Variations In Molecular Structure Research Articles

Preyssler-type phosphotungstate is a new family of negative-staining reagents for the TEM observation of viruses

Transmission electron microscopy (TEM) is an essential method in virology because it allows for direct visualization of virus morphology at a nanometer scale. Negative staining to coat virions with heavy metal ions must be performed before TEM observations to achieve sufficient contrast. Herein, we report that potassium salts of Preyssler-type phosphotungstates (K(15-n)[P5W30O110Mn+], M = Na+, Ca2+, Ce3+, Eu3+, Bi3+, or Y3+) are high-performance negative staining reagents. Additionally, we compare the staining abilities of these salts to those of uranyl acetate and Keggin-type phosphotungstate. The potassium salt of Preyssler-type phosphotungstates has the advantage of not requiring prior neutralization because it is a neutral compound. Moreover, the potassium counter-cation can be protonated by a reaction with H+-resin, allowing easy exchange of protons with other cations by acid–base reaction. Therefore, the counter-cations can be changed. Encapsulated cations can also be exchanged, and clear TEM images were obtained using Preyssler-type compounds with different encapsulated cations. Preyssler-type phosphotungstates may be superior negative staining reagents for observing virus. Polyoxotungstates (tungsten-oxide molecules with diverse molecular structures and properties) are thus promising tools to develop negative staining reagents for TEM observations.

Deep clustering of small molecules at large-scale via variational autoencoder embedding and K-means

BackgroundConverting molecules into computer-interpretable features with rich molecular information is a core problem of data-driven machine learning applications in chemical and drug-related tasks. Generally speaking, there are global and local features to represent a given molecule. As most algorithms have been developed based on one type of feature, a remaining bottleneck is to combine both feature sets for advanced molecule-based machine learning analysis. Here, we explored a novel analytical framework to make embeddings of the molecular features and apply them in the clustering of a large number of small molecules.ResultsIn this novel framework, we first introduced a principal component analysis method encoding the molecule-specific atom and bond information. We then used a variational autoencoder (AE)-based method to make embeddings of the global chemical properties and the local atom and bond features. Next, using the embeddings from the encoded local and global features, we implemented and compared several unsupervised clustering algorithms to group the molecule-specific embeddings. The number of clusters was treated as a hyper-parameter and determined by the Silhouette method. Finally, we evaluated the corresponding results using three internal indices. Applying the analysis framework to a large chemical library of more than 47,000 molecules, we successfully identified 50 molecular clusters using the K-means method with 32 embeddings based on the AE method. We visualized the clustering result via t-SNE for the overall distribution of molecules and the similarity maps for the structural analysis of randomly selected cluster-specific molecules.ConclusionsThis study developed a novel analytical framework that comprises a feature engineering scheme for molecule-specific atomic and bonding features and a deep learning-based embedding strategy for different molecular features. By applying the identified embeddings, we show their usefulness for clustering a large molecule dataset. Our novel analytic algorithms can be applied to any virtual library of chemical compounds with diverse molecular structures. Hence, these tools have the potential of optimizing drug discovery, as they can decrease the number of compounds to be screened in any drug screening campaign.

Predicting the Redox Potentials of Phenazine Derivatives Using DFT-Assisted Machine Learning.

This study investigates four machine-learning (ML) models to predict the redox potentials of phenazine derivatives in dimethoxyethane using density functional theory (DFT). A small data set of 151 phenazine derivatives having only one type of functional group per molecule (20 unique groups) was used for the training. Prediction accuracy was improved by a combined strategy of feature selection and hyperparameter optimization, using the external validation set. Models were evaluated on the external test set containing new functional groups and diverse molecular structures. High prediction accuracies of R2 > 0.74 were obtained on the external test set. Despite being trained on the molecules with a single type of functional group, models were able to predict the redox potentials of derivatives containing multiple and different types of functional groups with good accuracies (R2 > 0.7). This type of performance for predicting redox potential from such a small and simple data set of phenazine derivatives has never been reported before. Redox flow batteries (RFBs) are emerging as promising candidates for energy storage systems. However, new green and efficient materials are required for their widespread usage. We believe that the hybrid DFT-ML approach demonstrated in this report would help in accelerating the virtual screening of phenazine derivatives, thus saving computational and experimental costs. Using this approach, we have identified promising phenazine derivatives for green energy storage systems such as RFBs.

