Cytochrome c dissolved in 1-allyl-3-methylimidazolium chloride type ionic liquid undergoes a quasi-reversible redox reaction up to 140°C

Solubility of cytochrome c, a typical heme protein, in a various ionic liquids has been analyzed. The solubility has been discussed with polarity parameters of the ionic liquids. Both hydrogen bond basicity and dipolarity/polarizability of the ionic liquids were confirmed to be influential factors to control the solubilization of cytochrome c. Polar ionic liquids such as 1-butyl-3-methylimidazolium chloride and 1-allyl-3-methylimidazolium chloride solubilized cytochrome c at 80°C, and the dissolved cytochrome c was found to keep its redox activity in these ionic liquids. The redox response of the dissolved cytochrome c was detected in 1-allyl-3-methylimidazolium chloride up to 140°C.     

On the observation of a gem diol intermediate after O–O bond cleavage by extradiol dioxygenases. A hybrid DFT study

Catalytic cycle intermediates of a representative extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase (HPCD), have recently been characterized in crystallo by Kovaleva and Lipscomb. The structures of the identified species indicate that the process of inserting oxygen into the catechol ring occurs stepwise, and involves an Fe(II)-alkylperoxo intermediate and its O–O cleavage product: a gem diol species. In general, these findings corroborate the results of our previous computational studies; however, the fact that the gem diol species is stable enough to be observed in the crystal form seems to be at odds with the computational mechanistic data, which suggest that this intermediate should very readily and spontaneously convert to the epoxide species. The key question then becomes what is actually observed in the X-ray experiments. Here we report additional computational studies undertaken with the hope of clarifying this issue. The results obtained for active site models hosting both the native and the alternative (4-sulfonylcatechol) substrate indicate that the stability of the gem diol species is substantially increased if an electron and a proton are added. If this occurs somehow, the lifetime of the intermediate should be sufficient to observe it.     

Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria,using α-humulene as a model compound

Isoprenoids are an abundant and diverse class of natural products with various applications in the pharmaceutical, cosmetics and biofuel industries. A methanotroph-based biorefinery is an attractive scenario for the production of a variety of value-added compounds from methane, because methane is a promising alternative feedstock for industrial biomanufacturing. In this study, we metabolically engineered Methylotuvimicrobium alcaliphilum 20Z for de novo synthesis of a sesquiterpenoid from methane, using α-humulene as a model compound, via optimization of the native methylerythritol phosphate (MEP) pathway. Expression of codon-optimized α-humulene synthase from Zingiber zerumbet in M. alcaliphilum 20Z resulted in an initial yield of 0.04 mg/g dry cell weight. Overexpressing key enzymes (IspA, IspG, and Dxs) for debottlenecking of the MEP pathway increased α-humulene production 5.2-fold compared with the initial strain. Subsequently, redirecting the carbon flux through the Embden–Meyerhof–Parnas pathway resulted in an additional 3-fold increase in α-humulene production. Additionally, a genome-scale model using flux scanning based on enforced objective flux method was used to identify potential overexpression targets to increase flux towards isoprenoid production. Several target reactions from cofactor synthesis pathways were probed and evaluated for their effects on α-humulene synthesis, resulting in α-humulene yield up to 0.75 mg/g DCW with 18.8-fold enhancement from initial yield. This study first demonstrates production of a sesquiterpenoid from methane using methanotrophs as the biocatalyst and proposes potential strategies to enhance production of sesquiterpenoid and related isoprenoid products in engineered methanotrophic bacteria.     

A Curtin–Hammett mechanism for the copolymerization of ethylene and methyl acrylate monomer using a PymNox nickel catalyst as revealed by DFT computational studies

In this work, the copolymerization of ethylene and methyl acrylate (MA) as catalyzed by a new Ni-based PymNox organometallic compound was studied computationally. We recently tested the behavior of this type of catalyst in ethylene homopolymerization. Experimental results show that the unsubstituted catalyst Ni2 (aldimino PymNox catalyst) is unable to incorporate the MA monomer, whereas methyl-substituted Ni1 (acetaldimino PymNox catalyst) is able to achieve copolymerization. The reactivities of both catalysts were examined using density functional theory (DFT) models. Based on energy profiles calculated at the BP86 level, a Curtin–Hammett mechanism was proposed to explain the different reactivities of the catalysts in ethylene/MA copolymerization. Our results indicate that the methyl substituent Ni1 introduces additional steric hindrance that results in a catalyst conformation that is better suited to polar monomer incorporation. This model provides insights into the design of new catalysts to produce polar functionalized copolymers based on ethylene.     

