Recent Developments in Computational Bioinorganic Chemistry

Metal Ion Modeling Using Classical Mechanics

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.

Density functional theory for transition metals and transition metal chemistry

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

Computational Studies of Bioorganometallic Enzymes and Cofactors

Because of their complex geometric and electronic structures, the active sites and cofactors of bioorganometallic enzymes, which are characterized by their metal–carbon bonds, pose a major challenge for computational chemists. However, recent progress in computer technology and theoretical chemistry, along with insights gained from mechanistic, spectroscopic, and X-ray crystallographic studies, have established an excellent foundation for the successful completion of computational studies aimed at elucidating the electronic structures and catalytic cycles of these species. This chapter briefly reviews the most popular computational approaches employed in theoretical studies of bioorganometallic species and summarizes important information obtained from computational studies of (i) the enzymatic formation and cleavage of the Co–C bond of coenzyme B12; (ii) the catalytic cycle of methyl-coenzyme M reductase and its nickel-containing cofactor F430; (iii) the polynuclear active-site clusters of the bifunctional enzyme carbon monoxide dehydrogenase/acetyl-coenzyme A synthase; and (iv) the magnetic properties of the active-site cluster of Fe-only hydrogenases.

Reactions of the diiron(IV) intermediate Q in soluble methane monooxygenase with fluoromethanes

Soluble methane monooxygenases utilize a carboxylate-bridged diiron center and dioxygen to convert methane to methanol. A diiron(IV) oxo intermediate Q is the active species for this process. Alternative substrates and theoretical studies can help elucidate the mechanism. Experimental results for reactions with derivatized methanes were previously modeled by a combination of quantum mechanical/molecular mechanical techniques and the model was extended to predict the relative reactivity of fluoromethane. We therefore studied reactions of Q with CF(n)H(4-n) (n=1-3) to test the prediction. The kinetics of single-turnover reactions of Q with these substrates were monitored by double-mixing stopped-flow optical spectroscopy. For fluoro- and difluoromethane, conversion to the alcohols occurred with second-order rate constants less than that of methane, the values being 28,700 (CH4)>25,000 (CFH3)>9300 (CF2H2) M(-1) s(-1). KIE values for C-H versus C-D activation above the classical limit were observed, requiring modification of the theoretical predictions.