Molecular Reaction Research Articles

(Invited) Molecular Reaction Imaging of Charge Transport in MoS2 Nanoflake Photoelectrodes

Transition metal dichalcogenides (TMD) such as WSe2 and MoS2 are highly efficient and stable light absorbers in TMD∣I−,I3 −∣Pt liquid junction solar cells. It is generally accepted that TMD crystals with a large fraction of exposed edge sites exhibit lower power conversion efficiencies (PCEs) than apparently smooth crystals. However, one open question is why does the PCE vary significantly from one crystal to another? Answering this critical question could lead to robust syntheses for high quality and uniform TMD samples. In this work, we apply nanoscale photoelectrochemical microscopy techniques to study n-type TMD nano flake∣I−,I3 −∣Pt cells. Using a combination of near-diffraction-limited photocurrent mapping and molecular reaction imaging techniques, we reveal a previously hidden surface recombination process: photogenerated holes in hidden p-type domains travel micron-scale distances parallel to the solid/liquid interface and preferentially react with iodide at step-edges. The overall efficiency of the nanoflake, as evidenced from whole nanoflake-level photoelectrochemical measurements, is dictated by the size, efficiency, and location of n- and p-type domains. These results provide a unifying view of efficiency losses in smooth TMD photoelectrodes and open the possibility to design electrode architectures that leverage the long-range lateral charge transport property for photoelectrocatalysis.

Electrochemical Colloquium and Beyond: Opportunities for Online Education in Electrochemistry

Electrochemistry represents an exceptionally multifaceted and hard-to-teach subject. First, it requires knowledge of very distinct fields, including chemical thermodynamics, surface science, quantum mechanics, solid state ionics, catalysis, photovoltaics, cellular biology, and others. As a result, no electrochemistry curriculum can cover all the material needed for comprehensive understanding of the subject, meaning that the course is often shaped by the teacher’s personal preferences and agenda (e.g., fundamental electrochemistry, energy storage, corrosion, bioelectrochemistry, etc.). Second, the very core of electrochemistry – electrical double layer – is heavily debated within the professional community and does not have a satisfactory and consensual description suitable for textbooks and teaching. Unlike the kinetics of molecular reactions in solutions or at gas-solid interfaces, the kinetics of electrochemical reactions with the double layer region, even in simplest cases, is almost impossible to predict from first principles. All this causes confusion among both students and teachers – how should we teach when the key concept cannot be described adequately? Third, the field of electrochemistry is evolving, older concepts are reconsidered, and the new ones are introduced. This makes it difficult for students to relate course material to what is going on in real research. Finally, electrochemistry is vital for industry, which makes it particularly tempting for teachers to introduce a substantial “engineering” component into the curriculum and turn it into “applied electrochemistry course” (covering energy storage and conversion, corrosion, electroplating, etc.). While being well-intended, this leads to oversimplification of electrochemistry and offers a general (and often confusing) overview of the field.In my talk, I will discuss the difficulties of teaching electrochemistry courses and how online platforms can offer possible solutions. Specifically, I will draw on my experience with the Electrochemical Online Colloquium, which aims to make fundamental science and essential knowledge freely accessible to the public. My argument is that a holistic understanding of electrochemistry cannot be achieved if one ignores knowledge gained in neighboring fields. At the same time, discussion of open questions and critical assessment of concepts by experts helps a student understand what is truly well-established in the field and what is not. I will also discuss future opportunities for online education in electrochemistry and how we can improve the quality of research in this field.

Exploring the Conversion Limits of Bitumen Visbreaking through a Molecular Reaction Model

Exploring the Conversion Limits of Bitumen Visbreaking through a Molecular Reaction Model

Curl condition: Existence of sub‐Hilbert space for molecular species or chemical processes

AbstractThe “accuracy” of diabatic Hamiltonian matrix elements solely depends on the level of ab initio calculation and on the included set of coupled electronic manifold forming a “true” sub‐Hilbert space (SHS). If ab initio calculations are performed with enough accuracy, existence of SHS can be validated only when the Curl Condition attains zero within numerical precision. For the first time, we depict a theoretical and algorithmic formulation on the calculation of Curl Condition to demonstrate the existence of SHS on molecular processes or chemical reactions.

