Slow Step Research Articles

Hopping and crawling DNA-coated colloids

Understanding the motion of particles with multivalent ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or roll, depending on the study. We shed light on this problem by observing DNA-coated colloids diffusing near surfaces coated with complementary strands for a wide array of coating designs. We find colloids rapidly switch between 2 modes: They hop-with long and fast steps-and crawl-with short and slow steps. Both modes occur at all temperatures around the melting point and over various designs. The particles become increasingly subdiffusive as temperature decreases, in line with subsequent velocity steps becoming increasingly anticorrelated, corresponding to switchbacks in the trajectories. Overall, crawling (or hopping) phases are more predominant at low (or high) temperatures; crawling is also more efficient at low temperatures than hopping to cover large distances. We rationalize this behavior within a simple model: At lower temperatures, the number of bound strands increases, and detachment of all bonds is unlikely, hence, hopping is prevented and crawling favored. We thus reveal the mechanism behind a common design rule relying on increased strand density for long-range self-assembly: Dense strands on surfaces are required to enable crawling, possibly facilitating particle rearrangements.

A Dual CQD-Catalysis and H-Bond Acceptor for Controlling Product Selectivity and Regioselectivity in Symmetric/Unsymmetric Azoxy Arenes.

Azoxy arenes are valuable compounds in different areas of chemistry, such as organic chemistry, medicinal chemistry, and natural product chemistry. Despite their value, the regioselective synthesis of unsymmetric azoxybenzenes has remained a real challenge in the field. Herein, the product selectivity in oxidative homocoupling of anilines into symmetric azoxybenzenes was first achieved by an asparagine-functionalized CQD catalyst. Subsequently, in the cross-coupling of anilines into the unsymmetric azoxybenzenes via an ortho H-bond acceptor (HBA) on one of the coupling anilines, the regioselectivity was effectively controlled. It was demonstrated that ortho-HBA could mechanistically establish a six-membered intramolecular hydrogen-bonded ring on an N,N'-dihydroxy intermediate. The formed hydrogen bond makes the nearby nitrogen eminently suitable for the slow dehydration step. As a result, the functional oxygen of the azoxy compound is placed far from the HBA. The o-HBA mechanism also controls the regioselectivity ratio in which 1:0 (with an intramolecular H-bonded hexagonal ring), 2:1 (with an intramolecular H-bonded pentagonal ring), and 1:1 (without an ortho-HBA) isomeric mixtures could be achieved. The HBA mechanism was exploited by different substituted anilines, and various unsymmetric azoxybenzenes were synthesized. Finally, with the aid of mechanistic studies, a plausible mechanism for the reaction was proposed.

Gold(III) Auracycles Featuring C(sp3)-Au-C(sp2) Bonds: Synthesis and Mechanistic Insights into the Cycloauration Step.

The direct auration of arenes is a key step in numerous gold-catalyzed reactions. Although reported more than 100 years ago, understanding of its underlying mechanism has been hampered by the difficulties in the isolation of relevant intermediates given the propensity of gold(III) species to undergo reductive elimination. Here, we report the synthesis and isolation of a new family of intriguing zwitterionic [C(sp3)^C(sp2)]-auracyclopentanes, as well as of their alkyl-gold(III) precursors and demonstrate their value as mechanistic probes to study the C(sp2)-Au bond-forming event. Experimental investigations employing Kinetic Isotope Effects (KIE), Hammett plot, and Eyring analysis provided important insights into the formation of the auracycle. The data suggest a SEAr mechanism wherein the slowest step might be the π-coordination between the arene and the gold(III) center, en route to the Wheland intermediate. We also show that these auracyclopentanes can work as catalysts in several gold-promoted transformations.

Sorption of 32Si and 45Ca by isotopic exchange during recrystallisation of cement phases

The uptake kinetics of 32Si and 45Ca on cement minerals including C-S-H phases, portlandite, AFm phases, ettringite, and aged hardened cement paste were determined through batch sorption experiments. A two-step uptake kinetics was observed, with a fast initial step during ∼1 day followed by a much slower second step, not yet completed after one year. The working hypothesis that the fast uptake is caused by exchange of the radioisotopes with stable isotopes adsorbed on the mineral surface, whereas the slow uptake step is due to uptake in the crystal lattice during recrystallisation, was tested with the help of phenomenological models that combine surface adsorption and homogeneous recrystallisation. The experimental data could be reproduced satisfactorily using a refined version of the formerly published continuous homogeneous recrystallisation (CHOR) model, supporting the working hypothesis and allowing equilibrium sorption coefficients (Rd; L kg−1) for these radionuclides to be calculated on a mechanistic basis. This provides insight into the intrinsic rates and mechanisms of interaction between cementitious materials and their pore fluids which contain dissolved calcium and silicon.

