Publications

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2017

K. Klajman, G. Ciepielowski, R. Kaminski, P. Adamczyk, P. Paneth, Resolving Discrepancy between Theory and Experiment in 4-Nitrotoluene Oxidation, J. Phys. Chem. A 121 (2017) 6638, DOI: 10.1021/acs.jpca.7b05474

L. Szatkowski, R.N. Manna, A. Grzybkowska, R. Kaminski, A. Dybala-Defratyka, P. Paneth, Measurement and Prediction of Chlorine Kinetic Isotope Effects in Enzymatic Systems in Measurement and Analysis of Kinetic Isotope Effects (Eds. M.E. Harris, V.E. Anderson), Methods in Enzymology, 596 (2017) 179, DOI: 10.1016/bs.mie.2017.07.021

L. Ji, C. Wang, S. Ji, K.P. Kepp, and P. Paneth, Mechanism of Cobalamin-Mediated Reductive Dehalogenations of Chloroethylenes, ACS Catal. 7 (2017) 5294, DOI: 10.1021/acscatal.7b00540

S. Zaczek, F. Gelman, A. Dybala-Defratyka, A Benchmark Study of Kinetic Isotope Effects and Barrier Heights for the Finkelstein Reaction, J. Phys. Chem. A 121 (2017) 2311, DOI: 10.1021/acs.jpca.7b00230

A. Paneth, P. Staczek, T. Plech, A. Strzelczyk, D. Janowska, J. Stefanska, K. Dzitko, M. Wujec, S. Kosiek, P. Paneth, Synthesis and antibacterial activity of 1,4-dibenzoylthiosemicarbazide derivatives, Biomed. Pharmacother. 8 (2017) 1235-1242, DOI: 0.1016/j.biopha.2017.02.001

K. Świderek, S. Marti, I. Tunon, V. Moliner, J. Bertran, Molecular mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a twister ribozyme, Theor. Chem. Acc., 2017, DOI: 10.1007/s00214-017-2060-8

K. Świderek, K. Arafet, A. Kohen, V. Moliner, Benchmarking QM/MM Methods on the Thymidylate Synthase Catalyzed Hydride Transfer, J. Chem. Theor. Comp. 13 (2017) 1375, DOI: 10.1021/acs.jctc.6b01032

E. Budzisz, P. Paneth, I. Geromino, T. Muzioł, M. Rozalski, U. Krajewska, P. Pipiak, M. B. Ponczek, M. Małecka, B. Kupcewicz, The cytotoxic effect of spiroflavanone derivatives, their binding ability to human serum albumin (HSA) and a DFT study on the mechanism of their synthesis, J. Mol. Struct 1137 (2017) 267-276, DOI: 10.1016/j.molstruc.2017.02.037

2016

K. Kochel, M.D. Tomczyk, R. F. Simões, T. Fraczek, A. Sobon, P.J. Oliveira, K.Z. Walczak, A. Koceva-Chyla, Evaluation of biological properties of 3,3',4,4'-benzophenonetetracarboxylic dianhydride derivatives and their ability to inhibit hexokinase activity, Bioorg. Med. Chem. Lett. 2016, DOI:
10.1016/j.bmcl.2016.12.055

T. Fraczek, Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand–Protein Interactions, J. Chem. Inf. Model., 56 (2016) 2320-2335, DOI: 10.1021/acs.jcim.6b00391

A. Krzeminska, V. Moliner, K. Świderek, Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease, J. Am. Chem. Soc., 138 (2016) 16283-16298, DOI: 10.1021/jacs.6b06856

M. Ciężka, M. Kossowska, P. Paneth, M. Górka, Carbon, Nitrogen and Sulphur concentration and δ13C, δ15N values in Hypogymnia physodes within the montane area – preliminary data, Geosci. Rec. 3-1 (2016) 24, DOI: 10.1515/georec-2016-0004

A. Grzybkowska, D.J. Jedrzejczyk, M. Rostkowski, A. Chworos, A. Dybala-Defratyka, RNA Model Evaluation Based on MD Simulation of Four tRNA Analogs, RSC Adv. 6 (2016) 101788, DOI: 10.1039/C6RA14933B

K. Taran, T. Fraczek, A. Sikora-Szubert, A. Sitkiewicz, W. Młynarski, J. Kobos, P. Paneth, The first investigation of Wilms’ tumour atomic structure-nitrogen and carbon isotopic composition as a novel biomarker for the most individual approach in cancer disease, Oncotarget, 47 (2016) 76726-76734, DOI: 10.18632/oncotarget.12521

