Isomerization Step Research Articles

MpeV is a lyase isomerase that ligates a doubly linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus

Synechococcus cyanobacteria are widespread in the marine environment, as the extensive pigment diversity within their light-harvesting phycobilisomes enables them to utilize various wavelengths of light for photosynthesis. The phycobilisomes of Synechococcus sp. RS9916 contain two forms of the protein phycoerythrin (PEI and PEII), each binding two chromophores, green-light absorbing phycoerythrobilin and blue-light absorbing phycourobilin. These chromophores are ligated to specific cysteines via bilin lyases, and some of these enzymes, called lyase isomerases, attach phycoerythrobilin and simultaneously isomerize it to phycourobilin. MpeV is a putative lyase isomerase whose role in PEI and PEII biosynthesis is not clear. We examined MpeV in RS9916 using recombinant protein expression, absorbance spectroscopy, and tandem mass spectrometry. Our results show that MpeV is the lyase isomerase that covalently attaches a doubly linked phycourobilin to two cysteine residues (C50, C61) on the β-subunit of both PEI (CpeB) and PEII (MpeB). MpeV activity requires that CpeB or MpeB is first chromophorylated by the lyase CpeS (which adds phycoerythrobilin to C82). Its activity is further enhanced by CpeZ (a homolog of a chaperone-like protein first characterized in Fremyella diplosiphon). MpeV showed no detectable activity on the α-subunits of PEI or PEII. The mechanism by which MpeV links the A and D rings of phycourobilin to C50 and C61 of CpeB was also explored using site-directed mutants, revealing that linkage at the A ring to C50 is a critical step in chromophore attachment, isomerization, and stability. These data provide novel insights into β-PE biosynthesis and advance our understanding of the mechanisms guiding lyase isomerases.

Facile depolymerization of microcrystalline cellulose in ionic liquid medium catalyzed by carbon materials as catalysts

This study highlights novel approach for complete utilization of cellulose using metal immobilized modified activated carbon M-ACS and metal immobilized cellulose composite M ​− ​C in ionic liquid medium. Catalytic activity of the system was improved using metal immobilized modified activated carbon with varying impregnation ratios (0.5–25 ​wt%) respectively. Maximum yield of Total reducing sugars (TRS) was 64.68% and 5-Hydroxymethylfurfural (5-HMF) was 54.76% using Chromium immobilized modified activated carbon catalyst (15 ​wt%) in a reaction time of 60 ​min ​at 120 ​°C. Also, Chromium immobilized cellulose composite i.e. Cr–C: 20 ​wt% gave maximum 48.78% (TRS) and 39.67% (5-HMF) yield under similar operating conditions. Results revealed that metal immobilized cellulose composite M ​− ​C also gave appreciable product yield but at a lower rate than M-ACS. Also, the efficacy of cellulose pretreatment was evaluated using acids and results were found to be significant and effective. To understand hydrolysis rate during isomerization and dehydration steps, synthetic glucose and fructose solutions of varying concentration (3–45 ​wt%) were used. Complete utilization of cellulose with suitable acidity of the process has been proposed i.e cellulose solubilization without compromising with 5-HMF yield. Recyclability of catalyst, composite and ionic liquid at 1 ​atm pressure facilitate the economical and feasible production of TRS and 5-HMF. Development of environment friendly and economical ionic liquid/catalyst system can be considered as a potential alternative for the conversion of cellulose to bio-based products.

Illuminating anti-hydrozirconation: controlled geometric isomerization of an organometallic species.

A general strategy to enable the formal anti-hydrozirconation of arylacetylenes is reported that merges cis-hydrometallation using the Schwartz Reagent (Cp2ZrHCl) with a subsequent light-mediated geometric isomerization at λ = 400 nm. Mechanistic delineation of the contra-thermodynamic isomerization step indicates that a minor reaction product functions as an efficient in situ generated photocatalyst. Coupling of the E-vinyl zirconium species with an alkyne unit generates a conjugated diene: this has been leveraged as a selective energy transfer catalyst to enable E → Z isomerization of an organometallic species. Through an Umpolung metal–halogen exchange process (Cl, Br, I), synthetically useful vinyl halides can be generated (up to Z : E = 90 : 10). This enabling platform provides a strategy to access nucleophilic and electrophilic alkene fragments in both geometric forms from simple arylacetylenes.

