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.