Acid-catalyzed Research Articles

Regulating Nucleic Acid Catalysis Using Active Droplets.

Cells use transient membraneless organelles to regulate biological reaction networks. For example, stress granules selectively store mRNA to downregulate protein expression in response to heat or oxidative stress. Models mimicking this active behavior should be established to better understand in vivo regulation involving compartmentalization. Here we use active, complex coacervate droplets as a model for membraneless organelles to spatiotemporally control the activity of a catalytic DNA (DNAzyme). Upon partitioning into these peptide-RNA droplets, the DNAzyme unfolds and loses its ability to catalyze the cleavage of a nucleic acid strand. We can transiently pause the DNAzyme activity upon inducing droplet formation with fuel. After fuel consumption, the DNAzyme activity autonomously restarts. We envision this system could be used to up and downregulate multiple reactions in a network, helping understand the complexity of a cell's pathways. By creating a network where the DNAzyme could reciprocally regulate the droplet properties, we would have a powerful tool for engineering synthetic cells.

Catalytic Enantioselective Friedel–Crafts Allenylation

AbstractThe first enantioselective Friedel‐Crafts (FC) allenylation reaction for the creation of central chirality is developed under cooperative Ir(I)/(phosphoramidite,olefin) and Lewis acid catalysis. This enantioconvergent reaction utilizes racemic allenylic alcohol as the electrophile and shows compatibility with a variety of electron‐rich arenes and heteroarenes. The resulting highly enantioenriched (up to >99.5 : 0.5 e.r.) 1,1‐disubstituted allenylic methanes, bearing a benzylic carbon stereocenter, are obtained with complete regiocontrol – both on (hetero)arenes as well as on the allenylic fragment. This protocol allows for the enantioselective formal introduction of a 4‐carbon alkyl chain into (hetero)arenes, along with the creation of a benzylic stereocenter. Judicious synthetic elaborations not only lead to formal enantioselective FC alkylation products of less electron‐rich arenes but also of substituted arenes in ortho‐ and even meta‐selective fashion. An intramolecular version of this FC allenylation is shown to proceed with promising enantioselectivity under the same catalytic conditions. Mechanistic studies revealed the involvement of dynamic kinetic asymmetric transformation (DyKAT) of racemic allenylic alcohols in this reaction.

Catalytic Enantioselective Friedel-Crafts Allenylation.

The first enantioselective Friedel-Crafts (FC) allenylation reaction for the creation of central chirality is developed under cooperative Ir(I)/(phosphoramidite,olefin) and Lewis acid catalysis. This enantioconvergent reaction utilizes racemic allenylic alcohol as the electrophile and shows compatibility with a variety of electron-rich arenes and heteroarenes. The resulting highly enantioenriched (up to >99.5 : 0.5 e.r.) 1,1-disubstituted allenylic methanes, bearing a benzylic carbon stereocenter, are obtained with complete regiocontrol - both on (hetero)arenes as well as on the allenylic fragment. This protocol allows for the enantioselective formal introduction of a 4-carbon alkyl chain into (hetero)arenes, along with the creation of a benzylic stereocenter. Judicious synthetic elaborations not only lead to formal enantioselective FC alkylation products of less electron-rich arenes but also of substituted arenes in ortho- and even meta-selective fashion. An intramolecular version of this FC allenylation is shown to proceed with promising enantioselectivity under the same catalytic conditions. Mechanistic studies revealed the involvement of dynamic kinetic asymmetric transformation (DyKAT) of racemic allenylic alcohols in this reaction.

Single-Crystalline 3D Covalent Organic Frameworks with Exceptionally High Specific Surface Areas and Gas Storage Capacities.

