Molecular Reaction Research Articles

In-tube micro-pyramidal silicon nanopore for inertial-kinetic sensing of single molecules

Electrokinetic force has been the major choice for driving the translocation of molecules through a nanopore. However, the use of this approach is limited by an uncontrollable translocation speed, resulting in non-uniform conductance signals with low conformational sensitivity, which hinders the accurate discrimination of the molecules. Here, we show the use of inertial-kinetic translocation induced by spinning an in-tube micro-pyramidal silicon nanopore fabricated using photovoltaic electrochemical etch-stop technique for biomolecular sensing. By adjusting the kinetic properties of a funnel-shaped centrifugal force field while maintaining a counter-balanced state of electrophoretic and electroosmotic effect in the nanopore, we achieved regulated translocation of proteins and obtained stable signals of long and adjustable dwell times and high conformational sensitivity. Moreover, we demonstrated instantaneous sensing and discrimination of molecular conformations and longitudinal monitoring of molecular reactions and conformation changes by wirelessly measuring characteristic features in current blockade readouts using the in-tube nanopore device.

Hepatocyte-specific Selenoi deficiency predisposes mice to hepatic steatosis and obesity.

Selenoprotein I (Selenoi) is highly expressed in liver and plays a key role in lipid metabolism as a phosphatidylethanolamine (PE) synthase. However, the precise function of Selenoi in the liver remains elusive. In the study, we generated hepatocyte-specific Selenoi conditional knockout (cKO) mice on a high-fat diet to identify the physiological function of Selenoi. The cKO group exhibited a significant increase in body weight, with a 15.6% and 13.7% increase in fat accumulation in white adipose tissue (WAT) and the liver, respectively. Downregulation of the lipolysis-related protein (p-Hsl) and upregulation of the adipogenesis-related protein (Fasn) were observed in the liver of cKO mice. The cKO group also showed decreased oxygen consumption (VO2), carbon dioxide production (VCO2), and energy expenditure (p < .05). Moreover, various metabolites of the steroid hormone synthesis pathway were affected in the liver of cKO mice. A potential cascade of Selenoi-phosphatidylethanolamine-steroid hormone synthesis might serve as a core mechanism that links hepatocyte-specific Selenoi cKO to biochemical and molecular reactions. In conclusion, we revealed that Selenoi inhibits body fat accumulation and hepatic steatosis and elevates energy consumption; this protein could also be considered a therapeutic target for such related diseases.

Histamine-Responsive Hydrogel Biosensors Based on Aptamer Recognition and DNA-Driven Swelling Hydrogels.

Detection of chemical substances is essential for living a healthy and cultural life in the modern world. One type of chemical sensing technology, biosensing, uses biological components with molecular recognition abilities, enabling a broad spectrum of sensing targets. Short single-stranded nucleic acids called aptamers are one of the biological molecules used in biosensing, and sensing methods combining aptamers and hydrogels have been researched for simple sensing applications. In this research, we propose a hydrogel-based biosensor that uses aptamer recognition and DNA-driven swelling hydrogels for the rapid detection of histamine. Aptamer recognition and DNA-driven swelling hydrogels are directly linked via DNA molecular reactions, enabling rapid sensing. We selected histamine, a major food poisoning toxin, as our sensing target and detected the existence of histamine within 10 min with significance. Because this sensing foundation uses aptamers, which have a vast library of targets, we believe this system can be expanded to various targets, broadening the application of hydrogel-based biosensors.

SEM/EDX and FTIR/ATR Behavior of Ammonium Perchlorate Under Accelerated Aging in a New Solid Rocket Motor Fuel Composition with Superior Explosive and Mechanical Performance

Abstract The oxidation potential of perchlorates is high, which makes this material suitable for fuels with high specific impulse. Perchlorates are characterized by a ClO4- moiety/anion in their molecular structure and are crystalline materials used in the formation of solid fuels. Ammonium perchlorate (AP) particle size and shape influence the manufacturing process of fuels and their burning rate. The physical and chemical processes that can occur in the natural degradation process of composite fuels are related to molecular reactions and diffusion phenomena governed by kinetic processes and can be accelerated by increasing the temperature. The paper presents studies carried out by scanning electron microscopy and infrared spectrometry on the behavior of ammonium perchlorate in the new composite material of solid rocket motor fuel under the effect of high temperature, in the range of 65-85οC, at regular time intervals. The self-initiation temperature was also determined, with a temperature rise rate controlled at 5ºC/minute. It is very likely that these accelerated aging studies will show the changes that occur in the stability, sensitivity, mechanical and functional properties of fuels during their lifetime.

