Decay Pathway Research Articles

Molecular docking and ADME evaluation of plant-based bioactive molecules targeting nonsense-mediated mRNA decay pathway factors to modulate tumorigenesis

Cancer is a global health challenge that requires continuous efforts to discover effective anticancer drugs. Phytochemicals are compounds found in plants that often have medicinal properties. They possess a wide range of bioactive properties, including anticancer activity. Their multiple mechanisms of action in different physiological processes in humans make them promising candidates in the anticancer therapeutics development. The presence of these compounds makes plants valuable resources for traditional medicine and modern pharmaceutical research as well. Natural products from plants and marine sources are being used to find new anticancer agents. In humans, different cellular pathways are involved in the tumorigenesis process. Many studies have shown the role of the nonsense-mediated mRNA decay (NMD) pathway in the process of tumorigenesis. This NMD pathway is controlled by multiple proteins. In this study, we conducted a molecular docking analysis of 50 phytochemicals against the human NMD factor up-frameshit2 (UPF2) protein. The results of the molecular docking experiment and ADME properties indicate that 4 of these molecules (Genistein, Trihydroxyflavone, Baicalein and Epigallocatechin) have the potential to modulate the NMD pathway. Furthermore, these molecules comply with Lipinski's rule of five. The effects of these 4 phytochemicals may be further evaluated using in vitro and in vivo methods for novel anticancer therapeutic development.

Molecular Design and Synthetic Approaches for the Realization of Multichannel Radiative Decay Pathways in Gold(III) Complexes and Their Applications in Organic Light-Emitting Devices.

A unique class of tridentate diaryltriazine ligand-containing gold(III) complexes with thermally activated delayed fluorescence (TADF) and/or thermally stimulated delayed phosphorescence (TSDP) properties has been designed and synthesized. With a simple structural modification on the coordination of carbazole moiety in the monodentate ligand, a large spectral shift of ∼160 nm (ca. 4900 cm-1) spanning from sky blue to red emissions has been demonstrated in solid-state thin films. Three-state or four-state models have been employed in fitting the emission lifetimes of the gold(III) complexes at various temperatures. The findings clearly indicate the presence of three emitting states, S1, T1, and T1', suggesting the coexistence of TADF, phosphorescence, and TSDP. Notably, a minor structural change in the donor moiety between phenylcarbazolyl and diphenylaminoaryl has been demonstrated to turn on/off the TSDP, resulting in TADF-TSDP-phosphorescence or TADF-phosphorescence emitters. The TADF and/or TSDP properties have also been supported by temperature-dependent ultrafast transient absorption studies, with the direct observation of reverse intersystem crossing (RISC) and reverse internal conversion (RIC) and the determination of the activation parameters and excited state dynamics. Solution-processed and vacuum-deposited organic light-emitting devices (OLEDs) have been prepared, in which sky blue emitting devices based on 5 exhibit an operational lifetime LT70 ∼ 5 times longer than the previously reported sky blue emitting analogue that shows only TSDP property. These results have provided valuable insights into the manipulation of the excited states via rational molecular design toward the realization of gold(III)-based TSDP and/or TADF materials with multiple radiative decay pathways that show enhanced radiative decay rate constants (kr) for practical OLED applications.

A Compound Heterozygous Pathogenic Variant in ZP2 Gene Causes Female Infertility.

The oocyte maturation defect 6 is an autosomal recessive hereditary disease caused by a homozygous variant in ZP2 gene. It is characterized by female primary infertility due to an abnormally thin zona pellucida (ZP) and defective sperm binding. Here we identified a compound heterozygous variant (c.1924C > T and c.1695-2A > G) in ZP2 gene in a Chinese Han family. Quantitative real-time PCR showed that the variant c.1924C > T significantly decreased the expression of truncated ZP2message RNA by the nonsense-mediated decay pathway. Minigene assays showed the c.1695-2A > G variant led to an extra-61-nt preservation of intron 15 at the junction between exons 15 and 16 during transcription. Both variants (c.1924C > T and c.1695-2A > G) resulted in truncated ZP2 proteins (p.R642X and p.C566Hfs*2) that lost the transmembrane domain, which prevented the secretion of the mutant ZP2 proteins and produced a structurally abnormal ZP, thus resulting in female infertility. This study further elucidated the pathogenic mechanism of these two variants and provided new support for the genetic diagnosis of female infertility.