K. M. Romek, G. S. Remaud, V. Silvestre, R. J. Robins Richard, P. Paneth, Non- statistical 13C Fractionation Distinguishes Co-incident and Divergent Steps in the Biosynthesis of the Alkaloids Nicotine and Tropine, J. Biol. Chem. 291 (2016) 16620

K. Taran, T. Fraczek, P. Paneth, A. Sitkiewicz, A. Sikora-Szubert, J. Kobos, Hepatoblastoma Biology Using Isotope Ratio Mass Spectrometry: Utility of a Unique Technique for the Analysis of Oncological Specimens, Postępy higieny i medycyny doświadczalnej, 70 (2016) 797

A. Krzeminska, P. Paneth, DFT studies of SΝ2 dechlorination of polychlorinated biphenyls, Environ. Sci. Technol., 50 (2016) 6293, DOI: 10.1021/acs.est.6b00422

K. Dębowska, D. Dębski, B. Michałowski, A. Dybala-Defratyka, T. Wójcik, R. Michalski, M. Jakubowska, A. Selmi, R. Smulik, Ł. Piotrowski, J. Adamus, A. Marcinek, S. Chlopicki, and A. Sikora, Characterization of Fluorescein-Based Monoboronate Probe and Its Application to the Detection of Peroxynitrite in Endothelial Cells Treated with Doxorubicin, Chem. Res. Toxicol., 29 (2016) 735, DOI: 10.1021/acs.chemrestox.5b00431

S. Pati, H.-P. E. Kohler, A. Pabis, P. Paneth, R. Parales, and T.B. Hofstetter, Substrate and Enzyme Specificity of the Kinetic Isotope Effects Associated with the Dioxygenation of Nitroaromatic Contaminants, Environ. Sci. Technol., 50 (2016) 6708, DOI: 10.1021/acs.est.5b05084

E. Szumiło-Pilarska, A. Grajewska, L. Falkowska, J. Hajdrych, W. Meissner, T. Frączek, M. Bełdowska, S. Bzoma, Species differences in total mercury concentration in gulls from the Gulf of Gdansk (Southern Baltic), J. Trace Elem. Med. Biol., 33 (2016) 100, DOI: 10.1016/j.jtemb.2015.09.005

A. Krzeminska, K. Swiderek, P. Paneth, Theoretical studies of energetics and binding isotope effects of binding a triazole-based inhibitor to HIV-1 reverse transcriptase, Phys. Chem. Chem. Phys., 18 (2016) 310, DOI: 10.1039/C5CP06050H

N. Zhang, I. Geronimo, P. Paneth, J. Schindelka, T. Schaefer, H. Herrmann, C. Vogt, H.H. Richnow, Analyzing sites of OH radical attack (ring vs. side chain) in oxidation of substituted benzenes via dual stable isotope analysis (δ13C and δ2H), Sci. Total Environ. 542 (2016) 484, DOI: 10.1016/j.scitotenv.2015.10.075

A. Paneth, P. Stączek, T. Plech, A. Strzelczyk, K. Dzitko, M. Wujec, E. Kuśmierz, U. Kosikowska, A. Grzegorczyk, and P. Paneth, Biological evaluation and molecular modelling study of thiosemicarbazide derivatives as bacterial type IIA topoisomerases inhibitors,J. Enzym. Inhib. Med. Chem., 31 (2016) 14, DOI: 10.3109/14756366.2014.1003214

K. Swiderek and V. Moliner, Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases, J. Phys. Chem. B, 120 (2016) 2053, DOI: 10.1021/acs.jpcb.5b10527

L. Simon-Carballido, T. Vinicius Alves, A. Dybala-Defratyka, and A. Fernandez-Ramos, Kinetic Isotope Effects in Multipath VTST. Application to a Hydrogen Abstraction Reaction, J. Phys. Chem. B, 120 (2016) 1911, DOI: 10.1021/acs.jpcb.5b09671

T. Fraczek, A. Paneth, R. Kaminski, A. Krakowiak, and P. Paneth, Searching for novel scaffold of triazole non-nucleoside inhibitors of HIV-1 reverse transcriptase, J. Enzym. Inhib. Med. Chem., 31 (2016) 481, DOI: 10.3109/14756366.2015.1039531