Simulation of Chemical Reactions on a Quantum Computer.

Studying chemical reactions, particularly in the gas phase, relies heavily on computing scattering matrix elements. These elements are essential for characterizing molecular reactions and accurately determining reaction probabilities. However, the intricate nature of quantum interactions poses challenges, necessitating the use of advanced mathematical models and computational approaches to tackle the inherent complexities. In this study, we develop and apply a quantum computing algorithm for the calculation of scattering matrix elements. In our approach, we employ the time-dependent method based on the Møller operator formulation where the S-matrix element between the respective reactant and product channels is determined through the time correlation function of the reactant and product Møller wavepackets. We successfully apply our quantum algorithm to calculate scattering matrix elements for 1D semi-infinite square well potential and on the colinear hydrogen exchange reaction. As we navigate the complexities of quantum interactions, this quantum algorithm is general and emerges as a promising avenue, shedding light on new possibilities for simulating chemical reactions on quantum computers.

Operando Spectroscopy of Catalysts Exploiting Multi-technique and Modulated Excitation Approaches.

Operando spectroscopy combines the in situ determination of material structure by spectroscopy/diffraction techniques with the measurement of material performance, which is conversion/selectivity in the field of heterogeneous catalysis. A central question in operando spectroscopy is whether the signatures visible by the characterization methods are responsible for catalyst performance. Individual analytical methods can provide useful information, but their combination (multi-technique approach) is essential to obtain a complete perspective on molecular reaction mechanisms. This approach must be coupled to experimental protocols and mathematical algorithms enabling the ability to disentangle the contribution of the active structure from the unresponsive one. Here, we report an account with examples from our own research activities in catalysis science.

Accurate and efficient evaluation of the ionization potentials of extreme ultraviolet photoresists using density functionals and semi-empirical methods

Extreme ultraviolet (EUV) photoresists have become the core materials in lithography with nanometer-sized patterns and are actively explored on the path to realizing smaller critical dimensions. These photoresists can be small molecule-, polymer-, or organic–inorganic hybrid-based, with the full molecular working mechanism under investigation. For the rational design of EUV photoresists, theoretical guidance using tools like first-principle calculations and multi-scale simulations can be of great help. Considering the extremely high standard of accuracy in EUV lithography, it is critical to ensure the adoption of the appropriate methodologies in the theoretical evaluation of EUV photoresists. However, it is known that density functionals and semi-empirical methods differ in accuracy and efficiency, without a universal rule across materials. This poses a challenge in developing a reliable theoretical framework for calculating EUV photoresists. Here, we present a benchmark investigation of density functionals and semi-empirical methods on the three main types of EUV photoresists, focusing on the ionization potential, a key parameter in their microscopic molecular reactions. The vertical detachment energies (VDE) and adiabatic detachment energies (ADE) were calculated using 12 functionals, including pure functionals, hybrid functionals, Minnesota functionals, and the recently developed optimally tuned range-separated (OTRS) functionals. Several efficient semi-empirical methods were also chosen, including AM1, PM6, PM7, and GFN1-xTB in the extended tight-binding theoretical framework. These results guide the accurate and efficient calculation of EUV photoresists and are valuable for the development of multi-scale lithography protocols.Graphical

Frequency multiplexing enables parallel multi-sample EPR

Electron paramagnetic resonance (EPR) spectroscopy stands out as a powerful analytical technique with extensive applications in the fields of biology, chemistry, physics, and material sciences. It proves invaluable for investigating the molecular structure and reaction mechanisms of substances containing unpaired electrons, such as metal complexes, organic and inorganic radicals, and intermediate states in chemical reactions. However, despite their remarkable capabilities, EPR systems face significant limitations in terms of sample throughput, as current commercial systems only target the analysis of one sample at a time. Here we introduce a novel scheme for conducting ultra-high frequency continuous-wave EPR (CW EPR) targeting the EPR spectroscopy of multiple microliter volume samples in parallel. Our proof-of-principle prototype involves two decoupled detection cells equipped with high qualty factor Q=104\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$Q=104$$\\end{document} solenoidal coils tuned to 488 and 589 MHz, ensuring a significant frequency gap for effective radio frequency (RF) decoupling between the channels. To further enhance electromagnetic decoupling, an orthogonal alignment of the coils was adopted. The paper further presents an innovative radiofrequency circuit concept that utilizes a single physical RF channel to simultaneously conduct parallel EPR on up to eight cells. Parallel EPR experiments on two BDPA samples, each with a sample volume of 18.3 μL, registered signal-to-noise ratios of 255 and 252 for the two EPR measurement cells, with no observable coupling. The showcased prototype, built using cost-effective commercially available fabrication technology, is readily scalable and represents an initial step with promising potential for advancing sample screening with high-throughput parallel EPR.