Coacervation in Slow Motion: Kinetics of Complex Micelle Formation Induced by the Hydrolysis of an Antibiotic Prodrug.

Colistin methanesulfonate (CMS) is the less-toxic prodrug of highly nephrotoxic colistin. To develop and understand highly necessary new antibiotic formulations, the hydrolysis of CMS to colistin must be better understood. Herein, with the addition of poly(ethylene oxide)-b-poly(methacrylic acid) (PEO-b-PMAA) to CMS, we show that we can follow the hydrolysis kinetics, employing small-angle X-ray scattering (SAXS) through complex coacervation. During this hydrolysis, hydroxy methanesulfonate (HMS) groups from CMS are cleaved, while the newly formed cationic amino groups complex with the anionic charge from the PMAA block. As the hydrolysis of HMS groups is slow, we can follow the complex coacervation process by the gradual formation of complex micelles containing activated antibiotics. Combining mass spectrometry (MS) with SAXS, we quantify the hydrolysis as a function of pH. Upon modeling the kinetic pathways, we found that complexation only happens after complete hydrolysis into colistin and that the process is accelerated under acidic conditions. At pH = 5.0, effective charge switching was identified as the slowest step in the CMS conversion, constituting the rate-limiting step in colistin formation.

Kinetic and structural insights into the requirement of fungal tRNA ligase for a 2'-phosphate end.

Fungal RNA ligase (LIG) is an essential tRNA splicing enzyme that joins 3'-OH,2'-PO4 and 5'-PO4 RNA ends to form a 2'-PO4,3'-5' phosphodiester splice junction. Sealing entails three divalent cation-dependent adenylate transfer steps. First, LIG reacts with ATP to form a covalent ligase-(lysyl-Nζ)-AMP intermediate and displace pyrophosphate. Second, LIG transfers AMP to the 5'-PO4 RNA terminus to form an RNA-adenylate intermediate (A5'pp5'RNA). Third, LIG directs the attack of an RNA 3'-OH on AppRNA to form the splice junction and displace AMP. A defining feature of fungal LIG vis-à-vis canonical polynucleotide ligases is the requirement for a 2'-PO4 to synthesize a 3'-5' phosphodiester bond. Fungal LIG consists of an N-terminal adenylyltransferase domain and a unique C-terminal domain. The C-domain of Chaetomium thermophilum LIG (CthLIG) engages a sulfate anion thought to be a mimetic of the terminal 2'-PO4 Here, we interrogated the contributions of the C-domain and the conserved sulfate ligands (His227, Arg334, Arg337) to ligation of a pRNA2'p substrate. We find that the C-domain is essential for end-joining but dispensable for ligase adenylylation. Mutations H227A, R334A, and R337A slowed the rate of step 2 RNA adenylation by 420-fold, 120-fold, and 60-fold, respectively, vis-à-vis wild-type CthLIG. An R334A-R337A double-mutation slowed step 2 by 580-fold. These results fortify the case for the strictly conserved His-Arg-Arg triad as the enforcer of the 2'-PO4 end-specificity of fungal tRNA ligases and as a target for small molecule interdiction of fungal tRNA splicing.

Demonstrating the data integrity of routinely collected healthcare systems data for clinical trials (DEDICaTe): A proof-of-concept study.

Introduction/aims: Healthcare systems data (also known as real-world or routinely collected health data) could transform the conduct of clinical trials. Demonstrating integrity and provenance of these data is critical for clinical trials, to enable their use where appropriate and avoid duplication using scarce trial resources. Building on previous work, this proof-of-concept study used a data intelligence tool, the "Central Metastore," to provide metadata and lineage information of nationally held data. Methods: The feasibility of NHS England's Central Metastore to capture detailed records of the origins, processes, and methods that produce four datasets was assessed. These were England's Hospital Episode Statistics (Admitted Patient Care, Outpatients, Critical Care) and the Civil Registration of Deaths (England and Wales). The process comprised: information gathering; information ingestion using the tool; and auto-generation of lineage diagrams/content to show data integrity. A guidance document to standardise this process was developed. Results/Discussion: The tool can ingest, store and display data provenance in sufficient detail to support trust and transparency in using these datasets for trials. The slowest step was information gathering from multiple sources, so consistency in record-keeping is essential.

