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Carnosine (β-alanyl-L-histidine) is a naturally occurring endogenous dipeptide and an over-the-counter food supplement with a well-demonstrated multimodal mechanism of action that includes the detoxification of reactive oxygen and nitrogen species, the down-regulation of the production of pro-inflammatory mediators, the inhibition of aberrant protein formation, and the modulation of cells in the peripheral (macrophages) and brain (microglia) immune systems. Since its discovery more than 100 years ago, a plethora of in vivo preclinical studies have been carried out; however, there is still substantial heterogeneity regarding the route of administration, the dosage, the duration of the treatment, and the animal model selected, underlining the urgent need for "coordinated/aligned" preclinical studies laying the foundations for well-defined future clinical trials. The main aim of the present position paper is to critically and concisely consider these key points and open a discussion on the possible "alignment" for future studies, with the goal of validating the full therapeutic potential of this intriguing molecule. [ABSTRACT FROM AUTHOR]

MXene‐based thermal camouflage materials have gained increasing attention due to their low emissivity, however, the poor anti‐oxidation restricts their potential applications under complex environments. Various modification methods and strategies, e.g., the addition of antioxidant molecules and fillers have been developed to overcome this, but the realization of long‐term, reliable thermal camouflage using MXene network (coating) with excellent comprehensive performance remains a great challenge. Here, a MXene‐based hybrid network comodified with hyaluronic acid (HA) and hyperbranched polysiloxane (HSi) molecules is designed and fabricated. Notably, the presence of appreciated HA molecules restricts the oxidation of MXene sheets without altering infrared stealth performance, superior to other water‐soluble polymers; while the HSi molecules can act as efficient cross‐linking agents to generate strong interactions between MXene sheets and HA molecules. The optimized MXene/HA/HSi composites exhibit excellent mechanical flexibility (folded into crane structure), good water/solvent resistance, and long‐term stable thermal camouflage capability (with low infrared emissivity of ≈0.29). The long‐term thermal camouflage reliability (≈8 months) under various outdoor weathers and the scalable coating capability of the MXene‐coated textile enable them to disguise the IR signal of various targets in complex environments, indicating the great promise of achieved material for thermal camouflage, IR stealth, and counter surveillance. [ABSTRACT FROM AUTHOR]

The suggestion that the paper by Naef and Acree is the first one with the capability to treat "any molecule under the sun" is simply totally incorrect. In Ref. [[7]] (Neaf and Acree), reference to GC methods are only the previous publications by Naef and Acree. 10.3390/molecules25051147 7 Naef R., Acree W.E. Jr. Calculation of the Vapour Pressure of Organic Molecules by Means of a Group-Additivity Method and their Resultant Gibbs Free Energy and Entropy of Vaporization at 298.15 K. References 1 Naef R., Acree W.E. Jr. Revision and Extension of a Generally Applicable Group-Additivity Method for the Calculation of the Standard Heat of Combustion and Formation of Organic Molecules. [Extracted from the article]

The present comment concerns some doubtful results included in the above papers. [ABSTRACT FROM AUTHOR]

A database of thermally activated delayed fluorescent (TADF) molecules was automatically generated from the scientific literature. It consists of 25,482 data records with an overall precision of 82%. Among these, 5,349 records have chemical names in the form of SMILES strings which are represented with 91% accuracy; these are grouped in a subsidiary database. Each data record contains one of the following four properties: maximum emission wavelength (λEM), photoluminescence quantum yield (PLQY), singlet-triplet energy splitting (ΔEST), and delayed lifetime (τD). The databases were created through text mining using ChemDataExtractor, a chemistry-aware natural-language-processing toolkit, which has been adapted for TADF research. The text-mined corpus consisted of 2,733 papers from the Royal Society of Chemistry and Elsevier. To the best of our knowledge, these databases are the first databases that have been auto-generated for TADF molecules from existing publications. The databases have been publicly released for experimental and computational applications in the TADF research field. [ABSTRACT FROM AUTHOR]

The document titled "Advances in Amylases—What's Going on?" provides an overview of the classification and research on amylolytic enzymes, specifically α-amylases. It discusses the classification of α-amylase families within the CAZy database, highlighting GH13 and GH57 as the main families, and mentions the existence of subfamilies within GH13. The document also mentions a special issue of the journal Molecules, titled "Advances in Amylases," which includes thirteen papers covering various aspects of amylolytic enzymes. The papers discuss topics such as enzyme hydrolysis of starch granules, inactivation of α-amylase, protein content in rice flour, and the structure and function of different α-amylase subfamilies. The document concludes by expressing appreciation to the contributors and reviewers of the special issue. This article by Štefan Janeček explores the topic of molecules and their properties, providing an in-depth analysis of various types of molecules, their structures, functions, and interactions. It emphasizes the importance of understanding molecules in fields such as chemistry, biology, and medicine. The article is a valuable resource for library patrons conducting research on molecular science and its applications. [Extracted from the article]