Thermal Quenching Mechanism of Mn4+ in Na2SiF6, NaKSiF6, and K2SiF6 Phosphors: Insights from the First-Principles Analysis.

This study aims to identify the key factors governing the thermal quenching of Mn4+ ion luminescence in fluoride-based phosphor materials used as red emitters in modern-day phosphor-converted LED devices. Here, we employ first-principles calculations for Mn4+-doped Na2SiF6, NaKSiF6, and K2SiF6 hosts to explore how host properties and local coordination environments influence thermal quenching behavior. The ΔSCF method was used to model the geometric structures of the Mn4+4A2 (ground) and 2E, 4T2 (excited) states and the energies of the optical transitions between these states. Our results reveal that thermal quenching in Na2SiF6 and K2SiF6 phosphors occurs through thermally activated 2E → 4T2 → 4A2 crossover. In contrast, thermal quenching in NaKSiF6 is due to other nonradiative decay pathways. Investigations of the mechanical stability of these fluorides show that NaKSiF6 is mechanically unstable. We suggest that this property of the host limits the luminescence efficiency of the embedded Mn4+ ions. We also determined the reason for the difference in the intensity of the 2E → 4A2 emission transition (ZPL) in the systems. These findings advance our fundamental understanding of the thermal quenching mechanism of Mn4+ ion luminescence in fluorides, and the results can aid future discoveries of technologically useful phosphors through high-throughput design methodologies.

Bioinformatics-Driven Refinement of the Commonly Used TPI Nonsense-Mediated Decay Reporter System.

The cellular nonsense-mediated decay (NMD) pathway recognizes and degrades mRNAs with unusual structural features, such as long 3' UTRs or overlapping reading frames, and therefore serves as a transcript quality control mechanism. A broad spectrum of today's knowledge about the nonsense-mediated mRNA decay pathway has been discovered using NMD reporter systems, mostly consisting of multiple exons, with a wild type (WT) and a premature termination codon (PTC) containing variant. In a preliminary NMD study, we used the seven-exon triose phosphate isomerase (TPI) reporter and observed that in this well-known NMD reporter, surprisingly, not all splice sites are used constitutively, but additional cryptic splice sites are used. As this is more frequently observed in the construction of minigenes, especially when unknown splicing regulatory elements are removed, e.g. by shortening introns, this may affect the reliability of such reporters. To demonstrate how such minigenes can be improved in general with respect to constitutive splice site recognition, we restored an intron length in the TPI reporter or made bioinformatic adjustments to splice regulatory elements (SREs) or intrinsic strength of the splice sites themselves. As a result, this NMD reporter could be made more robust and specific for the evaluation of NMD sensitivity within a single transcript. The modifications of the TPI reporter shown here as examples can generally be used for the transfer of cellular multiexon transcripts to minigenes.

A Comparative Overview of the Role of Human Ribonucleases in Nonsense-Mediated mRNA Decay.