Single-crystalline covalent organic frameworks (COFs) are highly desirable toward understanding their pore chemistry and functions. Herein, two 50-100 μm single-crystalline three-dimensional (3D) COFs, TAM-TFPB-COF and TAPB-TFS-COF, were prepared from the condensation of 4,4',4″,4‴-methanetetrayltetraaniline (TAM) with 3,3',5,5'-tetrakis(4-formylphenyl)bimesityl (TFPB) and 3,3',5,5'-tetrakis(4-aminophenyl)bimesityl (TAPB) with 4,4',4″,4‴-silanetetrayltetrabenzaldehyde (TFS), respectively, in 1,4-dioxane under the catalysis of acetic acid. Single-crystal 3D electron diffraction reveals the triply interpenetrated dia-b networks of TAM-TFPB-COF with atom resolution, while the isostructure of TAPB-TFS-COF was disclosed by synchrotron single-crystal X-ray diffraction and synchrotron powder X-ray diffraction with Le Bail refinements. The nitrogen sorption measurements at 77 K disclose the microporosity nature of both activated COFs with their exceptionally high Brunauer-Emmett-Teller surface areas of 3533 and 4107 m2 g-1, representing the thus far record high specific surface area among imine-bonded COFs. This enables the activated COFs to exhibit also the record high methane uptake capacities up to 28.9 wt % (570 cm3 g-1) at 25 °C and 200 bar among all COFs reported thus far. This work not only presents the structures of two single-crystalline COFs with exceptional microporosity but also provides an example of atom engineering to adjust permanent microporous structures for methane storage.

Triazenolysis of alkenes as an aza version of ozonolysis.

Alkenes are broadly used in synthetic applications, thanks to their abundance and versatility. Ozonolysis is one of the most canonical transformations that converts alkenes into molecules bearing carbon-oxygen motifs via C=C bond cleavage. Despite its extensive use in both industrial and laboratory settings, the aza version-cleavage of alkenes to form carbon-nitrogen bonds-remains elusive. Here we report the conversion of alkenes into valuable amines via complete C=C bond disconnection. This process, which we have termed 'triazenolysis', is initiated by a (3 + 2) cycloaddition of triazadienium cation to an alkene. The triazolinium salt formed accepts hydride from borohydride anion and spontaneously decomposes to create new C-N motifs upon further reduction. The developed reaction is applicable to a broad range of cyclic alkenes to produce diamines, while various acyclic C=C bonds may be broken to generate two separate amine units. Computational analysis provides insights into the mechanism, including identification of the key step and elucidating the significance of Lewis acid catalysis.

Multi-omics analysis identifies BCAT2 as a potential pan-cancer biomarker for tumor progression and immune microenvironment modulation.

Branched-chain amino acid transaminase 2 (BCAT2) encodes a crucial protein involved in the initial catalysis of branched-chain amino acid (BCAA) catabolism, with emerging evidence suggesting its association with tumor progression. This study explores BCAT2 in a pan-cancer multi-omics context and evaluates its prognostic significance. We utilized a multi-database approach, analyzing cBioPortal for genetic alterations, RNA-Seq data from TCGA and GTEx for expression patterns, and RSEM for transcript analysis. Protein expression and interaction networks were assessed using the Human Protein Atlas, UniProt, and STRING. Prognostic value was determined through Cox regression analysis of TCGA clinical survival data, while immune cell infiltration across various cancers was examined using TCGA data and the TIMER2 platform. Our results revealed that BCAT2 alterations are primarily amplifications and is upregulated in various tumors, correlating with poor survival rates in several tumor types, including GBMLGG, LGG, and UVM. Elevated BCAT2 protein levels were common in pan-cancer, interacting with a range of metabolic enzymes. Additionally, BCAT2 expression significantly influenced CD4+ T cells, CD8+ T cells, and Treg cells infiltration, with varied correlations across cancer types. These findings indicate BCAT2 as a potential biomarker for cancer diagnosis and therapy, potentially regulating key metabolic and immune factors to mediate tumor progression and the microenvironment.

Solvent- and Catalyst-Controlled Regioselective O- and N-Alkylation of 2-Pyridones by 2H-Azirines.