A drug molecule is a substance that changes an organism's mental or physical state. Every approved drug has an indication, which refers to the therapeutic use of that drug for treating a particular medical condition. While the Large Language Model (LLM), a generative Artificial Intelligence (AI) technique, has recently demonstrated effectiveness in translating between molecules and their textual descriptions, there remains a gap in research regarding their application in facilitating the translation between drug molecules and indications (which describes the disease, condition or symptoms for which the drug is used), or vice versa. Addressing this challenge could greatly benefit the drug discovery process. The capability of generating a drug from a given indication would allow for the discovery of drugs targeting specific diseases or targets and ultimately provide patients with better treatments. In this paper, we first propose a new task, the translation between drug molecules and corresponding indications, and then test existing LLMs on this new task. Specifically, we consider nine variations of the T5 LLM and evaluate them on two public datasets obtained from ChEMBL and DrugBank. Our experiments show the early results of using LLMs for this task and provide a perspective on the state-of-the-art. We also emphasize the current limitations and discuss future work that has the potential to improve the performance on this task. The creation of molecules from indications, or vice versa, will allow for more efficient targeting of diseases and significantly reduce the cost of drug discovery, with the potential to revolutionize the field of drug discovery in the era of generative AI. [ABSTRACT FROM AUTHOR]

Medulloblastoma (MB) is a highly malignant childhood brain tumor. Group 3 MB (Gr3 MB) is considered to have the most metastatic potential, and tailored therapies for Gr3 MB are currently lacking. Gr3 MB is driven by PRUNE-1 amplification or overexpression. In this paper, we found that PRUNE-1 was transcriptionally regulated by lysine demethylase LSD1/KDM1A. This study aimed to investigate the therapeutic potential of inhibiting both PRUNE-1 and LSD1/KDM1A with the selective inhibitors AA7.1 and SP-2577, respectively. We found that the pharmacological inhibition had a substantial efficacy on targeting the metastatic axis driven by PRUNE-1 (PRUNE-1-OTX2-TGFβ-PTEN) in Gr3 MB. Using RNA seq transcriptomic feature data in Gr3 MB primary cells, we provide evidence that the combination of AA7.1 and SP-2577 positively affects neuronal commitment, confirmed by glial fibrillary acidic protein (GFAP)-positive differentiation and the inhibition of the cytotoxic components of the tumor microenvironment and the epithelial–mesenchymal transition (EMT) by the down-regulation of N-Cadherin protein expression. We also identified an impairing action on the mitochondrial metabolism and, consequently, oxidative phosphorylation, thus depriving tumors cells of an important source of energy. Furthermore, by overlapping the genomic mutational signatures through WES sequence analyses with RNA seq transcriptomic feature data, we propose in this paper that the combination of these two small molecules can be used in a second-line treatment in advanced therapeutics against Gr3 MB. Our study demonstrates that the usage of PRUNE-1 and LSD1/KDM1A inhibitors in combination represents a novel therapeutic approach for these highly aggressive metastatic MB tumors. [ABSTRACT FROM AUTHOR]

While a country-western song title may seem out of place in a I Molecules i Editorial, the words nevertheless seem most appropriate to define the journal's trajectory since volume 1 was published in 1996, to the occasion we now aim to celebrate with the Special Issue being announced herein. 1 Kulkarni B.A., Chattopadhyay S., Chattopadhyay A., Mamdapur V.R. Synthesis of the demospongic compounds, (6Z,11Z)-octadecadienoic acid and (6Z,11Z)-eicosadienoic acid. [Extracted from the article]

Biophysical models can predict the behavior of cell cultures including 3D cell aggregates (3DCAs), thereby reducing the need for costly and time-consuming experiments. Specifically, mass transfer models enable studying the transport of nutrients, oxygen, signaling molecules, and drugs in 3DCA. These models require the defining of boundary conditions (BC) between the 3DCA and surrounding medium. However, accurately modeling the BC that relates the inner and outer boundary concentrations at the border between the 3DCA and the medium remains a challenge that this paper addresses using both theoretical and experimental methods. The provided biophysical analysis indicates that the concentration of molecules inside boundary is higher than that at the outer boundary, revealing an amplification factor that is confirmed by a particle-based simulator (PBS). Due to the amplification factor, the PBS confirms that when a 3DCA with a low concentration of target molecules is introduced to a culture medium with a higher concentration, the molecule concentration in the medium rapidly decreases. The theoretical model and PBS simulations were used to design a pilot experiment with liver spheroids as the 3DCA and glucose as the target molecule. Experimental results agree with the proposed theory and derived properties. [ABSTRACT FROM AUTHOR]

Ferritin (Ft) is a protein with a peculiar three-dimensional architecture. It is characterized by a hollow cage structure and is responsible for iron storage and detoxification in almost all living organisms. It has attracted the interest of the scientific community thanks to its appealing features, such as its nano size, thermal and pH stability, ease of functionalization, and low cost for large-scale production. Together with high storage capacity, these properties qualify Ft as a promising nanocarrier for the development of delivery systems for numerous types of biologically active molecules. In this paper, we introduce the basic structural and functional aspects of the protein, and summarize the methods employed to load bioactive molecules within the ferritin nanocage. [ABSTRACT FROM AUTHOR]

The article discusses a group contribution (GC) method used to calculate the partition coefficients of organic molecules. The GC method assumes that certain aspects of chemical groups are consistent across different molecules. The authors of the article criticize previous publications by Naef and Acree for overlooking relevant research and not providing a rebuttal. They also compare Naef and Acree's results on the octanol-water partition coefficient to previous studies and highlight the limitations of their method. The authors suggest that Naef and Acree's claims of unmatched versatility are not supported by the literature. [Extracted from the article]

