Publications

Publications at UCT

Coming soon.

Prior to UCT

2024 /35/ 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.
/34/ 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.
/33/ 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 /32/ 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.
/31/ 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.
/30/ 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.
/29/ 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 /28/ 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.
/27/ 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.
/26/ 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.
/25/ 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.
/24/ 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 /23/ Electrostatic regulation of blue copper sites Bím, D.; Alexandrova, A. N. Chem. Sci. 2021, 12, 11406-11413.
/22/ Local Electric Fields As a Natural Switch of Heme-Iron Protein Reactivity Bím, D.; Alexandrova, A. N. ACS Catal. 2021, 11, 6534-6546.
2020 /21/ 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.
/20/ 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 /19/ 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.
/18/ 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.
/17/ 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.
/16/ 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.
/15/ 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 /14/ Toward a Selective Activation of Inert C–H Bonds Bím, D.; Srnec, M. Chemické Listy 2018, 112, 648‑654.
/13/ 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.
/12/ 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.
/11/ 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.
/10/ 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.
/9/ 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 /8/ 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.
/7/ 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.
/6/ 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 /5/ 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.
/4/ 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.
/3/ 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.
/2/ Theoretical Bioinorganic Chemistry and Spectroscopy Bím, D.; Gutten, O.; Chalupský, J.; Srnec, M.; Rulíšek, L. Chemické Listy 2016, 110, 354-364.
2015 /1/ Synthetic Models of Metalloenzymes Capable of Catalyzing Phosphodiester Bond Cleavage Bím, D.; Rulíšek, L.; Hodačová, J. Chemické Listy 2015, 109, 658-665.