Publications

2021

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]
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 Accepted
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]


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]
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]
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]
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 B76, 296-306, Published: 2020
[DOI: /10.1107/S2052520620002917]
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 ]
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]
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]
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]


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]
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]
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]

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]


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]
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]

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]
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]

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]
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]

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]
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]
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
[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]
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]