A. Paneth, T. Plech, B. Kapron, D. Hage, U. Kosikowska, E. Kusmierz, K. Dzitko, and P. Paneth, Design, synthesis and biological evaluation of 4-benzoyl-1-dichlorobenzoylthiosemicarbazides as potent Gram-positive antibacterial agents, J. Enzym. Inhib. Med. Chem., 31 (2016) 434, DOI: 10.3109/14756366.2015.1036050

2015

K. Taran, T. Frączek, A. Sitkiewicz, P. Paneth, J. Kobos, Rhabdomyosarcoma in children in the light of isotope ratio mass spectrometry, Pol. J. Pathol. 66 (2015) 383, DOI: 10.5114/pjp.2015.57251m

K. Taran, T. Frączek, R. Kamiński, A. Sitkiewicz, J. Kobos, P. Paneth, The first protocol of stable isotope ratio assessment in tumor tissues based on original research, Pol. J. Pathol. 66 (2015) 288, DOI: 10.5114/pjp.2015.54963

I. Bordes, J. Recatá, K. Świderek, V. Moliner, Is Promiscuous CALB a Good Scaffold for Designing New Epoxidases, Molecules 20 (2015) 17789, DOI: 10.3390/molecules201017789

R.N. Manna, K. Zinovjev, I. Tunon, and A. Dybala-Defratyka, Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study, J. Phys. Chem. B, 119 (2015) 15100, DOI: 10.1021/acs.jpcb.5b07538

K. Świderek, S. Marti, I. Tunon, V. Moliner, J. Bertran, Peptide Bond Formation Mechanism Catalyzed by Ribosome, J. Am. Chem. Soc. 137 (2015) 120024, DOI: 10.1021/jacs.5b05916

K.M. Romek, P. Nun, G. S. Remaud, V. Silvestre, G. S. Taïwe, F. Lecerf-Schmidt, A. Boumendjel, M. De Waard, and R.J. Robins, A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol, PNAS 112 (2015) 8296, doi: 10.1073/pnas.1506011112

K. Świderek, A. Kohen and V. Moliner, The influence of active site conformations on the hydride transfer step of the thymidylate synthase reaction mechanism, Phys. Chem. Chem. Phys., 17 (2015) 30793, DOI: 10.1039/C5CP01239B

K. Swiderek, I. Tunon, V. Moliner, J. Bertran, Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalysed by HG3.17, ACS Catal. 5 (2015) 2587, DOI: 10.1021/cs501904w

K. Świderek, I. Tunon, V. Moliner, J. Bertran, Computational strategies for the design of new enzymatic functions, Arch. Biochem. Biophys. 582 (2015) 68, DOI: 10.1016/j.abb.2015.03.013

T. Plech, B. Kaproń, A. Paneth, M. Wujec, R. Czarnomysy, A. Bielawska, K. Bielawski, N. Trotsko, E. Kuśmierz, and P. Paneth, Search for human DNA topoisomerase II poisons in the group of 2,5-disubstituted-1,3,4-thiadiazoles, J. Enzym. Inhib. Med. Chem., 30 (2015) 1021, DOI: 10.3109/14756366.2014.995179

A. Grajewska, L. Falkowska, E. Szumiło-Pilarska, J. Hajdrych, M. Szubska, T. Frączek, W. Meissner, S. Bzoma, M. Bełdowska, A. Przystalski, T. Brauze, Mercury in the eggs of aquatic birds from the Gulf of Gdansk and Wloclawek Dam (Poland), Environ. Sci. Poll. Res. 22 (2015) 9889, DOI: 10.1007/s11356-015-4154-y

H.K.V. Schürner, J.L. Seffernick, A. Grzybkowska, A. Dybala-Defratyka, L.P. Wackett, and M. Elsner, Characteristic Isotope Fractionation Patterns in s Triazine Degradation Have Their Origin in Multiple Protonation Options in the s Triazine Hydrolase TrzN, Environ. Sci. Technol., 49 (2015) 3490, DOI: 10.1021/es5055385

K. Świderek, I. Tunon, S. Marti, and V. Moliner, Protein Conformational Landscapes and Catalysis. Influence of active site conformations in the reaction catalyzed by L-Lactate Dehydrogenase, ACS Catal., 5 (2015) 1172, DOI: 10.1021/cs501704f