Eukaryotic cells possess surveillance mechanisms that detect and degrade defective transcripts. Aberrant transcripts include mRNAs with a premature termination codon (PTC), targeted by the nonsense-mediated decay (NMD) pathway, and mRNAs lacking a termination codon, targeted by the nonstop decay (NSD) pathway. The eukaryotic exosome, a ribonucleolytic complex, plays a crucial role in mRNA processing and turnover through its catalytic subunits PM/Scl100 (Rrp6 in yeast), DIS3 (Rrp44 in yeast), and DIS3L1. Additionally, eukaryotic cells have other ribonucleases, such as SMG6 and XRN1, that participate in RNA surveillance. However, the specific pathways through which ribonucleases recognize and degrade mRNAs remain elusive. In this study, we characterized the involvement of human ribonucleases, both nuclear and cytoplasmic, in the mRNA surveillance mechanisms of NMD and NSD. We performed knockdowns of SMG6, PM/Scl100, XRN1, DIS3, and DIS3L1, analyzing the resulting changes in mRNA levels of selected natural NMD targets by RT-qPCR. Additionally, we examined the levels of different human β-globin variants under the same conditions: wild-type, NMD-resistant, NMD-sensitive, and NSD-sensitive. Our results demonstrate that all the studied ribonucleases are involved in the decay of certain endogenous NMD targets. Furthermore, we observed that the ribonucleases SMG6 and DIS3 contribute to the degradation of all β-globin variants, with an exception for βNS in the former case. This is also the case for PM/Scl100, which affects all β-globin variants except the NMD-sensitive variants. In contrast, DIS3L1 and XRN1 show specificity for β-globin WT and NMD-resistant variants. These findings suggest that eukaryotic ribonucleases are target-specific rather than pathway-specific. In addition, our data suggest that ribonucleases play broader roles in mRNA surveillance and degradation mechanisms beyond just NMD and NSD.

Rise and Decay of Photoluminescence in Upconverting Lanthanide-Doped Nanocrystals.

Nanocrystals (NCs) doped with lanthanides are capable of efficient photon upconversion, i.e., absorbing long-wavelength light and emitting shorter-wavelength light. The internal processes that enable upconversion are a complex network of electronic transitions within and energy transfer between dopant centers. In this work, we study the rise and decay dynamics of upconversion emission from β-NaYF4 NCs codoped with Er3+ and Yb3+. The rise dynamics of the red and green upconverted emissions are nonlinear, reflecting the nonlinear nature of upconversion and revealing the mechanisms that populate the emitting states. The excited-state decay dynamics are nonexponential. We unravel the underlying decay pathways using photonic experiments. These reveal the contributions of different upconversion pathways visually, as each pathway exhibits a distinct response to systematic variation of the local density of optical states. Moreover, the effect of the local density of optical states on core-only NCs is qualitatively different from core-shell NCs. This is due to the different balance between feeding and decay of the electronic levels that produce upconverted emission. The understanding of the upconversion dynamics provided here could lead to better imaging and sensing methods relying on upconversion lifetimes or guide the rational optimization of the dopant concentrations for brighter upconversion.

Structure of the Nmd4-Upf1 complex supports conservation of the nonsense-mediated mRNA decay pathway between yeast and humans.

The nonsense-mediated mRNA decay (NMD) pathway clears eukaryotic cells of mRNAs containing premature termination codons (PTCs) or normal stop codons located in specific contexts. It therefore plays an important role in gene expression regulation. The precise molecular mechanism of the NMD pathway has long been considered to differ substantially from yeast to metazoa, despite the involvement of universally conserved factors such as the central ATP-dependent RNA-helicase Upf1. Here, we describe the crystal structure of the yeast Upf1 bound to its recently identified but yet uncharacterized partner Nmd4, show that Nmd4 stimulates Upf1 ATPase activity and that this interaction contributes to the elimination of NMD substrates. We also demonstrate that a region of Nmd4 critical for the interaction with Upf1 in yeast is conserved in the metazoan SMG6 protein, another major NMD factor. We show that this conserved region is involved in the interaction of SMG6 with UPF1 and that mutations in this region affect the levels of endogenous human NMD substrates. Our results support the universal conservation of the NMD mechanism in eukaryotes.

Uridylation regulates mRNA decay directionality in fission yeast.

Cytoplasmic mRNA decay is effected by exonucleolytic degradation in either the 5' to 3' or 3' to 5' direction. Pervasive terminal uridylation is implicated in mRNA degradation, however, its functional relevance for bulk mRNA turnover remains poorly understood. In this study, we employ genome-wide 3'-RACE (gw3'-RACE) in the model system fission yeast to elucidate the role of uridylation in mRNA turnover. We observe widespread uridylation of shortened poly(A) tails, promoting efficient 5' to 3' mRNA decay and ensuring timely and controlled mRNA degradation. Inhibition of this uridylation process leads to excessive deadenylation and enhanced 3' to 5' mRNA decay accompanied by oligouridylation. Strikingly we found that uridylation of poly(A) tails and oligouridylation of non-polyadenylated substrates are catalysed by different terminal uridyltransferases Cid1 and Cid16 respectively. Our study sheds new light on the intricate regulatory mechanisms underlying bulk mRNA turnover, demonstrating the role of uridylation in modulating mRNA decay pathways.

