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The effects of a variety of ortho-substituents (CH3, OH, OCH3, SH, SCH3, NH2, NO2, F, Cl, CN, and imidazole) on the acidity of phenol are investigated using hybrid density functional theory. Substitutions are made at the ortho-position to model modified tyrosine residues found in enzymes. Although the experimental trends are reproduced, the calculations tend to exaggerate the substituent effects. It is shown that the cysteine cross-link to tyrosine, present in the radical enzyme galactose oxidase, has a small effect on the pKa of the residue. The histidine cross-link present in cytochrome c oxidase, on the other hand, will contribute more to lower the pKa. Comparing the substituent effects on the O−H bond strengths and the acidities, no simple correlation is found between the two.

Reaction mechanisms of redox-active enzymes have for a long time been challenging targets for theoretical research. In this review, a quantum chemical approach will be described which during recent years has been applied in our laboratory to a number of the most interesting of these enzymes. Hybrid density functional theory is used where full geometry optimizations are done with a medium basis and final energies are evaluated using a much larger basis. Models consisting of 40−50 atoms and which contain the active site metal complex, including only the first-shell amino acid ligands, are normally employed. The protein surrounding is treated as a homogeneous dielectric medium. Results demonstrating the accuracy reached in this type of model are given, and a number of examples are described, showing the type of problems that can be treated. The most important of these are taken from studies on photosynthesis and oxidative phosphorylation (respiration).

Complexes [(C2H2X2)2M]nwith ligating atoms X = O, S and central atoms M = Li (n= 0, ± 1) and Be (n= 0, ± 2) have been studied by quantum chemical ab initiocalculations. Total energies, relative binding energies and orbital energies of mainly planar complexes of standard geometry have been studied. The effect of variation of geometry including non‐planarity has also been considered. The primary binding region is found to contain appreciable interactions not only within pairs MX but for the sulfur case also of the type XX'. The chelate form of the ligands is shown to be essential to the properties of the complexes.

Density functional theory in its B3LYP variant has been used to explore quantitative details of the adiabatic potential energy surface leading from Ni⁺ + C3H8 reactants through a deep Ni⁺(C3H8) well to NiC2H4⁺ + CH4 and NiC3H6⁺ + H2 elimination products. The lowest energy path to CH4 elimination involves facile CC bond insertion followed by a high multicenter transition state (MCTS) leading directly to the exit-channel complex Ni⁺(C2H4)(CH4). The lowest energy path to H2 elimination involves comparably facile secondary CH insertion followed by a comparably high MCTS leading directly to the Ni⁺(C3H6)(H2) complex. Primary CH insertion leads to significantly higher barriers to both CH4 and H2 elimination; in particular, β-methyl migration is energetically very costly. These results support a mechanism significantly different from the stepwise mechanisms invoked earlier but the same as that found in recent calculations on the Fe⁺ + C3H8 reaction by Holthausen and Koch. The geometries suggest that agostic interactions are important in stabilizing the key MCTSs. We use the B3LYP geometry (moments of inertia) and harmonic vibrational frequencies at each stationary point to construct a detailed rate model of the reaction, applying RRKM theory to each reaction step on the adiabatic ground-state surface. A steady-state approximation holds well and leads to a simple parallel decay model for the long-lived Ni⁺(C3H8) complexes. By adjusting the energies of the key MCTSs downward by 5−7 kcal/mol from the values from B3LYP theory, we can explain the range of experimental time scales, the product branching fractions, total cross section vs kinetic energy, and deuterium isotope effects. Differential centrifugal effects arising from the substantial variation of the mass distribution along the reaction coordinates lead to a strong J-dependence of the Ni⁺(C3H8) decay rate and of product branching fractions as well. The resulting mechanistic picture indicates that at low energy only low-J complexes (formed at small impact parameter) can overcome the centrifugal barriers atop the MCTSs and produce elimination products. High-J complexes live as Ni⁺(C3H8) for nanoseconds−microseconds, repeatedly insert in CC and CH bonds, but eventually revert to Ni⁺ + C3H8 reactants. We suggest possible reasons why the new model cannot explain the bimodal kinetic energy release distribution observed by Bowers and co-workers in the NiC3H6⁺ + H2 channel.

The potential energy surface of the endothermic reaction Rh⁺ + CH4 → %@mt;sys@%RhCH%@sx@%2%@be@%+%@sxx@%%@mx@% + H2 is calculated using high-accuracy quantum chemical methods. The results agree with recent results from ion beam mass spectrometry, indicating that there is no barrier in excess of the endothermicity of the H2 elimination reaction. All structures on the potential surface are optimized at the density functional theory level, using the empirically parametrized hybrid functional B3LYP. Relative energies are calculated both at the B3LYP level, using large basis sets, and at the parametrized configuration interaction (PCI-80 (MCPF)) level.

The oxidation of methane with molecular oxygen using the atomic platinum cation as a catalyst, yielding methanol, formaldehyde, and higher oxidation products, has been studied both computationally and experimentally. The most relevant reaction pathways have been followed in detail. To this end a large number of stationary points, both minima and transition states, have been optimized using a hybrid density functional theory method (B3LYP). At these optimized geometries, energies have been calculated using both an empirical scaling scheme (PCI-80) and the B3LYP method employing extended basis sets with several polarization functions. Good agreement with available experimental data has been obtained. For the parts of the catalytic cycle where detailed experimental results have not been available, the new calculated results have complemented the experimental picture to reach an almost complete understanding of the reaction mechanisms. Spin−orbit effects have been incorporated using an empirical approach, which has lead to improved agreement with experiments. The new FTICR experiments reported in the present study have helped to clarify some of the most complicated reaction sequences.