Publications
Publications at UCT
2025
Nucleophilic aromatic substitutions enable diversity-oriented synthesis of heterocyclic atropisomers via non-atropisomeric intermediates.
Šimek, M.; Dey, P.; Blahout, V.; Mondal, K.; Ernenwein, J.; Dračínský, M.; Bím, D.; Paioti, H. S. P.
Nat. Commun., 2025, 16, 4856.Methods for Theoretical Treatment of Local Fields in Proteins and Enzymes.
Eberhart, M. E.; Alexandrova, A. A.; Ajmera, P.; Bím, D.; Chaturvedi, S. S.; Vargas, S.; Wilson, T. R.
Chem. Rev., 2025, 125, 3772–3813.
Prior to UCT
2024
Bioinspired intramolecular spirocyclopropanation of quinones as an interrupted photoredox process.
Fadeev, A. A.; Bím, D.; Císařová, I.; Kotora, M.
Org. Chem. Front., 2024, 11, 5703–5711.Toward liquid cell quantum sensing: Ytterbium complexes with ultranarrow absorption.
Shin, A. J.; Zhao, C.; Shen, Y.; Dickerson, C. E.; Li, B.; Roshandel, H.; Bím, D.; Atallah, T. L.; Oyala, P. H.; He, Y.; Alson, L. K.; Kerr, T. A.; Alexandrova, A. N.; Diaconescu, P. L.; Campbell, W. C.; Caram, J. C.
Science, 2024, 385, 651–656.Mechanisms of Photoredox Catalysis Featuring Nickel–Bipyridine Complexes.
Cagan, D. A.; Bím, D.; Kazmierczak, N. P.; Hadt, R. G.
ACS Catal., 2024, 14, 9055–9076.Light Activation and Photophysics of a Structurally Constrained Nickel(II)–Bipyridine Aryl Halide Complex.
Bím, D.; Luedecke, K. M.; Cagan, D. A.; Hadt, R. G.
Inorg. Chem., 2024, 63, 4120–4131.
2023
Electronic Structures of Nickel(II)-Bis(indanyloxazoline)-dihalide Catalysts: Understanding Ligand Field Contributions That Promote C(sp2)–C(sp3) Cross-Coupling.
McNicholas, B. J.; Tong, J. Z.; Bím, D.; Turro, R. F.; Kazmierczak, N. P.; Chalupský, J.; Reisman, S. E.; Hadt, R. G.
Inorg. Chem., 2023, 62, 14010–14027.Photogenerated Ni(I)–Bipyridine Halide Complexes: Structure–Function Relationships for Competitive C(sp2)–Cl Oxidative Addition and Dimerization Reactivity Pathways.
Cagan, D. A.; Bím, D.; McNicholas, B. J.; Kazmierczak, N. P.; Oyala, P. H.; Hadt, R. G.
Inorg. Chem., 2023, 62, 9538–9551.From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics.
Chaturvedi, S. S.; Bím, D.; Christov, C. Z.; Alexandrova, A. N.
Chem. Sci., 2023, 14, 10997–11011.Electrochemical Carbon Dioxide Capture and Concentration.
Zito, A. M.; Clarke, L. E.; Barlow, J. M.; Bím, D.; Zhang, Z.; Ripley, K. M.; Li, C.; Kummeth, A.; McLaid, L. E.; Alexandrova, A. N.; Brushett, F. R.; Yang, J. Y.
Chem. Rev., 2023, 123, 8069–8098.
2022
Computational and Experimental Design of Quinones for Electrochemical CO2 Capture and Concentration.
Zito, A. M.; Bím, D.; Vargas, S.; Alexandrova, A. N.; Yang, J. Y.
ACS Sust. Chem. Eng., 2022, 10, 11387–11395.Elucidating the Mechanism of Excited-State Bond Homolysis in Nickel–Bipyridine Photoredox Catalysts.
Cagan, A. D.; Bím, D.; Silva, B.; Kazmierczak, N. P.; McNicholas, B. J.; Hadt, R. G.
J. Am. Chem. Soc., 2022, 144, 6516–6531.Molecular design of redox carriers for electrochemical CO2 capture and concentration.
Barlow, J. M.; Clarke, L. E.; Zhang, Z.; Bím, D.; Ripley, K. M.; Zito, A. M.; Brushett, F. R.; Alexandrova, A. N.; Yang, J. Y.
Chem. Soc. Rev., 2022, 51, 8415–8433.Understanding desaturation/hydroxylation activity of castor stearoyl Δ9‑Desaturase through rational mutagenesis.
Tupec, M.; Culka, M.; Machara, A.; Macháček, S.; Bím, D.; Svatoš, A.; Rulíšek, L.; Pichová, I.
Comput. Struct. Biotechnol. J., 2022, 20, 1378–1388.Predicting Effects of Site‑Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II.
Bím, D.; Navrátil, M.; Gutten, O.; Konvalinka, J.; Kutil, Z.; Culka, M.; Návrátil, V.; Alexandrova, A. N.; Bařinka, C.; Rulíšek, L.
J. Phys. Chem. B, 2022, 126, 132–143.
2021
Electrostatic regulation of blue copper sites.
Bím, D.; Alexandrova, A. N.
Chem. Sci., 2021, 12, 11406–11413.Local Electric Fields As a Natural Switch of Heme‑Iron Protein Reactivity.
Bím, D.; Alexandrova, A. N.
ACS Catal., 2021, 11, 6534–6546.
2020
From Synthetic to Biological Fe4S4 Complexes: Redox Properties Correlated to Function of Radical S‑Adenosylmethionine Enzymes.
Bím, D.; Alonso‑Gil, S.; Srnec, M.
ChemPlusChem, 2020, 85, 2534–2541.Proton–Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9‑Desaturase.