In remote sensing applications, such as differential optical absorption spectroscopy (DOAS), atmospheric scattering processes need to be considered. After inelastic scattering on N2 and O2 molecules, the scattered photons occur as additional intensity at a different wavelength, effectively leading to filling-in of both solar Fraunhofer lines and absorptions of atmospheric constituents. Measured spectra in passive DOAS applications are typically corrected for rotational Raman scattering (RRS), also called Ring effect, which represents the main contribution to inelastic scattering. In contrast to that, vibrational Raman scattering (VRS) of N2 and O2 has often been thought to be negligible, but also contributes. Consequences of VRS are red-shifted Fraunhofer structures in scattered light spectra and filling-in of Fraunhofer lines, additional to RRS. We describe how to calculate VRS correction spectra in analogy to the Ring spectrum. We discuss further the impact of VRS cross-sections for O2 and N2 on passive DOAS measurements. The relevance of VRS is shown for the first time in spectral evaluations of Multi-Axis DOAS data. This measurement data yields in agreement with calculated scattering cross-sections, that the observed VRS cross-section amounts to 2.2±0.4% of the cross-section of RRS under tropospheric conditions. It is concluded, that this phenomenon has to be included in the spectral evaluation of weak absorbers as it reduces the measurement error significantly and can cause apparent differential optical depth of up to 2.5 × 10-4. Its influence on the spectral retrieval of IO, Glyoxal, water vapour and NO2 in the blue wavelength range is evaluated. For measurements with a large Ring signal a significant and systematic bias of NO2 dSCDs up to (-3.8±0.4) × 1014 molec cm-2 at low elevation angles is observed if this effect is not considered. [ABSTRACT FROM AUTHOR]

Our new density functional theory calculations by Gaussian reproduce the bond lengths and Raman spectra of a number of model tetrahedral Si and P compounds [the ten compounds in the SiHxD4−x and SiFxCl4−x (x = 0–4) series, and the tetramer P4O10]. The number of symmetric A1 peaks is determined by group theory, and the center of mass is especially important for the assignment of the three A1 peaks for P4O10 to the two P–O stretches and the O–P–O bend. Additional Gaussian calculations on isolated C3v PO4 tetrahedra, using the P–O bond lengths and O–P–O bond angles from the P4O10 optimization, also reproduce the three peak P4O10 Raman spectra and provide an important guide to the assignment of the two low energy peaks at ∼500 and ∼700 cm−1 to the P–BO (BO = P–O–P) stretch and BO–P–BO bend, respectively, in contrast to all earlier assignments. In the SiFxCl4−x series, there is a regular increase in the Si–F A1 frequency and a decrease in the Si–Cl A1 frequency across the series. Similar trends are seen in the SiClx(CH3)4−x series, and these trends are due to changes in the electron densities in the tetrahedron when an electronegative F or Cl is replaced by a less electronegative Cl or CH3, as measured by previous Si 2p, F 1s, Cl 2p, and C 1s x-ray photoelectron spectroscopy. These considerations serve as a guide for the interpretation of the Raman spectra of silicate glasses in Paper II [Bancroft et al., AIP Adv. 13, 125216 (2023)]. [ABSTRACT FROM AUTHOR]

This document is a list of contributions to a special issue titled "Molecules from Side Reactions II" in the journal Molbank. The special issue focuses on the synthesis and characterization of molecules obtained from unexpected and unpredictable synthetic routes. The research on side products is important as they can lead to new syntheses and provide insights into reaction mechanisms. The special issue includes 17 papers, with Italy contributing the most research. The topics covered in the special issue include the synthesis of heterocycles, carbohydrates, modified nucleosides, mechanisms of reactions, green chemistry, and chemistry of natural substances. The document also acknowledges the rigorous review process and the support of the editor-in-chief and editorial office staff. [Extracted from the article]

Research Highlights: Long-term exposure of paper birch to elevated carbon dioxide (CO2) and ozone (O3) modified metabolite content of over-wintering buds, but no evidence of reduced freezing tolerance was found. Background and Objectives: Atmospheric change may affect the metabolite composition of over-wintering buds and, in turn, impact growth onset and stress tolerance of perennial plant species in spring. Materials and Methods: Low molecular weight compounds of paper birch (Betula papyrifera) buds, including lipophilic, polar and phenolic compounds were analyzed, and freezing tolerance (FT) of the buds was determined prior to bud break after 11 growing seasons exposure of saplings to elevated concentrations of CO2 (target concentration 560 µL L−1) and O3 (target concentration 1.5 × ambient) at the Aspen FACE (Free-Air CO2 and O3 Enrichment) facility. Results: The contents of lipophilic and phenolic compounds (but not polar compounds) were affected by elevated CO2 and elevated O3 in an interactive manner. Elevated O3 reduced the content of lipids and increased that of phenolic compounds under ambient CO2 by reallocating carbon from biosynthesis of terpenoids to that of phenolic acids. In comparison, elevated CO2 had only a minor effect on lipophilic and polar compounds, but it increased the content of phenolic compounds under ambient O3 by increasing the content of phenolic acids, while the content of flavonols was reduced. Conclusions: Based on the freezing test and metabolite data, there was no evidence of altered FT in the over-wintering buds. The impacts of the alterations of bud metabolite contents on the growth and defense responses of birches during early growth in spring need to be uncovered in future experiments. [ABSTRACT FROM AUTHOR]

Aggregation-induced emission (AIE) can exhibit different properties in different situations, such as non-emission and highly fluorescent in the dissolved state of the molecule and in the aggregate or solid state, respectively. This property of AIE is distinguished from aggregation-induced quenching (ACQ) or even the opposite. Combining the AIE phenomenon with different polymers yields different polymers with corresponding AIE properties. In this paper, the mechanism, synthesis, branching and application of AIE in the fields of optoelectronic functional materials, sensors, biology, and environment are reviewed. It is hoped that this review will stimulate more research on molecular aggregates and promote further cross-fertilisation and greater development in the disciplines of materials, chemistry and biomedicine. [ABSTRACT FROM AUTHOR]

