Publications

2026

Hawash, M., Çapan, İ., Henawi, H., Jawabre, B., Nassif, Y., Zorba, I., Kamiński, M. D., Góral, T., Sutuła, S., Dominiak, P. M., Bsharat, R., Sobuh, S., & Tari, O. (2026). Structure-guided design of Benzodioxole–acrylamide hybrids as potent and low-toxicity α-amylase inhibitors: Integration of MicroED and molecular docking analyses. Journal of Molecular Structure, 1368, 146300. https://doi.org/10.1016/j.molstruc.2026.146300

Femoen, V. J., Pacoste, L., Chodkiewicz, M. L., Afonine, P. V., Poon, B. K., Kulik, M., Golon, Ł., Moriarty, N. W., Adams, P. D., Hofer, G., Dominiak, P. M., Liebschner, D., & Zou, X. (2026). pyDiSCaMB  : enabling the use of multipolar scattering factors in Phenix. Journal of Applied Crystallography, 59(2), 662–672. https://doi.org/10.1107/s1600576726000828

2025

Kulik, M., & Dominiak, P. M. (2025). Protein electrostatic potential Fourier maps calculated using the transferable aspherical atom model and the independent atom model across resolutions IUCrJ, 12, 616-632. https://doi.org/10.1107/S2052252525008383

Dominiak, P. M., Martín Pendás, Á., & Woźniak, K. (2025). Focus on Quantum Crystallography IUCrJ, 12, 610-613. https://doi.org/10.1107/S2052252525008759

Hawash, M., Shweiki, N., Qaoud, M. T., Çapan, I., Abualhasan, M., Kumar, A., Olech, B., & Dominiak, P. M. (2025). Trifluoromethyl–pyrazole–carboxamides as COX inhibitors: synthesis, microed structural analysis, computational profiling, and biological evaluation BMC Chemistry 19, 288. https://doi.org/10.1186/s13065-025-01659-z

Ziemniak, M., Budniak, U., Dominiak, P. M., & Woźniak, K.(2025) Computational analysis of energetic features and intermolecular interactions in protein-inhibitor USP7 complexes Organic & Biomolecular Chemistry, 23(25), 6138–6161. https://doi.org/10.1039/d4ob01953a

2024

Ignat’ev, V., & Dominiak, P. M. (2024). Towards expansion of the MATTS data bank with heavier elements: the influence of the wavefunction basis set on the multipole model derived from the wavefunction. Journal of Applied Crystallography, 57(Pt 6), 1884–1895. https://doi.org/10.1107/S1600576724009841

Pacoste, L., Ignat’ev, V. M., Dominiak, P. M., & Zou, X. (2024). On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors. IUCrJ, 11(Pt 5), 878–890. https://doi.org/10.1107/S2052252524006730

Chodkiewicz, M. L., Olech, B., Jha, K. K., Dominiak, P. M., & Woźniak, K. (2024). Hirshfeld atom refinement and dynamical refinement of hexagonal ice structure from electron diffraction data. IUCrJ, 11(Pt 5), 730–736. https://doi.org/10.1107/S2052252524006808

Kumar, A., Jha, K. K., Olech, B., Goral, T., Malinska, M., Woźniak, K., & Dominiak, P. M. (2024). TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules. Acta Crystallographica. Section C, Structural Chemistry, 80(Pt 7), 264–277. https://doi.org/10.1107/S2053229624005357

Hawash, M., Qneibi, M., Natsheh, H., Mohammed, N. H., Hamda, L. A., Kumar, A., Olech B., Dominiak P.M. , Bdir S., Bdair, M. (2024). Evaluating the neuroprotective potential of novel benzodioxole derivatives in Parkinson’s disease via AMPA receptor modulation. ACS Chemical Neuroscience, 15(11), 2334–2349. https://doi.org/10.1021/acschemneuro.4c00163

Olech, B., Brázda, P., Palatinus, L., & Dominiak, P. M. (2024). Dynamical refinement with multipolar electron scattering factors. IUCrJ, 11(Pt 3), 309–324. https://doi.org/10.1107/S2052252524001763