Effect of surface hydroxyls on dimethyl ether synthesis over the γ-Al2O3 in liquid paraffin: a computational study

In a recent paper (Zuo et al., Appl Catal A 408:130–136, 2011), the mechanism of dimethyl ether (DME) synthesis from methanol dehydration over γ-Al₂O₃ (110) was studied using density functional theory (DFT). Using the same method, the effect of surface hydroxyls on γ-Al₂O₃ in liquid paraffin during DME synthesis from methanol dehydration is investigated. It is found that DME is mainly formed from two adsorbed CH₃O groups via methanol dehydrogenation on both dehydrated and hydrated γ-Al₂O₃ in liquid paraffin. No close correlation between catalytic activity and acid intensity was found. Before and after water adsorption at typical catalytic conditions (e.g., 553 K), the reaction rate is not obviously changed on γ-Al₂O₃(100) surface in liquid paraffin, but the reaction rate decreases by about 11 times on the (110) in liquid paraffin. Considering the area of the (110) and (100) surfaces under actual conditions, the catalytic activity decreased mainly because the Al3 sites on the (110) surface gradually become inactive. Catalytic activity decreased mainly due to surface hydrophilicity. The calculated results were consistent with the experiment.

DFT study of geometrical and vibrational features of a 3′,5′-deoxydisugar-monophosphate (dDSMP) DNA model in the presence of counterions and solvent

The B3LYP/6–31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li⁺, Na⁺, K⁺) and divalent (Mg²⁺) metal counterions in interaction with the charged PO₂^? group, on the geometrical and vibrational characteristics of the DNA fragments of 3′,5′-dDSMP, represented by four conformers (g⁺g⁺, g⁺t, g^?g^? and g^?t). All complexes were optimized through two solvation models [the explicit model (6H₂O) and the hybrid model (6H₂O/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li⁺, Na⁺, K⁺, Mg²⁺) always remain in the bisector plane of the O1–P–O2 angle. When these counterions are explicitly hydrated, the smallest counterions (Li⁺, Na⁺) deviate from the bisector plane, while the largest counterions (K⁺ and Mg²⁺) always remain in the same plane. On the other hand, the present calculations reveal that the g⁺g⁺ conformer is the most stable in the presence of monovalent counterions, while conformers g⁺t and g^?t are the most stable in the presence of the divalent counterion Mg²⁺. Finally, the hybrid solvation model seems to be in better agreement with the available crystallographic and spectroscopic (Raman) experiments than the explicit model. Indeed, the six conformational torsions of the C4′-C3′-O3′-PO^?₂-O5′-C5′-C4′ segment of all complexes of the g^?g^? conformer in 6H₂O/Continuum remain similar to the available experimental data of A- and B-DNA forms. The calculated wavenumbers of the g⁺g⁺ conformer in the presence of the monovalent counterion and of g^?t conformer in presence of the divalent counterion in the hybrid model are in good agreement with the Raman experimental data of A- and B-DNA forms. In addition, the maximum deviation between the calculated wavenumbers in the 6H₂O/Continuum for the g⁺g⁺ conformer and experimental value measured in an aqueous solution of the DMP-Na⁺ complex, is <1.07% for the PO₂^? (asymmetric and symmetric) stretching modes and <2.03% for the O5′-C5′ and O3′-C3′ stretching modes.

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Graphical abstract dDSMP-(OO)^? Mg²⁺/6W/Continuum

     

Ground state intermolecular proton transfer in the supersystems thymine–(H2O)n and thymine–(CH3OH)n, n = 1,2: a theoretical study

Twelve binary and eight ternary supersystems between thymine and methanol, and water were investigated in the ground state at the B3LYP and MP2 levels of theory using B3LYP/6-311 + + G(d,p) basis functions. The thermodynamics of complex formations and the mechanisms of intermolecular proton transfers were clarified in order to find out the most stable H-boned system. It was established that the energy barriers of the water/methanol-assisted proton transfers are several times lower than those of the intramolecular proton transfers in the DNA/RNA bases. The X-ray powder spectra of thymine, and this precrystallized from water and methanol showed that water molecules are incorporated in the crystal lattice of thymine forming H-bridges between thymine molecules. Figure Intermolecular H-bonding of thymine     

A Monte Carlo simulation study to predict the solubility of H2S in ionic liquids with 1-butyl-3-methylimidazolium ([C4mim+]) cation and tetrafluoroborate ([BF4−]), hexaflorophosphate ([PF6−]) and bis(trifluoromethanesulfonyl)amide ([Tf2N−]) anions