M. Sanchez Tarin, K. Świderek, M. Roca, and I. Tunon, Enzyme Promiscuity in Enolase Superfamily. A Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods, J. Phys. Chem. B, 119 (2015) 1899, DOI: 10.1021/jp511147b

A. Krzeminska, P. Paneth, V. Moliner, and K. Świderek, Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT, J. Phys. Chem. B, 119 (2015) 917, DOI: 10.1021/jp506119h

2014

A. Siwek, T. Plech, N. Trotsko, U. Kosikowska, A. Malm, K. Dzitko, P. Paneth, Conformational preference of potassium salts of N-acylhydrazinecarbodithioates with antifungal activity. Combined experimental and theoretical approach, Curr. Comput.-Aid. Drug 10 (2014) 205-216, DOI: 10.2174/1573409910666140521152701

Winiecka-Klimek et al. PIN3 duplication may be partially responsible for TP53 haploinsufficiency, BMC Cancer 14 (2014) 669, DOI: 10.1186/1471-2407-14-669

K. Dzitko, A. Paneth, T. Plech, J. Pawełczyk, L. Weglinska, and P. Paneth, Triazole-based compound as the candidate to develop a novel medicines to treat toxoplasmosis, Antimicrob. Agents and Chemother., 58 (2014) 7583, DOI: 10.1128/AAC.03832-14

K. Świderek, I. Tunon, and V. Moliner, Predicting enzymatic reactivity: from theory to design, WIREs Comput Mol Sci, 4 (2014) 407, DOI: 10.1002/wcms.1173

R.N. Manna and A. Dybala-Defratyka, A computational study of the dechlorination of β-hexachlorocyclohexane (β-HCH) catalyzed by the haloalkane dehalogenase LinB, Arch. Biochem. Biophys. 562 (2014) 43, DOI: 10.1016/j.abb.2014.07.028

K. Huben, M. Jewgiński, A. Pabis, P. Paluch, B. Luy, and S. Jankowski, The structure of cyclolinopeptide A in chloroform refined by RDC measurements, J. Peptide Sci. 20 (2014) 901, DOI: 10.1002/psc.2683

K. Dzitko, A. Paneth, T. Plech, J. Pawełczyk, P. Stączek, J. Stefańska, and P. Paneth, 1,4-Disubstituted Thiosemicarbazide Derivatives are Potent Inhibitors of Toxoplasma gondii Proliferation, Molecules 19 (2014) 9926, DOI: 10.3390/molecules19079926

A. Siwek, T. Plech, N. Trotsko, U. Kosikowska, A. Malm, K. Dzitko, P. Paneth, Conformational Preference of Potassium Salts of N-Acylhydrazinecarbodithioates with Antifungal Activity. Combined Experimental and Theoretical Approach, Curr. Comput. Aided Drug Des. 2014

A. Grzybkowska, R. Kaminski, and A. Dybala-Defratyka, Theoretical predictions of isotope effects versus their experimental values on an example of uncatalyzed hydrolysis of atrazine, Phys. Chem. Chem. Phys., 16 (2014) 15164, DOI: 10.1039/C4CP00914B

K. Świderek, J. Ruiz-Pernia, V. Moliner, and I. Tunon, Heavy enzymes - experimental and computational insights in enzyme dynamics, Current Opinion in Chemical Biology, 21 (2014) 11, DOI: 10.1016/j.cbpa.2014.03.005

I. Geronimo and P. Paneth, A DFT and ONIOM study of C–H hydroxylation catalyzed by nitrobenzene 1,2-dioxygenase, Phys. Chem. Chem. Phys., 13 (2014) 13889, DOI: 10.1039/C4CP01030B

A.H. Meyer, A. Dybala-Defratyka, P.J. Alaimo, I. Geronimo, A.D. Sanchez, C.J. Cramer and M. Elsner, Cytochrome P450-Catalyzed Dealkylation of Atrazine by Rhodococcus sp. strain NI86/21 Involves Hydrogen Atom Transfer rather than Single Electron Transfer, Dalton Trans., 43 (2014) 12175 DOI: 10.1039/C4DT00891J

A. Pabis, I. Geronimo, D.M. York, and P. Paneth, Molecular dynamics simulation of nitrobenzene dioxygenase using AMBER force field, J. Chem. Theory Comput. 10 (2014) 2246, DOI: 10.1021/ct500205z

