Density functional theory

Density functional theory (DFT) finds increasing use in applications related to biological systems. Advancements in methodology and implementations have reached a point where predicted properties of reasonable to high quality can be obtained. Thus, DFT studies can complement experimental investigations, or even venture with some confidence into experimentally unexplored territory. In the present contribution, we provide an overview of the properties that can be calculated with DFT, such as geometries, energies, reaction mechanisms, and spectroscopic properties. A wide range of spectroscopic parameters is nowadays accessible with DFT, including quantities related to infrared and optical spectra, X-ray absorption and Mössbauer, as well as all of the magnetic properties connected with electron paramagnetic resonance spectroscopy except relaxation times. We highlight each of these fields of application with selected examples from the recent literature and comment on the capabilities and limitations of current methods

The oxidative inactivation of FeFe hydrogenase reveals the flexibility of the H-cluster

International audienceNature is a valuable source of inspiration in the design of catalysts, and various approaches are used to elucidate the mechanism of hydrogenases, the enzymes that oxidize or produce H2. In FeFe hydrogenases, H2 oxidation occurs at the H-cluster, and catalysis involves H2 binding on the vacant coordination site of an iron centre. Here, we show that the reversible oxidative inactivation of this enzyme results from the binding of H2 to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the coordination sphere around the reactive iron centre confers on the enzyme the ability to avoid harmful reactions under oxidizing conditions, including exposure to O2. The versatile chemistry of the diiron cluster in the natural system might inspire the design of novel synthetic catalysts for H2 oxidation

Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases

International audienceHow living organisms create carbon-sulfur bonds during the biosynthesis of critical sulfur-containing compounds is still poorly understood. The methylthiotransferases MiaB and RimO catalyze sulfur insertion into tRNAs and ribosomal protein S12, respectively. Both belong to a subgroup of radical–S-adenosylmethionine (radical-SAM) enzymes that bear two [4Fe-4S] clusters. One cluster binds S-adenosylmethionine and generates an Ado• radical via a well-established mechanism. However, the precise role of the second cluster is unclear. For some sulfur-inserting radical-SAM enzymes, this cluster has been proposed to act as a sacrificial source of sulfur for the reaction. In this paper, we report parallel enzymological, spectroscopic and crystallographic investigations of RimO and MiaB, which provide what is to our knowledge the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur cosubstrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction

Applications of the Density Matrix Renormalization Group to Exchange-Coupled Transition Metal Systems

Transition metal complexes containing magnetically interacting open-shell ions are important for diverse areas of molecular science. The reliable prediction and computational analysis of their electronic structure and magnetic properties, either in qualitative or quantitative terms, remain a central challenge for theoretical chemistry. The use of multireference methods is in principle the ideal approach to the inherently multireference problem of exchange coupling in oligonuclear transition metal complexes; however, the applicability of such methods has been severely restricted due to their computational cost. In recent years, the introduction of the density matrix renormalization group (DMRG) to quantum chemistry has enabled the multireference treatment of chemical problems with previously unattainable numbers of active electrons and orbitals. This development also paved the way for the first-principles multireference treatment of magnetic properties in the case of exchange-coupled transition metal systems. Here, the first detailed applications of DMRG-based methods to exchange-coupled systems are reviewed and the lessons learned so far regarding the applicability, apparent limitations, and future promise of this approach are discussed