The synthesis of O-substituted 2-hydroxypyridines and N-substituted 2-pyridones, crucial for many bioactive compounds and drugs, faces challenges due to the tautomeric nature of 2-pyridones, which complicates selective alkylation. Here we developed an efficient method for regioselective O- and N-alkylation of 2-pyridones using Bro̷nsted acid-catalyzed ring opening of 2H-azirines. The process involves triflic acid for O-alkylation and p-toluenesulfonic acid for N-alkylation, achieving high yields under optimized conditions. For O-alkylation, a variety of 2-pyridones and 2H-azirines were used, resulting in significant yields of the desired products. Similarly, for N-alkylation, the optimized conditions produced excellent yields, highlighting the method's versatility. This methodology was further demonstrated through scaled-up syntheses and subsequent transformations, showcasing its practicality for complex molecular architectures. The proposed mechanism involves the protonation of 2H-azirine, followed by a regioselective SN2-type attack and acid-catalyzed hydrolysis, leading to the desired alkylated products. This innovative approach, emphasizing Bro̷nsted acid catalysis and careful control of reaction conditions, represents a significant advancement in the selective alkylation of 2-pyridones, with broad implications for medicinal chemistry.

Polymers Containing Diethylsiloxane Segment and Active Functional Group by Ring-Opening Polymerization of Hexaethylcyclotrisiloxane under the Catalysis of Linear Chlorinated Phosphazene Acid.

Linear chlorinated phosphazene acid is prepared using PCl5 and NH4Cl as raw materials. Using hexaethylcyclotrisiloxane as the monomer, 1,1,3,3-tetramethyldisiloxane or 1,3-divinyl-1,1,3,3-tetramethyldisiloxane as the end-capping agent, and linear chlorinated phosphazene acid as the catalyst, polydiethylsiloxane oligomers terminated with active Si-H or Si-CH=CH2 groups have been prepared. Using hexaethylcyclotrisiloxane and 1,3,5,7-octamethylcyclotetrasiloxane as comonomers, 1,1,3,3-tetramethyldisiloxane or hexamethyldisiloxane as the end-capping agent, or using hexaethylcyclotrisiloxane and octamethylcyclotetrasiloxane as comonomers, 1,1,3,3-tetramethyldisiloxane as the end-capping agent, copolymers containing active Si-H bonds and dimethylsiloxane segments have been prepared under the catalysis of linear chlorinated phosphazene acid. The effects of catalyst dosage, reaction temperature, reaction time, end-capping agent, and polymerization monomer dosage on polymer yield and structure were investigated. Using 300 ppm of linear chlorinated phosphazene acid, oligomers and copolymers containing an active Si-H bond and diethylsiloxane segment were prepared under mild conditions. The molecular weight of the obtained polymers was close to their designed values, but their PDI values were small. The highest yield of α, ω-bisdimethylsiloxyl-terminated PDES oligomers reached 93%. Using oligomers and copolymers containing Si-H bonds and diethylsiloxane segments as crosslinkers, a silicone gel containing diethylsiloxane segments was prepared by hydrosilylation reaction. With the introduction of a diethylsiloxane segment, the glass transition temperature of the silicone gel decreased relative to that of the PDMS oligomer, but the temperature at 5% weight loss in nitrogen atmosphere decreased from 347 °C to 312 °C. The mechanism of the ring-opening polymerization of hexaethylcyclotrisiloxane catalyzed by linear chlorinated phosphazene acid is also discussed.