The solubilities of H₂S in ionic liquids, 1-butyl-3-methylimidazolium tetrafluoroborate ([C₄mim⁺][BF₄^?]), 1-butyl-3-methylimidazolium hexaflorophosphate ([C₄mim⁺][PF₆^?]) and -butyl-3-methylimidazolium tetrafluoroborate bis(trifluoromethanesulphonyl)amide ([C₄mim⁺][Tf₂N^?]) are predicted using isothermal–isobaric Gibbs ensemble Monte Carlo method (NPT-GEMC) at temperatures ranging from 333 to 453 K and pressure up to 20 bar. The low pressure points (up to 3 bar) of the absorption isotherms are fitted to a straight line to get a rough estimation of the Henry’s law constants. The van’t Hoff relationship is used to estimate the partial molar enthalpy of the absorption. The obtained results are in a good agreement with Jou and Mather [18], and Jalili et al. [13]. When comparing the solubility in ILs, it is found that H₂S solubility is highest for [C₄mim⁺][Tf₂N^?], followed by [C₄mim⁺][PF₆^?]. The lowest solubility is observed in [C₄mim⁺][BF₄^?]. The highest solubility in [C₄mim⁺][Tf₂N^?] is consistent with Jalili et al. [13]. However, their results indicate slightly higher solubility in [C₄mim⁺][BF₄^?] than in [C₄mim⁺][PF₆^?], and do not agree with the predictions. Upon absorption, the molar volumes of the mixtures decrease linearly, showing only small changes in volume. The effect of H₂S absorption on ILs is further studied by calculating the radial distribution functions between the ions. The results indicate that the solute molecules accommodate themselves in the cavities without significantly disturbing the ionic arrangement of the ions, similar to CO₂ absorption in ILs. The spatial distribution functions show similar spatial distribution for H₂S around cation in all of the studied ILs, whereas the distribution around anion depends on the shape and flexibility of the anion. The mechanism of H₂S absorption is studied by computing the van der Waals (VDW) and electrostatic (ELEC) energies. It is observed that the solubility of H₂S in the studied ILs is primarily controlled by VDW interaction. When comparing the interaction of H₂S with the ions, it is found that solute molecules interact with cations mainly due to VDW interaction. Both VDW and ELEC energies contribute in the interaction between H₂S and anions.     

Presence of a [3Fe–4S] cluster in a PsaC variant as a functional component of the photosystem I electron transfer chain in <Emphasis Type="Italic">Synechococcus</Emphasis> sp. PCC 7002

A site-directed C14G mutation was introduced into the stromal PsaC subunit of Synechococcus sp. strain PCC 7002 in vivo in order to introduce an exchangeable coordination site into the terminal F_B [4Fe–4S] cluster of Photosystem I (PSI). Using an engineered PSI-less strain (psaAB deletion), psaC was deleted and replaced with recombinant versions controlled by a strong promoter, and the psaAB deletion was complemented. Modified PSI accumulated at lower levels in this strain and supported slower photoautotrophic growth than wild type. As-isolated PSI complexes containing PsaC_C14G showed resonances with g values of 2.038 and 2.007 characteristic of a [3Fe–4S]¹⁺ cluster. When the PSI complexes were illuminated at 15 K, these resonances partially disappeared and two new sets of resonances appeared. The majority set had g values of 2.05, 1.95, and 1.85, characteristic of F_A ^?, and the minority set had g values of 2.11, 1.90, and 1.88 from F_B′ in the modified site. The S?=?1/2 spin state of the latter implied the presence of a thiolate as the terminal ligand. The [3Fe–4S] clusters could be partially reconstituted with iron, producing a larger population of [4Fe–4S] clusters. Rates of flavodoxin reduction were identical in PSI complexes isolated from wild type and the PsaC_C14G variant strain; this implied equivalent capacity for forward electron transfer in PSI complexes that contained [3Fe–4S] and [4Fe–4S] clusters. The development of this cyanobacterial strain is a first step toward translation of in vitro PSI-based biosolar molecular wire systems in vivo and provides new insights into the formation of Fe/S clusters.     

Discovery of 1-benzoyl-3-cyanopyrrolo[1,2-a]quinolines as a new series of apoptosis inducers using a cell- and caspase-based high-throughput screening assay. 2: Structure–activity relationships of the 4-, 5-, 6-, 7- and 8-positions

As a continuation of our efforts to discover and develop the apoptosis inducing 1-benzoyl-3-cyanopyrrolo[1,2-a]quinolines as potential anticancer agents, we explored substitutions at the 4-, 5-, 6-, 7- and 8-positions of pyrrolo[1,2-a]quinoline. SAR studies showed that substitution at the 6-position by a small group such as Cl resulted in potent compounds. Substitutions at the 5- and 8-positions were tolerated while substitutions at the 4- and 7-position led to inactive compounds. Several compounds, including 2c, 3a, 3b and 3f, were found to be highly active against human breast cancer cells T47D with EC₅₀ values of 0.053–0.080 μM, but much less active against human colon cancer cells HCT116 and hepatocellular carcinoma cancer cells SNU398 in the caspase activation assay. Compound 3f also was found to be highly active with a GI₅₀ value of 0.018 μM against T47D cells in a growth inhibition assay.