M. Wujec, E. Kędzierska, E. Kuśmierz, T. Plech, A. Wróbel, A. Paneth, J. Orzelska, S. Fidecka, and P. Paneth, Pharmacological and Structure-Activity Relationship Evaluation of 4-aryl-1-Diphenylacetyl(thio)semicarbazides, Molecules, 19 (2014) 4745, DOI: 10.3390/molecules19044745

A. Pabis, I. Geronimo, P. Paneth, A DFT Study of the Cis-dihydroxylation of Nitroaromatic Compounds Catalyzed by Nitrobenzene Dioxygenase, J. Phys. Chem. B, 118 (2014) 3245, DOI: 10.1021/jp4076299

P. Adamczyk, R.S. Wijker, T.B. Hofstetter and P. Paneth, A DFT study of permanganate oxidation of toluene and its ortho-nitroderivatives, J. Mol. Model. 20 (2014) 2091, DOI: 10.1007/s00894-014-2091-1

2013

K.M. Romek, M. Julien, M. Frasquet-Darrieux, I. Tea, I. Antheaume, R. Hankard, R.J. Robins, Human baby hair amino acid natural abundance 15N-isotope values are not related to the 15N-isotope values of amino acids in mother’s breast milk protein, Amino Acids, 45 (2013) 1365, DOI: 10.1007/s00726-013-1597-7

T. Fraczek, A. Siwek, and P. Paneth, Assessing molecular docking tools for relative biological activity prediction: a case study of triazole HIV-1 NNRTIs, J. Chem. Inf. Model. 53 (2013) 3326, DOI: 10.1021/ci400427a

R.S. Wijker, P. Adamczyk, J. Bolotin, P. Paneth, and T.B. Hofstetter, Isotopic analysis of oxidative pollutant degradation pathways exhibiting large H isotope fractionation, Environ. Sci. Technol., 47 (2013) 13459, DOI: 10.1021/es403597v

A. Siwek, R. Omib, K. Hirotsu, K. Jitsumori, N. Esaki, T. Kurihara, P.Paneth, Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies, Arch. Biochem. Biophys., 540 (2013) 26, link

K. Świderek and P. Paneth, Binding Isotope Effects, Chem. Rev., 113 (2013) 7851, DOI: 10.1021/cr300515x

B. Kupcewicz, G. Balcerowska-Czerniak, M. Malecka, P. Paneth, U. Krajewska, M. Rozalski, Structure–cytotoxic activity relationship of 3-arylideneflavanone and chromanone (E,Z isomers) and 3-arylflavones, Bioorg. Med. Chem. Lett., 23 (2013) 4102, DOI: 10.1016/j.bmcl.2013.05.044

R. N. Manna and A. Dybala-Defratyka, Insights into the elimination mechanisms employed for the degradation of different hexachlorocyclohexane isomers using kinetic isotope effects and docking studies, J. Phys. Org. Chem., 26 (2013) 797, DOI: 10.1002/poc.3163

A. Sikora, J. Zielonka, J. Adamus, D. Dębski, A. Dybala-Defratyka, B. Michalowski, J. Joseph, R. C. Hartley, M. P. Murphy, and B. Kalyanaraman, Reaction between peroxynitrite and triphenylphosphonium-substituted arylboronic acid isomers – Identification of diagnostic marker products and biological implications, Chem. Res. Toxicol., 26 (2013) 856, DOI: 10.1021/tx300499c

I. Tea, A. Le Guennec, M. Frasquet-Darrieux, M. Julien, K. Romek, I. Antheaume, R. Hankard and R. J. Robins, Simultaneous determination of natural-abundance d15N values and quantities of individual amino acids in proteins from milk of lactating women and from infant hair using gas chromatography/isotope ratio mass spectrometry; Rapid Commun. Mass Spectrom. 27 (2013) 1345, DOI: 10.1002/rcm.6582

K. Świderek, I. Tunon, S. Marti, V. Moliner, and J. Bertran, Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects, J. Am. Chem. Soc., 135 (2013) 8707, DOI: 10.1021/ja403038t

L. Szatkowski, A. Dybala-Defratyka, C. Batarseh, J. Blum, L. Halicz and F. Gelman, Bromine kinetic isotope effects: insight into Grignard reagent formation, New J. Chem., 37 (2013) 2241, DOI: 10.1039/C3NJ00197K