Recent Advances and Prospects of Nucleic Acid Therapeutics for Anti-Cancer Therapy

Nucleic acid therapeutics are promising alternatives to conventional anti-cancer therapy, such as chemotherapy and radiation therapy. While conventional therapies have limitations, such as high side effects, low specificity, and drug resistance, nucleic acid therapeutics work at the gene level to eliminate the cause of the disease. Nucleic acid therapeutics treat diseases in various forms and using different mechanisms, including plasmid DNA (pDNA), small interfering RNA (siRNA), anti-microRNA (anti-miR), microRNA mimics (miRNA mimic), messenger RNA (mRNA), aptamer, catalytic nucleic acid (CNA), and CRISPR cas9 guide RNA (gRNA). In addition, nucleic acids have many advantages as nanomaterials, such as high biocompatibility, design flexibility, low immunogenicity, small size, relatively low price, and easy functionalization. Nucleic acid therapeutics can have a high therapeutic effect by being used in combination with various nucleic acid nanostructures, inorganic nanoparticles, lipid nanoparticles (LNPs), etc. to overcome low physiological stability and cell internalization efficiency. The field of nucleic acid therapeutics has advanced remarkably in recent decades, and as more and more nucleic acid therapeutics have been approved, they have already demonstrated their potential to treat diseases, including cancer. This review paper introduces the current status and recent advances in nucleic acid therapy for anti-cancer treatment and discusses the tasks and prospects ahead.

Synthesis and Performance Evaluation of Metallocene Polyalphaolefins (mPAO) Base Oil with Anti-Friction and Anti-Wear Properties

Anti-wear and anti-oxidation abilities are two key properties of lubricants that play a crucial role in ensuring long-term stable equipment operation. In this study, we aimed to develop a base oil with good anti-oxidation and anti-wear properties for use under extreme pressure. The as-prepared metallocene polyalphaolefin (mPAO) was chemically modified using the trifluoromethanesulfonic acid (TfOH) catalysis through an alkylating reaction with triphenyl phosphorothioate (TPPT). During the experiments, when the reaction temperature exceeded 70 °C or the concentration of TfOH exceeded 2.67%, the β-scission reaction in the alkylation process became significantly more pronounced. The physical and chemical properties of TPPT-modified mPAO (T-mPAO) were evaluated by nuclear magnetic resonance spectroscopy, Fourier trans-form infrared spectroscopy, gel–permeation chromatography, and ASTM standards. T-mPAO showed significantly improved antioxidant capacity, with the initial oxidation temperature increasing by 32 °C compared to the base oil, and it exhibited the slowest increase in acid number in the 96-h oven oxidation test. The tribological tests showed that T-mPAO had the lowest friction coefficient, wear track, and wear rate (72.7% lower than that of mPAO) as well as the highest PB (238 kg) and PD (250 kg) among all tested samples. Compared to mPAO, the average friction coefficient of TPPT-modified mPAO in the four-ball friction test was reduced by 30.5%, and by 16.4% in the TE77 reciprocating friction test. Based on the experimental results, T-mPAO had strong anti-oxidation ability and excellent lubricating performance.The successful synthesis of multifunctional mPAO has enabled lubricant base oil additization, making it possible to use it in more demanding work scenarios, greatly broadening its application scope and making lubricant formulation blending more flexible.

Triple Catalysis for the Tandem Transformation of Cyclopropyl Ketones to SCF3-Substituted Dihydrofurans.

In this study, we have developed an effective and general strategy for synthesizing various 4-[(trifluoromethyl)thio]-2,3-dihydrofuran derivatives with high regioselectivity from easily prepared cyclopropyl ketone under mild reaction conditions. By the combination of photoredox, copper, and Lewis acid catalysis into a triple catalytic system, this methodology facilitates the selective cleavage of the carbon-carbon bonds and the formation of new carbon-oxygen and carbon-sulfur bonds. In addition, to enhance the synthetic feasibility of this protocol, we demonstrate its broad applicability across a wide range of substrates and its scalability for large-scale synthesis.

The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.

