| Summary: | This thesis deals with application of modern theoretical methods for studying enzymatic reactivity as well as with the efficient implementation of second analytical energy derivatives on the self-consistent field (SCF) theory level. The enzymatic mechanisms were investigated in the framework of electronic structure theory with special accent put on kinetics, proton-coupled electron transfer and theoretical support of EPR and Mössbauer experiments. In particular, cytochrome c nitrite reductase (C c NiR) enzyme mechanism was under consideration. The possible role of second-sphere active site amino acids as proton donors was investigated by taking different possible protonation states and geometrical conformations into account. It was found that the most probable proton donor is His 277 , whose spatial orientation and fine-tuned acidity lead to energetically feasible, low-barrier protonation reactions. However, substrate protonation may also be accomplished by Arg 114 . The activation barriers for the various proton and electron transfer steps were estimated in the framework of Marcus theory. The cd 1 nitrite reductase (NIR) enzyme was also investigated. NIR is a key enzyme in the denitrification process that reduces nitrite to nitric oxide (NO). There are three residues at the “distal” side of the active site heme (Tyr 10 , His 327 and His 369 ) and in this work the focus was set on the identification and characterization of possible H-bonds they can form with the NO, thereby affecting the stability of the complex. It was shown that the NO in the nitrosyl d 1 -heme complex of cd 1 NIR forms H-bonds with Tyr 10 and His 369 whereas the second conserved histidine, His 327 , appears to be less involved in NO H-bonding. Moreover, it was shown that the H-bonding network within the active site is dynamic and that a change in the protonation state of one of the residues does affect the strength and position of the H-bonds formed by the others. The electronic structure of the [4Fe-3S] cluster in Hydrogenase I (Hase I) was ...
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