Effect of charge-transfer enhancement on the efficiency and rotary mechanism of an oxindole-based molecular motor.

Harvesting energy and converting it into mechanical motion forms the basis for both natural and artificial molecular motors. Overcrowded alkene-based light-driven rotary motors are powered through sequential photochemical and thermal steps. The thermal helix inversion steps are well characterised and can be manipulated through adjustment of the chemical structure, however, the insights into the photochemical isomerisation steps still remain elusive. Here we report a novel oxindole-based molecular motor featuring pronounced electronic push–pull character and a four-fold increase of the photoisomerization quantum yield in comparison to previous motors of its class. A multidisciplinary approach including synthesis, steady-state and transient absorption spectroscopies, and electronic structure modelling was implemented to elucidate the excited state dynamics and rotary mechanism. We conclude that the charge-transfer character of the excited state diminishes the degree of pyramidalisation at the alkene bond during isomerisation, such that the rotational properties of this oxindole-based motor stand in between the precessional motion of fluorene-based molecular motors and the axial motion of biomimetic photoswitches.

Visible-Light-Driven Rotation of Molecular Motors in Discrete Supramolecular Metallacycles.

The organization of molecular motors in supramolecular assemblies to allow the amplification and transmission of motion and collective action is an important step toward future responsive systems. Metal-coordination-driven directional self-assembly into supramolecular metallacycles provides a powerful strategy to position several motor units in larger structures with well-defined geometries. Herein, we present a pyridyl-modified molecular motor ligand (MPY) which upon coordination with geometrically distinct di-Pt(II) acceptors assembles into discrete metallacycles of different sizes and shapes. This coordination leads to a red-shift of the absorption bands of molecular motors, making these motorized metallacycles responsive to visible light. Photochemical and thermal isomerization experiments demonstrated that the light-driven rotation of the motors in the metallacycles is similar to that in free MPY in solution. CD studies show that the helicity inversions associated with each isomerization step in the rotary cycle are preserved. To explore collective motion, the trimeric motor-containing metallacycle was aggregated with heparin through multiple electrostatic interactions, to construct a multi-component hierarchical system. SEM, TEM, and DLS measurements revealed that the photo- and thermal-responsive molecular motor units enabled selective manipulation of the secondary supramolecular aggregation process without dissociating the primary metallacycle structures. These visible-light-responsive metallacycles, with intrinsic multiple rotary motors, offer prospects for cooperative operations, dynamic hierarchical self-assembled systems, and adaptive materials.

Manganese-Catalyzed Hydroboration of Terminal Olefins and Metal-Dependent Selectivity in Internal Olefin Isomerization-Hydroboration.

In the past decade, the use of earth-abundant metals in homogeneous catalysis has flourished. In particular, metals such as cobalt and iron have been used extensively in reductive transformations including hydrogenation, hydroboration, and hydrosilylation. Manganese, on the other hand, has been considerably less explored in these reductive transformations. Here, we report a well-defined manganese complex, [Mn(iPrBDI)(OTf)2] (2a; BDI = bipyridinediimine), that is an active precatalyst in the hydroboration of a variety of electronically differentiated alkenes (>20 examples). The hydroboration is specifically selective for terminal alkenes and occurs with exclusive anti-Markovnikov selectivity. In contrast, when using the analogous cobalt complex [Co(iPrBDI)(OTf)2] (3a), internal alkenes are hydroborated efficiently, where a sequence of isomerization steps ultimately leads to their hydroboration. The contrasting terminal versus internal alkene selectivity for manganese and cobalt was investigated computationally and is further discussed in the herein-reported study.

Positioning Bacillus subtilis as terpenoid cell factory.

SummaryIncreasing demands for bioactive compounds have motivated researchers to employ micro‐organisms to produce complex natural products. Currently, Bacillus subtilis has been attracting lots of attention to be developed into terpenoids cell factories due to its generally recognized safe status and high isoprene precursor biosynthesis capacity by endogenous methylerythritol phosphate (MEP) pathway. In this review, we describe the up‐to‐date knowledge of each enzyme in MEP pathway and the subsequent steps of isomerization and condensation of C5 isoprene precursors. In addition, several representative terpene synthases expressed in B. subtilis and the engineering steps to improve corresponding terpenoids production are systematically discussed. Furthermore, the current available genetic tools are mentioned as along with promising strategies to improve terpenoids in B. subtilis, hoping to inspire future directions in metabolic engineering of B. subtilis for further terpenoid cell factory development.