Broadband Up‐Conversion Mid‐Infrared Time‐Stretch Spectroscopy

AbstractTime‐stretch spectroscopy is a powerful tool for studying transient and nonrepetitive physical events. Its extension to the fundamental molecular fingerprint region is promising for chemical and biological research but encounters difficulties in mid‐infrared photodetection and strong attenuation of aqueous environments. Here, mid‐infrared time‐stretch spectroscopy via coincidently‐pumped nonlinear frequency conversion for efficient mid‐infrared generation and detection is demonstrated. Broadband (≈200 cm−1) mid‐infrared spectra at 77.5 Mspectra s−1 with high signal‐to‐noise ratio are recorded. The single‐shot signal‐to‐noise ratio (SNR) measured within 2 ns exceeds 200. The method reveals fast spectral dynamics in a laser‐induced liquid evaporation process with a temporal resolution of 12.9 ns. Furthermore, probing transient spectra during evaporation opens up a new opportunity for interrogating chemicals inside or behind a thick water layer. Integrating high speed, broad bandwidth, high SNR, and the potential for operating under an aqueous environment, this method will benefit many applications including molecular dynamics, chemical reactions, and biological diagnostics.

Antibacterial mechanism of vanillin against Escherichia coli O157: H7

Vanillin, a plant-derived antimicrobial volatile substance, has potential microbial control applications in the food industry. However, the effect of vanillin on the food-borne pathogen Escherichia coli (E. coli) O157:H7 has not been well studied. This study aims to explore the antibacterial mechanism of vanillin against E. coli O157:H7. The minimum inhibitory concentration (MIC) and antibacterial effect of vanillin were determined by microdilution. Scanning electron microscopy (SEM) was used to observe the damage of vanillin to the cell membrane, while cell membrane potential and the leakage of nucleic acid protein were measured to explore the effect of vanillin on the membrane system. Confocal laser scanning and intracellular adenosine triphosphate (ATP) concentration determination were utilized to investigate the effects of vanillin on the energy, life, and death of E. coli. Finally, transcriptome sequencing was conducted to investigate the gene expression differences induced by vanillin treatment. The results showed that vanillin treatment effectively controlled E. coli O157:H7 with an MIC of 2 mg/mL. After treatment, damage to the membrane system, depolarization of the membrane, and leakage of nucleic acid and protein were observed. Meanwhile, vanillin treatment caused decreased ATP content and cell death. Transcriptome analysis showed that vanillin treatment significantly affected the expression of genes involved in cell membrane formation, tricarboxylic acid (TCA) cycling pathway, and oxidative phosphorylation pathway in E. coli O157:H7. In conclusion, membrane damage and energy metabolism disruption are important mechanisms of vanillin's inhibitory effect on E. coli O157:H7. This study provides new insights into the molecular reaction mechanism of vanillin against E. coli O157:H7, highlighting its potential as an antibacterial substance for preventing E. coli contamination in the food industry.

Temperature-dependent determination of NO2 dimerization reaction based on dual-comb spectroscopy.

Dimerization reactions play a critical role in various fields of research, including cell biology, biomedicine, and chemistry. In particular, the dimerization reaction of 2NO2⇌N2O4 has been extensively applied in pollution control and raw material preparation. Spectroscopy, as a powerful tool for investigating molecular structures and reaction kinetics, has been increasingly employed to study dimerization reactions in recent years. In this study, we successfully demonstrated the application of dual-comb spectroscopy (DCS) to analyze NO2 dimerization reactions, making the first report on the application of this technique in this context. Parallel measurements of NO2 and N2O4 fingerprints spectra with high resolution at 3000 cm-1 was performed, benefiting from the unprecedented broadband and high-precision capability of DCS. The absorption cross-sections of N2O4 from 296 to 343 K was obtained from the measured spectra, which contributes to further research on the molecular spectrum of N2O4. These results demonstrate the potential of DCS for studying the dimerization reaction mechanism.