Hawash, M., Abdallah, S., Abudayyak, M., Melhem, Y., Abu Shamat, M., Aghbar, M., Çapan I., Abualhasan M., Kumar A., Kamiński M., Góral T., Dominiak P.M., Sobuh, S. (2024). Exploration of isoxazole analogs: Synthesis, COX inhibition, anticancer screening, 3D multicellular tumor spheroids, and molecular modeling. European Journal of Medicinal Chemistry, 271(116397), 116397. https://doi.org/10.1016/j.ejmech.2024.116397

Bick, T., Dominiak, P. M., & Wendler, P. (2024). Exploiting the full potential of cryo-EM maps. BBA Advances, 5(100113), 100113. https://doi.org/10.1016/j.bbadva.2024.100113

2023

Hawash, M., Al-Smadi, D., Kumar, A., Olech, B., Dominiak, P. M., Jaradat, N., … Natsheh, H. (2023). Characterization and investigation of novel benzodioxol derivatives as antidiabetic agents: An in vitro and in vivo study in an animal model. Biomolecules, 13(10), 1486. https://doi.org/10.3390/biom13101486

Jha, K. K., Kleemiss, F., Chodkiewicz, M. L., & Dominiak, P. M. (2023). Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time-accuracy trade-off. Journal of Applied Crystallography, 56(Pt 1), 116–127. https://doi.org/10.1107/S1600576722010883

Landeros-Rivera, B., Ramírez-Palma, D., Cortés-Guzmán, F., Dominiak, P. M., & Contreras-García, J. (2023). How do density functionals affect the Hirshfeld atom refinement? Physical Chemistry Chemical Physics, 25(18), 12702–12711. https://doi.org/10.1039/d2cp04098k

2022

Budniak, U. A., Karolak, N. K., Kulik, M., Młynarczyk, K., Górna, M. W., & Dominiak, P. M. (2022). The role of electrostatic interactions in IFIT5-RNA complexes predicted by the UBDB+EPMM method. The Journal of Physical Chemistry. B, 126(45), 9152–9167. https://doi.org/10.1021/acs.jpcb.2c04519

https://doi.org/10.1016/j.csbj.2022.10.018

https://doi.org/10.1107/s2052520622008800

Rybicka, P. M., Kulik, M., Chodkiewicz, M. L., & Dominiak, P. M. (2022). Multipolar atom types from theory and statistical clustering (MATTS) data bank: Impact of surrounding atoms on electron density from cluster analysis. Journal of Chemical Information and Modeling, 62(16), 3766–3783. https://doi.org/10.1021/acs.jcim.2c00145Jha, K. K., Gruza, B., Sypko, A., Kumar, P., Chodkiewicz, M. L., & Dominiak, P. M. (2022). Multipolar Atom Types from Theory and Statistical clustering (MATTS) data bank: Restructurization and extension of UBDB. Journal of Chemical Information and Modeling, 62(16), 3752–3765. https://doi.org/10.1021/acs.jcim.2c00144

Kulik, M., Chodkiewicz, M. L., & Dominiak, P. M. (2022). Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank. Acta Crystallographica. Section D, Structural Biology, 78(Pt 8), 1010–1020. https://doi.org/10.1107/S2059798322005836

Ziemniak, Marcin, Pawlędzio, S., Zawadzka-Kaźmierczuk, A., Dominiak, P. M., Trzybiński, D., Koźmiński, W., Zieliński R., Fokt I., Priebe W., Woźniak K., & Pająk, B. (2022). X-ray wavefunction refinement and comprehensive structural studies on bromo-substituted analogues of 2-deoxy-d-glucose in solid state and solution. RSC Advances, 12(14), 8345–8360. https://doi.org/10.1039/d1ra08312k