Strong and Weakly Acidic OH Groups of HY Zeolite into the Different Routes of Cyclohexene Reaction: An IR Operando Study

IR operando study of cyclohexene reaction on HY zeolite (Si/Al = 15) was performed to determine the role of the OH groups located in the different zeolitic cages and the silanol groups (SiOH). A parallel between the product yield and type and amount of OH groups poisoned by coking and pyridine pulses was established. The role of silanol and zeolitic OH groups during cyclohexene conversion and the coverage rate of surface groups of the dealuminated HY zeolite, were evaluated by FT-IR operando study. At the beginning of the reaction, zeolite exhibited a very intense deactivation due to coke formation. Coke is initially deposited on strong acid sites, inhibiting the H-transfer activity. Further, coke formation decreased. At this stage of the reaction, pyridine addition markedly decreased the isomerization activity. In parallel, it is noted that mainly SiOH, OH groups at hexagonal prisms, and perturbed OH groups in sodalite cages were mainly affected, indicating that these groups are responsible for the isomerization steps. These results showed that even weakly acidic sites are active sites for isomerization reaction. In cyclohexene conversion, hydrogen transfer occurs on supercage OH groups of HY zeolite. In contrast, perturbed sodalite OH and hexagonal prisms OH, as well as SiOH groups, are responsible for isomerization steps, as revealed by pyridine pulse addition during the reaction.

Fluorine Effects for Tunable C–C and C–S Bond Cleavage in Fluoro-Julia–Kocienski Intermediates

Classical Julia–Kocienski fluoroolefination represents an indispensable platform for the construction of monofluoroalkenes. Nevertheless, its complex multistep mechanistic manifold along with the u...

Impact of Thermal Treatment of Nb2O5 on Its Performance in Glucose Dehydration to 5-Hydroxymethylfurfural in Water.

The cascade dehydration of glucose to 5-hydroxymethylfurfural (HMF) was carried out in water over a series of Nb2O5 catalysts, which were derived from the thermal treatment of niobic acid at 300 and 550 °C, under air or inert atmosphere. Amorphous niobic acid showed high surface area (366 m2/g) and large acidity (2.35 mmol/g). With increasing the temperature of the thermal treatment up to 550 °C, the amorphous Nb2O5 was gradually transformed into a pseudohexagonal phase, resulting in a decrease in surface area (27–39 m2/g) and total acidity (0.05–0.19 mmol/g). The catalysts’ performance in cascade dehydration of glucose realized in pure water was strongly influenced by the total acidity of these materials. A remarkable yield of 37% HMF in one-pot reaction in water was achieved using mesoporous amorphous niobium oxide prepared by thermal treatment of niobic acid at 300 °C in air. The best-performing catalyst displayed a total acidity lower than niobic acid (1.69 mmol/g) which afforded a correct balance between a high glucose conversion and limited further conversion of the target product to numerous polymers and humins. On the other hand, the treatment of niobic acid at 550 °C, independently of the atmosphere used during the sample preparation (i.e., air or N2), resulted in Nb2O5 catalysts with a high ratio of Lewis to Brønsted acid sites and poor total acidity. These materials excelled at catalyzing the isomerization step in the tandem process.

Recent Advances in Carboxylation of Furoic Acid into 2,5-Furandicarboxylic Acid: Pathways towards Bio-Based Polymers.

2,5-furandicarboxylic acid (FDCA) is one of the most important bio-sourced building blocks and several routes have been reported for its synthesis. FDCA is presumed to be an ideal green alternative to terephthalate, which is one of the predominant monomers in polymer industry. This Minireview concerns the synthesis of FDCA by using various carboxylation reactions and discusses the synthesis of FDCA starting from furoic acid and CO2 and using different catalytic and stoichiometric processes. This process is of high interest, as it avoids the glucose isomerization step and selectivity issues observed during the 5-hydroxymethylfurfural oxidation step of the current alternative route to FDCA. Discussion focuses on the main parameters that govern selectivity and activity in the carboxylation processes. Moreover, various previously described processes, such as the Henkel reaction and enzymatic, homogeneous catalytic, and photoelectrocatalytic processes, are also discussed.