From L-mode to the L–H transition, experiments on ASDEX upgrade and related gyrokinetic simulations

This work combines experimental observations from the ASDEX Upgrade tokamak with related gyrokinetic simulations of the turbulence moving from L-mode toward, and beyond, the L–H transition. Dedicated experiments have been performed with slow steps of increasing electron cyclotron heating power. Gyrokinetic simulations of the edge turbulence of these plasmas highlight the key roles of the non-linear electromagnetic effects and the external flow shear (E × B shear), both related to the evolution of the plasma pressure profile with increasing heating power. The increase in the plasma βe destabilizes turbulence at low toroidal mode numbers, that, in turn, is strongly suppressed by the external flow shear. This allows the plasma pressure profiles to evolve without a sharp rise in the turbulent fluxes. When all the experimentally measured plasma parameters are consistently included as inputs of the local gyrokinetic simulations, both the experimental electron and ion heat fluxes are quantitatively reproduced on the whole L-mode phase of the selected discharge. Simulations carried out with edge parameters of an ELM-free H-mode phase still show the importance of the mechanisms discussed earlier while also indicating possible limitations of the local approach.

Investigation on the steam gasification mechanism of different chars using isotopic tracing method

Gasification can provide syn-gas for consequent chemical production from carbon resources. The control of CO2 emission produced from gasification calls for the lower temperature and the more biomass char for the feed compared with traditional gasification, and the mechanism for steam gasification of different chars is more important. The gasification behaviors of four biomass chars and four coal chars are studied. The mechanism is probed using H216O/H218O period step tracing method coupled with various solid-state analyses on char structures. The increment of intermediates with increasing conversion demonstrate other slow step exists during gasification, and the solid state spectra of chars after and before gasification demonstrates that the condensation of poly-aromatic clusters in chars occurs accompanied with gasification. The addition reactions of radicals generated from gasifying agents and unsaturated carbon bonds C = C in chars is the slower step during gasification and enhancing the addition of radicals to unsaturated C = C bonds may be helpful for the higher gasification rate.

Preparation and Characterization of Chitosan Nanofiber: Kinetic Studies and Enhancement of Insulin Delivery System.

Insulin-loaded nanofibers were prepared using chitosan as a natural polymer. The loaded insulin with polyethylene oxide was used for preparing monolayer batch S1. Nanofiber S1 was coated by seven layers of film on both sides to form batch S2 as a sandwich containing Layer A (CS, PEG and PEO) and Layer B (PEG and PEO) using electrospinning apparatus. SEM, TEM and FT-IR techniques were used to confirm the drug loading within the composite nanofibers. The in vitro activity that provided a sustained and controlled release of the drug from the nanofiber batch was studied at different pH values spectrophotometrically using a dialysis method. In batches S1 and S2, the release of insulin from nanofiber proceeds via burst release necessary to produce the desired therapeutic activity, followed by slow step. The rate and the percentage release of insulin in batch S2 are found to be higher at all pH values.

Mechanism of Nitrone Formation by a Flavin-Dependent Monooxygenase.

OxaD is a flavin-dependent monooxygenase (FMO) responsible for catalyzing the oxidation of an indole nitrogen atom, resulting in the formation of a nitrone. Nitrones serve as versatile intermediates in complex syntheses, including challenging reactions like cycloadditions. Traditional organic synthesis methods often yield limited results and involve environmentally harmful chemicals. Therefore, the enzymatic synthesis of nitrone-containing compounds holds promise for more sustainable industrial processes. In this study, we explored the catalytic mechanism of OxaD using a combination of steady-state and rapid-reaction kinetics, site-directed mutagenesis, spectroscopy, and structural modeling. Our investigations showed that OxaD catalyzes two oxidations of the indole nitrogen of roquefortine C, ultimately yielding roquefortine L. The reductive-half reaction analysis indicated that OxaD rapidly undergoes reduction and follows a "cautious" flavin reduction mechanism by requiring substrate binding before reduction can take place. This characteristic places OxaD in class A of the FMO family, a classification supported by a structural model featuring a single Rossmann nucleotide binding domain and a glutathione reductase fold. Furthermore, our spectroscopic analysis unveiled both enzyme-substrate and enzyme-intermediate complexes. Our analysis of the oxidative-half reaction suggests that the flavin dehydration step is the slow step in the catalytic cycle. Finally, through mutagenesis of the conserved D63 residue, we demonstrated its role in flavin motion and product oxygenation. Based on our findings, we propose a catalytic mechanism for OxaD and provide insights into the active site architecture within class A FMOs.