2021

Landeros-Rivera, B., Contreras-García, J., & Dominiak, P. M. (2021). The influence of refinement strategies on the wavefunctions derived from an experiment. Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials, 77(5), 715–727. https://doi.org/10.1107/s2052520621008258
Kumar, P., & Dominiak, P. M. (2021). Combining molecular dynamic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in multimeric protein-ligand complex: A case study for HIV-1 protease. Molecules, 26(13), 3872. https://doi.org/10.3390/molecules26133872
Jha, K. K., Gruza, B., Chodkiewicz, M. L., Jelsch, C., & Dominiak, P. M. (2021). Refinements on electron diffraction data of β-glycine in MoPro: a quest for an improved structure model. Journal of Applied Crystallography, 54(4), 1234–1243. https://doi.org/10.1107/s160057672100580x
Cabaj, M. K., & Dominiak, P. M. (2021). Phase transition of hypoxanthinium nitrate monohydrate. Crystal Growth & Design, 21(1), 424–435. https://doi.org/10.1021/acs.cgd.0c01252

2020

Brunner, J. S., Vogel, A., Lercher, A., Caldera, M., Korosec, A., Pühringer, M., Hofmann M., Hajto A., Kieler M., Garrido L.Q., Kerndl M., Kuttke M., Mesteri I., Górna M.W., Kulik M., Dominiak P.M., Brandon A.E., Estevez E., Egan C.L., Gruber F., Schweiger M., Menche J., Bergthaler A., Weichhart T., Klavins K., Febbraio M.A., Sharif O., & Schabbauer, G. (2020). The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages. Nature Metabolism, 2(12), 1427–1442. https://doi.org/10.1038/s42255-020-00311-5

Sanjuan-Szklarz, W. F., Woińska, M., Domagała, S., Dominiak, P. M., Grabowsky, S., Jayatilaka, D., Gutmannd M., Woźniak, K. (2020). On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model. IUCrJ, 7(Pt 5), 920–933. https://doi.org/10.1107/S2052252520010441

Cabaj, M. K., & Dominiak, P. M. (2020). Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals. Nucleic Acids Research, 48(15), 8302–8319. https://doi.org/10.1093/nar/gkaa629

Jha, K. K., Gruza, B., Kumar, P., Chodkiewicz, M. L., & Dominiak, P. M. (2020). TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data. Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials, 76(Pt 3), 296–306. https://doi.org/10.1107/S2052520620002917

Gruza, B., Chodkiewicz, M. L., Krzeszczakowska, J., & Dominiak, P. M. (2020). Refinement of organic crystal structures with multipolar electron scattering factors. Acta Crystallographica. Section A, Foundations and Advances, 76(Pt 1), 92–109. https://doi.org/10.1107/S2053273319015304

2019

Kumar, P., Cabaj, M. K., & Dominiak, P. M. (2019). Intermolecular interactions in ionic crystals of nucleobase chlorides—combining topological analysis of electron densities with energies of electrostatic interactions. Crystals, 9(12), 668. https://doi.org/10.3390/cryst9120668

Cabaj, M. K., Gajda, R., Hoser, A., Makal, A., & Dominiak, P. M. (2019). Differences and similarities among hypoxanthinium nitrate hydrate structures. Acta Crystallographica. Section C, Structural Chemistry, 75(Pt 8), 1036–1044. https://doi.org/10.1107/s2053229619008702

Kumar, P., Gruza, B., Bojarowski, S. A., & Dominiak, P. M. (2019). Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure-activity studies. Acta Crystallographica. Section A, Foundations and Advances, 75(Pt 2), 398–408. https://doi.org/10.1107/S2053273319000482

