Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Molecular mechanics force field for structure, dynamics and conformation of carbohydrates involving furanoses

2015/18/E/ST4/00234

Keywords:

furanoses molecular dynamics carbohydrate conformation force fields

Descriptors:

  • ST4_15: Colloid chemistry
  • ST4_13: Solid-state chemistry, surface physicochemistry
  • ST4_4: Theoretical and computational chemistry

Panel:

ST4 - Chemistry: physical chemistry/chemical physics, theoretical chemistry, analytical chemistry, inorganic chemistry, organic chemistry, method development

Host institution :

Instytut Katalizy i Fizykochemii Powierzchni im. Jerzego Habera Polskiej Akademii Nauk

woj. małopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Wojciech Płaziński 

Number of co-investigators in the project: 4

Call: SONATA BIS 5 - announced on 2015-06-15

Amount awarded: 917 600 PLN

Project start date (Y-m-d): 2016-06-15

Project end date (Y-m-d): 2021-06-14

Project duration:: 60 months (the same as in the proposal)

Project status: Project settled

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Equipment purchased [PL]

  1. komputer przenośny typu laptop, zasilacz UPC, dyski trawde do serwera HPC.
  2. Prznośny komputer (laptop) (8 000 PLN)
  3. Wysokowydajny serwer obliczeniowy HPC (168 000 PLN)

Information in the final report

  • Publication in academic press/journals (15)
  1. A GROMOS Force Field for Furanose-Based Carbohydrates
    Authors:
    Nester, K., Gaweda, K., Plazinski, W.
    Academic press:
    Journal of Chemical Theory and Computation (rok: 2019, tom: 15, strony: 1168-1186), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jctc.8b00838 - link to the publication
  2. Comparison of Carbohydrate Force Fields in Molecular Dynamics Simulations of Protein–Carbohydrate Complexes
    Authors:
    Plazinska, A., Plazinski, W.
    Academic press:
    Journal of Chemical Theory and Computation (rok: 2021, tom: 17, strony: 2575–2585), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jctc.1c00071 - link to the publication
  3. Conformations of saturated five-membered heterocycles evaluated by MP2 calculations
    Authors:
    Gaweda, K., Plazinska, A., Plazinski, W.
    Academic press:
    Chemistry of Heterocyclic Compounds (rok: 2020, tom: 56, strony: 1599–1604), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s10593-020-02855-6 - link to the publication
  4. Extension of the GROMOS 56a6CARBO/CARBO_R Force Field for Charged, Protonated and Esterified Uronates
    Authors:
    Karina Panczyk, Karolina Gaweda, Mateusz Drach, Wojciech Plazinski
    Academic press:
    Journal of Physical Chemistry B (rok: 2018, tom: 122, strony: 3696-3710), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.7b11548 - link to the publication
  5. Tautomers of N-acetyl-D-allosamine: an NMR and computational chemistry study
    Authors:
    W. Plazinski, M.U. Roslund, E. Säwén, O. Engström, P. Tähtinen, G. Widmalm
    Academic press:
    Organic & Biomolecular Chemistry (rok: 2021, tom: 19, strony: 7190-7201), Wydawca: The Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/d1ob01139a - link to the publication
  6. The endo- and exo-Anomeric Effects in Furanosides. A Computational Study
    Authors:
    Gaweda, K., Plazinski, W.
    Academic press:
    European Journal of Organic Chemistry (rok: 2020, tom: 6, strony: 674-679), Wydawca: Royal Chemical Society
    Status:
    Published
    DOI:
    10.1002/ejoc.201901473 - link to the publication
  7. Efficient sampling of high-energy states by machine learning force fields
    Authors:
    Plazinski, W., Plazinska, A., Brzyska, A.
    Academic press:
    Physical Chemistry Chemical Physics (rok: 2020, tom: 22, strony: 14364-14374), Wydawca: Royal Chemical Society
    Status:
    Published
    DOI:
    10.1039/D0CP01399D - link to the publication
  8. Molecular Structure of Cefuroxime Axetil Complexes with α-, β-, γ-, and 2-Hydroxypropyl-β-Cyclodextrins: Molecular Simulations and Raman Spectroscopic and Imaging Studies
    Authors:
    B. Gieroba, G. Kalisz, A. Sroka-Bartnicka, A. Płazińska, W. Płaziński, M. Starek, M. Dąbrowska
    Academic press:
    International Joural of Molecular Sciences (rok: 2021, tom: 22 (10), strony: 5238), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22105238 - link to the publication
  9. Pyranose ring puckering in aldopentoses, ketohexoses and deoxyaldohexoses. A molecular dynamics study
    Authors:
    Panczyk, K., Plazinski, W.
    Academic press:
    Carbohydrate Research (rok: 2018, tom: 455, strony: 67-70), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.carres.2017.11.011 - link to the publication
  10. Pyranose ring conformations in mono- and oligosaccharides: A combined MD and DFT approach
    Authors:
    Gaweda, K., Plazinski, W.
    Academic press:
    Physical Chemistry Chemical Physics (rok: 2017, tom: 19, strony: 20760-20772), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/C7CP02920A - link to the publication
  11. Relation between the NMR data and the pseudorotational free energy profile for oxolane
    Authors:
    Plazinski, W.; Gaweda, K.; Plazinska, A.
    Academic press:
    Journal of Theoretical and Computational Chemistry (rok: 2019, tom: 18, strony: 1950012), Wydawca: World Scientific
    Status:
    Published
    DOI:
    10.1142/S0219633619500123 - link to the publication
  12. The systematic influence of solvent on the conformational features of furanosides
    Authors:
    Gaweda, K., Plazinski, W.
    Academic press:
    Organic and Biomolecular Chemistry (rok: 2019, tom: 17, strony: 2479-2485), Wydawca: Royal Chemical Society
    Status:
    Published
    DOI:
    10.1039/C9OB00043G - link to the publication
  13. Conformational properties of inulin, levan and arabinan studied by molecular dynamics simulations
    Authors:
    Nester, K., Plazinski, W.
    Academic press:
    Carbohydrate Polymers (rok: 2020, tom: 240, strony: 116266-116278), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.carbpol.2020.116266 - link to the publication
  14. Deciphering the conformational preferences of furanosides. A molecular dynamics study
    Authors:
    Nester, K., Plazinski, W.
    Academic press:
    Journal of Biomolecular Structure and Dynamics (rok: 2020, tom: 38, strony: 3359-3370), Wydawca: Taylor and Francis
    Status:
    Published
    DOI:
    10.1080/07391102.2019.1656670 - link to the publication
  15. Tautomeric and epimeric equilibria of aldo- and ketohexoses studied by the MD simulations and QM calculations
    Authors:
    Gaweda, K., Plazinski, W.
    Academic press:
    Carbohydrate Research (rok: 2019, tom: 474, strony: 45519), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.carres.2019.01.004 - link to the publication

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