Switch In Mechanism Research Articles

Time-varying stimuli that prolong IKK activation promote nuclear remodeling and mechanistic switching of NF-κB dynamics.

Temporal properties of molecules within signaling networks, such as sub-cellular changes in protein abundance, encode information that mediate cellular responses to stimuli. How dynamic signals relay and process information is a critical gap in understanding cellular behaviors. In this work, we investigate transmission of information about changing extracellular cytokine concentrations from receptor-level supramolecular assemblies of IκB kinases (IKK) downstream to the nuclear factor κB (NF-κB) transcription factor (TF). In a custom robot-controlled microfluidic cell culture, we simultaneously measure input-output (I/O) encoding of IKK-NF-κB in dual fluorescent-reporter cells. When compared with single cytokine pulses, dose-conserving pulse trains prolong IKK assemblies and lead to disproportionately enhanced retention of nuclear NF-κB. Using particle swarm optimization, we demonstrate that a mechanistic model does not recapitulate this emergent property. By contrast, invoking mechanisms for NF-κB-dependent chromatin remodeling to the model recapitulates experiments, showing how temporal dosing that prolongs IKK assemblies facilitates switching to permissive chromatin that sequesters nuclear NF-κB. Remarkably, using simulations to resolve single-cell receptor data accurately predicts same-cell NF-κB time courses for more than 80% of our single cell trajectories. Our data and simulations therefore suggest that cell-to-cell heterogeneity in cytokine responses are predominantly due to mechanisms at the level receptor-associated protein complexes.

International Simple Glass (ISG) dissolution rate in a (Si, Ca)-rich environment at 90 °C and alkaline conditions

The dissolution of International Simple Glass (ISG) was investigated at 90 °C and alkaline conditions with various concentrations of dissolved Si and Ca to unravel the combined effects of those elements on ISG reactivity. Experiments were conducted over durations ranging from 20 days to 3 months. Through morphological, structural, and chemical characterizations, the glass dissolution rate was proven to be strongly correlated with the activity of dissolved silica in the solution. While dissolved calcium did not significantly impact the dissolution rate, precipitation of calcium silicate hydrates (CSH) during the experiments enhanced ISG dissolution rate, though to a modest extent. The 3-months experiments highlighted the strong correlation between the dissolution mechanism and the evolution of the nature of secondary phases in saturated solution. During the first 20 days and at high Si and Ca concentrations, CSH precipitated and aggregated, without preventing the passivating impact of the gel layer at the surface of the glass: the dissolution was controlled by diffusion. Then, a resumption of dissolution occurred between 19 days and 76 days, corresponding to the CSH growth, and a possible mechanistic switch to a hydrolysis-controlled reaction rate. Finally, in some experiments, a drop in pH due to carbonate precipitation was observed along with a decrease in the dissolution rate, falling back in a diffusion-limited regime. Overall, this study shows that at 90 °C, pH = 10 and concentrations of SiO2(aq) exceeding 50 % of saturation with respect to amorphous silica, irrespective of Ca concentration but in presence of CO2(aq), ISG exhibits a very good chemical durability.

Intermolecular O-O Bond Formation between High-Valent Ru-oxo Species.

Despite extensive research on water oxidation catalysts over the past few decades, the relationship between high-valent metal-oxo intermediates and the O-O bond formation pathway has not been well clarified. Our previous study showed that the high spin density on O in RuV=O is pivotal for the interaction of two metal-oxyl radical (I2M) pathways. In this study, we found that introducing an axially coordinating ligand, which is favorable for bimolecular coupling, into the Ru-pda catalyst can rearrange its geometry. The shifts in geometric orientation altered its O-O bond formation pathway from water nucleophilic attack (WNA) to I2M, resulting in a 70-fold increase in water oxidation activity. This implies that the I2M pathway is concurrently influenced by the spin density on oxo and the geometry organization of the catalysts. The observed mechanistic switch and theoretical studies provide insights into controlling reaction pathways for homogeneous water oxidation catalysis.