Structure, Stability, and Spectroscopic Properties of Small Acetonitrile Cation Clusters.

Ionization and fragmentation pathways induced by ionizing agents are key to understanding the formation of complex molecules in astrophysical environments. Acetonitrile (CH3CN), the simplest organic nitrile, is an important molecule present in the interstellar medium. In this work, DFT and MP2 calculations were performed in order to obtain the low energy structures of the most relevant cations formed from electron-stimulated ion desorption of CH3CN ices. Selected reaction pathways and spectroscopic properties were also calculated. Our results indicate that the most stable acetonitrile cation structure is CH2CNH+ and that hydrogenation can occur successively without isomerization steps until its complete saturation. Moreover, the stability of distinct cluster families formed from the interaction of acetonitrile with small fragments, such as CHn+, C2Hn+, and CHnCNH+, is discussed in terms of their respective binding energies. Some of these molecular clusters are stabilized by hydrogen bonds, leading to species whose infrared features are characterized by a strong redshift of the N-H stretching mode. Finally, the rotational spectra of CH3CN and protonated acetonitrile, CH3CNH+, were simulated using distinct computational protocols based on DFT, MP2, and CCSD(T) considering centrifugal distortion, vibrational-rotational coupling, and vibrational anharmonicity corrections. By adopting an empirical scaling procedure for calculating spectroscopic parameters, we were able to estimate the rotational frequencies of CH3CNH+ with an expected average error below 1 MHz for J values up to 10.

The reconstruction and biochemical characterization of ancestral genes furnish insights into the evolution of terpene synthase function in the Poaceae

Key MessageDistinct catalytic features of the Poaceae TPS-a subfamily arose early in grass evolution and the reactions catalyzed have become more complex with time.The structural diversity of terpenes found in nature is mainly determined by terpene synthases (TPS). TPS enzymes accept ubiquitous prenyl diphosphates as substrates and convert them into the various terpene skeletons by catalyzing a carbocation-driven reaction. Based on their sequence similarity, terpene synthases from land plants can be divided into different subfamilies, TPS-a to TPS-h. In this study, we aimed to understand the evolution and functional diversification of the TPS-a subfamily in the Poaceae (the grass family), a plant family that contains important crops such as maize, wheat, rice, and sorghum. Sequence comparisons showed that aside from one clade shared with other monocot plants, the Poaceae TPS-a subfamily consists of five well-defined clades I–V, the common ancestor of which probably originated very early in the evolution of the grasses. A survey of the TPS literature and the characterization of representative TPS enzymes from clades I–III revealed clade-specific substrate and product specificities. The enzymes in both clade I and II function as sesquiterpene synthases with clade I enzymes catalyzing initial C10-C1 or C11-C1 ring closures and clade II enzymes catalyzing C6-C1 closures. The enzymes of clade III mainly act as monoterpene synthases, forming cyclic and acyclic monoterpenes. The reconstruction and characterization of clade ancestors demonstrated that the differences among clades I–III were already present in their ancestors. However, the ancestors generally catalyzed simpler reactions with less double-bond isomerization and fewer cyclization steps. Overall, our data indicate an early origin of key enzymatic features of TPS-a enzymes in the Poaceae, and the development of more complex reactions over the course of evolution.

Understanding the mechanism of cis–trans isomerism in photo-active palladium(II) complexes derived from the N,N-di-substituted benzoylthioureas