The molecular movement in single particle tracking (SPT) experiments shows a crucial role of diffusion in many biological processes such as signaling, cellular organization, transport mechanisms, and more. The SPT analysis detects not only classical Brownian motion but diffusion with other features. These include directed diffusion and confined motion. The behavior remains a challenging problem for several reasons. Due to the action of many physical processes, random trajectories of cellular molecules are segmented in different diffusive modes. Often their study requires sophisticated algorithms for the analysis of statistical properties. In this paper we consider the segment analysis for trajectories of G proteins and coupled-receptors in living cells. Their movement is often transient and switches among free diffusion, confined diffusion, directed diffusion, and immobility. Moreover, the confined segments can have both Gaussian and non-Gaussian statistics. The types of alternation of diffusive modes along the trajectories of G proteins and coupled-receptors are analyzed. [ABSTRACT FROM AUTHOR]

Dynamic control of the motion in a catenane remains a big challenge as it requires precise design and sophisticated well‐organized structures. This paper reports the design and synthesis of a donor‐acceptor [2]catenane through mechanical interlocking, employing a crown ether featuring two dibenzylammonium salts on its side arms as the host and a cyclobis(paraquat‐p‐phenylene) (CBPQT ⋅ 4PF6) ring as the guest molecule. By addition of external acid or base, the catenane can form self‐complexed or decomplexed compounds to alter the cavity size of the crown ether ring, consequently affecting circumrotation rate of CBPQT ⋅ 4PF6 ring of the catenane. This study offers insights for the design and exploration of artificial molecular machines with intricate cascading responsive mechanisms. [ABSTRACT FROM AUTHOR]

Domination is an important factor in determining the robustness of a graph structure. A thorough examination of the graph's topological structure is necessary for analyzing and examining it for various aspects. Understanding the stability of a chemical compound is a significant criterion in chemistry, which necessitates conducting numerous experimental tests. The domination number and power domination number are pivotal in defining a wide range of physical properties, which include physiochemical properties, thermodynamic properties, chemical activities, and biological activities. The one-pentagonal carbon nanocone (1-PCNC) is a member of the carbon nanocone family and has a structure similar to that of honeycomb networks, which are renowned for their robustness. In this paper, we find the domination number and power domination number of 1-PCNC by considering it as an (m-1)-layered infinite graph. [ABSTRACT FROM AUTHOR]

This article concerns the spasmolytic activities of some novel 1,3-disubstituted 3,4-dihydroisoquinolines. These compounds can be evaluated as potential therapeutic candidates according to Lipinski's rule of five, showing high gastrointestinal absorption and the ability to cross the blood–brain barrier, which is a very important parameter in the drug discovery processes. In silico simulation predicted smooth muscle relaxant activity for all the compounds. Since smooth muscle contractile failure is a characteristic feature of many disorders, in the current paper, we concentrate on the parameters of the spontaneous contractile responses of smooth muscle (SM) cells compared to the well-known drug mebeverine. Two of the newly synthesized substances can be identified as essential modulating regulators and potentially used as therapeutic molecules. One of these molecules also showed significant DPPH antioxidant activity compared to rutin. [ABSTRACT FROM AUTHOR]

Cell and cYTOkine CONcentrations DataBase (CYTOCON DB) is a project undertaken by the InSysBio team and aimed at the development of a database that allows collecting, processing, and visualizing publicly available in vivo human data on baseline concentrations of cells, cytokines, chemokines, and other molecules. Besides manual curation, an important feature of CYTOCON is that most values found in papers are converted from a huge variety of original units (i.e., mg/ml and number of cells per mm2 of biopsy surface section) to unified units: "pM" for cytokine and "kcell/L" for cell concentration. These features of the database can help researchers facilitate the creation and calibration of quantitative systems pharmacology (QSP) models. Possible applications can be: estimation of the average value or variability of the cell, cytokine or chemokine concentrations for patient groups with different characteristics, such as age, gender, disease severity, disease subtype, etc.; and analysis of correlations among the cell, cytokine, or chemokine concentrations in patients with different characteristics, such as severity of the disease. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Physics is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Molecular biology is crucial for drug discovery, protein design, and human health. Due to the vastness of the drug-like chemical space, depending on biomedical experts to manually design molecules is exceedingly expensive. Utilizing generative methods with deep learning technology offers an effective approach to streamline the search space for molecular design and save costs. This paper introduces a novel E(3)-equivariant score-based diffusion framework for 3D molecular generation via SDEs, aiming to address the constraints of unified Gaussian diffusion methods. Within the proposed framework EMDS, the complete diffusion is decomposed into separate diffusion processes for distinct components of the molecular feature space, while the modeling processes also capture the complex dependency among these components. Moreover, angle and torsion angle information is integrated into the networks to enhance the modeling of atom coordinates and utilize spatial information more effectively. Results: Experiments on the widely utilized QM9 dataset demonstrate that our proposed framework significantly outperforms the state-of-the-art methods in all evaluation metrics for 3D molecular generation. Additionally, ablation experiments are conducted to highlight the contribution of key components in our framework, demonstrating the effectiveness of the proposed framework and the performance improvements of incorporating angle and torsion angle information for molecular generation. Finally, the comparative results of distribution show that our method is highly effective in generating molecules that closely resemble the actual scenario. Conclusion: Through the experiments and comparative results, our framework clearly outperforms previous 3D molecular generation methods, exhibiting significantly better capacity for modeling chemically realistic molecules. The excellent performance of EMDS in 3D molecular generation brings novel and encouraging opportunities for tackling challenging biomedical molecule and protein scenarios. [ABSTRACT FROM AUTHOR]