Changing Mechanisms for CO2 Reduction to Formate Via Protonation of the Catalyst

Electrochemical reduction reaction of CO2 (CO2RR) is a promising method to transform CO2 to useful products for consumption such as formic acid, carbon monoxide, or methane. Simply increasing the driving force of a catalytic process to speed up the rate of CO2 reduction is unviable because of the competing Hydrogen Evolution Reaction (HER) pathway and of increased energy cost. Controlling the reactivity of active intermediates is of substantial importance for such processes. [Fe4N(CO)12]− is a formate selective electrocatalyst previously studied by our group and was modified through protonation and replacement of several CO ligands with triethylphosphines (PEt3) to synthesize [HFe4N(PEt3)4(CO)8] . This PEt3 substituted, pre-protonated analog of [Fe4N(CO)12]− exhibits altered rates compared to a non-protonated analog which we attribute to a switch in mechanism. We further explore explanations for different rates despite similar “active intermediates” and similar driving force using Cyclic Voltammetry (CV).

Diastereodivergent nucleophile–nucleophile alkene chlorofluorination

The selective hetero-dihalogenation of alkenes provides useful building blocks for a broad range of chemical applications. Unlike homo-dihalogenation, selective hetero-dihalogenation reactions, especially fluorohalogenation, are underdeveloped. Current approaches combine an electrophilic halogen source with a nucleophilic halogen source, which necessarily leads to anti-addition, and regioselectivity has only been achieved using highly activated alkenes. Here we describe an alternative, nucleophile–nucleophile approach that adds chloride and fluoride ions over unactivated alkenes in a highly regio-, chemo- and diastereoselective manner. A curious switch in the reaction mechanism was discovered, which triggers a complete reversal of the diastereoselectivity to promote either anti- or syn-addition. The conditions are demonstrated on an array of pharmaceutically relevant compounds, and detailed mechanistic studies reveal the selectivity and the switch between the syn- and anti-diastereomers are based on different active iodanes and which of the two halides adds first.

Substitution-Induced Mechanistic Switching in SNAr-Warheads for Cysteine Proteases.

The aim of this study was to investigate the transition from non-covalent reversible over covalent reversible to covalent irreversible inhibition of cysteine proteases by making delicate structural changes to the warhead scaffold. To this end, dipeptidic rhodesain inhibitors with different N-terminal electrophilic arenes as warheads relying on the SNAr mechanism were synthesized and investigated. Strong structure-activity relationships of the inhibition potency, the degree of covalency, and the reversibility of binding on the arene substitution pattern were found. The studies were complemented and substantiated by molecular docking and quantum-mechanical calculations of model systems. Furthermore, the improvement in the membrane permeability of peptide esters in comparison to their corresponding carboxylic acids was exemplified.

The complexity of extracellular vesicles: Bridging the gap between cellular communication and neuropathology.

Brain-derived extracellular vesicles (EVs) serve a prominent role in maintaining homeostasis and contributing to pathology in health and disease. This review establishes a crucial link between physiological processes leading to EV biogenesis and their impacts on disease. EVs are involved in the clearance and transport of proteins and nucleic acids, responding to changes in cellular processes associated with neurodegeneration, including autophagic disruption, organellar dysfunction, aging, and other cell stresses. In neurodegenerative disorders (e.g., Alzheimer's disease, Parkinson's disease, etc.), EVs contribute to the spread of pathological proteins like amyloid β, tau, ɑ-synuclein, prions, and TDP-43, exacerbating neurodegeneration and accelerating disease progression. Despite evidence for both neuropathological and neuroprotective effects of EVs, the mechanistic switch between their physiological and pathological functions remains elusive, warranting further research into their involvement in neurodegenerative disease. Moreover, owing to their innate ability to traverse the blood-brain barrier and their ubiquitous nature, EVs emerge as promising candidates for novel diagnostic and therapeutic strategies. The review uniquely positions itself at the intersection of EV cell biology, neurophysiology, and neuropathology, offering insights into the diverse biological roles of EVs in health and disease.

Competing Mechanisms in Palladium-Catalyzed Alkoxycarbonylation of Styrene.

