Base-catalyzed Research Articles

Ornithine carbamoyltransferase from psychrophiles to thermophiles: structural evolution of catalytic fold to accommodate physiological diversity.

Here, we have analyzed the enzyme ornithine carbamoyltransferase (OCTase) in different classes of microorganisms belonging to psychrophiles, mesophiles and thermophiles. This OCTase catalyzes the formation of citrulline from carbamoyl phosphate (CP) and ornithine (ORN) in arginine biosynthesis pathway and has certain unique adaptations to regulate metabolic pathways in extreme conditions. The tertiary structure of OCTase showed two binding domains, the CP domain and ORN-binding domain at N and C terminals, respectively. We propose general acid-base catalysis in Pseudomonas gessardii between His259 and Asp220 in which later may act as a recipient of proton in the process. The comparative docking analysis showed that substrate-binding loops have been evolved to accommodate their lifestyles across the physiological temperature range where two substrates bind on two distinct loops in psychrophiles and mesophiles, whereas both the substrates bind on a single-substrate-binding loop in thermophiles and bring down the flexibility of the active site pocket to improve its evolutionary fitness.

Cover Feature: Lewis Base Catalysis Enables the Activation of Alcohols by means of Chloroformates as Phosgene Substitutes (ChemCatChem 22/2020)

Cover Feature: Lewis Base Catalysis Enables the Activation of Alcohols by means of Chloroformates as Phosgene Substitutes (ChemCatChem 22/2020)

Correction to “The Catalytic Acid–Base in GH109 Resides in a Conserved GGHGG Loop and Allows for Comparable α-Retaining and β-Inverting Activity in an N-Acetylgalactosaminidase from Akkermansia muciniphila”

Correction to “The Catalytic Acid–Base in GH109 Resides in a Conserved GGHGG Loop and Allows for Comparable α-Retaining and β-Inverting Activity in an <i>N</i>-Acetylgalactosaminidase from <i>Akkermansia muciniphila</i>”

Production of Aromatic Compounds by Catalytic Depolymerization of Technical and Downstream Biorefinery Lignins.

Lignocellulosic materials are promising alternatives to non-renewable fossil sources when producing aromatic compounds. Lignins from Populus salicaceae. Pinus radiata and Pinus pinaster from industrial wastes and biorefinery effluents were isolated and characterized. Lignin was depolymerized using homogenous (NaOH) and heterogeneous (Ni-, Cu- or Ni-Cu-hydrotalcites) base catalysis and catalytic hydrogenolysis using Ru/C. When homogeneous base catalyzed depolymerization (BCD) and Ru/C hydrogenolysis were combined on poplar lignin, the aromatics amount was ca. 11 wt.%. Monomer distributions changed depending on the feedstock and the reaction conditions. Aqueous NaOH produced cleavage of the alkyl side chain that was preserved when using modified hydrotalcite catalysts or Ru/C-catalyzed hydrogenolysis in ethanol. Depolymerization using hydrotalcite catalysts in ethanol produced monomers bearing carbonyl groups on the alkyl side chain. The analysis of the reaction mixtures was done by size exclusion chromatography (SEC) and diffusion ordered nuclear magnetic resonance spectroscopy (DOSY NMR). 31P NMR and heteronuclear single quantum coherence spectroscopy (HSQC) were also used in this study. The content in poly-(hydroxy)-aromatic ethers in the reaction mixtures decreased upon thermal treatments in ethanol. It was concluded that thermo-solvolysis is key in lignin depolymerization, and that the synergistic effect of Ni and Cu provided monomers with oxidized alkyl side chains.

Lewis Base Catalysis Enables the Activation of Alcohols by means of Chloroformates as Phosgene Substitutes

AbstractNucleophilic substitutions (SN) are typically promoted by acid chlorides as sacrificial reagents to improve the thermodynamic driving force and lower kinetic barriers. However, the cheapest acid chloride phosgene (COCl2) is a highly toxic gas. Against this background, phenyl chloroformate (PCF) was discovered as inherently safer phosgene substitute for the SN‐type formation of C−Cl and C−Br bonds using alcohols. Thereby, application of the Lewis bases 1‐formylpyrroldine (FPyr) and diethylcyclopropenone (DEC) as catalysts turned out to be pivotal to shift the chemoselectivity in favor of halo alkane generation. Primary, secondary and tertiary, benzylic, allylic and aliphatic alcohols are appropriate starting materials. A variety of functional groups are tolerated, which includes even acid labile moieties such as tert‐butyl esters and acetals. Since the by‐product phenol can be isolated, a recycling to PCF with inexpensive phosgene would be feasible on a technical scale. Eventually, a thorough competitive study demonstrated that PCF is indeed superior to phosgene and other substitutes.

Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant.

SummaryAn oxidative DNA-cleaving DNAzyme (PL) employs a double-cofactor model “X/Cu2+” for catalysis. Herein, we verified that reduced nicotinamide adenine dinucleotide (NADH), flavin mononucleotide, cysteine, dithiothreitol, catechol, resorcinol, hydroquinone, phloroglucinol, o-phenylenediamine, 3,3′,5,5'-tetramethylbenzidine, and hydroxylamine acted as cofactor X. According to their structural similarities or fluorescence property, we further confirmed that reduced nicotinamide adenine dinucleotide phosphate (NADPH), 2-mercaptoethanol, dopamine, chlorogenic acid, resveratrol, and 5-carboxyfluorescein also functioned as cofactor X. Superoxide anions might be the commonality behind these cofactors. We subsequently determined the conservative change of individual nucleotides in the catalytic core under four different cofactor X. The nucleotides A4 and C5 are highly conserved, whereas the conservative levels of other nucleotides are dependent on the types of cofactor X. Moreover, we observed that the minor change in the PL's secondary structure affects electrophoretic mobility. Finally, we characterized a highly efficient variant T3G and converted its double-cofactor NADH/Cu2+ to sole-cofactor NADH.

Lewis Acid–Base Interactions between Polysulfides and Boehmite Enables Stable Room‐Temperature Sodium–Sulfur Batteries

AbstractRoom‐temperature sodium–sulfur (RT Na–S) batteries are among the ideal candidates for grid‐scale energy storage due to their high theoretical energy density. However, rapid dissolution of polysulfides along with extremely slow redox kinetics lead to a low practical cell capacity and inferior cycling stability, inhibiting their practical applications. Herein, an innovative design strategy is introduced for a chemical and structural synergistic immobilization of sodium‐polysulfides in the cathode structure. An aluminum oxyhydroxide (AlOOH) nanosheets decorated sulfur/carbon black nanocomposite (S@CB@AlOOH) is used as an efficient cathode material for stable RT Na–S batteries. The cathode material exhibits extremely stable cycling performance, delivering an initial specific capacity of 392 mA h g–1and retains 378 mA h g–1after 500 cycles at 1C. The excellent performance is attributed to the synergistic effect of the structural encapsulation as well as chemical immobilization of polysulfides, significantly suppressing their gradual dissolution into liquid electrolyte. Density functional theory (DFT) calculations reveal that through favorable Lewis acid–base interactions, AlOOH catalyzes the redox conversion of the higher‐order polysulfides (Na2Sn, 6 ≤n≤ 8) to the lower‐order polysulfides (Na2Sx, 1 ≤x≤ 2). The importance of Lewis acid–base catalysis to enhance the overall performance of these batteries is demonstrated.

Divergent Synthesis of Bicyclo[3.2.1]octenes and Cyclohexenes via Catalytic Annulations of Nazarov Reagent and Vinyl 1,2-Diketones.

Bicyclo[3.2.1]octanes and related structures are unique units that widely exist in natural products, but the rapid and stereoselective construction of this skeleton is a challenging issue. We report the stereodivergent synthesis of bicyclo[3.2.1]octenes using Nazarov reagents and alkenyl 1,2-diketones with Brønsted base catalysis under mild conditions. Both stereoisomers of the bridged products can be obtained by tuning the reaction conditions, and cyclohexene product can also be selectively formed.

Dichotomous Si–H Bond Activation by Alkoxide and Alcohol in Base-Catalyzed Dehydrocoupling of Silanes