Recently, increasing attention of researchers in the field of membrane technology has been paid to the development of membranes based on biopolymers. One of the well-proven polymers for the development of porous membranes is cellulose acetate (CA). This paper is devoted to the study of the influence of different parameters on ultrafiltration CA membrane formation and their transport properties, such as the variation in coagulation bath temperature, membrane shrinkage (post-treatment at 80 °C), introduction to casting CA solution of polymers (polyethylene glycol (PEG), polysulfone (PS), and Pluronic F127 (PL)) and carbon nanoparticles (SWCNTs, MWCNTs, GO, and C60). The structural and physicochemical properties of developed membranes were studied by scanning electron and atomic force microscopies, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, and contact angle measurements. The transport properties of developed CA-based membranes were evaluated in ultrafiltration of bovine serum albumin (BSA), dextran 110 and PVP K-90. All developed membranes rejected 90% compounds with a molecular weight from ~270,000 g/mol. It was shown that the combination of modifications (addition of PEG, PS, PL, PS-PL, and 0.5 wt% C60) led to an increase in the fluxes and BSA rejection coefficients with slight decrease in the flux recovery ratio. These changes were due to an increased macrovoid number, formation of a more open porous structure and/or thinner top selective, and decreased surface roughness and hydrophobization during C60 modification of blend membranes. Optimal transport properties were found for CA-PEG+C60 (the highest water—394 L/(m2h) and BSA—212 L/(m2h) fluxes) and CA-PS+C60 (maximal rejection coefficient of BSA—59%) membranes. [ABSTRACT FROM AUTHOR]

Recently, we have demonstrated a method to record the longitudinal phase-space distribution of a pulsed cryogenic buffer gas cooled beam of barium fluoride molecules with high resolution. In this paper, we use this method to determine the influence of various source parameters. Besides the expected dependence on temperature and pressure, the forward velocity of the molecules is strongly correlated with the time they exit the cell, revealing the dynamics of the gas inside the cell. Three observations are particularly noteworthy: (1) The velocity of the barium fluoride molecules increases rapidly as a function of time, reaches a maximum 50–200 µ s after the ablation pulse and then decreases exponentially. We attribute this to the buffer gas being heated up by the plume of hot atoms released from the target by the ablation pulse and subsequently being cooled down via conduction to the cell walls. (2) The time constant associated with the exponentially decreasing temperature increases when the source is used for a longer period of time, which we attribute to the formation of a layer of isolating dust on the walls of the cell. By thoroughly cleaning the cell, the time constant is reset to its initial value. (3) The velocity of the molecules at the trailing end of the molecular pulse depends on the length of the cell. For short cells, the velocity is significantly higher than expected from the sudden freeze model. We attribute this to the target remaining warm over the duration of the molecular pulse giving rise to a temperature gradient within the cell. Our observations will help to optimize the source parameters for producing the most intense molecular beam at the target velocity. [ABSTRACT FROM AUTHOR]

The Wiener index is one of the most classic and widely used indicators in topology. It reflects the average distance of any node pair in the graph. It not only makes the boundaries of given graphs clearer but also continuously generates topological indices that are more suitable for new fields, such as the Gutman index. The Wiener index and Gutman index are two important topological indices, which are commonly used to describe the characteristics of molecular structure. They are closely related to the physical and chemical properties of molecular compounds. And they are widely used to predict the physical and chemical properties and biological activity of molecular compounds. In this paper, we study the vertex Gutman index and Gutman index and describe the structural characteristics of all cases of two simple cycles intersecting. We comprehensively analyze the Gutman index and vertex Gutman index in these cases in detail by means of classification discussion and analogical reasoning and characterize their maximum and minimum accordingly. [ABSTRACT FROM AUTHOR]

Revealing the interaction mechanisms between anticancer drugs and target DNA molecules at the single-molecule level is a hot research topic in the interdisciplinary fields of biophysical chemistry and pharmaceutical engineering. When fluorescence imaging technology is employed to carry out this kind of research, a knotty problem due to fluorescent dye molecules and drug molecules acting on a DNA molecule simultaneously is encountered. In this paper, based on self-made novel solid active substrates NpAA/(ZnO-ZnCl2)/AuNPs, we use a surface-enhanced Raman spectroscopy method, inverted fluorescence microscope technology, and a molecular docking method to investigate the action of the fluorescent dye YOYO-1 and the drug DOX on calf thymus DNA (ctDNA) molecules and the influencing effects and competitive relationships of YOYO-1 on the binding properties of the ctDNA-DOX complex. The interaction sites and modes of action between the YOYO-1 and the ctDNA-DOX complex are systematically examined, and the DOX with the ctDNA-YOYO-1 are compared, and the impact of YOYO-1 on the stability of the ctDNA-DOX complex and the competitive mechanism between DOX and YOYO-1 acting with DNA molecules are elucidated. This study has helpful experimental guidance and a theoretical foundation to expound the mechanism of interaction between drugs and biomolecules at the single-molecule level. [ABSTRACT FROM AUTHOR]