Bím, D.; Chalupský, J.; Culka, M.; Solomon, E. I.; Rulíšek, L.; Srnec, M.
J. Am. Chem. Soc., 2020, 142, 10412–10423.
2019
Reactive mode composition factor analysis of transition states: the case of coupled electron–proton transfers.
Maldonado‑Domínguez, M.; Bím, D.; Fučík, R.; Čurík, R.; Srnec, M.
Phys. Chem. Chem. Phys., 2019, 21, 24912–24918.Dissecting the Temperature Dependence of Electron–Proton Transfer Reactivity.
Bím, D.; Maldonado‑Domínguez, M.; Fučík, R.; Srnec, M. J.
Phys. Chem. C, 2019, 123, 21422–21428.Preparation and redox properties of fluorinated 1,3‑diphenylisobenzofurans.
Kaleta, J.; Šimková, L.; Liška, A.; Bím, D.; Madridejos, J.; Pohl, R.; Ludvík, J.; Rulíšek, L.; Michl, J.
Electrochim. Acta, 2019, 321, 134659.Preparation of (Pentafluorosulfanyl)benzenes by Direct Fluorination of Diaryldisulfides: Synthetic Approach and Mechanistic Aspects.
Ajenjo, J.; Klepetářová, B.; Greenhall, M.; Bím, D.; Culka, M.; Rulíšek, L.; Beier, P.
Chem. Eur. J., 2019, 25, 11375–11382.Structural and computational basis for potent inhibition of glutamate carboxypeptidase II by carbamate‑based inhibitors.
Bařinka, C.; Nováková, Z.; Hin, N.; Bím, D.; Ferraris, D. V.; et al.
Bioorg. Med. Chem., 2019, 27, 255–264.
2018
Toward a Selective Activation of Inert C–H Bonds.
Bím, D.; Srnec, M.
Chemické Listy, 2018, 112, 648–654.Beyond the classical thermodynamic contributions to hydrogen atom abstraction reactivity.
Bím, D.; Maldonado‑Domínguez, M.; Rulíšek, L.; Srnec, M.
Proc. Natl. Acad. Sci. U.S.A., 2018, 115, E10287–E10294.Computational Electrochemistry as a Reliable Probe of Experimentally Elusive Mononuclear Nonheme Iron Species.
Bím, D.; Rulíšek, L.; Srnec, M.
J. Phys. Chem. C, 2018, 122, 10773–19782.Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set.
Řezáč, J.; Bím, D.; Gutten, O.; Rulíšek, L.
J. Chem. Theory Comput., 2018, 14, 1254–1266.Near-UV Water Splitting by Cu, Ni, and Co Complexes in the Gas Phase.
Dang, A.; Shaffer, C. J.; Bím, D.; Lawler, J.; Lesslie, M.; Ryzhov, V.; Tureček, F.
J. Phys. Chem. A, 2018, 122, 2069–2078.Macrocycle Conformational Sampling by DFT‑D3/COSMO‑RS Methodology.
Gutten, O.; Bím, D.; Řezáč, J.; Rulíšek, L.
J. Chem. Inf. Model., 2018, 58, 48–60.
2017
Increase in Solubility of Poorly-Ionizable Pharmaceuticals by Salt Formation: A Case of Agomelatine Sulfonates.
Skořepová, E.; Bím, D.; Hušák, M.; Klimeš, J.; Chatziadi, A.; Ridvan, L.; Boleslavská, T.; Beránek, J.; Šebek, P.; Rulíšek, L.
Cryst. Growth Des., 2017, 17, 5283–5294.Radical Reactions Affecting Polar Groups in Threonine Peptide Ions.
Nguyen, H. T. H.; Andrikopoulos, P. C.; Bím, D.; Rulíšek, L.; Dang, A.; Tureček, F.
J. Phys. Chem. B, 2017, 121, 6557–6569.Cytosine Radical Cations: A Gas-Phase Study Combining IRMPD Spectroscopy, UVPD Spectroscopy, Ion–Molecule Reactions, and Theoretical Calculations.
Lesslie, M.; Lawler, J. T.; Dang, A.; Korn, J. A.; Bím, D.; Steinmetz, V.; Maitre, P.; Tureček, F.; Ryzhov, V.
ChemPhysChem, 2017, 18, 1293–1301.
2016
Copper(II) and Zinc(II) Complexes of Conformationally Constrained Polyazamacrocycles as Efficient Catalysts for RNA Model Substrate Cleavage in Aqueous Solution at Physiological pH.
Bím, D.; Svobodová, E.; Eigner, V.; Rulíšek, L.; Hodačová, J. Chem. Eur. J., 2016, 22, 10426–10437.Accurate Prediction of One-Electron Reduction Potentials in Aqueous Solution by Variable-Temperature H‑Atom Addition/Abstraction Methodology.
Bím, D.; Rulíšek, L.; Srnec, M.
J. Phys. Chem. Lett., 2016, 7, 7–13.Mono- and binuclear non-heme iron chemistry from a theoretical perspective.
Rokob, T. A.; Chalupský, J.; Bím, D.; Andrikopoulos, P. C.; Srnec, M.; Rulíšek, L.
J. Biol. Inorg. Chem., 2016, 21, 619–644.Theoretical Bioinorganic Chemistry and Spectroscopy.
Bím, D.; Gutten, O.; Chalupský, J.; Srnec, M.; Rulíšek, L.
Chemické Listy, 2016, 110, 354–364.
2015
- Synthetic Models of Metalloenzymes Capable of Catalyzing Phosphodiester Bond Cleavage.
Bím, D.; Rulíšek, L.; Hodačová, J.
Chemické Listy, 2015, 109, 658–665.