Palladium-catalyzed carbonylation is a versatile method for the synthesis of various aldehydes, esters, lactones, or lactams. Alkoxycarbonylation of alkenes with carbon monoxide and alcohol produces either saturated or unsaturated esters as a result of two distinct catalytic cycles. The existing literature presents an inconsistent account of the procedures favoring oxidative carbonylation products. In this study, we have monitored the intermediates featured in both catalytic cycles of the methoxycarbonylation of styrene PhCH=CH2 as a model substrate, including all short-lived intermediates, using mass spectrometry. Comparing the reaction kinetics of the intermediates in both cycles in the same reaction mixture shows that the reaction proceeding via alkoxy intermediate [PdII]-OR, which gives rise to the unsaturated product PhCH=CHCO2Me, is faster. However, with an advancing reaction time, the gradually changing reaction conditions begin to favor the catalytic cycle dominated by palladium hydride [PdII]-H and alkyl intermediates, affording the saturated products PhCH2CH2CO2Me and PhCH(CO2Me)CH3 preferentially. The role of the oxidant proved to be crucial: using p-benzoquinone results in a gradual decrease of the pH during the reaction, swaying the system from oxidative conditions toward the palladium hydride cycle. By contrast, copper(II) acetate as an oxidant guards the pH within the 5-7 range and facilitates the formation of the alkoxy palladium complex [PdII]-OR, which favors the oxidative reaction producing PhCH=CHCO2Me with high selectivity. Hence, it is the oxidant, rather than the catalyst, that controls the reaction outcome by a mechanistic switch. Unraveling these principles broadens the scope for developing alkoxycarbonylation reactions and their application in organic synthesis.

Mechanistic Insights into the Origins of Selectivity in a Cu-Catalyzed C-H Amidation Reaction.

The catalytic transformation of C-H to C-N bonds offers rapid access to fine chemicals and high-performance materials, but achieving high selectivity from undirected aminations of unactivated C(sp3)-H bonds remains an outstanding challenge. We report the origins of the reactivity and selectivity of a Cu-catalyzed C-H amidation of simple alkanes. Using a combination of experimental and computational mechanistic studies and energy decomposition techniques, we uncover a switch in mechanism from inner-sphere to outer-sphere coupling between alkyl radicals and the active Cu(II) catalyst with increasing substitution of the alkyl radical. The combination of computational predictions and detailed experimental validation shows that simultaneous minimization of both Cu-C covalency and alkyl radical size increases the rate of reductive elimination and that both strongly electron-donating and electron-withdrawing substituents on the catalyst accelerate the selectivity-determining C-N bond formation process as a result of a change in mechanism. These findings offer design principles for the development of improved catalyst scaffolds for radical C-H functionalization reactions.

Increased α-ketoglutarate links the C3-C4 intermediate state to C4 photosynthesis in the genus Flaveria.

As a complex trait, C4 photosynthesis has multiple independent origins in evolution. Phylogenetic evidence and theoretical analysis suggest that C2 photosynthesis, which is driven by glycine decarboxylation in the bundle sheath cell, may function as a bridge from C3 to C4 photosynthesis. However, the exact molecular mechanism underlying the transition between C2 photosynthesis to C4 photosynthesis remains elusive. Here, we provide evidence suggesting a role of higher α-ketoglutarate (AKG) concentration during this transition. Metabolomic data of 12 Flaveria species, including multiple photosynthetic types, show that AKG concentration initially increased in the C3-C4 intermediate with a further increase in C4 species. Petiole feeding of AKG increases the concentrations of C4-related metabolites in C3-C4 and C4 species but not the activity of C4-related enzymes. Sequence analysis shows that glutamate synthase (Fd-GOGAT), which catalyzes the generation of glutamate using AKG, was under strong positive selection during the evolution of C4 photosynthesis. Simulations with a constraint-based model for C3-C4 intermediate further show that decreasing the activity of Fd-GOGAT facilitated the transition from a C2-dominant to a C4-dominant CO2 concentrating mechanism. All these results provide insight into the mechanistic switch from C3-C4 intermediate to C4 photosynthesis.