Effects of Doxycycline Treatment on Hematological Parameters, Viscosity, and Cytokines in Canine Monocytic Ehrlichiosis.

This study aimed to analyze the hematological parameters, blood viscosity, and cytokines of dogs infected by Ehrlichia canis untreated and treated with doxycycline. Initially, 47 dogs were examined, and 36 were suspected to have canine monocytic ehrlichiosis, which was confirmed through molecular polymerase chain reaction tests. This study consisted of 25 dogs, with 11 being healthy and 14 testing positive for E. canis. The dogs were divided into experimental groups based on their test results, including a control group of healthy dogs (N = 11), a group of infected dogs without treatment (N = 7), and a group of infected dogs treated with doxycycline (N = 7) at a 10 mg/kg dose every 12 h for 28 days. Blood samples were taken to determine hematological parameters, viscosity, and cytokine levels. It was observed that, regardless of doxycycline treatment, there was a reduction in total leukocytes and lymphocytes in infected dogs with Ehrlichia canis. The eosinophils and platelets decreased in dogs with Ehrlichia canis infections without treatment. Monocytes, eosinophils, and platelets increased when the dogs were treated with doxycycline. Regardless of treatment, infected dogs' blood viscosity was lower than uninfected dogs. Infected dogs showed lower TNF-α and increased IL-1β. There was a correlation between the blood viscosity with the cytokines IL-10 and IL-12 in the infected dogs. The eosinophil count correlated with TNF-α in the group of infected and untreated dogs. In conclusion, treating dogs with monocytic ehrlichiosis using doxycycline can increase platelet and eosinophil levels but may also increase IL-1β and monocyte levels, exacerbating inflammation. Therefore, evaluating viscosity and cytokine levels is important when treating dogs with this condition.

Optimizing molecular potential models by imposing kinetic constraints with path reweighting.

Empirical force fields employed in molecular dynamics simulations of complex systems are often optimized to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the interconversion rates between metastable states in such systems is hardly ever incorporated in a force field due to a lack of an efficient approach. Here, we introduce such a framework based on the relationship between dynamical observables, such as rate constants, and the underlying molecular model parameters using the statistical mechanics of trajectories. Given a prior ensemble of molecular dynamics trajectories produced with imperfect force field parameters, the approach allows for the optimal adaption of these parameters such that the imposed constraint of equally predicted and experimental rate constant is obeyed. To do so, the method combines the continuum path ensemble maximum caliber approach with path reweighting methods for stochastic dynamics. When multiple solutions are found, the method selects automatically the combination that corresponds to the smallest perturbation of the entire path ensemble, as required by the maximum entropy principle. To show the validity of the approach, we illustrate the method on simple test systems undergoing rare event dynamics. Next to simple 2D potentials, we explore particle models representing molecular isomerization reactions and protein-ligand unbinding. Besides optimal interaction parameters, the methodology gives physical insights into what parts of the model are most sensitive to the kinetics. We discuss the generality and broad implications of the methodology.

Orthogonal activation of a DNA molecular reaction network for proteinase-free and highly specific mRNA imaging in live cells

Construction of artificial DNA molecular reaction networks (DMRNs) represents an effective approach in biosensing. Here we developed a reaction network consisting of a dual catalytic hairpin assembly-mediated tandem molecular circuit combined with strand displacement reaction (DCHA-SDR) for proteinase-free and highly specific mRNA imaging in living cells. The strand displacement reaction (SDR) was designed to be orthogonally activated in exact order by two fuel strands that separately split into inactive species and grafted into the dual catalytic hairpin assembly-mediated molecular tandem circuit (DCHA). The fuel strands can be activated only when the specific mRNA is introduced, and DCHA is initiated by using two different pieces of mRNA sequences as target. In this way, the target mRNA can be automatically matched twice to obtain an accurate and amplified recognition. Comparative analysis indicates that this orthogonal strategy for target identification is superior to the strategy consisting of single CHA-mediated molecular circuit and strand displacement reaction (SCHA-SDR). Moreover, we demonstrate that the DCHA-SDR system comes with the benefit of proteinase-free progress, which makes the approach suitable for operation in living cells. Final application in various cancer cells and normal cells reveals its enormous potential for highly specific mRNA imaging in biological systems.