Synthesis, DFT calculations, and investigation of catalytic and biological activities of back‐bond functionalized re‐NHC‐Cu complexes

Five copper complexes (3a–e) stabilized by ring‐expanded back‐bond functionalized N‐heterocyclic carbene ligands (re‐NHCs) were produced in the glovebox by reacting free re‐NHC with CuI precursor. The potential of these re‐NHC‐Cu complexes as catalysts on the synthesis of mono‐ and di‐(1,4‐disubstituted‐1,2,3‐triazoles) by Cu‐catalyzed azide–alkyne cycloaddition (CuAAC) reactions was investigated. Various spectroscopic approaches were utilized to completely characterize the structures of the re‐Cu‐NHC complexes. Furthermore, density functional theory (DFT) calculations were carried out to get further insights into their molecular geometry and CuAAC reaction mechanism. The re‐NHC‐Cu complexes showed high activity on the CuAAC reaction in an open‐air atmosphere at rt. The Gibbs free energies as well as the optimized geometries of the intermediates and the transition states of the determining step of the reactions catalyzed by 3a, 3e, and 3b complexes were computed. Complex 3e was found to be the most efficient catalyst among these re‐NHC‐Cu complexes. Additionally, re‐Cu‐NHC complexes were investigated for their biological activities, including antiproliferative, antioxidant, AChE and TyrE inhibition, and antiparasitic activity. The results showed that the 3b, 3d, and 3e complexes possessed strong antiproliferative activity against human colon carcinoma (HCT‐116) and moderate cytotoxic activity against hepatocellular carcinoma (HepG‐2) cell lines. In addition, effective selective antileishmanial effects were observed for the 3e compound against both promastigotes and amastigotes stages of L. major with an IC50 value of 0.027 and 0.39 μM mL−1, respectively. These results demonstrate that these compounds are promising candidates for the treatment of colorectal cancer and leishmaniasis.

Effect of β-fluorinated porphyrin in changing selectivity for electrochemical O2 reduction

The development of catalytic systems that selectively convert O2 to water is required to progress fuel cell technology. As an alternative to platinum catalysts, derivatives of iron and cobalt porphyrin molecular catalysts provide one benchmark for catalyst design. However, the inclusion of these catalysts into homogeneous platforms remains a difficulty. Co-porphyrins have been studied as heterogeneous O2 reduction catalysts; however, they have not been explored much in homogeneous systems. Moreover, they suffer from poor selectivity for the desired four-electron reduction of O2 to H2O. Herein, we present two cobalt-based β-fluorinated porphyrin complexes (CoTPF8(OH)2 and CoTPF8(OH)4) and demonstrate applicability as effective catalysts for the oxygen reduction reaction. Using rotating ring-disk electrochemistry, the catalysts, CoTPF8(OH)2 and CoTPF8(OH)4, showed maximum Faradaic efficiency for H2O of 92 % and 97 %, respectively. DFT calculations suggest that the formation of a phlorin intermediate could occur before O2 reduction and that a stronger H2O2 binding in the cobalt-based β-fluorinated porphyrin species compared to the unsubstituted parent compound, CoTP(OH)2, was responsible for the observed experimental selectivity for H2O. These results reveal that the β-fluorinated porphyrin catalyst serves as a novel platform for investigating molecular electrocatalytic reactions.

Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution

The 3D architecture of RNAs governs their molecular interactions, chemical reactions, and biological functions. However, a large number of RNAs and their protein complexes remain poorly understood due to the limitations of conventional structural biology techniques in deciphering their complex structures and dynamic interactions. To address this limitation, we have benchmarked an integrated approach that combines cryogenic OrbiSIMS, a state-of-the-art solid-state mass spectrometry technique, with computational methods for modelling RNA structures at atomic resolution with enhanced precision. Furthermore, using 7SK RNP as a test case, we have successfully determined the full 3D structure of a native RNA in its apo, native and disease-remodelled states, which offers insights into the structural interactions and plasticity of the 7SK complex within these states. Overall, our study establishes cryo-OrbiSIMS as a valuable tool in the field of RNA structural biology as it enables the study of challenging, native RNA systems.