MTR1 is an in vitro-selected alkyl transferase ribozyme that transfers an alkyl group from O 6-alkylguanine to N1 of the target adenine in the RNA substrate (A63). The structure of the ribozyme suggested a mechanism in which a cytosine (C10) acts as a general acid to protonate O 6-alkylguanine N1. Here, we have analyzed the role of the C10 general acid and the A63 nucleophile by atomic mutagenesis and computation. C10 was substituted by n1c and n1c, c5n variants. The n1c variant has an elevated pK a (11.4 as the free nucleotide) and leads to a 104-fold lower activity that is pH-independent. Addition of the second c5n substitution with a lower pK a restored both the rate and pH dependence of alkyl transfer. Quantum mechanical calculations indicate that protonation of O 6-alkylguanine lowers the barrier to alkyl transfer and that there is a significantly elevated barrier to proton transfer for the n1c single substitution. The calculated pK a values are in good agreement with the apparent values from measured rates. Increasing the pK a of the nucleophile by A63 n7c substitution led to a 6-fold higher rate. The increased reactivity of the nucleophile corresponds to a βnuc of ∼0.5, indicating significant C-N bond formation in the transition state. Taken together, these results are consistent with a two-step mechanism comprising protonation of the O 6-alkylguanine followed by alkyl transfer.

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generates the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional active site in the γβ-domain and a vestigial ɑ-domain. Substrate docking into the active site of the GrTPS2 apo protein structure predicted catalytic amino acids. Biochemical characterization of protein variants identified residues with impact on enzyme activity and catalytic specificity. Specifically, mutagenesis of Y457 provided mechanistic insight into the position-specific deprotonation of the intermediary carbocation to form the characteristic 7,13 double bond of 7,13-copalyl diphosphate.

Linking Ab initio density functional theory with modelling reaction microkinetics to understand catalytic fatty acids hydro-deoxygenation intermediate species selectivity

Catalyst surfaces enable the catalytic reactions via binding of substrates and lowering the reaction barriers to obtain the desired products. Separating the binding process from the reaction barriers enables us the understanding of surface properties and enables the reaction engineering strategies such as choice of solvents or functional groups protections. Through the modelling of the hydrodeoxygenation (HDO) of fatty acids, namely Stearic, Oleic, Linoleic, Myristic and Decanoic acid we show why the alkanes are the ideal solvent choice for NiMoS catalyst, why the alcohols side products form, regardless of the kinetic constant indicating fast dehydration, why the aldehydes intermediates are rarely detected and why hydrogenation of double bonds supersedes other kinetics events. We confirm the DFT calculations by integrating them into the kinetic model which confirms that the obtained results are sensible and usable in reaction engineering. The results are supported by the detailed characterization of the NiMoS catalyst.

Acidity and stability of Nb(V) active sites doped in SBA-15 and ZrSBA-15: A DFT study

Mesoporous silicas are of great interest in heterogeneous catalysis due to the structural characteristics of their pores and the adjustable catalytic properties that arise from incorporating heteroatoms. The substitution of Zr and Nb into SBA-15 introduces active sites into the material, rendering it a potential catalyst for acid catalysis reactions. However, discussions regarding the acid properties and metal-support interactions in amorphous silicas functionalized with metals are limited in computational chemistry. This study aims to determine the acid strength and charge transfer effects between Zr(IV) and Nb(V) species in mesoporous silica by proposing a representative SBA-15 cluster of type 5–6. Density Functional Theory (DFT) simulations were conducted using the B3LYP/6-31G(d,p)/def2TZVP levels. The model successfully replicated trends from larger clusters, demonstrating that the more grafted onto the silica structure (i.e. have more Si-O-M bonds), the greater the acid strength of the active site. Additionally, it was found that ZrSBA-15 structures are more stable than NbSBA-15 and possess higher acid strength, a trend supported by experimental observations. The results also suggest that Nb(V) species are more effectively stabilized in ZrSBA-15 than SBA-15, likely due to the presence of Zr(IV) centers in ZrSBA-15. This research contribute to a better understanding of how the support affects the stabilization of active phases, paving the way for the rational design of silica-based heterogeneous catalysts.