Bye bye, linearity, bye: quantification of the mean for linear CRNs in a random environment

Molecular reactions within a cell are inherently stochastic, and cells often differ in morphological properties or interact with a heterogeneous environment. Consequently, cell populations exhibit heterogeneity both due to these intrinsic and extrinsic causes. Although state-of-the-art studies that focus on dissecting this heterogeneity use single-cell measurements, the bulk data that shows only the mean expression levels is still in routine use. The fingerprint of the heterogeneity is present also in bulk data, despite being hidden from direct measurement. In particular, this heterogeneity can affect the mean expression levels via bimolecular interactions with low-abundant environment species. We make this statement rigorous for the class of linear reaction systems that are embedded in a discrete state Markov environment. The analytic expression that we provide for the stationary mean depends on the reaction rate constants of the linear subsystem, as well as the generator and stationary distribution of the Markov environment. We demonstrate the effect of the environment on the stationary mean. Namely, we show how the heterogeneous case deviates from the quasi-steady state (Q.SS) case when the embedded system is fast compared to the environment.

DNA droplets for intelligent and dynamical artificial cells: from the viewpoint of computation and non-equilibrium systems.

Living systems are molecular assemblies whose dynamics are maintained by non-equilibrium chemical reactions. To date, artificial cells have been studied from such physical and chemical viewpoints. This review briefly gives a perspective on using DNA droplets in constructing artificial cells. A DNA droplet is a coacervate composed of DNA nanostructures, a novel category of synthetic DNA self-assembled systems. The DNA droplets have programmability in physical properties based on DNA base sequence design. The aspect of DNA as an information molecule allows physical and chemical control of nanostructure formation, molecular assembly and molecular reactions through the design of DNA base pairing. As a result, the construction of artificial cells equipped with non-equilibrium behaviours such as dynamical motions, phase separations, molecular sensing and computation using chemical energy is becoming possible. This review mainly focuses on such dynamical DNA droplets for artificial cell research in terms of computation and non-equilibrium chemical reactions.

Meta-DNA Strand Displacement for Sub-Micron-Scale Autonomous Reconfiguration.

Dynamic molecular interactions in chemical reaction networks lead to complex behaviors in living systems. Whereas recent advances in programming DNA molecular reactions have reached a high level of complexity at molecular and nanometer scales, achieving programmable autonomous behavior at submicron or even larger scales remains challenging. Here, we present a mechanism of meta-DNA strand displacement reactions (M-SDRs) that is mediated solely by meta-toehold (M-toehold) using versatile submicron building blocks of meta-DNA (M-DNA). M-SDR emulates the toehold binding and branch migration processes of conventional strand displacement. Importantly, the kinetics of M-SDR can be modulated over a range of five orders of magnitude reaching a maximum rate of about 1.62 × 105 M-1 s-1. Further, we demonstrate the use of M-SDR to program autonomous reconfiguration in information transmission and logical computation systems. We envision that M-SDR serves as a versatile mechanism for emulating autonomous behavior approaching the cellular level.

The development of a zero-dimensional collisional-radiative model for interpreting plasma emission in low temperature divertor plasmas in tokamaks

Collisional-radiative models are commonly used to analyse atomic and molecular processes in low temperature plasmas by determining the distribution functions of excited states as functions of various plasma parameters. This paper outlines the improvements to a zero-dimensional collisional-radiative model, developed at Keio University, for purposes relevant to the analysis of emission measurements in low temperature hydrogen plasmas. The extension of this 0D model centres on the inclusion of additional molecular species and reactions, a calculation of emission intensity in order to directly compare with experimental work, and the addition of a simple wall model to allow for a deeper understanding of recycling of atoms and molecules in low temperature plasmas close to plasma facing components in fusion machines. Results from the improved model are then compared with both an existing CR model for benchmarking and experimental emission spectroscopy data from an inductively-coupled plasma device at the University of Liverpool. These results show how the developments to the model have increased the relevance to experimental plasmas, such as those in the power exhaust regions of fusion machines, with the ratio of the Hβ/Hα line intensities outputted from the improved CR model mirroring more closely the emission measured experimentally in the ICP device.