2018

Bojarowski, S. A., Kumar, P., Wandtke, C. M., Dittrich, B., & Dominiak, P. M. (2018). Universal method for electrostatic interaction energies estimation with charge penetration and easily attainable point charges. Journal of Chemical Theory and Computation, 14(12), 6336–6345. https://doi.org/10.1021/acs.jctc.8b00781
Genoni, A., Bučinský, L., Claiser, N., Contreras-García, J., Dittrich, B., Dominiak, P. M., Espinosa E., Gatti, C., Giannozzi, P., Gillet, J.-M., Jayatilaka, D., Macchi, P., Madsen, A. Ø., Massa, L., Matta, C. F., Merz Jr., K. M., Nakashima, P. N. H., Ott, H., Ryde, U., Schwarz, K., Sierka, M., Grabowsky, S. (2018). Quantum crystallography: Current developments and future perspectives. Chemistry—A European Journal, 24(43), 10881–10905. https://doi.org/10.1002/chem.201705952
Kumar, P., Cabaj, M. K., Pazio, A., & Dominiak, P. M. (2018). Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions. IUCrJ, 5(Pt 4), 449–469. https://doi.org/10.1107/S2052252518006346
Chodkiewicz, Michał L., Migacz, S., Rudnicki, W., Makal, A., Kalinowski, J. A., Moriarty, N. W., Grosse-Kunstleve R. W., Afonine P. V., Adams P. D., Dominiak, P. M. (2018). DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs. Journal of Applied Crystallography, 51(Pt 1), 193–199. https://doi.org/10.1107/S1600576717015825
Budniak, U. A., & Dominiak, P. M. (2018). Molecular tapes in the structure of isoguaninium chloride. Acta Crystallographica. Section C, Structural Chemistry, 74(Pt 1), 108–112. https://doi.org/10.1107/S2053229617017685]

2017

Woińska, M., Jayatilaka, D., Dittrich, B., Flaig, R., Luger, P., Woźniak, K., Dominiak P.M., Grabowsky, S. (2017). Validation of X-ray wavefunction refinement. Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, 18(23), 3334–3351. https://doi.org/10.1002/cphc.201700810
Jarzembska, K. N., Ślepokura, K., Kamiński, R., Gutmann, M. J., Dominiak, P. M., & Woźniak, K. (2017). Multi-temperature study of potassium uridine-5’-monophosphate: electron density distribution and anharmonic motion modelling. Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials, 73(Pt 4), 550–564. https://doi.org/10.1107/S2052520617005534
Bojarowski, S. A., Kumar, P., & Dominiak, P. M. (2017). Interplay of point multipole moments and charge penetration for intermolecular electrostatic interaction energies from the University at Buffalo pseudoatom databank model of electron density. Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials, 73(Pt 4), 598–609. https://doi.org/10.1107/S2052520617005510

2016

Bojarowski, S. A., Kumar, P., & Dominiak, P. M. (2016). A universal and straightforward approach to include penetration effects in electrostatic interaction energy estimation. Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, 17(16), 2455–2460. https://doi.org/10.1002/cphc.201600390
Woińska, M., Grabowsky, S., Dominiak, P. M., Woźniak, K., & Jayatilaka, D. (2016). Hydrogen atoms can be located accurately and precisely by x-ray crystallography. Science Advances, 2(5), e1600192. https://doi.org/10.1126/sciadv.1600192

2015

Adamczyk-Woźniak, A., Cabaj, M. K., Dominiak, P. M., Gajowiec, P., Gierczyk, B., Lipok, J., Popenda L., Schroeder G., Tomecka E., Urbanski P., Wieczorek D., Sporzyński, A. (2015). The influence of fluorine position on the properties of fluorobenzoxaboroles. Bioorganic Chemistry, 60, 130–135. https://doi.org/10.1016/j.bioorg.2015.05.004
Kulik, M., Goral, A. M., Jasiński, M., Dominiak, P. M., & Trylska, J. (2015). Electrostatic interactions in aminoglycoside-RNA complexes. Biophysical Journal, 108(3), 655–665. https://doi.org/10.1016/j.bpj.2014.12.020

2014

Woińska, M., Jayatilaka, D., Spackman, M. A., Edwards, A. J., Dominiak, P. M., Woźniak, K., Nishibori E., Sugimoto K., Grabowsky, S. (2014). Hirshfeld atom refinement for modelling strong hydrogen bonds. Acta Crystallographica. Section A, Foundations and Advances, 70(Pt 5), 483–498. https://doi.org/10.1107/S2053273314012443

Malińska, M., Jarzembska, K. N., Goral, A. M., Kutner, A., Woźniak, K., & Dominiak, P. M. (2014). Sunitinib: from charge-density studies to interaction with proteins. Acta Crystallographica. Section D, Biological Crystallography, 70(Pt 5), 1257–1270. https://doi.org/10.1107/S1399004714002351

