Electrochemical, Computational, And Reactivity Studies Of Strongly Stabilized Cerium(iv) Hydroxylaminato Coordination Complexes And Pyrroloquinoline Quinone Cofactor Surrogates

A series of electron rich, air-stable hydroxylamine ligands and their strongly stabilized cerium(IV) hydroxylaminato complexes are described. Monotopic, ditopic, and tetratopic hydroxylaminato ligands are described. The synthesis and characterization of HLNOx, H2ODiNOx, H2PhNDiNOx, and H4TetraNOx were accomplished through modified literature procedures from their parent aryl bromides. The cerium(IV) complexes Ce(LNOx)4, Ce(ODiNOx)2 were synthesized by protonolysis reactions, crystallized, and characterized electrochemically and computationally. The cerium(IV) complexes exhibited significant stabilization of the Ce(III/IV) couple as observed in their cyclic voltammetry data. The pyrroloquinoline quinone (PQQ) is an important cofactor that shuttles redox equivalents in diverse metalloproteins. Quinoline 7,8-quinones have been synthesized and characterized as surrogates for PQQ to elucidate redox energetics within metalloenzyme active sites. The quinoline 7,8-quinones were synthesized, and the compounds were evaluated using solution electrochemistry. Together with a family of quinones, the products were evaluated computationally and used to generate a predictive correlation between a computed ΔG and the experimental reduction potentials. The methoxy substituted derivative exhibited catalytic activity in the dehydrogenation of benzylamines. The stoichiometric dehydrogenation of benzyl alcohols was also achieved with irradiation

Enzymatic reduction of acetophenone derivatives with a benzil reductase from Pichia glucozyma (KRED1-Pglu): electronic and steric effects on activity and enantioselectivity

A recombinant ketoreductase from Pichia glucozyma (KRED1-Pglu) was used for the enantioselective reduction of various mono-substituted acetophenones. Reaction rates of meta- and para-derivatives were consistent with the electronic effects described by \u3c3-Hammett coefficients; on the other hand, enantioselectivity was determined by an opposite orientation of the substrate in the binding pocket. Reduction of ortho-derivatives occurred only with substrates bearing substituents with low steric impact (i.e., F and CN). Reactivity was controlled by stereoelectronic features (C[double bond, length as m-dash]O length and charge, shape of LUMO frontier molecular orbitals), which can be theoretically calculated

Structure-activity approaches for prediction of chemical reactivity and pharmacological properties of some heterocyclic compounds

Benzodiazepine drugs are widely prescribed to treat many psychiatric and neurologic disorders. As its pharmacological action is exerted in a sensitive area of the brain; ''the central nervous system'', it is crucial to provide detailed reports on the chemistry of benzodiazepines, model the mechanism of action that occurs with GABAA receptors, identify the overlap with other modulators, as well as explore the structural requirements that better potentiate the receptor response to benzodiazepines. This dissertation consists of two original studies that consider the new lines of research related to benzodiazepines, particularly the identification of three new TMD binding sites. The first study provides, on the one hand, an overview of the chemistry of six Benzodiazepine basic rings starting from structural characteristics, electronic properties, Global/local reactivities, up to intermolecular interactions with long-range nucleophilic/electrophilic reactants. This was achieved by combining a DFT investigation with a quantitative MEP analysis on the vdW surface. On the other hand, the performed molecular docking simulations allowed identifying the best binding modes, binding interactions, and binding affinities with residues, which helped to validate the quantitative MEP analysis predictions. The second study was conducted on a dataset of [3H]diazepam derivatives. First, molecular docking simulation was used to initially screen the dataset and select the best ligand/target complexes. Afterwise, the best-docked complexes were refined by performing molecular dynamics simulation for 1000 picoseconds. For both simulations, the binding modes, binding interactions, and binding affinities were thoroughly discussed and compared with each other and with outcomes collected from the literature. Additionally, the good pharmacokinetic properties (ADME prediction) as well as compliance with all druglikeness rules were checked via in silico tools for all the dataset compounds. Finally, a QSAR analysis was carried out using an improved version of PLS regression. Briefly, the dataset is randomly split into 10 000 training and test sets that involve, respectively, 80% and 20% of chemicals. Subsequently, 10 000 statistical simulations were conducted that; after excluding outlying observations, yielded 10 000 best training models following the Bayesian Information Criterion. Among these 10 000 best models, the best predictors with the highest probability of occurrence were selected. As a consequence, the derived PLS regression equation explains 63.2% of the variability in BDZ activity around its mean. Furthermore, Internal and external validation metrics assure the robustness and predictability of the developed model. The developed model was interpreted based on literature investigations and a combination of implemented approaches