Mixed-field effect at the hyperfine level of 127I79Br in its rovibronic ground state: Toward field manipulation of cold molecules

The mixed-field effect at the hyperfine level of the rovibronic ground state of the 127I79Br (X1Σ, v = 0, J = 0) molecule is computed on the J–I uncoupled basis of |JMJI 1 M 1 I 2 M 2〉, where J is the molecular total angular momentum excluding nuclear spin, MJ is the projection number of J, I 1 and I 2 are the nuclear spins of the iodine and bromine atoms, and M 1 and M 2 are the projection numbers of I 1 and I 2, respectively. When the two applied electric and magnetic fields are parallel, the perturbations are rare and only one perturbation is observed in a relatively large field regime in our computation range. However, when the two fields are off-parallel, the perturbations increase significantly and some sublevels show the Feshbach-like resonance phenomenon. Therefore, such sublevels transit between weak-field seeking and strong-field seeking repeatedly, which can be utilized to enhance or suppress cold molecular collision and chemical reaction rates. Such behavior of the molecular hyperfine structure in the mixed off-parallel fields may also be utilized to construct an electric-field-assisted anti-Helmholtz magnetic trap for cold molecules and to realize evaporative cooling of cold molecules (sub-mK) into the ultracold regime (μK).

Nanoscale molecular reactions in microbiological medicines in modern medical applications

Abstract Everything around us is made up of atoms and molecules. The properties of quantum atoms are sought to understand the behavior of a particular object. But with the advent of research, it was discovered that there is a quantity smaller than the molecular size. The nanoscale measures a fraction of a billionth of a meter. The atom of an object measures 0.1 nm. Since atoms are the building blocks of matter, at the nanoscale one can combine these atoms to create new materials. The proposed model displays the properties of these nano-scale elements in modern medical applications. The nano-scale research of matter is fascinating because it is the basic phase in which atoms are held together. Therefore, by manipulating material at this level, one can create many different types of objects. This proposed model calculates the operation requirements and expects the results. Based on the operational requirements, the proposed model provides the suggestions. This will be helpful for the medical researchers to identify the proper medical treatments based on the microbiological requirements.

Characterizing Reaction Route Map of Realistic Molecular Reactions Based on Weight Rank Clique Filtration of Persistent Homology.

A reaction route map (RRM) constructed using the GRRM program is a collection of elementary reaction pathways, each of which comprises two equilibrium (EQ) geometries and one transition state (TS) geometry connected by an intrinsic reaction coordinate (IRC). An RRM can be mathematically represented by a graph with weights assigned to both vertices, corresponding to EQs, and edges, corresponding to TSs, representing the corresponding energies. In this study, we propose a method to extract topological descriptors of a weighted graph representing an RRM based on persistent homology (PH). The work of Mirth et al. [ J. Chem. Phys. 2021, 154, 114114], in which PH analysis was applied to the (3N - 6)-dimensional potential energy surface of an N atomic system, is related to the present method, but our method is practically applicable to realistic molecular reactions. Numerical assessments revealed that our method can extract the same information as the method proposed by Mirth et al. for the 0-th and 1-st PHs, except for the death of the 1-st PH. In addition, the information obtained from the 0-th PH corresponds to the analysis using the disconnectivity graph. The results of this study suggest that the descriptors obtained using the proposed method accurately reflect the characteristics of the chemical reactions and/or physicochemical properties of the system.