The activation of silanes in dehydrogenative coupling with alcohols under general base catalysis was studied experimentally (using multinuclear NMR, IR, and UV-visible spectroscopies) and computationally (at DFT M06/6-311++G(d,p) theory level) on the example of Ph4-nSiHn (n = 1-3) interaction with (CF3)2CHOH in the presence of Et3N. The effect of the phenyl groups' number and H- substitution by the electron-withdrawing (CF3)2CHO- group on Si-H bond hydricity (quantified as hydride-donating ability, HDA) and Lewis acidity of silicon atom (characterized by maxima of molecular electrostatic potential) was accessed. Our results show the coordination of Lewis base (Y = Me3N, ROH, OR-) leads to the increased hydricity of pentacoordinate hypervalent Ph4-nSi(Y)Hn complexes and a decrease of the reaction barrier for H2 release. The formation of tertiary complexes [Ph4-nSi(Y)Hn]···HOR is a critical prerequisite for the dehydrocoupling with alkoxides being ideal activators. The latter can be external or internal, generated by in situ HOR deprotonation. The mutual effect of tetrel interaction and dihydrogen bonding in tertiary complexes (RO-)Ph4-nSiHn···HOR leads to dichotomous activation of Si-H bond promoting the proton-hydride transfer and H2 release.

Unconventional Transformations of Morita–Baylis–Hillman Adducts

Morita–Baylis–Hillman (MBH) adducts are versatile starting materials widely employed in Lewis base catalysis. A myriad of different transformations have been reported based on either allylic alkylations with stabilised nucleophiles or annulations with diverse dipolarophiles. Apart from these two conventional types of reactivity, MBH adducts have recently been implemented in alternative and complementary catalytic strategies, including: (i) one-pot and cascade transformations, where additional chemical bonds are formed following the asymmetric allylic alkylation event in a single synthetic operation; (ii) regioselective α-allylations for the synthesis of trisubstituted alkenes; and (iii) dual activation strategies, involving Lewis base catalysis together with transition metal complexes or light, enabling allylic alkylations with nonstabilised nucleophiles and cascade processes. The present Short Review summarises the most significant unconventional catalytic transformations of racemic MBH adducts reported within the last decade.1 Introduction2 Multi-Step Single-Vessel Transformations (path iii)2.1 One-Pot Transformations2.2 Cascade Transformations3 α-Allylations (path iv)3.1 SN2′ Mechanism3.2 SN2′–SN2 Mechanism3.3 Miscellaneous Mechanisms4 Dual Activation (path v)4.1 MBH Adduct as Electrophile4.2 MBH Adduct as Nucleophile5 Summary and Outlook

Progress in polyoxometalate catalysis

Polyoxometalates (POMs) is a kind of metal-oxygen clusters with well-defined structures, controllable composition, and excellent properties including acidity, redox properties, etc . In recent years, POMs have shown potential application in the field of catalysis, materials, energy conversion and pharmaceuticals and become a hot interdisciplinary research area. This review focuses on the recent progress in the structure design of POMs and their catalytic properties, mainly including POM structure chemistry, acid-base catalysis, redox catalysis, photocatalysis, the catalytic conversion of CO2 and toxic molecules. In addition, the future development of POMs-based catalysis is prospected.

Comparative study of gas-phase “dehydration” of alkyl lactates and lactic acid for acrylic acid production over hydroxyapatite catalysts

Gas-phase “dehydration” of methyl (ML) and ethyl lactates (EL) for acrylic acid (AA) production was studied and compared with the dehydration of lactic acid (LA) over serial hydroxyapatite catalysts of varying compositions (HAPm-360, molar Ca/P ratio m = 1.58–1.68, calcination temperature: 360 °C). The product distribution from both lactic esters was found very similar to that from LA; AA but not methyl (MA) or ethyl acrylate (EA) also appeared as the prevailing product (> 50 mol% by selectivity) from both ML and EL. Compared with the reaction of LA, both esters showed much lower reactivity but higher AA selectivity. Among the two esters EL was less reactive but produced a higher selectivity for AA formation. Correlating the AA selectivity or yield with the catalyst surface acid-base property uncovers that a suitable balance between the surface acidity and basicity (or acidity/basicity ratio) is the key to the lactic ester-to-AA reactions. However, the optimum surface acidity/basicity ratio for producing the highest AA selectivity from both esters was higher than that from LA. These results suggest that the lactic ester-to-AA reactions proceeded by catalytic tandem processes involving a formation of LA (or adsorbed lactate) as the key intermediate at the catalyst surface. Acid-base catalysis responsible for these observations is discussed.