PRMT1 Modulates Alternative Splicing to Enhance HPV18 mRNA Stability and Promote the Establishment of Infection.

Only persistent HPV infections lead to the development of cancer. Thus, understanding the virus-host interplay that influences the establishment of viral infection has important implications for HPV biology and human cancers. The ability of papillomaviruses to establish in cells requires the strict temporal regulation of viral gene expression in sync with cellular differentiation. This control primarily happens at the level of RNA splicing and polyadenylation. However, the details of how this spatio-temporal regulation is achieved still need to be fully understood. Until recently, it has been challenging to study the early events of the HPV lifecycle following infection. We used a single-cell genomics approach to identify cellular factors involved in viral infection and establishment. We identify protein arginine N-methyltransferase 1 (PRMT1) as an important factor in viral infection of primary human cervical cells. PRMT1 is the main cellular enzyme responsible for asymmetric dimethylation of cellular proteins. PRMT1 is an enzyme responsible for catalyzing the methylation of arginine residues on various proteins, which influences processes such as RNA processing, transcriptional regulation, and signal transduction. In this study, we show that HPV18 infection leads to increased PRMT1 levels across the viral lifecycle. PRMT1 is critical for the establishment of a persistent infection in primary cells. Mechanistically, PRMT1 inhibition leads to a highly dysregulated viral splicing pattern. Specifically, reduced PRMT1 activity leads to intron retention and a change in the E6 and E7 expression ratio. In the absence of PRMT1, viral transcripts are destabilized and subject to degradation via the nonsense-mediated decay (NMD) pathway. These findings highlight PRMT1 as a critical regulator of the HPV18 lifecycle, particularly in RNA processing, and position it as a potential therapeutic target for persistent HPV18 infections.

Disruption of cotranscriptional splicing suggests RBM39 is a therapeutic target in acute lymphoblastic leukemia

AbstractThere are only a few options for patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL), thus, this is a major area of unmet medical need. In this study, we reveal that the inclusion of a poison exon in RBM39, which could be induced by both CDK9 or CDK9 independent cyclin-dependent kinases, mitogen-activated protein kinases, glycogen synthase kinases, CDC-like kinases (CMGC) kinase inhibition, is recognized by the nonsense-mediated messenger RNA decay pathway for degradation. Targeting this poison exon in RBM39 with CMGC inhibitors led to protein downregulation and the inhibition of ALL growth, particularly in relapsed/refractory B-ALL. Mechanistically, disruption of cotranscriptional splicing by the inhibition of CMGC kinases, including DYRK1A, or inhibition of CDK9, which phosphorylate the C-terminal domain of RNA polymerase II (Pol II), led to alteration in the SF3B1 and Pol II association. Disruption of SF3B1 and the transcriptional elongation complex altered Pol II pausing, which promoted the inclusion of a poison exon in RBM39. Moreover, RBM39 ablation suppressed the growth of human B-ALL, and targeting RBM39 with sulfonamides, which degrade RBM39 protein, showed strong antitumor activity in preclinical models. Our data reveal that relapsed/refractory B-ALL is susceptible to pharmacologic and genetic inhibition of RBM39 and provide 2 potential strategies to target this axis.