Gelation mechanisms of granular and non-granular starches with variations in molecular structures

Gelation is a critical functional property that determines the applications of starch. This study aimed to elucidate the gelation mechanisms of granular and non-granular starches varying in molecular structures. Five representative starches – including waxy maize (containing 1.9% amylose), normal maize (32.0% amylose), tapioca (29.1% amylose), pea (39.2% amylose), and high-amylose maize (HA7; 69.7% amylose) – were pasted in both physical forms at 95 °C with 8.0% concentration (w/w, dry basis) to examine the gelation behaviors. The gelation process of cooling (2 °C/min) and 2-h curing at 25 °C was monitored using dynamic rheological tests. The derived starch gels/pastes were further characterized using uniaxial compression test and scanning electron microscopy (SEM). The granular starches showed gelling ability in an order of pea > normal maize > HA7 > tapioca, waxy maize. For native, granular starches, the existence of swollen starch granules/remnants that were able to deform with each other to fill the whole volume of a mold was crucial for developing a strong, true gel; additionally, amylose molecules diffusing out from granules could act as a glue to further enhance the firmness of gel network, such as in pea starch gel. After the granular structure was destroyed, only non-granular HA7 – having linear amylose as the predominant component – could generate a firm and rigid gel, resulting from the re-association and alignment of amylose chains to establish stable junction zones. This study provided fundamental knowledge for using starch of various physical states as a gelling agent to achieve desirable textural attributes of foods and other industrial products.

Interaction between fructan metabolism and plant growth regulators.

The relationship of fructan to plant growth regulators is clearly more complicated than it looks and is likely related to differences between fructan molecules in size and structure as well as localization. Fructans are a complex group of carbohydrates composed mainly of fructose units linked to a sucrose molecule. Fructans are present in plants as heterogeneous mixtures with diverse molecular structures and mass, different polymerization degrees, and linkage types between fructosyl residues. Like sucrose, they are frequently stored in leaves and other organs, acting as carbohydrate reserves. Fructans are synthesized in the cell vacuole by fructosyltransferase enzymes and catabolized by fructan exohydrolase enzymes. Several publications have shown that fructan metabolism varies with the stage of plant development and in response to the environment. Recent studies have shown a correlation between plant growth regulators (PGR), fructan metabolism, and tolerance to drought and cold. PGR are compounds that profoundly influence the growth and differentiation of plant cells, tissues, and organs. They play a fundamental role in regulating plant responses to developmental and environmental signals. In this review, we summarize the most up-to-date knowledge on the metabolism of fructans and their crosstalk with PGR signaling pathways. We identify areas that require more research to complete our understanding of the role of fructans in plants.

MICROBIAL SURFACTANTS: CLASSIFICATIONS, PROPERTIES, RECOVERY, AND APPLICATIONS

Surface-active agents or surfactants are amphiphilic compounds derived naturally or chemically synthesized. Natural surfactants or so-called biosurfactants can be obtained from bacteria, yeasts, and fungi as well as plants. Due to their hydrophilic and hydrophobic molecules, biosurfactants offer the ability to reduce surface or interfacial tension and create microemulsion between aqueous and organic phases. Many studies have suggested biosurfactants as a better substitution to chemical surfactants since they are more environment friendly, biocompatible, and has lower toxicity. This review article is provided to introduce some general information regarding microbial-derived biosurfactants including five main classes of biosurfactants and several distinctive properties that confer them as promising surface-active agents. Due to their diverse molecular structures, biosurfactants have been applied in various applications. Thus, several common biosurfactant recovery methods are discussed and examples of biosurfactant applications in hydrocarbon removal as well as in industrial processing are highlighted.