Carbon nanotubes filled with organic molecules can serve as chemical nanoreactors. Recent experimental results show that, by introducing cyclic hydrocarbon molecules inside carbon nanotubes, they can be transformed into nanoribbons or inner tubes, depending on the experimental conditions. In this paper, we present our results obtained as a continuation of our previous molecular dynamics simulation work. In our previous work, the initial geometry consisted of independent carbon atoms. Now, as an initial condition, we have placed different molecules inside a carbon nanotube (18,0): C5H5 (fragment of ferrocene), C5, C5+H2; C6H6 (benzene), C6, C6+H2; C20H12 (perylene); and C24H12 (coronene). The simulations were performed using the REBO-II potential of the LAMMPS software package, supplemented with a Lennard-Jones potential between the nanotube wall atoms and the inner atoms. The simulation proved difficult due to the slow dynamics of the H abstraction. However, with a slight modification of the parameterization, it was possible to model the formation of carbon nanoribbons inside the carbon nanotube. [ABSTRACT FROM AUTHOR]

Many industrial processes, several natural processes involving non-living matter, and all the processes occurring within living organisms take place in solution. This means that the molecules playing active roles in the processes are present within another medium, called solvent. The solute molecules are surrounded by solvent molecules and interact with them. Understanding the nature and strength of these interactions, and the way in which they modify the properties of the solute molecules, is important for a better understanding of the chemical processes occurring in solution, including possible roles of the solvent in those processes. Computational studies can provide a wealth of information on solute–solvent interactions and their effects. Two major models have been developed to this purpose: a model viewing the solvent as a polarisable continuum surrounding the solute molecule, and a model considering a certain number of explicit solvent molecules around a solute molecule. Each of them has its advantages and challenges, and one selects the model that is more suitable for the type of information desired for the specific system under consideration. These studies are important in many areas of chemistry research, from the investigation of the processes occurring within a living organism to drug design and to the design of environmentally benign solvents meant to replace less benign ones in the chemical industry, as envisaged by the green chemistry principles. The paper presents a quick overview of the modelling approaches and an overview of concrete studies, with reference to selected crucial investigation themes. [ABSTRACT FROM AUTHOR]

This correction notice addresses inaccuracies in an article about two products used in the animal breeding industry in China. The names of the products and a picture were incorrectly used, and the term "impurity" should be replaced with "trace components." The correction provides the accurate names of the products and clarifies their use as safe and effective Chinese veterinary medicine. Additionally, errors in figures and sample preparation information are corrected. The scientific conclusions of the article remain unaffected by these changes. [Extracted from the article]

Highlights: Critical solvation structure changes the hydrogen bond network through "catchers". Catcher further arrests the active molecules to promote Zn2+ deposition. The Zn||Zn symmetric battery can stably cycle for 2250 h. Zn||V6O13 full battery achieved a capacity retention rate of 99.2% after 10,000 cycles. Aqueous Zn-ion batteries (AZIBs) have attracted increasing attention in next-generation energy storage systems due to their high safety and economic. Unfortunately, the side reactions, dendrites and hydrogen evolution effects at the zinc anode interface in aqueous electrolytes seriously hinder the application of aqueous zinc-ion batteries. Here, we report a critical solvation strategy to achieve reversible zinc electrochemistry by introducing a small polar molecule acetonitrile to form a "catcher" to arrest active molecules (bound water molecules). The stable solvation structure of [Zn(H2O)6]2+ is capable of maintaining and completely inhibiting free water molecules. When [Zn(H2O)6]2+ is partially desolvated in the Helmholtz outer layer, the separated active molecules will be arrested by the "catcher" formed by the strong hydrogen bond N–H bond, ensuring the stable desolvation of Zn2+. The Zn||Zn symmetric battery can stably cycle for 2250 h at 1 mAh cm−2, Zn||V6O13 full battery achieved a capacity retention rate of 99.2% after 10,000 cycles at 10 A g−1. This paper proposes a novel critical solvation strategy that paves the route for the construction of high-performance AZIBs. [ABSTRACT FROM AUTHOR]

The natural product Desmosdumotin D (hereafter referred to as Des-D), isolated from the plant Desmos dumosus, showed potent anti-HIV activity. However, the subsequent pharmacological activity and clinical studies are limited due to the low content of Des-D in the plant. Therefore, the total synthesis path of Des-D was optimized in this paper, and the total yield was increased from 4.4% to 11.9%. Additionally, twelve analogues were obtained following the synthesis route of Des-D. The anti-HIV activity evaluation results in vitro showed that Des-D had the highest activity, with an IC50 value of 13.6 μM, and compounds 17 and 11 had the lowest anti-HIV activity, with IC50 values of 101.3 μM and 161.0 μM, respectively. Through the molecular docking of compounds Des-D and 17 with HIV-IN, the results show that phenolic hydroxyl groups and two benzene rings interact with HIV-IN and are possible pharmacodynamic groups. [ABSTRACT FROM AUTHOR]