Biallelic EPB41L3 variants underlie a developmental disorder with seizures and myelination defects

Abstract Erythrocyte Membrane Protein Band 4.1 Like 3 (EPB41L3: NM_012307.5), also known as DAL-1, encodes the ubiquitously expressed, neuronally enriched 4.1B protein, part of the 4.1 superfamily of membrane-cytoskeleton adaptors. 4.1B plays key roles in cell spreading, migration, and cytoskeletal scaffolding that support oligodendrocyte axon adhesions essential for proper myelination. We herein describe six individuals from five unrelated families with global developmental delay, intellectual disability, seizures, hypotonia, neuroregression, and delayed myelination. Exome sequencing identified biallelic variants in EPB41L3 in all affected individuals: two nonsense (c.466C>T, p.(R156*); c.2776C>T, p.(R926*)) and three frameshift (c.666delT, p.(F222Lfs*46); c.2289dupC, p.(V764Rfs*19); c.948_949delTG, p.(A317Kfs*33)). Quantitative-real time PCR and Western blot analysis in human fibroblasts harbouring EPB41L3:c.666delT, p.(F222Lfs*46) indicate ablation of EPB41L3 mRNA and 4.1B protein expression. Inhibition of the nonsense mediated decay (NMD) pathway led to an upregulation of EPB41L3:c.666delT transcripts, supporting NMD as a pathogenic mechanism. Epb41l3-deficient mouse oligodendroglia cells showed significant reduction in mRNA expression of key myelin genes, reduced branching, and increased apoptosis. Our report provides the first clinical description of an autosomal recessive disorder associated with variants in EPB41L3, which we refer to as EPB41L3-associated developmental disorder (EADD). Moreover, our functional studies substantiate the pathogenicity of EPB41L3 hypothesized loss-of-function variants.

NMDtxDB: data-driven identification and annotation of human NMD target transcripts.

The nonsense-mediated RNA decay (NMD) pathway is a crucial mechanism of mRNA quality control. Current annotations of NMD substrate RNAs are rarely data-driven, but use generally established rules. We present a data set with four cell lines and combinations for SMG5, SMG6, and SMG7 knockdowns or SMG7 knockout. Based on this data set, we implemented a workflow that combines Nanopore and Illumina sequencing to assemble a transcriptome, which is enriched for NMD target transcripts. Moreover, we use coding sequence information (CDS) from Ensembl, Gencode consensus Ribo-seq ORFs, and OpenProt to enhance the CDS annotation of novel transcript isoforms. In summary, 302,889 transcripts were obtained from the transcriptome assembly process, out of which 24% are absent from Ensembl database annotations, 48,213 contain a premature stop codon, and 6433 are significantly upregulated in three or more comparisons of NMD active versus deficient cell lines. We present an in-depth view of these results through the NMDtxDB database, which is available at https://shiny.dieterichlab.org/app/NMDtxDB, and supports the study of NMD-sensitive transcripts. We open sourced our implementation of the respective web-application and analysis workflow at https://github.com/dieterich-lab/NMDtxDB and https://github.com/dieterich-lab/nmd-wf.

Exploiting the Potential of Iridium(III) bis-Nitrone Complexes as Phosphorogenic Bifunctional Reagents for Phototheranostics.

Cross-linking strategies have found wide applications in chemical biology, enabling the labeling of biomolecules and monitoring of protein-protein interactions. Nitrone exhibits remarkable versatility and applicability in bioorthogonal labeling due to its high reactivity with strained alkynes via the strain-promoted alkyne-nitrone cycloaddition (SPANC) reaction. In this work, four cyclometalated iridium(III) polypyridine complexes functionalized with two nitrone units were designed as novel phosphorogenic bioorthogonal reagents for bioimaging and phototherapeutics. The complexes showed efficient emission quenching, which is attributed to an efficient nonradiative decay pathway via the low-lying T1/S0 minimum energy crossing point (MECP), as revealed by computational studies. However, the complexes displayed significant emission enhancement and lifetime extension upon reaction with (1R,8S,9s)-bicyclo[6.1.0]non-4-yne (BCN) derivatives. In particular, they showed a remarkably higher reaction rate toward a bis-cyclooctyne derivative (bis-BCN) compared with its monomeric counterpart (mono-BCN). Live-cell imaging and (photo)cytotoxicity studies revealed higher photocytotoxicity in bis-BCN-pretreated cells, which is ascribed to the enhanced singlet oxygen (1O2) photosensitization resulting from the elimination of the nitrone-associated quenching pathway. Importantly, the cross-linking properties and enhanced reactivity of the complexes make them highly promising candidates for the development of hydrogels and stapled/cyclized peptides, offering intriguing photophysical, photochemical, and biological properties. Notably, a nanosized hydrogel (2-gel) demonstrated potential as a drug delivery system, while a stapled peptide (2-bis-pDIKK) exhibited p53-Mdm2 inhibitory activity related to apoptosis and a cyclized peptide (2-bis-RGD) showed cancer selectivity.