Sulfamic acid catalyzed grinding: A facile one-pot approach for the synthesis of polysubstituted pyrazoles under green conditions

A competent, rapid and simple grinding procedure for the synthesis of pharmacologically relevant polysubstituted pyrazoles catalyzed by sulfamic acid is reported via multicomponent reaction of substituted arylaldehydes, 4-nitrophenylacetonitrile, hydrazine hydrate, ethyl acetoacetate under solvent-free reaction conditions. In our reported protocol, four different reactants featuring diverse functional groups are assembled in one pot, enabling the synthesis of more diverse molecular structures in a facile manner.

IR spectra of paracetamol

Paracetamol is a very popular medication used to treat pain and fever. IR spectra of paracetamol have been measured for powder crystals. Ab initio calculations of its equilibrium geometry and vibrational spectra were carried out for spectrum interpretation. Differences between the experimental IR spectra of crystalline samples have been analyzed. Variations of molecular structure from the isolated state to molecular crystal were estimated based on the difference between the optimized molecular parameters of free molecules and the experimental bond lengths and angles evaluated for the crystal forms of the title compounds. The role of hydrogen bonds in the structure of molecular crystals of paracetamol is investigated.
 Bangladesh J. Sci. Ind. Res.56(4), 255-262, 2021

Molecular structure modification of ovalbumin through controlled glycosylation with dextran for its emulsibility improvement

Ovalbumin (OVA) is a high nutritious protein, but the poor emulsibility limited its application. The present study glycosylated OVA with dextran (Dex) by controlled wetheating (60–90 °C for 3 h). Temperature was an inductive factor for glycosylation degree (DG and browning intensity), and higher temperature could accelerate the reaction. Variations in molecular structure of OVA were analyzed by SDS-PAGE, FTIR, fluorescence spectroscopy and UV spectroscopy, which verified successes in the generation of glycoconjugate with more flexible structure. Emulsifying activity index (EAI) and emulsion stability index (ESI) for the emulsion of OVA-Dex glycoconjugates were significantly enhanced with the increasing of glycosylation temperature. Moreover, confocal laser scanning results revealed that the emulsion exhibited smaller size and more uniform distribution, and slower transmission profiles were checked by LUMiSizer centrifugal analysis as well, confirming the emulsibility improvement of OVA. Thus, controlled glycosylation reaction is an available method to improve the emulsifying properties of OVA.

Carbon-Based Nanocomposite Smart Sensors for the Rapid Detection of Mycotoxins.

Carbon-based nanomaterials have become the subject of intensive interest because their intriguing physical and chemical properties are different from those of their bulk counterparts, leading to novel applications in smart sensors. Mycotoxins are secondary metabolites with different structures and toxic effects produced by fungi. Mycotoxins have low molecular weights and highly diverse molecular structures, which can induce a spectrum of biological effects in humans and animals even at low concentrations. A tremendous amount of biosensor platforms based on various carbon nanocomposites have been developed for the determination of mycotoxins. Therefore, the contents of this review are based on a balanced combination of our own studies and selected research studies performed by academic groups worldwide. We first address the vital preparation methods of biorecognition unit (antibodies, aptamers, molecularly imprinted polymers)-functionalized carbon-based nanomaterials for sensing mycotoxins. Then, we summarize various types of smart sensors for the detection of mycotoxins. We expect future research on smart sensors to show a significant impact on the detection of mycotoxins in food products.

Short Peptides Make a Big Difference: The Role of Botany-Derived AMPs in Disease Control and Protection of Human Health.

Botany-derived antimicrobial peptides (BAMPs), a class of small, cysteine-rich peptides produced in plants, are an important component of the plant immune system. Both in vivo and in vitro experiments have demonstrated their powerful antimicrobial activity. Besides in plants, BAMPs have cross-kingdom applications in human health, with toxic and/or inhibitory effects against a variety of tumor cells and viruses. With their diverse molecular structures, broad-spectrum antimicrobial activity, multiple mechanisms of action, and low cytotoxicity, BAMPs provide ideal backbones for drug design, and are potential candidates for plant protection and disease treatment. Lots of original research has elucidated the properties and antimicrobial mechanisms of BAMPs, and characterized their surface receptors and in vivo targets in pathogens. In this paper, we review and introduce five kinds of representative BAMPs belonging to the pathogenesis-related protein family, dissect their antifungal, antiviral, and anticancer mechanisms, and forecast their prospects in agriculture and global human health. Through the deeper understanding of BAMPs, we provide novel insights for their applications in broad-spectrum and durable plant disease prevention and control, and an outlook on the use of BAMPs in anticancer and antiviral drug design.