Context. The G31.41+0.31 Unbiased ALMA sPectral Observational Survey (GUAPOS) project targets the hot molecular core (HMC) G31.41+0.31 (G31) to reveal the complex chemistry of one of the most chemically rich high-mass star-forming regions outside the Galactic center (GC). Aims. In the third paper of the project we present a study of nine O-bearing (CH3OH, 13CH3OH, CH318OH , CH3CHO, CH3OCH3, CH3COCH3, C2H5OH, aGg′-(CH2OH)2, and gGg′-(CH2OH)2) and six N-bearing (CH3CN,13CH3CN, CH313CN, C2H3CN, C2H5CN, and C2H513CN) complex organic molecules toward G31. The aim of this work is to characterize the abundances in G31 and to compare them with the values estimated in other sources. Moreover, we searched for a possible chemical segregation between O-bearing and N-bearing species in G31, which hosts four compact sources as seen with higher angular resolution data. In the discussion we also include the three isomers of C2H4O2 and the O- and N-bearing molecular species NH2CHO, CH3NCO, CH3C(O)CH2, and CH3NHCHO, which were analyzed in previous GUAPOS papers. Methods. Observations were carried out with the interferometer ALMA and cover the entire Band 3 from 84 to 116 GHz (~32 GHz bandwidth) with an angular resolution of 1.2″ × 1.2″ (~4400 au × 4400 au) and a spectral resolution of ~0.488 MHz (~1.3–1.7 km s−1). The transitions of the 14 molecular species were analyzed with the tool SLIM of MADCUBA to determine the physical parameters of the emitting gas. Moreover, we analyzed the morphology of the emission of the molecular species. Results. The values of abundances with respect to H2 in G31 range from 10−6 to 10−10 for the different species. We compared the abundances with respect to methanol of O-bearing, N-bearing, and O- and N-bearing COMs in G31 with 27 other sources, including other hot molecular cores inside and outside the GC, hot corinos, shocked regions, envelopes around young stellar objects, and quiescent molecular clouds, and with chemical models. Conclusions. From the comparison with other sources there is not a unique template for the abundances in hot molecular cores, pointing toward the importance of the thermal history for the chemistry of the various sources. The abundances derived from the chemical models are in good agreement, within a factor of 10, with those of G31. From the analysis of the maps we derived the peak positions of all the molecular species toward G31. Different species peak at slightly different positions, and this, together with the different central velocities of the lines obtained from the spectral fitting, point to chemical differentiation of selected O-bearing species. [ABSTRACT FROM AUTHOR]

Watson-Crick automata are belonging to the natural computing paradigm as these finite automata are working on strings representing DNA molecules. Watson-Crick automata have two reading heads, and in the 5' → 3' models these two heads start from the two extremes of the input. This is well motivated by the fact that DNA strands have 5' and 3' ends based on the fact which carbon atoms of the sugar group is used in the covalent bonds to continue the strand. However, in the two stranded DNA, the directions of the strands are opposite, so that, if an enzyme would read the strand it may read each strand in its 5' to 3' direction, which means physically opposite directions starting from the two extremes of the molecule. On the other hand, enzymes may not have inner states, thus those Watson-Crick automata which are stateless (i.e. have exactly one state) are more realistic from this point of view. In this paper these stateless 5' → 3' Watson-Crick automata are studied and some properties of the language classes accepted by their variants are proven. We show hierarchy results, and also a "pumping", i.e., iteration result for these languages that can be used to prove that some languages may not be in the class accepted by the class of stateless 5' → 3' Watson-Crick automata. [ABSTRACT FROM AUTHOR]

The investigation of the relation between chemistry and quantum mechanics includes examining how the two theories each describe an isolated molecule. This paper focuses on one particular characteristic of chemistry's and quantum mechanics' descriptions of an isolated molecule; namely on the assumptions made by each description that an isolated molecule is stable and has structure. The paper argues that these assumptions are an idealisation. First, this is because stability and structure are partially determined by factors that concern the context in which a molecule is considered (i.e. thermodynamic conditions, time-range of experiment, environment, etc.). Secondly, the stability and structure of a molecule can only be empirically identified with reference to those factors. This paper examines these assumptions in the context of the philosophical literature on idealisations. This examination is a novel contribution that raises interesting questions about the relation between the two theories, the nature of stability and structure, and the function of these assumptions in the two theories. [ABSTRACT FROM AUTHOR]

Aconitine (AC), which is the primary bioactive diterpene alkaloid derived from Aconitum L plants, have attracted considerable interest due to its unique structural feature. Additionally, AC demonstrates a range of biological activities, such as its ability to enhance cardiac function, inhibit tumor growth, reduce inflammation, and provide analgesic effects. However, the structure-activity relationships of AC are remain unclear. A clear understanding of these relationships is indeed critical in developing effective biomedical applications with AC. In line with these challenges, this paper summarized the structural characteristics of AC and relevant functional and bioactive properties and the structure-activity relationships presented in biomedical applications. The primary temporal scope of this review was established as the period spanning from 2010 to 2023. Subsequently, the objective of this review was to provide a comprehensive understanding of the specific action mechanism of AC, while also exploring potential novel applications of AC derivatives in the biomedical field, drawing upon their structural characteristics. In conclusion, this review has provided a comprehensive analysis of the challenges and prospects associated with AC in the elucidation of structure-bioactivity relationships. Furthermore, the importance of exploring modern biotechnology approaches to enhance the potential biomedical applications of AC has been emphasized. [ABSTRACT FROM AUTHOR]

In this paper, all molecules (1,2-ethanediol, ethanol, methoxymethanol, dimethyl ether, and dimethyl peroxide) predicted to be produced as a result of C–C, C–O, or O–O bond formation between methanol molecules induced by laser-driven shock wave were detected and identified by gas chromatography-mass spectroscopy. In this process, the ultrahigh pressure resulting from the shock wave is considered to reduce the interatomic distance between molecules to mechanically create a new chemical bond. Methoxymethanol production was further verified by infrared absorption spectroscopy of the laser-irradiated methanol concentrated by vacuum distillation. In the concentrated sample, polyoxymethylene hemiformals, which are presumably produced by the polymerization of methoxymethanol, were also found. [ABSTRACT FROM AUTHOR]

