2024
| Ignat’ev VM, Dominiak PM 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 J. Appl. Cryst., Volume 57, Part 6, 1884-1895, Published: 2024 [DOI: 10.1107/S1600576724009841] |
| Pacoste L, Ignat’ev VM, Dominiak PM, Zou X On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors IUCrJ, 11, 878-890, Published: 2024 [DOI: 10.1107/S2052252524006730] |
| Chodkiewicz ML, Olech B, Jha KK, Dominiak PM, Woźniak K Hirshfeld atom refinement and dynamical refinement of hexagonal ice structure from electron diffraction data IUCrJ, 11, 730-736, Published: 2024 [DOI: 10.1107/S2052252524006808] |
| Kumar A, Jha KK, Olech B, Goral T, Malinska M, Woźniak K, Dominiak PM TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules Acta Cryst. C80, 264-277, Published: 2024 [DOI: 10.1107/S2053229624005357] |
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| Hawash M, Qneibi M, Natsheh H, Mohammed NH, Hamda LA, Kumar A, Olech B, Dominiak PM , Bdir S, Bdair M Evaluating the Neuroprotective Potential of Novel Benzodioxole Derivatives in Parkinson’s Disease via AMPA Receptor Modulation ACS Chem. Neurosci. 15 (11), 2334-2349, Published: 2024 [DOI: 10.1021/acschemneuro.4c00163] |
| Olech B, Brázda P, Palatinus L, Dominiak PM Dynamical refinement with multipolar electron scattering factors IUCrJ, Volume 11, part 3, 309-324, Published: 2024 [DOI: 10.1107/S2052252524001763] |
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| Hawash M, Abdallah S, Abudayyak M, Melhem Y, Shamat MA, Aghbar M, Çapan I, Abualhasan M, Kumar A, Kamiński M, Góral T, Dominiak PM, Sobuh S Exploration of isoxazole analogs: Synthesis, COX inhibition, anticancer screening, 3D multicellular tumor spheroids, and molecular modeling European Journal of Medicinal Chemistry, Volume 271, 116397, Published: 2024 [DOI: 10.1016/j.ejmech.2024.116397] |
| Bick T, Dominiak PM, Wendler P Exploiting the full potential of cryo-EM maps BBA Advances, Volume 5, 100113, Published: 2024 [DOI: 10.1016/j.bbadva.2024.100113] |
2023
| Hawash M, Al-Smadi D, Kumar A, Olech B, Dominiak PM, Jaradat, N, Antari S, Mohammed S, Nasasrh A, Abualhasan M, Musa A, Suboh S, Çapan İ, Qneibi M, Natsheh H Characterization and Investigation of Novel Benzodioxol Derivatives as Antidiabetic Agents: An In Vitro and In Vivo Study in an Animal Model Biomolecules, 13, 1486, Published: 2023 [DOI: 10.3390/biom1310148] |
| Jha KK, Kleemiss F, Chodkiewicz ML, Dominiak PM Aspherical Atom Refinements on X-Ray Data of Diverse Structures Including Disordered and Covalent Organic Framework Systems: A Time–Accuracy Trade-Off J. Appl. Crystallogr., 56 (1), 116–127, Published: 2023 [DOI: 10.1107/S1600576722010883] |
| Landeros-Rivera B, Ramírez-Palma D, Cortes-Guzman F, Dominiak PM, Contreras García J How do density functionals affect the Hirshfeld atom refinement? Phys. Chem. Chem. Phys., 25, 12702, Published: 2023 [DOI: 10.1039/D2CP04098K ] |
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2022
| Budniak UA, Karolak NK, Kulik M, Młynarczyk K, Górna MW, Dominiak PM The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method J. Phys. Chem. B., 126, 45, 9152–9167, Published: 2022 [DOI: 10.1021/acs.jpcb.2c04519] |
| Kulik M, Dominiak PM Electron density is not spherical: the many applications of the transferable aspherical atom model Computational and Structural Biotechnology Journal, 20, 6237-6243, Published: 2022 [DOI: 10.1016/j.csbj.2022.10.018] |
| Bojarowski SA, Gruza B, Trzybiński D, Kamiński R, Hoser AA, Kumar P, Woźniak K, Dominiak PM New refinement strategies for a pseudoatom databank – toward rapid electrostatic interaction energy estimations Acta Cryst. B78, 823-834, Published: 2022 [DOI: 10.1107/S2052520622008800] |
| Rybicka PM, Kulik M, Chodkiewicz ML, Dominiak PM Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis J. Chem. Inf. Model., 62 (16), 3766–3783, Published: 2022 [DOI: 10.1021/acs.jcim.2c00145]Jha KK, Gruza B, Sypko A, Kumar P, Chodkiewicz ML, Dominiak PM Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB J. Chem. Inf. Model., 62 (16), 3752–3765, Published: 2022 [DOI: 10.1021/acs.jcim.2c00144] |