L. Szatkowski, A. Dybala-Defratyka, A computational study on enzymatically driven oxidative coupling of chlorophenols: An indirect dehalogenation reaction, Chemosphere 91 (2013) 258, DOI: 10.1016/j.chemosphere.2012.11.022

A. Siwek, P. Staczek, M. Wujec, K. Bielawski, A. Bielawska, P. Paneth, Cytotoxic effect and molecular docking of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide-a novel topoisomerase II inhibitor, J. Mol. Model. 19 (2013) 1319, DOI: 10.1007/s00894-012-1679-6

T.-S. Lee, B.K. Radak, A. Pabis, D.M. York, A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations. J. Chem. Theory Comput. 9(1) (2013) 153, DOI: 10.1021/ct300703z

2012

A. Siwek, P. Stączek, U. Kosikowska, A. Malm, P. Paneth and S. Jankowski, Does dehydrocyclization of 4-benzoylthiosemicarbazides in acetic acid lead to s-triazoles or thiadiazoles? Struct. Chem., 23 (2012) 1441, DOI: 10.1007/s11224-012-0065-4

K. Świderek, A. Pabis, V. Moliner, A theoretical study of carbon-carbon bond formation by a Michael-type addition, Organic & Biomolecular Chemistry 10 (2012) 5598, DOI: 10.1039/c2ob25465d

R.A. Kwiecien, J.-V. Le Questel, J. Lebreton, M. Delaforge, F. Andre, E. Pihan, A. Roussel, A. Fournial, P. Paneth, R.J. Robins, Cytochrome P450-Catalyzed Degradation of Nicotine: Fundamental Parameters Determining Hydroxylation by Cytochrome P450 2A6 at the 5'-Carbon or the N-Methyl Carbon, J. Phys. Chem. B 116 (2012), 7827, DOI: 10.1021/jp304276v

K. Świderek and P. Paneth, Extending Limits of Chlorine Kinetic Isotope Effects, J. Org. Chem. 77 (2012) 5120, DOI: 10.1021/jo300682f

R.A. Kwiecień, K. Kosieradzka, J.-Y. Le Questel, J. Lebreton, A. Fournial, E. Gentil, M. Delaforge, P.Paneth, R. J. Robins, Cytochrome P450 Monooxygenase-Catalyzed Ring Opening of the Bicyclic Amine, Nortropine: An Experimental and DFT Computational Study, ChemCatChem 4 (2012) 530

P.Paneth, Isotopic fractionation – chemical v. environmental perspective, Environ. Chem. 9 (2012) 67 DOI: 10.1071/EN11110

2011

A. Siwek, P. Stączek, M. Wujec, J. Stefańska, U. Kosikowska, A. Malm, S. Jankowki, P. Paneth, Biological and docking studies of topoisomerase IV inhibition by thiosemicarbazides, J. Mol. Model. 17 (2011) 2297

L. Chomicz, J. Rak, P. Paneth, M. Sevilla, Y.J. Ko, H. Wang, and K.H. Bowen, Valence anions of N-acetylproline in the gas phase: Computational and anion photoelectron spectroscopic studies, J. Chem. Phys. 135 (2011) 114301, DOI: 10.1063/1.3625957

A. Pabis, R. Kaminski, G. Ciepielowski, S. Jankowski, and P. Paneth, Measurements of Heavy-Atom Isotope Effects Using 1H NMR Spectroscopy, J. Org. Chem. 76 (2011) 8033, DOI: 10.1021/jo201226g

R.A. Kwiecień, R. Molinié, P. Paneth, V. Silvestre, J. Lebretona, R.J. Robins, Elucidation of the mechanism of N-demethylation catalyzed by cytochrome P450 monooxygenase is facilitated by exploiting nitrogen-15 heavy isotope effects, Arch. Biochem. Biophys. 510 (2011) 35

K. Świderek and P. Paneth, Binding Ligands and Cofactor to L-Lactate Dehydrogenase from Human Skeletal and Heart Muscles, J. Phys. Chem. B, 115 (2011) 6366, DOI: 10.1021/jp201626k

A. Sikora, J.Zielonka, M. Lopez, A. Dybala-Defratyka, J. Joseph, A. Marcinek, and B. Kalyanaraman, Reaction between Peroxynitrite and Boronates: EPR Spin-Trapping, HPLC Analyses, and Quantum Mechanical Study of the Free Radical Pathway, Chem. Res. Toxicol. 24 (2011) 687, DOI: 10.1021/tx100439a