3+3] Cycloaddition of Azomethine Imine: Synthesis of Bi‐ or Tricyclic N‐Heterocycle

AbstractSynthesis of six‐membered bicyclic, tricyclic or tetracyclic N‐heterocycles are important due to enormous use of such scaffolds in bioactive natural products, agrochemicals and in pharmaceuticals. [3+3] cycloaddition of azomethine imine for the construction of such heterocycles is less explored but also a genuine approach with the other method like [4+2] and [2+2+2] cycloaddition. Hence, the literature survey in this area is utmost significant. The delights and difficulties of [3+3] cycloaddition of azomethine imine have been deliberated thoroughly to elucidate this highly mounting field in this literature study. Herein, we report a vast synthetic method [base catalyzed, metal catalyzed (racemic and asymmetric), phosphine catalyzed, NHC and Lewis acid catalyzed] for the synthesis of di, tri and tetra‐nitrogen containing heterocycles via [3+3] cycloadditon reaction of azomethine imine.

Rearrangement of Epoxide Derivatives Semisynthesized from β-Himachalene using Lewis and Bronsted Acids Catalysis

The acid-catalyzed rearrangement of epoxides 3a, 4a, 6a, and 7a derived from β-himachalene, the major constituent of Cedrus atlantica essential oil, has been studied using various Lewis and Bronsted acids. Several new enantiomerically pure ketones were obtained in good yields and high selectivities. All products obtained were fully characterized by 1H and 13C NMR, and the mechanistic explanations for their formation were proposed.

Brønsted Base-Catalyzed Transformation of α,β-Epoxyketones Utilizing [1,2]-Phospha-Brook Rearrangement for the Synthesis of Allylic Alcohols Having a Tetrasubstituted Alkene Moiety.

A stereoselective transformation of α,β-epoxyketones into alkenylphosphates having a hydroxymethyl group on the β-carbon was established by utilizing the [1,2]-phospha-Brook rearrangement under Brønsted base catalysis. The reaction involves the catalytic generation of an α-oxygenated carbanion located at the α-position of an epoxide moiety through the [1,2]-phospha-Brook rearrangement and the following epoxide opening. Further transformation of the alkenylphosphates by the palladium-catalyzed cross-coupling reaction with Grignard reagents provided allylic alcohols having a stereodefined all-carbon tetrasubstituted alkene moiety.

Hybrid Materials Based on Silica Matrices Impregnated with Pt-Porphyrin or PtNPs Destined for CO2 Gas Detection or for Wastewaters Color Removal.

Multifunctional hybrid materials with applications in gas sensing or dye removal from wastewaters were obtained by incorporation into silica matrices of either Pt(II)-5,10,15,20-tetra-(4-allyloxy-phenyl)-porphyrin (PtTAOPP) or platinum nanoparticles (PtNPs) alone or accompanied by 5,10,15,20-tetra-(4-allyloxy-phenyl)-porphyrin (TAOPP). The tetraethylorthosilicate (TEOS)-based silica matrices were obtained by using the sol-gel method performed in two step acid-base catalysis. Optical, structural and morphological properties of the hybrid materials were determined and compared by UV-vis, fluorescence and FT-IR spectroscopy techniques, by atomic force microscopy (AFM) and high resolution transmission electron microscopy (HRTEM) and by Brunauer–Emmett–Teller (BET) analysis. PtTAOPP-silica hybrid was the most efficient material both for CO2 adsorption (0.025 mol/g) and for methylene blue adsorption (7.26 mg/g) from wastewaters. These results were expected due to both the ink-bottle mesopores having large necks that exist in this hybrid material and to the presence of the porphyrin moiety that facilitates chemical interactions with either CO2 gas or the dye molecule. Kinetic studies concerning the mechanism of dye adsorption demonstrated a second order kinetic model, thus it might be attributed to both physical and chemical processes.

EXPERIMENTAL INVESTIGATION AND MODELING OF MODIFICATION AGENT ON SURFACE PROPERTY OF AEROGEL PRODUCED VIA AMBIENT PRESSURE DRYING

A crucial properties for hydrophobic silica aerogels such as surface free energy surface tension contact angle has been determines experimentally and theoretically in the present work, the modification was by hexamethyldisilazane (HMDZ) and trimethylchlorosilane (TMCS) with different concentration from 5% to 15% , two step acid base catalysis followed in preparation, using (TEOS) ethanol and [0.001M] hydrochloride acid with molar ratio was 1:2.8:0.19*10 -3 respectively , the effect study upon analysis of FTIR spectra and the degree of hydrophobicity was estimated by contact angle measurements. The results refer that the contact angle of aerogel from 130 to 151 by modifying by HMDZ and from 122 to 153 by modifying by TMCS, Neumann’s and Young’s equation of state depend to determine surface free energy and surface tension of samples, while the specific surface area is measured by using the Brunauer –Emmett–Teller (BET) method. Here, we have confirmed that the surface free energy of samples can be regulated in varied range from 4.4997 to 0.3115 and 4.1419 to 0.5112 mJ/m 2 by adjusting their surface by TMCS and HMDZ. From results the modification with TMCS is best from HMDZ, theoretical part give a good results to estimate the important information about hydrophobic silica aerogel. Article DOI: https://dx.doi.org/10.20319/mijst.2019.51.8598 This work is licensed under the Creative Commons Attribution-Non-commercial 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