Gold(III) Auracycles featuring C(sp3)−Au−C(sp2) Bonds: Synthesis and Mechanistic Insights into the Cycloauration Step

The direct auration of arenes is a key step in numerous gold‐catalyzed reactions. Although reported more than 100 years ago, understanding of its underlying mechanism has been hampered by the difficulties in the isolation of relevant intermediates given the propensity of gold(III) species to undergo reductive elimination. Here, we report the synthesis and isolation of a new family of intriguing zwitterionic [C(sp3)^C(sp2)]‐auracyclopentanes, as well as of their alkyl‐gold(III) precursors and demonstrate their value as mechanistic probes to study the Csp2‐Au bond‐forming event. Experimental investigations employing Kinetic Isotope Effects (KIE), Hammett plot, and Eyring analysis provided important insights into the formation of the auracycle. The data suggest a SEAr mechanism wherein the slowest step might be the p‐coordination between the arene and the gold(III) center, en route to the Wheland intermediate. We also show that these auracyclopentanes can work as catalysts in several gold‐promoted transformations.

An Overview Analysis of Current Research Status in Iron Oxides Reduction by Hydrogen

This paper focuses on the study of current knowledge regarding the use of hydrogen as a reducing agent in the metallurgical processes of iron and steel production. This focus is driven by the need to introduce environmentally suitable energy sources and reducing agents in this sector. This theoretical study primarily examines laboratory research on the reduction of Fe-based, metal-bearing materials. The article presents a critical analysis of the reduction in iron oxides using hydrogen, highlighting the advantages and disadvantages of this method. Most experimental facilities worldwide employ their unique original methodologies, with techniques based on Thermogravimetric analysis (TGA) devices, fluidized beds, and reduction retorts being the most common. The analysis indicates that the mineralogical composition of the Fe ores used plays a crucial role in hydrogen reduction. Temperatures during hydrogen reduction typically range from 500 to 900 °C. The reaction rate and degree of reduction increase with higher temperatures, with the transformation of wüstite to iron being the slowest step. Furthermore, the analysis demonstrates that reduction of iron ore with hydrogen occurs more intensively and quickly than with carbon monoxide (CO) or a hydrogen/carbon monoxide (H2/CO) mixture in the temperature range of 500 °C to 900 °C. The study establishes that hydrogen is a superior reducing agent for iron oxides, offering rapid reduction kinetics and a higher degree of reduction compared to traditional carbon-based methods across a broad temperature range. These findings underscore hydrogen’s potential to significantly reduce greenhouse gas emissions in the steel production industry, supporting a shift towards more sustainable manufacturing practices. However, the implementation of hydrogen as a primary reducing agent in industrial settings is constrained by current technological limitations and the need for substantial infrastructural developments to support large-scale hydrogen production and utilization.

Unveiling kinetics post rate-determining step in Brønsted acid-catalyzed reactions of fructose: A strategy for 5-hydroxymethylfurfural production from concentrated feedstock

The development of high-yielding catalytic systems is pivotal in biomass upgrading. However, the investigation of kinetics in these complex reaction systems is often highly challenging, especially when reactions leading to byproduct formation are obscured by a preceding, slow rate-determining step. In this work, we introduce a unique approach to kinetic analysis that enables the investigation of reactions occurring post rate-determining step. The technique was applied to the conversion of sugars to 5-hydroxymethylfurfural (HMF), an important platform molecule for sustainable chemical production. First, screening experiments were carried out to identify a catalytic solvent system that achieves a balance between solvent stability, HMF yield, and cost-effectiveness. Our kinetic analysis on the identified system reveals that the fructose reactant undergoes a rate-determining dehydration step to form an unstable reactive intermediate. This intermediate further reacts competitively with other reactive species, such as the hexose reactants or the HMF product, ultimately lowering the HMF selectivity. The calculated relative activation energies of these reactions post rate-determining step provide intuitive insights into the effects of temperature, co-existing reactive species, as well as the previously unexplained effect of feed concentration on HMF selectivity. Additionally, we propose a novel reaction strategy that significantly enhances HMF yield when compared to a traditional batch synthesis. Notably, a high HMF yield of 74 % was achieved with an extreme 55 wt% fructose loading on an aqueous basis (20 wt% loading on a total weight basis) in a low-boiling 80 wt% dioxane/water mixture using an HCl catalyst at 393 K.