A. Siwek, N. Trotsko, M. Wujec, R. Kamiński, P. Paneth, Synthetic route to isotopically labelled-oxamate, 54 (2011) 344, DOI: 10.1002/jlcr.1876

P. Adamczyk, A. Dybala-Defratyka, P. Paneth, DFT Study of Trichloroethene Reaction with Permanganate in Aqueous Solution, Environ. Sci. Technol. 45 (2011) 3006, DOI: 10.1021/es103251u

K. Swiderek, A. Dybala-Defratyka, D.R. Rohr, A New Scheme to Calculate Isotope Effects, J. Mol. Model., 17 (2011) 2175, DOI: 10.1007/s00894-010-0868-4

P. Adamczyk and P. Paneth, Theoretical evaluation of isotopic fractionation factors in oxidation reactions of benzene, phenol and chlorophenols, J. Mol. Model., 17 (2011) 2285, DOI: 10.1007/s00894-011-1038-z

L. Szatkowski, M.K. Thompson, R. Kaminski, S. Franzen, A. Dybala-Defratyka, Oxidative dechlorination of halogenated phenols catalyzed by two distinct enzymes: horseradish peroxidase and dehaloperoxidase, Arch. Biochem. Biophys. 505 (2011) 22, DOI: 10.1016/j.abb.2010.09.018

K. Świderek and P. Paneth, Differences and similarities in binding of pyruvate and l-lactate in the active site of M4 and H4 isoforms of human lactate dehydrogenase, Arch. Biochem. Biophys. 505 (2011) 33, DOI: 10.1016/j.abb.2010.10.010

2010


K. Świderek and P. Paneth, Importance of the Lactate Dehydrogenase Quaternary Structure in Theoretical Calculations, Journal of Physical Chemistry B 114 (2010) 3393, DOI:10.1021/jp100026z

P. Paneth, A. Dybala-Defratyka (Eds), Kinetics and Dynamics, From Nano- to Bio-Scale, Vol. 12 in Challenges and Advances in Computational Chemistry and Physics (series editor: J. Leszczynski), Springer, 2010

Isotope Effects in the Chemical, Geological and Bio Sciences, M. Wolfsberg, A. Van Hook, P. Paneth, Springer, London, 2010

2009

A. Dybala-Defratyka, P. Paneth, D.G. Truhlar, Quantum Catalysis in Enzymes  in Quantum Tunneling in Enzyme Catalyzed Reactions, edited by N. Scrutton and R. Allemann (RSC Publishing, Cambridge, UK) 2009, DOI:10.1039/9781847559975-00036

X. Li, L.W. Chung, P. Paneth and K. Morokuma, DFT and ONIOM(DFT:MM) Studies on Co-C Bond Cleavage and Hydrogen Transfer in B12-Dependent Methylmalonyl-CoA Mutase. Stepwise or Concerted Mechanism? J. Am. Chem. Soc. 131 (2009) 5115, DOI:10.1021/ja807677z

A. Pabis, P. Paluch, J. Szala and P. Paneth, A DFT study of the kinetic isotope effects on the competing SN2 and E2 reactions between hypochlorite anion and ethyl chloride, J. Chem. Theory and Comput. 5 (2009) 33, DOI:10.1021/ct800412h

T. Humphry, S. Iyer, O. Iranzo, J.R. Morrow, J.P. Richard, P.Paneth, and A.C. Hengge, An Altered Transition State for the Reaction of an RNA Model Catalyzed by a Dinuclear Zinc(II) Catalyst, J. Am. Chem. Soc. 130 (2009) 17858, DOI:10.1021/ja8059864

K. Świderek, A. Panczakiewicz, A. Bujacz, G. Bujacz, P. Paneth, Modeling of isotope effects on binding oxamate to lactic dehydrogenase,  J. Phys Chem. B 113 (2009) 12782

Y. Kim, A.V. Marenich, J.Zheng, K.H. Kim, M. Kołodziejska-Huben, M. Rostkowski, P. Paneth, D.G. Truhlar, Mechanistic Analysis of the Base-Catalyzed HF Elimination from
4-Fluoro-4-(4'-nitrophenyl)butane-2-one Based on Liquid-Phase Kinetic Isotope Effects Calculated by Dynamics Modeling with Multidimensional Tunneling, J. Chem. Theory Comp. 5 (2009) 59