The reaction of a series of N,N-di-substituted aroylthioureas (HL1−3; L1 = H, L2 = Cl, L3 = OMe) with the Pd(II) centre in K2PdCl4 leads to cis-[Pd(L1−3-κS,O)2] complexes exclusively which then undergoes photo-induced isomerism to the trans-[Pd(L1−3-κS,O)2] isomer upon broadband UV irradiation. The photochemical isomerization allows these unstable trans-[Pd(L1−3-κS,O)2] products to be isolated in pure forms if the conversion is completed in acetonitrile after slow evaporation of the solvent. The molecular structures of both cis-[Pd(L2-κS,O)2] and trans-[Pd(L2-κS,O)2] isomers have been determined by single-crystal X-ray diffraction. Upon dissolving trans-[Pd(L1−3-κS,O)2] in chloroform in the dark, spontaneous trans → cis isomerism occurs. In-situ laser photolysis in conjunction with NMR spectroscopy allows the time course of both these photochemical and thermal isomerisations to be monitored. The results indicate that a photostationary state is reached, that the back reaction is promoted both photochemically and thermally, and that the established photostationary state reverts back to the initial composition once photolysis stops. The presence of an electron-withdrawing chloro substituent on the para position of the phenyl ring increases the rate of the thermally initiated trans → cis isomerisation step. Furthermore, the addition of trace amounts of the HL1−3 ligands, a coordinating solvent or a two electron donor such as pyridine also speeds up this process in accordance with an associative mechanism. Mixed-ligand complexes were detected by reverse phase (RP) chromatography when cross-reactions were performed in accordance with this hypothesis. All the experimental evidence fits with a mechanism involving a competitive photochemical and associative ligand exchange.

The investigation on ibuprofen methyl ester isomerization as a fundamental stage in the preparation of antipyretic medicine (R)-ibuprofen: a computational insight

The isomerization of the widely used nonsteroid anti-inflammatory medicine ibuprofen was investigated by employing the hybrid density functional theory. The rearrangement reaction of (R)-(−)-ibuprofen to its (S)-( +)-isomer consists of a [1,3]-hydrogen shifts. This process causes an inversion of configuration at C7. The obtained results revealed that the rate-limiting step of ibuprofen isomerization is the excitation of (R)-(−)-ibuprofen methyl ester in its initial structure to the first excited singlet state S1 at λ = 231 nm. In addition, the C7-H19 distance was investigated and analyzed for the excited singlet to obtain more information about the isomerization reaction occurring upon excitation. Based upon the calculations, passing through a barrier of around 72 kcal/mol is necessary for this isomerization reaction. Furthermore, the -0.944 kcal/mol of thermodynamic stability of the (S)-( +)-ibuprofen methyl ester elucidates the more photostability of (S)-( +)-ibuprofen methyl ester than (R)-(−)-isomer. The overall reactions with the different components belonging to each reaction step have been fully analyzed.

Isomerization of Glucose to Fructose in Hydrolysates from Lignocellulosic Biomass Using Hydrotalcite

The isomerization of glucose-containing hydrolysates to fructose is a key step in the process from lignocellulosic biomass to the platform chemical hydroxymethylfurfural. We investigated the isomerization reaction of glucose to fructose in water catalyzed by hydrotalcite. Catalyst characterization was performed via IR, XRD, and SEM. Firstly, glucose solutions at pH-neutral conditions were converted under variation of the temperature, residence time, and catalyst loading, whereby a maximum of 25 wt.% fructose yield was obtained at a 38 wt.% glucose conversion. Secondly, isomerization was performed at pH = 2 using glucose solutions as well as glucose-containing hydrolysates from lignocellulosic biomass. Under acidic conditions, the hydrotalcite loses its activity for isomerization. Consequently, it is unavoidable to neutralize the acidic hydrolysate before the isomerization step with an inexpensive base. As a neutralizing agent NaOH is preferred over Ba(OH)2, since higher fructose yields are achieved with NaOH. Lastly, a pH-neutral hydrolysate from lignocellulose was subjected to isomerization, yielding 16 wt.% fructose at a 32 wt.% glucose conversion. This work targets the application of catalytic systems on real biomass-derived samples.