Divergent asymmetric reactions of α-alkenyl ketones with β,γ-alkynyl-α-imino esters enabled by chiral phosphoric acids

Divergent asymmetric synthesis provides access to a wide range of isomers from the same starting material by modifying the reaction conditions, which plays an important role in the efficient construction of a structurally diverse molecular library for structure-activity relationship studies. In this work, we present the divergent asymmetric addition of α-alkenyl ketones with β,γ-alkynyl-α-imino esters enabled by chiral phosphoric acid catalysis. Despite the challenging presence of multiple reactive sites in both components, we successfully achieved the regioselective synthesis of both α-1,2-addition α-tertiary amines and γ-1,4-addition allenes with good to high regio-, diastereo- and enantioselectivities by modifying the reaction conditions. Moreover, the stereodivergent asymmetric synthesis of the four allene stereoisomers bearing contiguous central and axial chirality was achieved by adjusting the E/Z configuration of the α-alkenyl ketone substrates.

A mild and chemoselective photoredox-catalyzed reduction of aromatic ketones

A mild, chemoselective reduction of aromatic ketones was discovered and investigated. The combination of photoredox and Lewis acid catalysis with an organic hydrogen source reduced aromatic ketones in good to high yield. Optimization found 2-phenylbenzothiazoline to be a sufficiently strong source of hydrogen in combination with an iridium photosensitizer and lanthanum triflate. Effective photomediated reduction of some substrates was also observed in the absence of photocatalyst and Lewis acid or with photocatalyst only. While yields were typically higher under catalytic conditions, some acid-sensitive substrates were more effectively reduced in the absence of Lewis acid. The reaction was generally high yielding, and chemoselecte, while tolerant of complex and functionally rich molecules.

Erratum for the Research Article "Electrically driven proton transfer promotes Brønsted acid catalysis by orders of magnitude" by K. S. Westendorff et al.

Erratum for the Research Article "Electrically driven proton transfer promotes Brønsted acid catalysis by orders of magnitude" by K. S. Westendorff et al.

Comparative Study of PtM (M=Cu, Zn, Ga, Mn, Fe, In, Ce) Bimetals on Zincosilicate for Propane Dehydrogenation Reaction.

Silicoaluminate zeolites have relatively strong Brönsted (B) acid properties that can easily lead to deep cracking reactions, making them less favourable as carriers for propane dehydrogenation. Here, we utilise zincosilicate zeolite with less B-acid produced by the introduction of the heteroatom Zn into the framework as a carrier, followed by simultaneous ion exchange (IE) of M monometallic or PtM bimetallic (M = Cu, Zn and Ga, etc.). The optimized PtZn/Zn-4 exhibits a superior propane dehydrogenation performance over PtCu/Zn-4 and PtGa/Zn-4, which can achieve a propane conversion of about 30% in a pure propane atmosphere at 550 °C and can be operated for at least 168 h without significant deactivation. Characterization techniques such as spherical aberration corrected transmission electron microscopy, in situ X-ray photoelectron spectroscopy, and in situ diffuse reflectance infrared fourier transform spectroscopy with different gas adsorptions are used to investigate these PtM@zeolite catalysts in order to deepen the understanding of acid site identification, promoter effect and catalysis.

Organocatalytic Asymmetric (4 + 3) Cycloaddition toward Optically Active Cyclohepta Fused Diindoles.

A novel asymmetric (4 + 3) cycloaddition of indole-2,3-quinodimethanes in situ generated from 3-methyl-2-indolylmethanols with 3-indolylmethanols via chiral phosphoric acid catalysis has been established. The cycloaddition reaction exhibits a broad substrate scope affording the diverse enantioenriched cyclohepta fused diindoles in high yields with good enantioselectivities. Significantly, this work represents the first application of 3-methyl-2-indolylmethanols as 4C synthons instead of the commonly reported three-atom synthons in cycloaddition reactions.