Cyclic Voltammetry for Accurate Icing Detection on Simulated Aircraft Surfaces.

Icing and ice accretion on aerodynamically critical surfaces of an aircraft increase drag, reduce lift, and raise stalling speed, which pose significant safety hazards to aircraft while in flight. Icephobic coatings have been intensively investigated by the Canadian and global aerospace industries for passive ice protection. Nevertheless, effective icephobic coatings suitable for aerospace applications are far from ideal. Ice protection of an aircraft still relies on active ice protection systems based on heating, mechanical expulsion, and deicing fluids, which are heavy-weight, power-intensive, and unfriendly to the environment. To address these challenges, rapid and accurate detection of icing is highly desirable to activate these ice protection systems only when needed. To this end, cyclic voltammetry was used for the first time to detect the initiation of icing on aircraft surfaces with or without icephobic coatings. In this study, a water droplet was sandwiched between a screen-printed electrode and a simulated aircraft surface. Cyclic voltammograms were then collected as the temperature was slowly decreased until the droplet froze to form ice. A sharp spike in faradaic current was recorded in the voltammograms during the phase transition, suggesting a switch in the mass transfer mechanism from diffusion to a surface-confined pathway. This electrochemical signal could then be used to precisely indicate the onset of icing. The developed sensing method shows potential in icing detection to manage active ice protections and ameliorate icing risks in the aerospace and aviation industries.

SN 2 versus E2 Competition of Cyclic Ethers.

We have quantum chemically studied the influence of ring strain on the competition between the two mechanistically different SN 2 and E2 pathways using a series of archetypal ethers as substrate in combination with a diverse set of Lewis bases (F- , Cl- , Br- , HO- , H3 CO- , HS- , H3 CS- ), using relativistic density functional theory at ZORA-OLYP/QZ4P. The ring strain in the substrate is systematically increased on going from a model acyclic ether to a 6- to 5- to 4- to 3-membered ether ring. We have found that the activation energy of the SN 2 pathway sharply decreases when the ring strain of the system is increased, thus on going from large to small cyclic ethers, the SN 2 reactivity increases. In contrast, the activation energy of the E2 pathway generally rises along this same series, that is, from large to small cyclic ethers. The opposing reactivity trends induce a mechanistic switch in the preferred reaction pathway for strong Lewis bases from E2, for large cyclic substrates, to SN 2, for small cyclic substrates. Weak Lewis bases are unable to overcome the higher intrinsic distortivity of the E2 pathway and, therefore, always favor the less distortive SN 2 reaction.

Dynamic subcanopy leaf traits drive resistance of net primary production across a disturbance severity gradient

Across the globe, the forest carbon sink is increasingly vulnerable to an expanding array of low- to moderate-severity disturbances. However, some forest ecosystems exhibit functional resistance (i.e., the capacity of ecosystems to continue functioning as usual) following disturbances such as extreme weather events and insect or fungal pathogen outbreaks. Unlike severe disturbances (e.g., stand-replacing wildfires), moderate severity disturbances do not always result in near-term declines in forest production because of the potential for compensatory growth, including enhanced subcanopy production. Community-wide shifts in subcanopy plant functional traits, prompted by disturbance-driven environmental change, may play a key mechanistic role in resisting declines in net primary production (NPP) up to thresholds of canopy loss. However, the temporal dynamics of these shifts, as well as the upper limits of disturbance for which subcanopy production can compensate, remain poorly characterized. In this study, we leverage a 4-year dataset from an experimental forest disturbance in northern Michigan to assess subcanopy community trait shifts as well as their utility in predicting ecosystem NPP resistance across a wide range of implemented disturbance severities. Through mechanical girdling of stems, we achieved a gradient of severity from 0% (i.e., control) to 45, 65, and 85% targeted gross canopy defoliation, replicated across four landscape ecosystems broadly representative of the Upper Great Lakes ecoregion. We found that three of four examined subcanopy community weighted mean (CWM) traits including leaf photosynthetic rate (p = 0.04), stomatal conductance (p = 0.07), and the red edge normalized difference vegetation index (p < 0.0001) shifted rapidly following disturbance but before widespread changes in subcanopy light environment triggered by canopy tree mortality. Surprisingly, stimulated subcanopy production fully compensated for upper canopy losses across our gradient of experimental severities, achieving complete resistance (i.e., no significant interannual differences from control) of whole ecosystem NPP even in the 85% disturbance treatment. Additionally, we identified a probable mechanistic switch from nutrient-driven to light-driven trait shifts as disturbance progressed. Our findings suggest that remotely sensed traits such as the red edge normalized difference vegetation index (reNDVI) could be particularly sensitive and robust predictors of production response to disturbance, even across compositionally diverse forests. The potential of leaf spectral indices to predict post-disturbance functional resistance is promising given the capabilities of airborne to satellite remote sensing. We conclude that dynamic functional trait shifts following disturbance can be used to predict production response across a wide range of disturbance severities.