Mutual Transformations of Polysulfide Chromophore Species in Sodalite-Group Minerals: A DFT Study on S6 Decomposition.

It is known that various polysulfide species determine the color of sodalite-group minerals (haüyne, lazurite, and slyudyankaite), and that heating induces their transformations and color change, but the mechanisms of the transitions are unknown. A prominent example is the decay of cyclic S6 molecule. Using density-functional simulations, we explore its main decay pathways into the most probable final reaction products (the pairs of radical anions S3⋅-+S3⋅- and S2⋅-+S4⋅-). It was found that the most favorable reaction path involves initial capture of one electron by the S6 molecule, which greatly facilitates its decay of S6 and leads to the opening of the S6 cycle, and subsequent decomposition of the thus formed chain radical anion, with a limiting energy barrier of ~0.4 eV. Neutral polysulfide molecules capture one electron with a significant energy reduction. The radical anions Sn⋅- (n=2-6) are the most stable ones among corresponding species with the same n values and different charges. The capture of the second electron by S6⋅- occurs with a huge energy barrier (~2 eV). The results of the DFT calculations are in agreement with experimental data on the products of thermal conversions of extra-framework S-bearing groups in sodalite-group minerals.

Structure and Kinetics of Organic Acid Radicals Formed in Reaction with •OH Radicals.

The study investigated •OH-derived radicals from certain organic acids employed in nuclear fuel processing and separation using EPR spectroscopy and quantum chemistry methods. Hydroxyl radicals were generated through a Fenton-like reaction within the EPR resonator under both acidic and basic conditions, allowing for the detection of neutral and radical anions, respectively. The spectral assignment and analysis were conducted using a combination of literature data and quantum chemical calculations employing DFT theory with B3LYP or LPBE functionals and the L2a_3 basis set. The reaction of the •OH radical with lactic and glycolic acids yielded primary C-centered radicals through hydrogen abstraction from these acids. In contrast, the •OH radical exclusively generated secondary radicals from oxalic acid, whereas for citric acid, it resulted in both primary and secondary species induced by decarboxylation. The EPR spectrum of acetohydroxamic acid, upon reaction with the •OH radical, displayed a complex pattern featuring primary •N-type and N-O•-type radicals. The decay pathways of the generated radicals were primarily attributed to radical-radical reactions, with the extracted reaction rate constants generally falling within the typical range observed for such reactions. The EPR parameters calculated for potential radicals using B3LYP and LPBE functionals with L2a_3 basis set demonstrated good accuracy for neutral radicals, albeit requiring minor adjustments for radical anions.

Distinct vibrational motions promote disparate excited-state decay pathways in cofacial perylenediimide dimers.

A complex interplay of structural, electronic, and vibrational degrees of freedom underpins the fate of molecular excited states. Organic assemblies exhibit a myriad of excited-state decay processes, such as symmetry-breaking charge separation (SB-CS), excimer (EX) formation, singlet fission, and energy transfer. Recent studies of cofacial and slip-stacked perylene-3,4:9,10-bis(dicarboximide) (PDI) multimers demonstrate that slight variations in core substituents and H- or J-type aggregation can determine whether the system follows an SB-CS pathway or an EX one. However, questions regarding the relative importance of structural properties and molecular vibrations in driving the excited-state dynamics remain. Here, we use a combination of two-dimensional electronic spectroscopy, femtosecond stimulated Raman spectroscopy, and quantum chemistry computations to compare the photophysics of two PDI dimers. The dimer with 1,7-bis(pyrrolidin-1'-yl) substituents (5PDI2) undergoes ultrafast SB-CS from a photoexcited mixed state, while the dimer with bis-1,7-(3',5'-di-t-butylphenoxy) substituents (PPDI2) rapidly forms an EX state. Examination of their quantum beating features reveals that SB-CS in 5PDI2 is driven by the collective vibronic coupling of two or more excited-state vibrations. In contrast, we observe signatures of low-frequency vibrational coherence transfer during EX formation by PPDI2, which aligns with several previous studies. We conclude that key electronic and structural differences between 5PDI2 and PPDI2 determine their markedly different photophysics.