A. Siwek, M. Wujec, J. Stefanska, P. Paneth, Antimicrobial properties of 4-aryl-3-(2-methyl-furan-3-yl)-Δ2-1,2,4-triazoline-5-thiones, Phosphorus, Sulfur 184 (2009) 3149, DOI:10.1080/10426500802705297

M. Ciolkowski, P. Paneth, I.-P. Lorenz, P. Mayer, M. Rozalski, U. Krajewska, E. Budzisz, Tautomeric forms study of 1H-(2'-pyridyl)-3-methyl-5-hydroxypyrazole and 1H-(2'-pyridyl)-3-phenyl-5-hydroxypyrazole. Synthesis, structure, and cytotoxic activity of their complexes with palladium(II) ions, J. Enzym. Inhib. Med. Ch. 24 (2009) 1257, DOI:10.3109/14756360902827653

K. Świderek, P. Paneth, Modeling excitation properties of iridium complexes, J. Phys. Org. Chem. 22 (2009) 845, DOI:10.1002/poc.1531

J. Flieger, P. Paneth, K. Gielzak-Kocwin, M. Tatarczak, Micropreparative isolation of Cu(II) complexes of isoniazid and ethambutol and determination of their structures, JPC-J. Planar Chromat. 22 (2009) 83, DOI:10.1556/JPC.22.2009.2.2

2008

A. Dybala-Defratyka, L. Szatkowski, R. Kaminski, M. Wujec, A. Siwek, P. Paneth, Kinetic isotope effects on dehalogenation at an aromatic carbon,  Environ. Sci. Technol. 42 (2008) 7744

A. Siwek, M. Wujec, I. Wawrzycka-Gorczyca, M. Dobosz, P. Paneth. Thiol-thione tautomeric forms recognition on the example of 4-[3-(2-methyl-furan-3-yl)-5-thioxo-1,2,4-triazolin-4-yl]acetic acid, Heteroatom Chemistry 19 (2008), 337, DOI:10.1002/hc.20433

A. Dybala-Defratyka, M. Rostkowski, P. Paneth. Enzyme mechanisms from molecular modeling and isotope effects, Archives of Biochemistry and Biophysics 474 (2008), 274, DOI:10.1016/j.abb.2008.01.012

M. Wujec, P. Paneth, Mechanism of 4-methyl-1,2,4-triazole-3-thione reaction with formaldehyde, Journal of Physical Organic Chemistry 21 (2008) 345, DOI:10.1002/poc.1324

A. Siwek, M. Wujec, M. Dobosz, E. Jagiello-Wojtowicz, A. Chodkowska, A. Kleinrok, P. Paneth, Synthesis and pharmacological properties of 3-(2-methyl-furan-3-yl)-4-substituted-Δ2-1,2,4-triazoline-5-thiones, Cent Eur J Chem, 6 (2008) 47, DOI:10.2478/s11532-007-0058-0

M. Wujec, A. Siwek, J. Dzierzawska, M. Rostkowski, R. Kaminski, P. Paneth, Influence of the Solvent Description on the Predicted Mechanism of SN2 Reactions, J. Phys. Chem. B, 112 (2008) 12414, DOI:10.1021/jp8035956

A. Siwek, M. Wujec, M. Dobosz, E. Jagiello-Wojtowicz, A. Kleinrok, A. Chodkowska, P. Paneth, Chemical and pharmacological properties of 3-(thiophen-2-yl)-4-substituted-Δ2-1,2,4-triazoline-5-thiones, Phosphorus, Sulfur and Silicon and the Related Elements 183 (2008) 2669, DOI:10.1080/10426500801968136

E. Budzisz, I -P.Lorenz, P. Mayer, P. Paneth, L. Szatkowski, U. Krajewska, M. Rozalski, M. Miernicka, Synthesis, crystal structure, theoretical calculation and cytotoxic effect of new Pt(II), Pd(II) and Cu(II) complexes with pyridine-pyrazoles derivatives, New Journal of Chemistry 32 (2008) 2238, DOI:10.1039/b808301k

 

A. Siwek, K. Świderek, S. Jankowski, Problems with molecular mechanics implementations on the example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide, J. Mol. Model. 18 (2012) 843, DOI: 10.1007/s00894-011-1117-1