholar 

  39. P. Sorlier, A. Denuzière, C. Viton, A. Domard, Biomacromolecules, 2001, 2, 765; DOI: https://doi.org/10.1021/bm015531+.

    Article  CAS  PubMed  Google Scholar 

  40. A. Lammerts Van Bueren, M. G. Ghinet, K. Gregg, A. Fleury, R. Brzezinski, A. B. Boraston, J. Mol. Biol., 2009, 385, 131; DOI: https://doi.org/10.1016/j.jmb.2008.10.031.

    Article  CAS  Google Scholar 

  41. A. Ranok, J. Wongsantichon, R. C. Robinson, W. Suginta, J. Biol. Chem., 2015, 290, 2617; DOI: https://doi.org/10.1074/jbc.M114.588905.

    Article  CAS  PubMed  Google Scholar 

  42. S. Moradi, E. Hosseini, M. Abdoli, S. Khani, M. Shahlaei, Carbohydr. Polym., 2019, 203, 52; DOI: https://doi.org/10.1016/j.carbpol.2018.09.032.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Problems of Chemical Physics, Russian Academy of Sciences, 1 prosp. Akad. Semenova, 142432, Chernogolovka, Moscow Region, Russian Federation

    V. B. Krapivin & V. B. Luzhkov

  2. Department of Fundamental Physical and Chemical Engineering, Lomonosov Moscow State University, Build. 51, 1 Leninskie Gory, 119991, Moscow, Russian Federation

    V. B. Luzhkov

Authors
  1. V. B. Krapivin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. V. B. Luzhkov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to V. B. Luzhkov.

Additional information

The authors express their gratitude to the staff of Computing Center at the Institute of Problems of Chemical Physics, Russian Academy of Sciences, for help in performing calculations.

This work was carried out within the framework of the State Assignment Theme No. AAAA-A19-119071890015-6.

This paper does not contain descriptions of studies on animals or humans.

The authors declare no competing interests.

Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1523–1532, August, 2021.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Krapivin, V.B., Luzhkov, V.B. Molecular modeling of the conformational dynamics of nitroxide derivatives of chitosan in aqueous solution. Russ Chem Bull 70, 1523–1532 (2021). https://doi.org/10.1007/s11172-021-3247-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11172-021-3247-7

Key words

Search

Navigation