A Multi-modal Approach to Understanding Degradation of Organic Photovoltaic Materials.

State-of-the-art organic photovoltaic (OPV) materials are composed of complex, chemically diverse polymeric and molecular structures that form highly intricate solid-state interactions, collectively yielding exceptional tunability in performance and aesthetics. These properties are especially attractive for semitransparent power-generating windows or shades in living environments, greenhouses, or other architectural integrations. However, before such a future is realized, a broader and deeper understanding of property stability must be acquired. Stability during operating and environmental conditions is critical, namely, material color steadfastness, optoelectronic performance retention, morphological rigidity, and chemical robustness. To date, no single investigation encompasses all four distinct, yet interconnected, metrics. Here, we present a multimodal strategy that captures a dynamic and interconnected evolution of each property during the course of an accelerated photobleaching experiment. We demonstrate this approach across relevant length scales (from molecular to visual macroscale) using X-ray photoelectron spectroscopy, grazing-incidence X-ray scattering, microwave conductivity, and time-dependent photobleaching spectroscopies for two high-performance semitransparent OPV blends-PDPP4T:PC60BM and PDPP4T:IEICO-4F, with comparisons to the stabilities of the individual components. We present direct evidence that specific molecular acceptor (fullerene vs nonfullerene) designs and the resulting donor-acceptor interactions lead to distinctly different mechanistic routes that ultimately arrive at what is termed "OPV degradation." We directly observe a chemical oxidation of the cyano endcaps of the IEICO-4F that coincides with a morphological change and large loss in photoconductivity while the fullerene acceptor-containing blend demonstrates a significantly greater fraction of oxygen uptake but retains 55% of the photoconductivity. This experimental roadmap provides meaningful guidance for future high-throughput, multimodal studies, benchmarking the sensitivity of the different analytical techniques for assessing stability in printable active layers, independent of complete device architectures.

Mini Review of Current Combustion Research Progress of Biodiesel and Model Compounds for Gas Turbine Application

Biodiesel is one of the most promising low-carbon fuels and has been applied in internal combustion engines. In recent years, there have been emerging interests in the application of biodiesel in gas turbines, accompanied by the growing need for carbon reduction in the gas turbine industry. This mini review focuses on the fundamental combustion research of biodiesel and its model compounds, as well as its current application in gas turbines, mainly in the last 15 years. As for fundamental combustion research, selected advances in combustion chemistry and swirl combustion are reviewed. Diversity in molecular structures of biodiesel and its model compounds includes a vast amount of research on fuel molecular structure effects on combustion characteristics, including the effects of the functional group, chain length, and isomeric structure. Swirling flame studies of biodiesel are also reviewed, which focus on the flame shape, flame stability, atomization performance, and pollutant emissions. Combustion performances of biodiesel in aircraft and land-based gas turbine are also highlighted. Furthermore, some prospects of future research of biodiesel combustion with the purpose of gas turbine application are provided.

Spatial and Temporal Distribution of Bacterioplankton Molecular Ecological Networks in the Yuan River under Different Human Activity Intensity.

