The structure and function of self-assembled monolayers (SAMs) at the nanoscale are determined by the steric and electronic effects of their building blocks. Carboranethiol molecules form pristine monolayers that provide tunable two-dimensional systems to probe lateral and interfacial interactions. Additional omega-functionality, such as carboxyl groups, can be introduced to change the properties of the exposed surfaces. Here, two geometrically similar isomeric m-carborane analogues of m-mercaptobenzoic acid, 1-COOH-7-SH-1,7-C2B10H10 and racem-1-COOH-9-SH-1,7-C2B10H10, are characterized and their SAMs on Au{111} are examined. The latter isomer belongs to the rare group of chiral cage molecules and becomes, to our knowledge, the first example assembled on Au{111}. Although different in symmetry, molecules of both isomers assemble into similar hexagonal surface patterns. The nearest-neighbor spacing of 8.4 +/- 0.4 angstrom is larger than that of non-carboxylated isomers, consistent with the increased steric demands of the carboxyl groups. Computational modeling reproduced this spacing and suggests a tilt relative to the surface normal. However, tilt domains are not observed experimentally, suggesting the presence of strong lateral interactions. Analyses of the influence of the functional groups through the pseudo-aromatic m-carborane skeleton showed that the thiol group attached to either carbon or boron atoms increases the carboxyl group acidity in solution. In contrast, the acidity of the exposed carboxyl group in the SAMs decreases upon surface attachment; computational analyses suggest that the driving force of this shift is the dielectric of the environment in the monolayer as a result of confined intermolecular interactions, proximity to the Au surface, and partial desolvation.

Microbial aromatic catabolism offers a promising approach to convert lignin, a vast source of renewable carbon, into useful products. Aryl-O-demethylation is an essential biochemical reaction to ultimately catabolize coniferyl and sinapyl lignin-derived aromatic compounds, and is often a key bottleneck for both native and engineered bioconversion pathways. Here, we report the comprehensive characterization of a promiscuous P450 aryl-O-demethylase, consisting of a cytochrome P450 protein from the family CYP255A (GcoA) and a three-domain reductase (GcoB) that together represent a new two-component P450 class. Though originally described as converting guaiacol to catechol, we show that this system efficiently demethylates both guaiacol and an unexpectedly wide variety of lignin-relevant monomers. Structural, biochemical, and computational studies of this novel two-component system elucidate the mechanism of its broad substrate specificity, presenting it as a new tool for a critical step in biological lignin conversion.

We report a DFT computational study (M06-2X) of π-facial selectivity in the Diels-Alder reactions of thiophene 1-oxide. The preference for the syn cycloaddition arises because the ground state geometry of thiophene 1-oxide is predistorted into an envelope conformation that resembles the syn transition state geometry. The syn distortion occurs to minimize the effect of hyperconjugative antiaromaticity in the thiophene 1-oxide, arising from overlap of the σ*SO with the π-system. The syn selectivity follows through to the product structure that is stabilized by a π-σ*SO interaction, related to the 7-norbornenyl ion stability.

Histone Deacetylases (HDACs) are responsible for the removal of acetyl groups from histones resulting in gene silencing. Overexpression of HDACs is associated with cancer, and HDAC inhibitors are of particular interest as chemotherapeutics. The best studied in this category is HDAC8. The physiological metal utilized by HDAC8 is a matter of debate, but mechanistic studies have shown that a zinc-dependent HDAC8 is capable of shuttling protons to produce the desired products. We used QM/MM methods to test two conflicting mechanisms with Zn, Co, Fe, Mn, Mg, and Ni as the participating, bound divalent ion, and have found that previous studies omitted important pieces of the active site that assist in further elucidating the mechanism of proton shuttling.

Histone deacetylases (HDACs) are responsible for the removal of acetyl groups from histones, resulting in gene silencing. Overexpression of HDACs is associated with cancer, and their inhibitors are of particular interest as chemotherapeutics. However, HDACs remain a target of mechanistic debate. HDAC class 8 is the most studied HDAC, and of particular importance due to its human oncological relevance. HDAC8 has traditionally been considered to be a Zn-dependent enzyme. However, recent experimental assays have challenged this assumption and shown that HDAC8 is catalytically active with a variety of different metals, and that it may be a Fe-dependent enzyme in vivo. We studied two opposing mechanisms utilizing a series of divalent metal ions in physiological abundance (Zn(2+), Fe(2+), Co(2+), Mn(2+), Ni(2+), and Mg(2+)). Extensive sampling of the entire protein with different bound metals was done with the mixed quantum-classical QM/DMD method. Density functional theory (DFT) on an unusually large cluster model was used to describe the active site and reaction mechanism. We have found that the reaction profile of HDAC8 is similar among all metals tested, and follows one of the previously published mechanisms, but the rate-determining step is different from the one previously claimed. We further provide a scheme for estimating the metal binding affinities to the protein. We use the quantum theory of atoms in molecules (QTAIM) to understand the different binding affinities for each metal in HDAC8 as well as the ability of each metal to bind and properly orient the substrate for deacetylation. The combination of this data with the catalytic rate constants is required to reproduce the experimentally observed trend in metal-depending performance. We predict Co(2+) and Zn(2+) to be the most active metals in HDAC8, followed by Fe(2+), and Mn(2+) and Mg(2+) to be the least active.

Catalysis in protein tyrosine phosphatases (PTPs) involves movement of a protein loop called the WPD loop that brings a conserved aspartic acid into the active site to function as a general acid. Mutation of the tryptophan in the WPD loop of the PTP YopH to any other residue with a planar, aromatic side chain (phenylalanine, tyrosine, or histidine) disables general acid catalysis. Crystal structures reveal these conservative mutations leave this critical loop in a catalytically unproductive, quasi-open position. Although the loop positions in crystal structures are similar for all three conservative mutants, the reasons inhibiting normal loop closure differ for each mutant. In the W354F and W354Y mutants, steric clashes result from six-membered rings occupying the position of the five-membered ring of the native indole side chain. The histidine mutant dysfunction results from new hydrogen bonds stabilizing the unproductive position. The results demonstrate how even modest modifications can disrupt catalytically important protein dynamics. Crystallization of all the catalytically compromised mutants in the presence of vanadate gave rise to vanadate dimers at the active site. In W354Y and W354H, a divanadate ester with glycerol is observed. Such species have precedence in solution and are known from the small molecule crystal database. Such species have not been observed in the active site of a phosphatase, as a functional phosphatase would rapidly catalyze their decomposition. The compromised functionality of the mutants allows the trapping of species that undoubtedly form in solution and are capable of binding at the active sites of PTPs, and, presumably, other phosphatases. In addition to monomeric vanadate, such higher-order vanadium-based molecules are likely involved in the interaction of vanadate with PTPs in solution.

Acireductone dioxygenase (ARD) oxidizes 1,2-dihydroxy-3-keto-5-(methylthio)pentene to either formate and an α-keto acid, or formate, methylthiopropionate and CO, depending on the nature of the catalytic metal, Fe2+ or Ni2+. We recently showed that, contrary to established hypotheses, the mechanistic preference is driven solely by the RedOx behavior of the metal. Here, we address the functionality of Co2+-ARD. Using mixed quantum–classical dynamics simulations and density functional theory calculations, we show that both Fe2+-like and Ni2+-like routes are accessible to Co2+-ARD, but the mechanism involves a bifurcating transition state, and so the exact product distribution would be determined by the reaction dynamics.