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| Kulik M, Chodkiewicz ML, Dominiak PM Theoretical 3D ED electrostatic potential density maps of proteins modeled with multipolar pseudoatom data bank Acta Crystallographica Section D Structural Biology, 78 (8), 1010–1020, Published: 2022 [DOI: 10.1107/S2059798322005836] |
| Ziemniak M, Pawlędzio S, Zawadzka-Kaźmierczuk A, Dominiak PM, Trzybiński D, Koźmiński W, Zieliński R, Fokt I, Priebe W, Woźniak K, Pająk B X-Ray Wavefunction Refinement and Comprehensive Structural Studies on Bromo-Substituted Analogues of 2-Deoxy-d-Glucose in Solid State and Solution RSC Adv., 12 (14), 8345–8360, Published: 2022 [DOI: 10.1039/d1ra08312k] |
2021
| Landeros-Rivera B, Contreras-García J, Dominiak PM The influence of refinement strategies on the wavefunctions derived from an experiment Acta Crystallographica Section B 77, 715-727, Published: 2021 [DOI: 10.1107/S2052520621008258] |
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| Kumar P, Dominiak PM 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, 3872-3887, Published: 2021 [DOI: 10.3390/molecules26133872] |
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| Jha KK, Gruza B, Chodkiewicz ML, Jelsch Ch, Dominiak PM Refinements on electron diffraction data of β-glycine in MoPro: A quest for improved structure model Journal of Applied Crystallography 54, 1234-1243, Published: 2021 [DOI: 10.1107/S160057672100580X] |
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| Cabaj MK, Dominiak PM Phase transition of hypoxanthinium nitrate monohydrate Crystal Growth and Design 21, 424-435, Published: 2021 [DOI: 10.1021/acs.cgd.0c01252] |
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2020
| Brunner JS, Vogel A, Lercher A, Caldera M, Korosec A, Pühringer M, Hofmann M, Hajto A, Kieler M, Garrido LQ, Kerndl M, Kuttke M, Mesteri I, Górna MW, Kulik M, Dominiak PM, Brandon AE, Estevez E, Egan CL, Gruber F, Schweiger M, Menche J, Bergthaler A, Weichhart T, Klavins K, Febbraio MA, Sharif O, Schabbauer G The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages Nature Metabolism, Published: 2020 [DOI: 10.1038/s42255-020-00311-5] |
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| Sanjuan-Szklarz FW, Woińska M, Domagała S, Dominiak PM, Grabowsky S, Jayatilaka D, Gutmannd M, Woźniak K On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model IUCrJ, 7, 920-933, Published: 2020 [DOI: /10.1107/S2052252520010441] |
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| Cabaj MK, Dominiak PM Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals Nucleic Acids Research 48, 8302-8319, Published: 2020 [DOI: 10.1093/nar/gkaa629] |
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| Jha KK, Gruza B, Kumar P, Chodkiewicz ML, Dominiak PM TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data Acta Crystallographica Section B 76, 296-306, Published: 2020 [DOI: /10.1107/S2052520620002917] |
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| Gruza B, Chodkiewicz ML, Krzeszczakowska J, Dominiak PM Refinement of organic crystal structures with multipolar electron scattering factors Acta Crystallographica Section A 76, 92-109, Published: 2020 [DOI: 10.1107/S2053273319015304] |
2019
| Kumar P, Cabaj MK, Dominiak PM Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions Crystals 9, 688-705, Published: 2019 [DOI: 10.3390/cryst9120668 ] |
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| Cabaj MK, Gajda R, Hoser A, Makal A, Dominiak PM Differences and similarities among hypoxanthinium nitrate hydrate structures Acta Crystallographica Section C 75, 1036-1044, Published: 2019 [DOI: 10.1107/S2053229619008702] |
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| Kumar P, Gruza B, Bojarowski SA, Dominiak PM Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies Acta Crystallographica Section A 75, 398-408, Published: 2019 [DOI: 10.1107/S2053273319000482] |
2018
| Bojarowski SA, Kumar P, Wandtke CM, Bittrich B, Dominiak PM 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; Published: 2018 [DOI: 10.1021/acs.jctc.8b00781] |
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| Genoni A, Bucinsky L, Claiser N, Contreras-Garcia J, Dittrich B, Dominiak PM, et al. Quantum Crystallography: Current Developments and Future Perspectives Chemistry – A European Journal 24, 43, 10881-10905; Published: 2018 [DOI: 10.1002/chem.201705952] |