Do specific ion effects influence the physical chemistry of aqueous graphene-based supercapacitors? Perspectives from multiscale QMMD simulations

Whether or not specific ion effects determine the charge storage properties of aqueous graphene and graphite-based supercapacitors remains a highly debated topic. In this work we present a multiscale quantum mechanics – classical molecular dynamics (QMMD) investigation of aqueous mono- and divalent salt electrolytes in contact with fully polarizable charged graphene sheets. By computing both the electrochemical double layer (EDL) and quantum capacitance we observe a constant electrode specific capacitance with cationic radii and charge. Counterintuitively, we determine that a switch in the cation adsorption mechanism from inner to outer Helmholtz layers leads to negligible changes to the EDL capacitance, this appears to be due to the robust electronic structure of the graphene electrodes. However, the ability of ions (such as K+) with a relatively low hydration free energy to penetrate the inner Helmholtz plane and adsorb directly on the electrode surface is found to slow their diffusion parallel to the interface. Ions in the outer Helmholtz layer are found to have higher diffusivity at the surface due to their position in ion channels between water layers. Our results show that surface effects such as the surface polarization and the partial dehydration and local structuring of ions on the surface underpin the behaviour of cations at the interface and add a vital new perspective on trends in ion mobilities seen under confinement.

Direct π-Activation vs. O-Activation in Halogen-Bonding Catalysis.

Halogen bond donors had an increasing impact on catalysis in recent years, and their development is highly active. In particular, numerous iodine-based halogen bond donors have been developed and used to promote various reactions through coordinating carbonyl groups, a ubiquitous mode of activation in catalysis. We now report computational data which strongly suggests that an alternative activation mode, through direct π-complexation, is operative for unsaturated carbonyl substrates. Calculations also suggest that solvent polarity could have a clear impact on the preference of the mode of activation, raising the possibility of a mechanistic manifold switch through solvent variation. These findings could profoundly impact the development of the next generation of halogen-bond donor catalysts.

Direct π‐Activation vs. O‐Activation in Halogen‐Bonding Catalysis

AbstractHalogen bond donors had an increasing impact on catalysis in recent years, and their development is highly active. In particular, numerous iodine‐based halogen bond donors have been developed and used to promote various reactions through coordinating carbonyl groups, a ubiquitous mode of activation in catalysis. We now report computational data which strongly suggests that an alternative activation mode, through direct π‐complexation, is operative for unsaturated carbonyl substrates. Calculations also suggest that solvent polarity could have a clear impact on the preference of the mode of activation, raising the possibility of a mechanistic manifold switch through solvent variation. These findings could profoundly impact the development of the next generation of halogen‐bond donor catalysts.

Tunable [3+2] and [4+2] annulations for pyrrolidine and piperidine synthesis.

N-heterocycles are privileged pharmaceutical scaffolds in drug discovery and development. We disclose here divergent intermolecular coupling strategies that can access diverse N-heterocycles directly from olefins. The radical-to-polar mechanistic switching is key for the divergent cyclization processes. These distinctive annulations result in the coupling of alkenes with simple bifunctional reagents for divergent N-heterocycle syntheses.