Searching for A Better Educational System: Language Planning in Competency-Based School Curriculum

Purpose: The new European school curriculum focuses on innovation, competency-based learning and the integration of technology as ways to increase the quality of education and better prepare students for the challenges of the 21st century. This study investigates the effects of implementation of this curriculum, highlighting its benefits and potential challenges, especially in relation to the standard language. Theoretical Framework: The new European pre-university curriculum is explored in interdisciplinary approach, integrating the latest theories in teaching methodology with language planning and technology. Synthesizing the existing literature serves as a prerequisite for the analysis performed on the empirical research. Methodology: The impact of the implementation of the competence-based curriculum in Albanian school education are analyzed theoretically and empirically, emphasizing the advantages and shortcomings compared to the previous curriculum. Findings: The increase in the quality of school education is evident with the implementation of the new European curriculum, which prioritizes student-centered learning by incorporating technology into different learning scenarios. As shown by international evaluations such as Pisa, slow steps have been made in the national curriculum, which calls for further reforms by the educational authorities. Research Practical and Social Implication: The new national curriculum improves student outcomes and aligns with wider educational goals within the EU, influencing national identity and global social cohesion, which are important research areas. Originality/Value: This study values the competency-based curriculum as a necessity for preparing European students for a globally competitive world, pointing out some areas for improvements.

Porphyrin Aluminum Metal-Organic Framework in Liquid Water, its Interaction with the Oxidized Organosulfur Compound Diethyl Sulfoxide, and its Sorption from Aqueous Solution.

Oxidized organosulfur compounds and, in particular, sulfoxides are of interest as solvents in the semiconductor and pharmaceutical industry, environmental contaminants, and simulants in deactivation of chemical warfare agents. An experimental study is reported of the interaction of porphyrin aluminum metal-organic framework Al-MOF-TCPPH2 (Compound 2) with diethyl sulfoxide (DESO) in pure form and in aqueous solution. First, the suitability of Compound 2 as sorbent in aqueous solution was assessed; namely, its long-term stability (up to 15 days) in liquid water has been investigated at room temperature and under stirring. Here, a novel facile spectroscopic method has been used, a periodic micro-sampling of sorbent from suspension, followed by vacuum mini-filtration and an ex situ time-dependent attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR) analysis. Next, the interaction of Compound 2 with pure liquid DESO under ambient conditions was investigated, which yields the stoichiometric adsorption complex (Al-MOF-TCPPH2)1(DESO)2 denoted Compound 3. In this adsorption complex, molecules of DESO interact with the OH group and carboxylate group of the sorbent. Then, the removal of DESO from Compound 3 was assessed, using facile treatment with warm water in the micro Soxhlet apparatus followed by the ATR FT-IR analysis. Finally, Compound 2 was tested in sorption of DESO from diluted aqueous solution. In the initial step, the sorption proceeds very quickly (in <1 min the concentration of DESO decreases by about 20%) followed by a much slower step. The maximum amount of adsorbed DESO corresponds to half of the amount adsorbed from pure DESO as found by the high-performance liquid chromatography-ultraviolet detection method. This adsorbed amount corresponds to 1 mol DESO adsorbate per mol of sorbent. Porphyrin aluminum metal-organic framework Compound 2 is promising for the removal of DESO from diluted aqueous solution, and it is of interest for the removal of similar oxidized organosulfur compounds.

Composites of sodium alginate based - Functional materials towards sustainable adsorption of benzene phenol derivatives - Bisphenol A/Triclosan

The present study evaluates the adsorption efficiency of low-cost carbonaceous adsorbents as fly ash (FA), saw dust biochar (SDB) (untreated and alkali - treated), live/dead pulverized white rot fungus Hypocrea lixii biomass encapsulated in sodium alginate (SA) against the commercially available activated carbon (AC) and graphene oxide (GO) SA beads for removal of benzene phenol derivatives - Bisphenol A (BPA)/triclosan (TCS). Amongst bi - and tri - composites SA beads, tri-composite beads comprising of untreated flyash - dead fungal biomass - sodium alginate (UFA - DB - SA) showed at par results with commercial composite beads. The tri - composite beads with point zero charge (Ppzc) of 6.2 was characterized using FTIR, XRD, surface area BET and SEM-EDX. The batch adsorption using tri - composite beads revealed removal of 93% BPA with adsorption capacity of 16.6 mg/g (pH 6) and 83.72% TCS with adsorption capacity of 14.23 mg/g (pH 5), respectively at 50 ppm initial concentration with 6 % adsorbent dose in 5 h. Freundlich isotherm favoring multilayered adsorption provided a better fit with r2 of 0.9674 for BPA and 0.9605 for TCS respectively. Intraparticle diffusion model showed adsorption of BPA/TCS molecules to follow pseudo - second order kinetics with boundary layer diffusion governed by first step of fast adsorption and intraparticle diffusion within pores by second slow adsorption step. Thermodynamic parameters (ΔH°, ΔS°, ΔG°) revealed adsorption process as exothermic, orderly and spontaneous. Methanol showed better desorbing efficiency leading to five cycles reusability. The phytotoxicity assay revealed increased germination rate of mung bean (Vigna radiata) seeds, sprinkled with post adsorbed treated water (0 h, 5 h and 7 h) initially spiked with 50 ppm BPA/TCS. Overall, UFA - DB - SA tri - composite beads provides a cost effective and eco - friendly matrix for effective removal of hydrophobic recalcitrant compounds.