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| Kumar P, Cabaj MK, Pazio A, Dominiak PM Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions IUCrJ 5, 449-469; Published: 2018 [DOI: 10.1107/S2052252518006346] |
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| Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs Journal of Applied Crystallography 51, 193-199, Published: 2018 [DOI: 10.1107/S1600576717015825] |
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| Budniak UA, Dominiak PM Molecular tapes in the structure of isoguaninium chloride Acta Crystallographica Section C 74, 108-112, Published: 2018 [DOI: 10.1107/S2053229617017685] |
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2017
| Woinska M, Jayatilaka D, Dittrich B, Flaig R, Luger P, Wozniak K, Dominiak PM, Grabowsky S Validation of X-ray Wavefunction Refinement ChemPhysChem 18, 3334-3351, Published: 2017 [DOI: 10.1002/cphc.201700810] |
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| Jarzembska KN, Slepokura K, Kaminski R, Gutmann MJ, Dominiak PM, Wozniak K Multi-temperature study of potassium uridine-5 ‘ monophosphate: electron density distribution and anharmonic motion modelling Acta Crystallographica Section B 73, 550-564, Published: 2017 [DOI: 10.1107/S2052520617005534] |
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| Bojarowski SA, Kumar P, Dominiak PM 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 73, 598-609, Published: 2017 [DOI: 10.1107/S2052520617005510] |
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2016
| Bojarowski SA, Kumar P, Dominiak PM A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation ChemPhysChem 17, 2455-2460, Published: 2016 [DOI: 10.1002/cphc.201600390] |
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| Woinska M, Grabowsky S, Dominiak PM, Wozniak K, Jayatilaka D Hydrogen atoms can be located accurately and precisely by x-ray crystallography Science Advances 2, Published: 2016 [DOI: 10.1126/sciadv.1600192] |
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2015
| Adamczyk-Wozniak A, Cabaj MK, Dominiak PM, Gajowiec P, Gierczyk B, Lipok J, Popenda L, Schroeder G, Tomecka E, Urbanski P, Wieczorek D, Sporzynski A The influence of fluorine position on the properties of fluorobenzoxaboroles Bioorganic Chemistry 60, 130-135, Published: 2015 [DOI: 10.1016/j.bioorg.2015.05.004] |
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| Kulik M, Goral AM, Jasinski M, Dominiak PM, Trylska J Electrostatic Interactions in Aminoglycoside-RNA Complexes Biophysical Journal 108, 655-665, Published: 2015 [DOI: 10.1016/j.bpj.2014.12.020] |
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2014
| Woinska M, Jayatilaka D, Spackman MA, Edwards AJ, Dominiak PM, Wozniak K, Nishibori E, Sugimoto K, Grabowsky S Hirshfeld atom refinement for modelling strong hydrogen bonds Acta Crystallographica Section A 70, 483-498, Published: 2014 [DOI: 10.1107/S2053273314012443] |
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| Malinska M, Jarzembska KN, Goral AM, Kutner A, Wozniak K, Dominiak PM Sunitinib: from charge-density studies to interaction with proteins Acta Crystallographica Section D 70, 1257-1270, Published: 2014 [DOI: 10.1107/S1399004714002351] |
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| 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] |
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| 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 [YADDA: 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] |
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| 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] |
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| 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] |
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| 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] |
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| 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] |
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| 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] |
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| 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] |
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