Brain capillary pericytes are metabolic sentinels that control blood flow through a KATP channel-dependent energy switch

Despite the abundance of capillary thin-strand pericytes and their proximity to neurons and glia, little is known of the contributions of these cells to the control of brain hemodynamics. We demonstrate that the pharmacological activation of thin-strand pericyte KATP channels profoundly hyperpolarizes these cells, dilates upstream penetrating arterioles and arteriole-proximate capillaries, and increases capillary blood flow. Focal stimulation of pericytes with a KATP channel agonist is sufficient to evoke this response, mediated via KIR2.1 channel-dependent retrograde propagation of hyperpolarizing signals, whereas genetic inactivation of pericyte KATP channels eliminates these effects. Critically, we show that decreasing extracellular glucose to less than 1mM or inhibiting glucose uptake by blocking GLUT1 transporters invivo flips a mechanistic energy switch driving rapid KATP-mediated pericyte hyperpolarization to increase local blood flow. Together, our findings recast capillary pericytes as metabolic sentinels that respond to local energy deficits by increasing blood flow to neurons to prevent energetic shortfalls.

Facile Tandem Copolymerization of O-Carboxyanhydrides and Epoxides to Synthesize Functionalized Poly(ester-b-carbonates).

The synthesis of well-defined degradable block copolymers from mixtures of monomers is one of the foremost challenges in the sustainable plastics industry. For example, the currently available one-pot strategies for preparing poly(ester-co-carbonates)─which combine two commonly used degradable polymers─are energy- and material-intensive, requiring high-pressure CO2 gas and elevated temperatures. Here, we report an atom-economical, scalable method for block copolymerization of O-carboxyanhydrides (OCAs) and epoxides to prepare functionalized poly(ester-b-carbonates) with high molecular weights (MWs) (>200 kDa) and narrow MW distributions (D̵ < 1.1) by using a single Lewis acidic zinc complex at room temperature in the absence of pressurized CO2. Kinetic studies showed that the first stage of the process, ring-opening polymerization of the OCAs, exhibited zero-order kinetics, suggesting that the polymerization rate was independent of monomer concentration and thus allowing for a sharp switch in mechanism without the tapering effect. The obtained degradable poly(ester-b-carbonates) showed better toughness than their corresponding homopolymers and outperformed some commodity polyolefins.

A requirement for astrocyte IP3R2 signaling for whisker experience-dependent depression and homeostatic upregulation in the mouse barrel cortex.

Changes to sensory experience result in plasticity of synapses in the cortex. This experience-dependent plasticity (EDP) is a fundamental property of the brain. Yet, while much is known about neuronal roles in EDP, very little is known about the role of astrocytes. To address this issue, we used the well-described mouse whiskers-to-barrel cortex system, which expresses a number of forms of EDP. We found that all-whisker deprivation induced characteristic experience-dependent Hebbian depression (EDHD) followed by homeostatic upregulation in L2/3 barrel cortex of wild type mice. However, these changes were not seen in mutant animals (IP3R2–/–) that lack the astrocyte-expressed IP3 receptor subtype. A separate paradigm, the single-whisker experience, induced potentiation of whisker-induced response in both wild-type (WT) mice and IP3R2–/– mice. Recordings in ex vivo barrel cortex slices reflected the in vivo results so that long-term depression (LTD) could not be elicited in slices from IP3R2–/– mice, but long-term potentiation (LTP) could. Interestingly, 1 Hz stimulation inducing LTD in WT paradoxically resulted in NMDAR-dependent LTP in slices from IP3R2–/– animals. The LTD to LTP switch was mimicked by acute buffering astrocytic [Ca2+]i in WT slices. Both WT LTD and IP3R2–/– 1 Hz LTP were mediated by non-ionotropic NMDAR signaling, but only WT LTD was P38 MAPK dependent, indicating an underlying mechanistic switch. These results demonstrate a critical role for astrocytic [Ca2+]i in several EDP mechanisms in neocortex.