Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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More accurate models of the electrostatic potential of biological macromolecules and organic crystals necessary for proper interpretation of data from cryo-electron microscopy and from electron diffraction - feasibility study

2017/27/B/ST4/02721

Keywords:

electron atomic scattering factors quantum crystallography structure refinement electrostatic potential

Descriptors:

  • ST4_4: Theoretical and computational chemistry
  • NZ1_4: Structural biology
  • ST3_1: Structure of solids, material growth and characterisation

Panel:

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

Host institution :

Uniwersytet Warszawski, Wydział Chemii

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Paulina Dominiak 

Number of co-investigators in the project: 8

Call: OPUS 14 - announced on 2017-09-15

Amount awarded: 1 792 000 PLN

Project start date (Y-m-d): 2018-08-03

Project end date (Y-m-d): 2022-08-02

Project duration:: 48 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. Zestaw specjalistycznych komputerów wraz z niezbędnym oprogramowaniem i sprzętem uzupełniającym niezbędnym do realizacji projektu (35 000 PLN)

Information in the final report

  • Publication in academic press/journals (7)
  • Articles in post-conference publications (7)
  1. TAAM: A reliable and user friendly tool for hydrogen atom location using routine X-Ray diffraction data
    Authors:
    Kunal Kumar Jha, Barbara Gruza, Prashant Kumar, Michał Leszek Chodkiewicz, Paulina Maria Dominiak
    Academic press:
    Acta Crystallographica Section B-Structural Science Crystal Engineering And Materials (rok: 2020, tom: 76, strony: 296-306), Wydawca: INT UNION CRYSTALLOGRAPHY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Status:
    Published
    DOI:
    10.1107/S2052520620002917 - link to the publication
  2. Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
    Authors:
    Kunal Kumar Jha, Florian Kleemiss, Michal Leszek Chodkiewicz and Paulina Maria Dominiak
    Academic press:
    Journal of Applied Crystallography (rok: 2023, tom: 56, strony: brak), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Status:
    Published
    DOI:
    10.1107/S1600576722010883 - link to the publication
  3. Theoretical 3D ED electrostatic potential density maps of proteins modeled with multipolar pseudoatom data bank
    Authors:
    Marta Kulik, Michał Leszek Chodkiewicz, Paulina Maria Dominiak
    Academic press:
    Acta Crystallographica Section D STRUCTURAL BIOLOGY (rok: 2022, tom: 78, strony: 1010-1020), Wydawca: INT UNION CRYSTALLOGRAPHY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Status:
    Published
    DOI:
    10.1107/S2059798322005836 - link to the publication
  4. Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB
    Authors:
    Kunal Kumar Jha, Barbara Gruza, Aleksandra Sypko, Prashant Kumar, Michał Leszek Chodkiewicz, Paulina Maria Dominiak
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2022, tom: 62, strony: 3752-3765), Wydawca: AMER CHEMICAL SOC
    Status:
    Published
    DOI:
    10.1021/acs.jcim.2c00144 - link to the publication
  5. Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis
    Authors:
    Paulina Maria Rybicka, Marta Kulik, Michał Leszek Chodkiewicz, Paulina Maria Dominiak
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2022, tom: 62, strony: 3766-3783), Wydawca: AMER CHEMICAL SOC
    Status:
    Published
    DOI:
    10.1021/acs.jcim.2c00145 - link to the publication
  6. Refinement of organic crystal structures with multipolar electron scattering factors
    Authors:
    Barbara Gruza, Michał Leszek Chodkiewicz, Joanna Krzeszczakowska and Paulina Maria Dominiak
    Academic press:
    Acta Crystallographica Section A-Foundation And Advances (rok: 2020, tom: 76, strony: 92-109), Wydawca: INT UNION CRYSTALLOGRAPHY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Status:
    Published
    DOI:
    10.1107/S2053273319015304 - link to the publication
  7. Refinements on electron diffraction data of β-glycine in MoPro: a quest for an improved structure model
    Authors:
    K. K. Jha, B. Gruza, M. L. Chodkiewicz, C. Jelsch and P. M. Dominiak
    Academic press:
    Journal of Applied Crystallography (rok: 2021, tom: 54, strony: 1234-1243), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Status:
    Published
    DOI:
    10.1107/S160057672100580X - link to the publication
  1. Model dependence (IAM versus TAAM) of B factors – cases of X-ray and electron diffraction
    Authors:
    B. Gruza, C. Jelsch and P. M. Dominiak
    Conference:
    School on Electron Crystallography, the XXV IUCr Congress, Prague, Czech Republic (rok: 2021, ), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Data:
    konferencja 11-13.08.2021, 14-22.08.2021
    Status:
    Published
    DOI:
    link to the publication
  2. TAAM: a reliable and user-friendly tool for hydrogen-atom location using X-ray diffraction data
    Authors:
    M. Chodkiewicz, K. Jha, B. Gruza and P. Dominiak
    Conference:
    the 32nd European Crystallographic Meeting, Vienna, Austria (rok: 2019, ), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Data:
    konferencja 18-23.08.2019
    Status:
    Published
    DOI:
    link to the publication
  3. Refinement on electron diffraction data in MoPro: a quest for improved structure model
    Authors:
    K. K. Jha, B. Gruza, M. Chodkiewicz, C. Jelsch and P. Dominiak
    Conference:
    the XXV IUCr Congress, Prague, Czech Republic (rok: 2021, ), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Data:
    konferencja 14-22.08.2021
    Status:
    Published
    DOI:
    link to the publication
  4. Refinement of organic crystal structure with multipolar electron scattering factors
    Authors:
    B. Gruza, M. Chodkiewicz, J. Krzeszczakowska and P. Dominiak
    Conference:
    the 32nd European Crystallographic Meeting, Vienna, Austria (rok: 2019, ), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Data:
    konferencja 18-23.08.2019
    Status:
    Published
    DOI:
    link to the publication
  5. Moving quantum crystallography from sub-atomic XRD to near-atomic 3D-ED
    Authors:
    P. M. Dominiak, M. L. Chodkiewicz, B. Gruza, K. K. Jha, M. Kulik, P. Rybicka and A. Sypko
    Conference:
    the XXV IUCr Congress, Prague, Czech Republic (rok: 2021, ), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Data:
    konferencja 14-22.08.2021
    Status:
    Published
    DOI:
    link to the publication
  6. Refinement with multipolar scattering factors
    Authors:
    B. Gruza, M. L. Chodkiewicz and P. M. Dominiak
    Conference:
    the XXV IUCr Congress, Prague, Czech Republic (rok: 2021, ), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Data:
    konferencja 14-22.08.2021
    Status:
    Published
    DOI:
    link to the publication
  7. Theoretical electrostatic potential maps of macromolecules calculated with multipolar electron scattering factors
    Authors:
    M. Kulik, M. L. Chodkiewicz and P. M. Dominiak
    Conference:
    the XXV IUCr Congress, Prague, Czech Republic (rok: 2021, ), Wydawca: INT UNION CRYSTALLOGRAP HY, 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND
    Data:
    konferencja 14-22.08.2021
    Status:
    Published
    DOI:
    link to the publication

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