Comparing the Chemistry of Malvidin-3-O-glucoside and Malvidin-3,5-O-diglucoside Networks: A Holistic Approach to the Acidic and Basic Paradigms with Implications in Biological Studies.

The kinetics, thermodynamics, and degradation of malvidin mono- and diglucosides were studied following a holistic approach by extending to the basic medium. In acidic conditions, the reversible kinetics of the flavylium cation toward the equilibrium is controlled by the hydration and cis-trans isomerization steps, while in the basic medium, the OH- nucleophilic addition to the anionic quinoidal bases is the slowest step. There is a pH range (transition pHs), between the acidic and basic paradigms, that includes physiological pH (7.4), where degradation reactions occur faster, preventing the system from reaching the equilibrium. The transition pH of the diglucoside is narrower, and in contrast with the monoglucoside, there is no evidence for the formation of colored oligomers among the degradation products. Noteworthy, OH- addition in position 4 to form B42-, a kinetic product that decreases the overall equilibration rate, was observed only for the diglucoside.

Kinetic perspectives for the degradation of oxacillin: A penicillanic acid derivative

Oxidation of oxacillin, a penicillanic acid derivative, has been predicted by monoperiodatocuprate [MPC (III)] at 25°C with 0.10 mol dm-3 ionic strength, in an aqueous alkaline medium by UV/Visible spectrophotometric analysis, for which 1:4 stoichiometry of oxacillin: MPC (III) is visible. The appearance of a sharp peak by the spectrophotometer confirmed the formation of the complex. The reaction products have been recognized using spectral reports from the FT-IR, LC-MS, melting point, and other spot tests. A pseudo-first-order reaction has been confirmed for the oxidant, fractional order for the substrate, and alkali, even though periodate claimed a delaying effect due to the accumulation of periodate ions from both potassium periodate and monoperiodatocuprate as a common ion effect. The primary active species in the alkaline medium [Cu(H2IO6)(H2O)2] was discovered to be monoperiodatocuprate [MPC (III)]. To figure out the activation and thermodynamic parameters, it is helpful to know the uncatalyzed rate constants, the slow step rate constants, and the equilibrium constants. We have evaluated the dependence of reaction rates on different temperatures. We have calculated rate constants using absorbance data collected from the UV/visible spectrophotometer. We have thoroughly examined the potential rate constant derivation and a plausible mechanism that could explain the experimental findings.

Sensitive remote homology search by local alignment of small positional embeddings from protein language models

Accurately detecting distant evolutionary relationships between proteins remains an ongoing challenge in bioinformatics. Search methods based on primary sequence struggle to accurately detect homology between sequences with less than 20% amino acid identity. Profile- and structure-based strategies extend sensitive search capabilities into this twilight zone of sequence similarity but require slow pre-processing steps. Recently, whole-protein and positional embeddings from deep neural networks have shown promise for providing sensitive sequence comparison and annotation at long evolutionary distances. Embeddings are generally faster to compute than profiles and predicted structures but still suffer several drawbacks related to the ability of whole-protein embeddings to discriminate domain-level homology, and the database size and search speed of methods using positional embeddings. In this work, we show that low-dimensionality positional embeddings can be used directly in speed-optimized local search algorithms. As a proof of concept, we use the ESM2 3B model to convert primary sequences directly into the 3D interaction (3Di) alphabet or amino acid profiles and use these embeddings as input to the highly optimized Foldseek, HMMER3, and HH-suite search algorithms. Our results suggest that positional embeddings as small as a single byte can provide sufficient information for dramatically improved sensitivity over amino acid sequence searches without sacrificing search speed.