Kumar P, Bojarowski SA, Jarzembska KN, Domagala S, Vanommeslaeghe K, MacKerell AD, Dominiak PM A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers Journal of Chemical Theory and Computation 10, 1652-1664, Published: 2014 [DOI: 10.1021/ct4011129]

Dominiak PM The importance and examples of application of aspherical pseudoatom databanks in small-molecule crystallography and their potential use in makromolecular crystallography Wiadomości Chemiczne 68, 429–455, Published: 2014 [Link: bwmeta1.element.baztech-8d225708-fbd7-453f-8ac1-9645b48628d9], paper in Polish

2013

Jarzembska KN, Kaminski R, Wenger E, Lecomte C, Dominiak PM Interplay between Charge Density Distribution, Crystal Structure Energetic Features, and Crystal Morphology of 6-Methyl-2-thiouracil Journal of Physical Chemistry C 117, 7764-7775, Published: 2013 [DOI: 10.1021/jp312158m]

Woinska M, Dominiak PM Transferability of Atomic Multipoles in Amino Acids and Peptides for Various Density Partitions Journal of Physical Chemistry A 117, 1535-1547, Published: 2013 [DOI: 10.1021/jp204010v]

Wesela-Bauman G, Boinski T, Dominiak P, Hajmowicz H, Synoradzki L, Wierzbicki M, Wolinski B, Wozniak K, Zawada K Tartaric acid and its O-acyl derivatives. 7. Crystal structure of O-p-anisoyl-D-tartaric acid and its dimethylammonium salt trihydrate Journal of Structural Chemistry 54, 155-158, Published: 2013 [DOI: 10.1134/S0022476613010228]

Jarzembska KN, Goral AM, Gajda R, Dominiak PM Hoogsteen-Watson-Crick 9-Methyladenine:1-Methylthymine Complex: Charge Density Study in the Context of Crystal Engineering and Nucleic Acid Base Pairing Crystal Growth and Design 13, 239-254, Published: 2013 [DOI: 10.1021/cg301393e]

2012

Bak JM, Czyznikowska Z, Dominiak PM Is it possible to derive quantitative information on polarization of electron density from the multipolar model? Acta Crystallographica Section A 68, 705-714, Published: 2012 [DOI: 10.1107/S010876731203317X]

Jarzembska KN, Kubsik M, Kaminski R, Wozniak K, Dominiak PM From a Single Molecule to Molecular Crystal Architectures: Structural and Energetic Studies of Selected Uracil Derivatives Crystal Growth and Design 12, 2508-2524, Published: 2012 [DOI: 10.1021/cg300129z]

Jarzembska KN, Dominiak PM New version of the theoretical databank of transferable aspherical pseudoatoms, UBDB2011-towards nucleic acid modelling Acta Crystallographica Section A 68, 139-147, Published: 2012 [DOI: 10.1107/S0108767311042176]

2011

Bak JM, Domagala S, Hubschle C, Jelsch C, Dittrich B, Dominiak PM Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases Acta Crystallographica Section A 67, 141-153, Published: 2011 [DOI: 10.1107/S0108767310049731]

2010

Czyznikowska Z, Gora RW, Zalesny R, Lipkowski P, Jarzembska KN, Dominiak PM, Leszczynski J Structural Variability and the Nature of Intermolecular Interactions in Watson-Crick B-DNA Base Pairs Journal of Physical Chemistry B 114, 9629-9644, Published: 2010 [DOI: 10.1021/jp101258q]

2009

Bak JM, Dominiak PM, Wilson CC, Wozniak K Experimental charge-density study of paracetamol – multipole refinement in the presence of a disordered methyl group Acta Crystallographica Section A 65, 490-500, Published: 2009 [DOI: 10.1107/S0108767309031729]
Dominiak PM, Volkov A, Dominiak AP, Jarzembska KN, Coppens P Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme-substrate complex: influenza neuraminidase inhibition Acta Crystallographica Section D 65, 485-499, Published: 2009 [DOI: 10.1107/S0907444909009433]