Tunable Stochastic State Switching in 2D MoS2 Nanomechanical Resonators with Nonlinear Mode Coupling and Internal Resonance.

Coupled nanomechanical resonators have unveiled fascinating physical phenomena, including phonon-cavity coupling, coupled energy decay pathway, avoided crossing, and internal resonance. Despite these discoveries, the mechanisms and control techniques of nonlinear mode coupling phenomena with internal resonances require further exploration. Here, we report on the observation of stochastic switching between the two resonance states with coupled 1:1 internal resonance, for resonant two-dimensional (2D) molybdenum disulfide (MoS2) nanoelectromechanical systems (NEMS), which is directly driven to the critical coupling regime without parametric pumping. We further demonstrate that the probability of state switching is linearly tunable from ∼0% to ∼100% by varying the driving voltage. Furthermore, we gradually increase the white noise amplitude and show that the probability of obtaining the higher-energy state decreases, and the stochastic switching phenomenon eventually disappears. The results provide insights into the dynamics of coupled NEMS resonators and open up new possibilities for sensing and stochastic computing.

Re‐Examination of Self‐Decay Chemistry of Phthalimide‐N‐oxyl Redox‐Organocatalyst for Free‐Radical CH‐Functionalization – Puzzle Begins to Come Together

AbstractPhthalimide‐N‐oxyl radicals (PINO) are catalytically active hydrogen abstracting species generated from N‐hydroxyphthalimide (NHPI) – one of the most efficient and widely used organocatalysts for free‐radical oxidative CH‐functionalization processes. The self‐decay of PINO is one of the main limiting factors of NHPI usage, but currently there is no consensus on the mechanism of this important process. In the present work, quantitative EPR and NMR monitoring of PINO generation and degradation along with decay product analysis and control experiments allowed us to build a consistent picture of PINO decay chemistry and put together previously contradictory results. PINO yields achievable employing various oxidants were measured and compared for the first time. At least two PINO decay pathways were revealed: “trimerization” (with partial fragmentation, favored by high PINO concentrations at initial stage of decay), and medium oxidation favored by low PINO concentrations. The main PINO decomposition product, the “trimer” can easily be recycled back to NHPI.

Discovery of Molecular Intermediates and Nonclassical Nanoparticle Formation Mechanisms by Liquid Phase Electron Microscopy and Reaction Throughput Analysis

Formation kinetics of metal nanoparticles are generally described via mass transport and thermodynamics‐based models, such as diffusion‐limited growth and classical nucleation theory (CNT). However, metal monomers are commonly assumed as precursors, leaving the identity of molecular intermediates and their contribution to nanoparticle formation unclear. Herein, liquid phase transmission electron microscopy (LPTEM) and reaction kinetic modeling are utilized to establish the nucleation and growth mechanisms and discover molecular intermediates during silver nanoparticle formation. Quantitative LPTEM measurements show that their nucleation rate decreases while growth rate is nearly invariant with electron dose rate. Reaction kinetic simulations show that Ag4 and Ag− follow a statistically similar dose rate dependence as the experimentally determined growth rate. We show that experimental growth rates are consistent with diffusion‐limited growth via the attachment of these species to nanoparticles. The dose rate dependence of nucleation rate is inconsistent with CNT. A reaction‐limited nucleation mechanism is proposed and it is demonstrated that experimental nucleation kinetics are consistent with Ag42+ aggregation rates at millisecond time scales. Reaction throughput analysis of the kinetic simulations uncovered formation and decay pathways mediating intermediate concentrations. We demonstrate the power of quantitative LPTEM combined with kinetic modeling for establishing nanoparticle formation mechanisms and principal intermediates.