Transesterification Reaction of Palm Kernel Oil (PKO) on a Bed of Crushed Cashew Nut Shell (CCNS)

Biodiesel (GA1) was produced by the transesterification reaction of palm kernel oil (PKO) and methanol catalysed by crushed cashew nut shaft. Biodiesel samples GA2 – GA4 were also produced from the palm kernel oil using conventional base catalysis by NaOH and crushed cashew nut shaft combined with NaOH. The physico-chemical properties and spectroscopic data of the four samples were found to be similar and compared favourably to those of standard biodiesel.&#x0D; Keywords: Transesterification, palm kernel oil, cashew nut shell, methanolysis, biodiesel.

Study on the degradation of biodegradable poly (glycerol maleate) (PGM) microbeads

Plastics contributed from personal care products and plastic fragments are considered as one of the most common pollutants in the ocean since 1970s. In this study, poly (glycerol maleate) (PGM) is applied as the alternative of microbeads due to its high degradability in the water and the relatively low cost compared to other biodegradable polymers. The proposed PGM microbeads are fabricated via solvent evaporation methods with average diameter around 30 ± 13 μm and polydispersity index around 0.2 to 0.3. To identify the degradability of PGM microbeads in different water solutions, samples were examined in buffer solution with different pH values, DI water, sea water and enzyme solution through total organic carbon (TOC) analyzer/UV–Vis spectrometry, microscopy, and SEM. These microbeads were completely degraded in 45 min in alkaline solution (pH 10). In contrast, 60% of PGM microbeads were degraded in 30 days in the acidic solution (pH 4). It revealed that the base catalysis of hydrolysis was quicker than acid-catalysis. 50% more of PGM microbeads were degraded in the refreshed DI water in a month. However, only 36% of microbeads were degraded in synthetic sea water. The high salinity was suspected to obstruct the hydrolysis of PGM microbeads and slow down the degradation rate. Lipase solution is conducted to examine the possibility of bio-accumulation once PGM microbeads ingested inside the living organism, and the result shows that PGM microbeads degrade mostly in seven days. It is worthy to note that PLA microbeads only degrade at pH 10 in this study. With the comparison between PGM and PLA microbeads, PGM is more easily degraded and affordable, and it is thought to have great potential for being the alternative to plastic microbeads.

Catalytic mechanism of the mismatch-specific DNA glycosylase methyl-CpG-binding domain 4.

Thymine:guanine base pairs are major promutagenic mismatches occurring in DNA metabolism. If left unrepaired, these mispairs can cause C to T transition mutations. In humans, T:G mismatches are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (hMBD4) and thymine-DNA glycosylase. Unlike lesion-specific DNA glycosylases, T:G-mismatch-specific DNA glycosylases specifically recognize both bases of the mismatch and remove the thymine but only from mispairs with guanine. Despite the advances in biochemical and structural characterizations of hMBD4, the catalytic mechanism of hMBD4 remains elusive. Herein, we report two structures of hMBD4 processing T:G-mismatched DNA. A high-resolution crystal structure of Asp560Asn hMBD4-T:G complex suggests that hMBD4-mediated glycosidic bond cleavage occurs via a general base catalysis mechanism assisted by Asp560. A structure of wild-type hMBD4 encountering T:G-containing DNA shows the generation of an apurinic/apyrimidinic (AP) site bearing the C1'-(S)-OH. The inversion of the stereochemistry at the C1' of the AP-site indicates that a nucleophilic water molecule approaches from the back of the thymine substrate, suggesting a bimolecular displacement mechanism (SN2) for hMBD4-catalyzed thymine excision. The AP-site is stabilized by an extensive hydrogen bond network in the MBD4 catalytic site, highlighting the role of MBD4 in protecting the genotoxic AP-site.