Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.

We report on extensive measurements in the low-frequency limit of the ac conductivity of colloidal fluids and crystals formed from charged colloidal spheres suspended in de-ionized water. Temperature was varied in a range of $5°\mathrm{C}<\Theta <35°\mathrm{C}$ and the particle number density $n$ between 0.2 and $25\mu {\mathrm{m}}^{-3}$ for the larger, respectively, 2.75 and $210\mu {\mathrm{m}}^{-3}$ for the smaller of two investigated species. At fixed $\Theta$ the conductivity increased linearly with increasing $n$ without any significant change at the fluid-solid phase boundary. At fixed $n$ it increased with increasing $\Theta$ and the increase was more pronounced for larger $n$ . Lacking a rigorous electrohydrodynamic treatment for counterion-dominated systems we describe our data with a simple model relating to Drude’s theory of metal conductivity. The key parameter is an effectively transported particle charge or valence $Z^{*}$ . All temperature dependencies other than that of $Z^{*}$ were taken from literature. Within experimental resolution $Z^{*}$ was found to be independent of $n$ irrespective of the suspension structure. Interestingly, $Z^{*}$ decreases with temperature in near quantitative agreement with numerical calculations.

Biomimetic nitrogen fixation provides an attractive alternative for the century-old Haber–Bosch process; however, the performance of the currently available molecular biomimetic catalysts is very limited. In this work, we are aiming to understand the catalytic cycle of one of the most promising biomimetic complex families that can be the cornerstone of future computer-aided rational design of biomimetic complexes. We calculate the Gibbs free energy of all elementary reaction steps of homogeneous dinitrogen reduction to NH₃ on single-site iron complexes with EPPP tetradentate ligands (E = B, Si). We examine all possible mechanisms and identify the dominant pathways and the critical elementary steps that can be rate-determining in the catalytic cycle of nitrogen fixation. We find that the catalytic mechanism depends on the applied ligand and that the distal pathway observed with E = B is the most favorable route regarding the catalytic performance. Our calculations also reveal the lack of thermodynamic driving force in the last steps of the catalytic cycle that can be responsible for the low catalytic activity of the studied biomimetic catalysts. Our results can serve as a starting point for the rational design of biomimetic complexes, which should focus on establishing a steadily decreasing Gibbs free energy profile, as suggested by the Sabatier principle.

The effectiveness of metallocene catalysts in the cationic ring-opening polymerization (cationic ROP) of ε-caprolactone (CL) is influenced by the choice of metallocene/borate systems, particularly their bulkiness. Recent research examines this effect on the initiation and propagation stages of cationic ROP. We conducted a density functional theory study on the precatalyst activation of cationic CL ROP by zirconocene/borate catalysts, where four models of zirconocene precatalysts (Cp₂ZrMe₂ (a), (Me₅Cp)CpZrMe₂ (b), (Me₅Cp)₂ZrMe₂ (c), and Ind₂ZrMe₂ (d)) were combined with boron cocatalysts B(C₆F₅)₃ and [X⁺][B(C₆F₅)₄ ^-] (X⁺ = Ph₃C⁺ or PhMe₂NH⁺). We modeled and predicted their thermodynamic, steric, and electronic properties during ion-pair formation and separation. The calculated Gibbs energies of ion-pair formation correlated with the positive charge at the metal center and steric congestion of the catalyst. All catalyst precursors showed exothermic and exergonic insertion of CL, toluene solvent, and contact ion pairs; solvent-separated ion pairs were the preferred activation pathway. Catalyst c showed the most stable ion pair in precatalyst activation, with the lowest separation energy, aided by methyl group bulkiness and toluene solvent. We evaluated Cp'-based ligands using percent buried volume (%V _Bur) trends. Noncovalent interaction analysis indicated weak interactions at ion-pair contacts. This study enhances our understanding of cationic ROP and could aid in developing new polymerization catalysts for polyester synthesis.