Molecular data needs for advanced collisional-radiative modelling for hydrogen plasmas

Population models for molecular hydrogen (H2) are applicable in various fields of plasma physics and particularly in fusion research: they are necessary for the evaluation of plasma diagnostics (e.g. optical emission spectroscopy) or can be used to evaluate effective reaction rates for molecular processes (e.g. molecular-assisted recombination in divertor plasmas). The accuracy and completeness of population models for molecular hydrogen is strongly linked to the accuracy and availability of molecular reaction data. While there are recently huge improvements in the field of electron impact cross sections, the shortfalls regarding input data availability persist in the area of collisions between heavy particles and H2. An overview of the status of population models for H and H2 based on the Yacora solver is given. The data needs for collisional-radiative modelling are demonstrated by means of three examples comprising different detail levels, namely a purely electronic collisional-radiative model for the singlet system of H2, a corona model for the Fulcher-α band and a vibrationally resolved collisional-radiative model for the electronic ground state X1 of H2.Graphical abstractElectronic energy level diagram of the hydrogen molecule delimiting the population models discussed in this work

Molecular Investigation Using RAPD-PCR Marker Field Populations of Pectinophora gossypiella Saunders (Lepidoptera: Gelechiidae) Exposed to Some Insecticide

Seasonally the cotton plant cultivated in Egyptian fields is suffering from the cotton Pink Bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) attacking fruits and buds. Insecticide applications reported control failure by the most recommended conventional classes. Monitoring pest DNA changes after sublethal exposure become the new technique to investigate. Then four insecticide treatments were screened by using the molecular marker polymerase chain reaction (PCR) inspection, using four Random amplified polymorphic deoxyribonucleic acid analysis (RAPD-PCR) primers partitioned based on band reproducibility. Result of LC50 was 0.55, 61.1, 69.3, and 0.23 for spinoteram, novaluron, metaflumezone, and dimeuron respectively. The insecticide treatments band of gel produced detected 47 loci ranging from 87 to 63 % polymorphism. The primer efficiency value of PIC =0.361, 0.34, 0.34, 0.355, and 0.262, RP = 5.30, H = 0.473, 0.434, 0.434, 0.462 and 0.31, and MI = 0.10, 0.1386, 0.138, 0.167 and 0.0582 for the same treated samples respectively. Distance and similarity were quantified based on Nei’s and genetic dissimilarity by the UPMGA method then a phylogenetic tree was constructed and grouped the entire genotypes into 2 major clusters and 6 subclusters. The RAPD primers revealed the number of alleles (Na = 0.324, 0.318, 0.318, 0.326, and 0.328), and the effective number of alleles (Ne = 0.571, 0.569, 0.558, 0.574, and 0.5784). The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.626, 0.684, 0.684, 0.2, and 0.695) exists within the four treated samples respectively. The level of gene flow was (Nm = 0.239, 0.230, 0.230, 0.233, and 0.2187) respectively across the four genotypes studied. Results proved that the RAPD-PCR technique was suitable for distinguishing between insecticide treatments.

One-Pot Graphene Supported Pt3Cu Nanoparticles—From Theory towards an Effective Molecular Oxygen Reduction Reaction Catalyst

In this work, recent research progresses in the formation of Pt3Cu nanoparticles onto the surface of graphene are described, and the obtained results are contrasted with previously published theoretical studies. To form these nanoparticles, tetrabutylammonium hexachloroplatinate, and copper acetylacetonate are used as platinum and copper precursors, respectively. Oleylamine is used as a reductor and a solvent. The obtained catalyst is characterized via X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and energy dispersive spectroscopy X-ray (EDS). To assess the catalytic activity, the graphene-supported Pt3Cu material is tested with cyclic voltammetry, “CO stripping”, and oxygen reduction reaction potentiodynamic curves to find the nature and the intrinsic electrochemical activity of the material. It can be observed that the tetrabutylammonium cation plays a critical role in anchoring and supporting nanoparticles over graphene, from which a broad discussion about the true nature of the anchoring mechanism was derived. The growth mechanism of the nanoparticles on the surface of graphene was observed, supporting the conducted theoretical models. With this study, a reliable, versatile, and efficient synthesis of nanocatalysts is presented, demonstrating the potentiality of Pt3Cu/graphene as an effective cathode catalyst. This study demonstrates the importance of reliable ab inito theoretical results as a useful source of information for the synthesis of the Pt3Cu alloy system.