Chemical Synthesis and Isolation of Trans‐Palmitoleic Acid (Trans‐C16:1 n‐7) Suitable for Nutritional Studies

AbstractTrans‐palmitoleic acid (trans‐9 C16:1, or trans‐C16:1 n‐7, TPA) is typically found in ruminant‐derived foods (milk and meat). Of note, previous epidemiological studies associated high levels of circulating TPA with a lower risk of type 2 diabetes and metabolic syndrome in humans. At the current time, TPA intakes in humans are ensured by ruminant‐derived foods. However, due to the very low commercial availability of TPA, there are no supplementation studies carried out so far. Therefore, the ability for dietary TPA to prevent type 2 diabetes and metabolic syndrome has never been experimentally assessed. Here, a method (among others) to get dozens of grams of pure TPA as ethyl ester, to perform dedicated supplementation studies, is reported. For that purpose, it starts from food sources containing high amounts of cis‐palmitoleic acid (cis‐9 C16:1, or cis‐C16:1 n‐7, CPA), dealing with fatty acids ethyl esters all along the experiment. CPA is purified with flash liquid chromatography, then submitted to a cis/trans isomerization step. Finally, TPA is separated from CPA by low‐temperature crystallization in methanol. The final product is fully characterized by 1H and 13C nuclear magnetic resonance spectrometry. It is possible to produce ≈70 g of 85%‐purity TPA suitable for nutritional studies.Practical Applications: The synthesized trans‐palmitoleic acid may serve for supplementation (or nutritional) studies aiming at unravelling its physiological impacts suggested by epidemiological work. Depending on the amount of synthesized trans‐palmitoleic acid, one may carry out nutritional studies on rodents or even on humans.

Iridium catalysts featuring amine-containing ligands for the dehydrogenation of formic acid

The use of protic ligands to generate metal-ligand bifunctional catalysts has proved an excellent strategy to enhance the catalytic activity in formic acid dehydrogenation. We present here synthetic routes for complexes of general formula [Ir(H)2(IPr)(PR3)(CH3CN)2]BF4 (1a-c), [Ir (8-AQ)(H)2(IPr)(PR3)]BF4 (2a-c and 3), and [Ir(IPr)(C-N)(8-AQ)H]BF4 (5a-c) (8-AQ = 8-aminoquinoline; IPr = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene; C-N = 1-phenylpiridine-1H, 1-phenylpirazol-1H or 2-(p-tolyl-1H)pyridine-1H). Complexes 2a-c, 3, 5a and c were evaluated as catalysts for the dehydrogenation of formic acid in water. The nature of the phosphane in complexes 2a-c and 3 affects drastically the catalytic activity, with more basic and less encumbered phosphanes bringing about better performances. DFT calculations suggest that the coordinated NH2 moiety of the 8-AQ ligand plays a crucial role throughout the catalytic cycle. Two key steps are the protonation of the hydride ligand directed by the NH2 moiety (H2 formation), and the hydride abstraction to regenerate the dihydride active species (CO2 formation). Complexes 5a and 5c do not improve the results obtained with 2a-c and 3, probably due to the fact that a preactivation step is required. This may be attributable to an isomerization step that places the NH2, initially trans to the hydride ligand, in cis position.

PIN1 Provides Dynamic Control of MYC in Response to Extrinsic Signals.

PIN1 is a phosphorylation-directed member of the peptidyl-prolyl cis/trans isomerase (PPIase) family that facilitates conformational changes in phosphorylated targets such as c-MYC (MYC). Following signaling events that mediate phosphorylation of MYC at Serine 62, PIN1 establishes structurally distinct pools of MYC through its trans-cis and cis-trans isomerization activity at Proline 63. Through these isomerization steps, PIN1 functionally regulates MYC’s stability, the molecular timing of its DNA binding and transcriptional activity, and its subnuclear localization. Recently, our group showed that Serine 62 phosphorylated MYC can associate with the inner basket of the nuclear pore (NP) in a PIN1-dependent manner. The poised euchromatin at the NP basket enables rapid cellular response to environmental signals and cell stress, and PIN1-mediated trafficking of MYC calibrates this response. In this perspective, we describe the molecular aspects of PIN1 target recognition and PIN1’s function in the context of its temporal and spatial regulation of MYC.

Stereodivergent Anion Binding Catalysis with Molecular Motors.

A photoresponsive chiral catalyst based on an oligotriazole‐functionalized unidirectional molecular motor has been developed for stereodivergent anion binding catalysis. The motor function controls the helical chirality of supramolecular assemblies with chloride anions, which by means of chirality transfer enables the enantioselective addition of a silyl ketene acetal nucleophile to oxocarbenium cations. Reversal of stereoselectivity (up to 142 % Δee) was achieved through rotation of the motor core induced by photochemical and thermal isomerization steps.