Interfacial and ion-pairing catalysis for oxygen-tolerant large-scale ATRP in ab initio emulsion

Interfacial and ion-pairing catalysis for oxygen-tolerant large-scale ATRP in ab initio emulsion

Deleterious Effects of Heat Stress on the Tomato, Its Innate Responses, and Potential Preventive Strategies in the Realm of Emerging Technologies.

The tomato is a fruit vegetable rich in nutritional and medicinal value grown in greenhouses and fields worldwide. It is severely sensitive to heat stress, which frequently occurs with rising global warming. Predictions indicate a 0.2 °C increase in average surface temperatures per decade for the next three decades, which underlines the threat of austere heat stress in the future. Previous studies have reported that heat stress adversely affects tomato growth, limits nutrient availability, hammers photosynthesis, disrupts reproduction, denatures proteins, upsets signaling pathways, and damages cell membranes. The overproduction of reactive oxygen species in response to heat stress is toxic to tomato plants. The negative consequences of heat stress on the tomato have been the focus of much investigation, resulting in the emergence of several therapeutic interventions. However, a considerable distance remains to be covered to develop tomato varieties that are tolerant to current heat stress and durable in the perspective of increasing global warming. This current review provides a critical analysis of the heat stress consequences on the tomato in the context of global warming, its innate response to heat stress, and the elucidation of domains characterized by a scarcity of knowledge, along with potential avenues for enhancing sustainable tolerance against heat stress through the involvement of diverse advanced technologies. The particular mechanism underlying thermotolerance remains indeterminate and requires further elucidatory investigation. The precise roles and interplay of signaling pathways in response to heat stress remain unresolved. The etiology of tomato plants' physiological and molecular responses against heat stress remains unexplained. Utilizing modern functional genomics techniques, including transcriptomics, proteomics, and metabolomics, can assist in identifying potential candidate proteins, metabolites, genes, gene networks, and signaling pathways contributing to tomato stress tolerance. Improving tomato tolerance against heat stress urges a comprehensive and combined strategy including modern techniques, the latest apparatuses, speedy breeding, physiology, and molecular markers to regulate their physiological, molecular, and biochemical reactions.

Characterization of Bacillus velezensis DCJ 2 isolated from the rhizosphere soil of aglaonema ‘Maria’ and investigation of its plant growth-promoting effects

Aglaonema ‘Maria’ is one of the key foliage plants that has gained high demand in foreign destinations in the last few years. This study was conducted to characterize Bacillus velezensis DCJ 2, assess its plant growth promotion effect and investigate the effectiveness of different delivery methods of the bacterial inoculum for the growth promotion of Aglaonema ‘Maria’. In this context, DCJ 2, isolated from the rhizosphere soil of A. Maria was screened to investigate its potential as a plant growth-promoting bacterium. The pure culture of DCJ 2 maintained on nutrient agar was utilized for morphological, biochemical and physiological examinations. The molecular characterization of the strain was performed with different primer pairs targeting 16SrRNA, gyrA, pgsB and sugar kinase genes of DCJ 2. A pot experiment was carried out to investigate the plant growth promotion effect. It was conducted in the greenhouse as per the complete randomized block design with eight treatments and five replicates. . Healthy plants of A. ‘Maria’ established in field soil and solarized soil were treated with 100 ml of the suspension of the DCJ 2 at the rate of 10 8 CFU/ml either as a soil drench or foliar spray. The partial 16SrRNA, gyrA, pgsB and sugar kinase gene sequences of DCJ 2, BLAST searched in the NCBI database revealed that it has a high similarity to Bacillus velezensis. The pot experiment showed that the application of strain DCJ 2 as a soil drench to solarized soil (Treatment 6) yielded a significant increase in growth parameters at p=0.05. Based on molecular analysis, morphological, biochemical, and physiological reactions, DCJ 2 was identified as Bacillus velezensis. This study revealed that B. velezensis DCJ 2 has the potential to boost the growth of A. Maria and hence serve as a base for developing a biofertilizer.