Multiscale modeling study of methanol oxidation by ion-modified MDH enzymes

Enzymes have been considered as molecular electrocatalysts due to their extraordinary characteristics such as their ability to accelerate reactions enormously, to operate under physiological conditions, and to produce fewer by-products during a catalytic reaction. However, enzyme based fuel cells have been reported to have power output and stability limitations, which are restricting the use of this kind of fuel cell to small electronic devices. Methanol dehydrogenase (MDH) is one such enzyme, which oxidizes methanol and other primary alcohols to their corresponding aldehydes. The active site of MDH contains a divalent cation (Ca2+), a co-factor pyrrolo-quinoline quinone (PQQ), several amino acids, and water molecules. Ca2+ ion holds the PQQ in place, and also acts as a Lewis acid, contributing to the methanol electro-oxidation reaction mechanism by this enzyme. Among the proposed mechanisms for methanol oxidation by MDH in the literature, the Hydride Transfer (H-T) mechanism seems, to the best of our knowledge, to be the preferred one under normal conditions. Work reported in the literature shows that the binding of the substrate and the reaction energy barrier for substrate oxidation by dehydrogenase enzymes is influenced by the nature of the ion in the enzyme active site. Thus, understanding the role of the ion in the active site of MDH as well as the methanol oxidation mechanism may have major impacts on alternative power sources research as they could lead to the development of new bio-inspired synthetic catalysts that could impact the use of methanol as fuel. In this study, the binding energy of methanol to the active site models of ion-modified MDH is determined and the effect of ion on methanol oxidation is investigated. It has been observed that the binding affinity of methanol and free energy barrier for the rate determining step of the H-T mechanism decreases as the ionic size increases. This shows that replacing the naturally occurring ion (Ca2+) with Mg2+, Sr2+ and Ba2+ affect the methanol oxidation process and binding of methanol to the active site of MDH. Density Functional Theory (DFT) calculations at BLYP/DNP theory level are performed using the DMOL3 module of the Materials Studio software to evaluate binding energies and investigate the reaction pathways. Furthermore, polarization curves corresponding to the electrochemical methanol oxidation in biofuel cell anodic chambers when MDH enzymes are used as the anode catalysts are obtained using the kinetic Monte Carlo approach. Microscopic reaction rates, obtained from free energy barriers evaluated using DFT and Transition State Theory (TST), are provided as inputs in a kinetic Monte Carlo (kMC) program (CARLOS 4.1) to model the oxidation process at macroscopic level. These simulations gave a better understanding of the catalytic methanol oxidation mechanism by MDH, helping evaluate the enzyme catalysis and their dependence on various factors like the nature of the ion in the MDH active site

Unpicking the Cause of Stereoselectivity in Actinorhodin Ketoreductase Variants with Atomistic Simulations

Ketoreductase enzymes (KRs) with a high degree of regio- and stereoselectivity are useful biocatalysts for the production of small, specific chiral alcohols from achiral ketones. Actinorhodin KR (actKR), part of a type II polyketide synthase involved in the biosynthesis of the antibiotic actinorhodin, can also turn over small ketones. In vitro studies assessing stereocontrol in actKR have found that, in the “reverse” direction, the wild-type (WT) enzyme’s mild preference for S-α-tetralol is enhanced by certain mutations (e.g., P94L) and entirely reversed by others (e.g., V151L) in favor of R-α-tetralol. Here, we employ computationally cost-effective atomistic simulations to rationalize these trends in WT, P94L, and V151L actKR using trans-1-decalone (1) as the model substrate. Three potential factors (FI–FIII) are investigated: frequency of pro-R vs pro-S reactive poses (FI) is assessed with classical molecular dynamics (MD), binding affinity of pro-R vs pro-S orientations (FII) is compared using the binding free energy method MM/PBSA, and differences in reaction barriers toward trans-1-decalol (FIII) are assessed by hybrid semiempirical quantum/classical (QM/MM) MD simulations with umbrella sampling, benchmarked with density functional theory. No single factor is found to dominate stereocontrol: FI largely determines the selectivity of V151L actKR, whereas FIII is more dominant in the case of P94L. It is also found that formation of S-trans-1-decalol or R-trans-1-decalol mainly arises from the reduction of the trans-1-decalone enantiomers (4aS,8aR)-1 or (4aR,8aS)-1, respectively. Our work highlights the complexity of enzyme stereoselectivity as well as the usefulness of atomistic simulations to aid the design of stereoselective biocatalysts

"Radical clock investigation with a metalloporphyrin enzyme model"

A significant tool for better understanding the complex nature of the cofactor of heme thiolate proteins such as Cytochromes P450 is the investigation of model compounds. In this context a new family of iron porphyrins has been synthesized by replacing the native thiolate ligand for a SO3- group coordinating the heme iron. The porphyrin mimics designed and synthesized during the course of this thesis were successfully used as catalytic oxidants in radical clock experiments. trans-2-Phenyl-methylcyclopropane was oxidized using PhIO and the porphyrin model. Analysis of the product distribution revealed a ratio of 9:1 of the non-rearranged cyclopropyl methanol over 1,1-allyl phenyl methanol. Given the rate of rearrangement k = 1.8·1011 sec -1 of the phenyl cyclopropyl methyl radical in solution, the life time of the intermediate radical cluster IC- H can be calculated as 625 fsec. This time is analogous to the lifetimes observed in enzymatic hydroxylations. It was proposed that this intermediate is not a free radical but instead a cluster containing a CH2 group carrying spin density joined to the spin system of the …H…O-Fe(III) porphyrin radical cation. The two routes to the final oxidized products, originating from this intermediate I - H, are C divergent, the unrearranged alcohol is formed via a concerted route whereas the rearranged product is produced from either a high-spin or low spin pathway. The hydroxylation proceeds by concerted non-synchronous ‘O’-insertion into the C-H bond of the methyl group

