Catalytic divergencies in the mechanism of L-arginine hydroxylating nonheme iron enzymes

Many enzymes in nature utilize a free arginine (L-Arg) amino acid to initiate the biosynthesis of natural products. Examples include nitric oxide synthases, which generate NO from L-Arg for blood pressure control, and various arginine hydroxylases involved in antibiotic biosynthesis. Among the groups of arginine hydroxylases, several enzymes utilize a nonheme iron(II) active site and let L-Arg react with dioxygen and α-ketoglutarate to perform either C3-hydroxylation, C4-hydroxylation, C5-hydroxylation, or C4-C5-desaturation. How these seemingly similar enzymes can react with high specificity and selectivity to form different products remains unknown. Over the past few years, our groups have investigated the mechanisms of L-Arg-activating nonheme iron dioxygenases, including the viomycin biosynthesis enzyme VioC, the naphthyridinomycin biosynthesis enzyme NapI, and the streptothricin biosynthesis enzyme OrfP, using computational approaches and applied molecular dynamics, quantum mechanics on cluster models, and quantum mechanics/molecular mechanics (QM/MM) approaches. These studies not only highlight the differences in substrate and oxidant binding and positioning but also emphasize on electronic and electrostatic differences in the substrate-binding pockets of the enzymes. In particular, due to charge differences in the active site structures, there are changes in the local electric field and electric dipole moment orientations that either strengthen or weaken specific substrate C-H bonds. The local field effects, therefore, influence and guide reaction selectivity and specificity and give the enzymes their unique reactivity patterns. Computational work using either QM/MM or density functional theory (DFT) on cluster models can provide valuable insights into catalytic reaction mechanisms and produce accurate and reliable data that can be used to engineer proteins and synthetic catalysts to perform novel reaction pathways.

CuO Nanoparticles and Microaggregates: An Experimental and Computational Study of Structure and Electronic Properties

The link between morphology and properties is well-established in the nanoparticle literature. In this report, we show that different approaches in the synthesis of copper oxide can lead to nanoparticles (NPs) of different size and morphology. The structure and properties of the synthesized NPs are investigated with powder X-ray diffraction, scanning electron microscopy (SEM), and diffuse reflectance spectroscopy (DRS). Through detailed SEM analyses, we were able to correlate the synthetic pathways with the particles' shape and aggregation, pointing out that bare hydrothermal pathways yield mainly spheroidal dandelion-like aggregates, whereas, if surfactants are added, the growth of the nanostructures along a preferential direction is promoted. The effect of the morphology on the electronic properties was evaluated through DRS, which allowed us to obtain the electron bandgap in every system synthesized, and to find that the rearrangement of threaded particles into more compact structures leads to a reduction in the energy difference. The latter result was compared with Density Functional Theory (DFT) computational models of small centrosymmetric CuO clusters, cut from the tenorite crystal structure. The computed UV-Vis absorption spectra obtained from the clusters are in good agreement with experimental findings.

Mechanism of Action of Flavin-Dependent Halogenases

To rationally engineer the substrate scope and selectivity of flavin-dependent halogenases (FDHs), it is essential to first understand the reaction mechanism and substrate interactions in the active site. FDHs have long been known to achieve regioselectivity through an electrophilic aromatic substitution at C7 of the natural substrate Trp, but the precise role of a key active-site Lys residue remains ambiguous. Formation of hypochlorous acid (HOCl) at the cofactor-binding site is achieved by the direct reaction of molecular oxygen and a single chloride ion with reduced FAD and flavin hydroxide, respectively. HOCl is then guided 10 Å into the halogenation active site. Lys79, located in this site, has been proposed to direct HOCl toward Trp C7 through hydrogen bonding or a direct reaction with HOCl to form an -NH₂Cl⁺ intermediate. Here, we present the most likely mechanism for halogenation based on molecular dynamics (MD) simulations and active-site density functional theory "cluster" models of FDH PrnA in complex with its native substrate l-tryptophan, hypochlorous acid, and the FAD cofactor. MD simulations with different protonation states for key active-site residues suggest that Lys79 directs HOCl through hydrogen bonding, which is confirmed by calculations of the reaction profiles for both proposed mechanisms.

Desorption induced by low energy charge carriers on Si(111)-7 × 7: First principles molecular dynamics for benzene derivates

We use clusters for the modeling of local ion resonances caused by low energy charge carriers in STM-induced desorption of benzene derivates from Si(111)-7 × 7. We perform Born-Oppenheimer molecular dynamics for the charged systems assuming vertical transitions to the charged states at zero temperature, to rationalize the low temperature activation energies, which are found in experiment for chlorobenzene. Our calculations suggest very similar low temperature activation energies for toluene and benzene. For the cationic resonance transitions to physisorption are found even at 0 K, while the anion remains chemisorbed during the propagations. Further, we also extend our previous static quantum chemical investigations to toluene and benzene. In addition, an in depth analysis of the ionization potentials and electron affinities, which are used to estimate resonance energies, is given. © 2018 Wiley Periodicals, Inc.

Practical Cluster Models for a Layered β-NiOOH Material

Due to the high oxygen evolution reaction (OER) activity, stability, and abundance of NiOx materials, they are found to be promising catalysts, competitive with expensive metal oxides such as IrO₂ and RuO₂. From a theoretical point of view, studies reported in the literature so far are mostly based on density functional theory using periodic slab models for the bulk and surface of β-NiOOH, one of the active NiOx phases. However, cluster models are a valid method to investigate many aspects about structure, charge carrier transport properties, and OER activity of β-NiOOH. Hence, here we present new cluster models for the surface of β-NiOOH, where the oxygen atoms are bonded to Mg effective core potentials (ECPs) mimicking neighboring atom cores. This cluster embedding procedure is superior to saturating the cluster with hydrogen atoms, and to using other atomic ECPs for β-NiOOH. We find that layered materials such as β-NiOOH are more vulnerable to geometrical rupture and therefore a cluster approach requires additional care in choosing the embedding approach. We evaluated the models by using them to calculate the energy required for water adsorption and deprotonation, which are essential ingredients for OER. Specifically, our results agree with previous slab models that the first deprotonation reaction step requires a large amount of energy. In addition, we find that water and hydroxyl groups have high adsorption energy and therefore the first deprotonation step is limiting the reaction efficiency.