Simulation of 1D atmospheric pressure dielectric barrier discharge in argon

This work aims at modelling an atmospheric-pressure homogeneous barrier discharge in argon, using a time-dependent 1D fluid model coupled to the electric field and plasmo-chemical kinetic equations. The model is chosen to mimic a discharge when a sinusoidal 1 kV voltage at 10 MHz is applied to the terminals. Energy and mass transfer are considered for a macroscopic fluid representation, while energy transfer in molecular collisions and chemical reactions is treated at the microscopic level. The macroscopic model is represented by a set of coupled partial differential equations. Microscopic effects are studied within a discrete model for electronic and molecular collisions in the frame of ZDPlasKin, a plasma modelling numerical tool. The BOLSIG+ solver is employed in solving the electronic Boltzmann equation. An operator splitting technique is used to separate microscopic and macroscopic models. The spatial and temporal evolution of such species and electron transport parameters are presented and discussed.

Enhanced Efficiency and Stability of Inverted Perovskite Solar Cells via Primary Amine Molecular Reaction.

The inverted perovskite solar cells have drawn considerable attention owing to their low cost, good compatibility, and easy production processes. However, the device performance is still limited by some important factors, such as surface imperfections and interfacial nonradiative recombination losses. Here, N-acetylethylenediamine (N-AE) is introduced to bind to the surface of the perovskite film via an ammonia condensation reaction. This process creates a stable interfacial layer with n-type doping to enhance the open-circuit voltage (VOC). Moreover, during post-treatment, N-AE dissolves a portion of the perovskite on the surface, leading to perovskite recrystallization. This process enhances the surface quality of the perovskite film and reduces nonradiative recombination. As a result, the inverted perovskite solar cell exhibits a power conversion efficiency approaching 20%, with a rise in VOC from 0.96 to 1.05 V. More impressively, the unencapsulated devices display excellent stability at 85 °C annealing and retained 88% of the initial PCE for 816 h.

Experimental and computational study on antioxidant activity and molecular properties of novel ferrocenyl Schiff bases

Experimental and computational study on antioxidant activity and molecular properties of novel ferrocenyl Schiff bases

Selective aromatization of 1-hexene to BTX over core-shell structured Silicalite-1@ZSM-5 catalyst

Selective aromatization of 1-hexene to BTX over core-shell structured Silicalite-1@ZSM-5 catalyst

Breaking the Scaling Relationship in C-N Coupling via the Doping Effects for Efficient Urea Electrosynthesis.

Electrochemical C-N coupling reaction based on carbon dioxide and nitrate have been emerged as a new "green synthetic strategy" for the synthesis of urea, but the catalytic efficiency is seriously restricted by the inherent scaling relations of adsorption energies of the active sites, the improvement of catalytic activity is frequently accompanied by the decrease in selectivity. Herein, a doping engineering strategy was proposed to break the scaling relationship of intermediate binding and minimize the kinetic barrier of C-N coupling. A thus designed SrCo0.39Ru0.61O3-δ catalyst achieves a urea yield rate of 1522 μg h-1 mgcat. -1 and faradic efficiency of 34.1 % at -0.7 V versus reversible hydrogen electrode. A series of characterizations revealed that Co doping not only induces lattice distortion but also creates rich oxygen vacancies (OV) in the SrRuO3. The oxygen vacancies weaken the adsorption of *CO and *NH2 intermediates on the Co and Ru sites respectively, and the strain effects over the Co-Ru dual sites promoting the occurrence of C-N coupling of the two monomers instead of selective hydrogenating to form by-products. This work presents an insight into molecular coupling reactions towards urea synthesis via the doping engineering on SrRuO3.

Breaking the Scaling Relationship in C−N Coupling via the Doping Effects for Efficient Urea Electrosynthesis

AbstractElectrochemical C−N coupling reaction based on carbon dioxide and nitrate have been emerged as a new “green synthetic strategy” for the synthesis of urea, but the catalytic efficiency is seriously restricted by the inherent scaling relations of adsorption energies of the active sites, the improvement of catalytic activity is frequently accompanied by the decrease in selectivity. Herein, a doping engineering strategy was proposed to break the scaling relationship of intermediate binding and minimize the kinetic barrier of C−N coupling. A thus designed SrCo0.39Ru0.61O3−δ catalyst achieves a urea yield rate of 1522 μg h−1 mgcat.−1 and faradic efficiency of 34.1 % at −0.7 V versus reversible hydrogen electrode. A series of characterizations revealed that Co doping not only induces lattice distortion but also creates rich oxygen vacancies (OV) in the SrRuO3. The oxygen vacancies weaken the adsorption of *CO and *NH2 intermediates on the Co and Ru sites respectively, and the strain effects over the Co−Ru dual sites promoting the occurrence of C−N coupling of the two monomers instead of selective hydrogenating to form by‐products. This work presents an insight into molecular coupling reactions towards urea synthesis via the doping engineering on SrRuO3.