Separation and identification of molecules and biomolecules such as nucleic acids, proteins, and polysaccharides from complex fluids are known to be important due to unmet needs in various applications. Generally, many different separation techniques, including chromatography, electrophoresis, and magnetophoresis, have been developed to identify the target molecules precisely. However, these techniques are expensive and time consuming. "Lab‐on‐a‐chip" systems with low cost per device, quick analysis capabilities, and minimal sample consumption seem to be ideal candidates for separating particles, cells, blood samples, and molecules. From this perspective, different microfluidic‐based techniques have been extensively developed in the past two decades to separate samples with different origins. In this review, "lab‐on‐a‐chip" methods by passive, active, and hybrid approaches for the separation of biomolecules developed in the past decade are comprehensively discussed. Due to the wide variety in the field, it will be impossible to cover every facet of the subject. Therefore, this review paper covers passive and active methods generally used for biomolecule separation. Then, an investigation of the combined sophisticated methods is highlighted. The spotlight also will be shined on the elegance of separation successes in recent years, and the remainder of the article explores how these permit the development of novel techniques. [ABSTRACT FROM AUTHOR]

The piperazine moiety is often found in drugs or in bioactive molecules. This widespread presence is due to different possible roles depending on the position in the molecule and on the therapeutic class, but it also depends on the chemical reactivity of piperazine-based synthons, which facilitate its insertion into the molecule. In this paper, we take into consideration the piperazine-containing drugs approved by the Food and Drug Administration between January 2011 and June 2023, and the synthetic methodologies used to prepare the compounds in the discovery and process chemistry are reviewed. [ABSTRACT FROM AUTHOR]

Shellac is a natural resin composed of a complex mixture of hydroxy aliphatic acids, primarily aleuritic acid (AA), and sesquiterpenoid acids such as jalaric acid (JA). The paper puts forth valuable information on the polymerization mechanism considering AA and JA using Gaussian 16.0 software. Computations of energy, thermochemical values, and molecular orbital coefficients have been done using both Hartree-Fock (HF) and Density Functional Theory (DFT) to establish the mechanism. Global reactivity parameter study revealed that monomers of the shellac are hard whereas the polymer units are soft. HOMO-LUMO, ESP and theoretical FTIR results are coherent with the previously reported works for the prediction of possible polymeric species present in the shellac along with their thermodynamic stability. This is the first attempt to predict the linkages in shellac resin. This study helps understand the mechanism of formation of lac polymer and also highlights the associated properties of shellac. [ABSTRACT FROM AUTHOR]

As living standards advance, an escalating emphasis is placed on health, particularly in relation to prevalent chronic metabolic disorders. It is necessary to explore safe and effective functional foods or drugs. Fu brick tea (FBT) is a kind of dark tea fermented by fungi. The extracts are rich in compounds that can effectively relieve metabolic diseases such as hyperglycemia and hyperlipidemia, protect the liver, improve human immunity, enhance antioxidant activity, and regulate intestinal flora. This paper summarizes the biological activities and mechanisms of the extracts, polysaccharides, and small molecular compounds of FBT, which provides a certain theoretical basis for the rational, systematic, comprehensive development and utilization of the FBT resources. It is expected to develop and apply these active substances in health care products and natural medicines and provide more beneficial and diversified FBT products for human beings. [ABSTRACT FROM AUTHOR]

Designing 3D molecules with high binding affinity for specific protein targets is crucial in drug design. One challenge is that the atomic interaction between molecules and proteins in 3D space has to be taken into account. However, the existing target-aware methods solely model the joint distribution between the molecules and proteins, disregarding the binding affinities between them, which leads to limited performance. In this paper, we propose an explainable diffusion model to generate molecules that can be bound to a given protein target with high affinity. Our method explicitly incorporates the chemical knowledge of protein–ligand binding affinity into the diffusion model, and uses the knowledge to guide the denoising process towards the direction of high binding affinity. Specifically, an SE(3)-invariant expert network is developed to fit the Vina scoring functions and jointly trained with the denoising network, while the domain knowledge is distilled and conveyed from Vina functions to the expert network. An effective guidance is proposed on both continuous atom coordinates and discrete atom types by taking advantages of the gradient of the expert network. Experiments on the benchmark CrossDocked2020 demonstrate the superiority of our method. Additionally, an atom-level explanation of the generated molecules is provided, and the connections with the domain knowledge are established. [ABSTRACT FROM AUTHOR]

In past years, optical lattices have been demonstrated as an excellent platform for making, understanding, and controlling quantum matters at nonlinear and fundamental quantum levels. Shrinking experimental observations include matter-wave gap solitons created in ultracold quantum degenerate gases, such as Bose–Einstein condensates with repulsive interaction. In this paper, we theoretically and numerically study the formation of one-dimensional gap soliton molecules and clusters in ultracold coherent atom ensembles under electromagnetically induced transparency conditions and trapped by an optical lattice. In numerics, both linear stability analysis and direct perturbed simulations are combined to identify the stability and instability of the localized gap modes, stressing the wide stability region within the first finite gap. The results predicted here may be confirmed in ultracold atom experiments, providing detailed insight into the higher-order localized gap modes of ultracold bosonic atoms under the quantum coherent effect called electromagnetically induced transparency. [ABSTRACT FROM AUTHOR]