Where does the Oxygen go? – Pathways and Partitioning in Autothermal Pyrolysis

Autothermal fast pyrolysis (AFP), a variation of fast pyrolysis (FP) admitting a small amount of oxygen to provide process heat, has notable merit as a biomass-to-biofuels conversion process. As a result of heat transfer and product collection advantages over standard non-oxidative FP, it has the potential to generate a higher quality product in a more economically competitive manner. Initial investigation and process development efforts, first led by Kwang Ho Kim, and Joseph Polin, respectively, at the Bioeconomy Institute, generated many further questions about the process. One notable question was “where does the energy come from to support autothermal pyrolysis” – to which the obvious answer is exothermic reactions, but beyond that is not well understood. This work explored the chemistry underlying autothermal (partial oxidative) pyrolysis, as distinguished from standard non-oxidative pyrolysis of whole biomass. A critical literature review was carried out to develop a theoretical mechanistic framework which was then applied to a process base case, and experimentally tested. Key findings of the literature review included reaction mechanisms for the oxidation of: lignin interunit linkages, lignin monomers (and their functionalities), cellulose dimers and monomers, and hemicellulose units and functionalities. As discussed in the cellulose oxidation section, oxidation could occur by means of assisting glycosidic bond hydrolysis (either at a chain end (unzipping) or mid-chain (cracking)), effectively increasing levoglucosan yield, or by oxidation of ring functionalities. If cellulose’s substituents were to measurably react with Reactive Oxygen Species (ROS), the C6 primary alcohol would be the likely candidate, oxidizing to a C6 aldehyde or carboxylic acid, yet theoretically possible for ring-hydroxyls to oxidize. Similarly to celluloses, hemicellulose might be oxidized by four means; polymer-end-wise chain scission initiation (primary peeling), mid-chain scission, end-chain unit degradation (secondary peeling), or side-chain oxidation. Because of its branched and heterogeneous nature, and tendencies for decomposition of monomeric units following complete depolymerization during non-oxidative pyrolysis, fewer hemicellulose hexoses and pentoses would likely be recovered during oxidative pyrolysis. Lignin, also structurally diverse, has many possible routes for oxidation. From linkage studies, it is apparent that oxidation of the β- or γ-hydroxyl (in the case of a β-O-4’ linkage), or the α-hydroxyl (for α-O-4’ linkages) greatly weakens ether linkages, making susceptible to cleavage. Lignin’s phenolic substituents are prone to oxidation to aldehydes, carboxylic acids and ketones. Those side chains with reactive double bonds could be oxidatively cleaved or encourage a concerted decomposition reaction. Because products of oxidation can be further oxidized themselves, care must be taken in extrapolating out composition trends to scaled-operation. Even considering these routes which would effect a change in product composition, the most significant effects might come simply due to improved reaction conditions (heat transfer, heating rate, and ventilation (due to greater gas production)). Experimental work identified reactor limitations, and explored partial oxidation of a number of model compounds, representative of cellulose, hemicellulose, as well as lignin monomers and linkages. It is important to note that the findings of the micropyrolyzer studies are not directly applicable to continuous reactor chemistry due to the fundamentally different hydrodynamics and heat transfer. Additionally, biopolymer characteristics and interaction effects are not accounted for in the monomer and dimer model compound studies, as would be seen with whole biomass

Computational Structural Biology of S-nitrosylation of Cancer Targets

Nitric oxide (NO) plays an essential role in redox signaling in normal and pathological cellular conditions. In particular, it is well known to react in vivo with cysteines by the so-called S-nitrosylation reaction. S-nitrosylation is a selective and reversible post-translational modification that exerts a myriad of different effects, such as the modulation of protein conformation, activity, stability, and biological interaction networks. We have appreciated, over the last years, the role of S-nitrosylation in normal and disease conditions. In this context, structural and computational studies can help to dissect the complex and multifaceted role of this redox post-translational modification. In this review article, we summarized the current state-of-the-art on the mechanism of S-nitrosylation, along with the structural and computational studies that have helped to unveil its effects and biological roles. We also discussed the need to move new steps forward especially in the direction of employing computational structural biology to address the molecular and atomistic details of S-nitrosylation. Indeed, this redox modification has been so far an underappreciated redox post-translational modification by the computational biochemistry community. In our review, we primarily focus on S-nitrosylated proteins that are attractive cancer targets due to the emerging relevance of this redox modification in a cancer setting