Bacterioplankton communities play a crucial role in freshwater ecosystem functioning, but it is unknown how co-occurrence networks within these communities respond to human activity disturbances. This represents an important knowledge gap because changes in microbial networks could have implications for their functionality and vulnerability to future disturbances. Here, we compare the spatiotemporal and biogeographical patterns of bacterioplankton molecular ecological networks using high-throughput sequencing of Illumina HiSeq and multivariate statistical analyses from a subtropical river during wet and dry seasons. Results demonstrated that the lower reaches (high human activity intensity) network had less of an average degree (10.568/18.363), especially during the dry season, when compared with the upper reaches (low human activity intensity) network (10.685/37.552) during the wet and dry seasons, respectively. The latter formed more complexity networks with more modularity (0.622/0.556) than the lower reaches (high human activity intensity) network (0.505/0.41) during the wet and dry seasons, respectively. Bacterioplankton molecular ecological network under high human activity intensity became significantly less robust, which is mainly caused by altering of the environmental conditions and keystone species. Human activity altered the composition of modules but preserved their ecological roles in the network and environmental factors (dissolved organic carbon, temperature, arsenic, oxidation–reduction potential and Chao1 index) were the best parameters for explaining the variations in bacterioplankton molecular ecological network structure and modules. Proteobacteria, Actinobacteria and Bacteroidetes were the keystone phylum in shaping the structure and niche differentiations in the network. In addition, the lower reaches (high human activity intensity) reduce the bacterioplankton diversity and ecological niche differentiation, which deterministic processes become more important with increased farmland and constructed land area (especially farmland) with only 35% and 40% of the community variation explained by the neutral community model during the wet season and dry season, respectively. Keystone species in high human activity intensity stress habitats yield intense functional potentials and Bacterioplankton communities harbor keystone taxa in different human activity intensity stress habitats, which may exert their influence on microbiome network composition regardless of abundance. Therefore, human activity plays a crucial role in shaping the structure and function of bacterioplankton molecular ecological networks in subtropical rivers and understanding the mechanisms of this process can provide important information about human–water interaction processes, sustainable uses of freshwater as well as watershed management and conservation.

Anthracene‐Assisted Morphology Optimization in Photoactive Layer for High‐Efficiency Polymer Solar Cells

AbstractCurrently, morphology optimization methods for the fused‐ring nonfullerene acceptor‐based polymer solar cells (PSCs) empirically follow the treatments originally developed in fullerene‐based systems, being unable to meet the diverse molecular structures and strong crystallinity of the nonfullerene acceptors. Herein, a new and universal morphology controlling method is developed by applying volatilizable anthracene as solid additive. The strong crystallinity of anthracene offers the possibility to restrict the over aggregation of fused‐ring nonfullerene acceptor in the process of film formation. During the kinetic process of anthracene removal in the blend under thermal annealing, donor can imbed into the remaining space of anthracene in the acceptor matrix to form well‐developed nanoscale phase separation with bi‐continuous interpenetrating networks. Consequently, the treatment of anthracene additive enables the power conversion efficiency (PCE) of PM6:Y6‐based devices to 17.02%, which is a significant improvement with regard to the PCE of 15.60% for the reference device using conventional treatments. Moreover, this morphology controlling method exhibits general application in various active layer systems to achieve better photovoltaic performance. Particularly, a remarkable PCE of 17.51% is achieved in the ternary PTQ10:Y6:PC71BM‐based PSCs processed by anthracene additive. The morphology optimization strategy established in this work can offer unprecedented opportunities to build state‐of‐the‐art PSCs.

Bipolar Diimide Based Molecule for Nonaqueous Symmetric Redox Flow Battery

Redox flow batteries (RFBs) allow decoupling of power and energy capacity, a unique feature that makes them a promising energy storage technology for large scale applications[1]. In recent years, there has been a massive development in aqueous organic RFBs. However, their commercialization has been hindered by low energy density owing to low solubility of redox active materials and narrow electrochemical stability window of water which limits the cell voltage[2] .Nonaqueous redox flow batteries based on organic redox active material are a regarded as an alternative to aqueous organic RFBs[3] . Apart from enjoying the advantages of organic redox active materials such as low cost, diverse molecular structure and tailorability, nonaqueous RFBs also benefits from using organic supporting electrolytes which provide a wider voltage window (2-5V) facilitating a high energy capacity and low-cost storage system[4, 5] .Herein, a diimide based molecule is designed, chemically modified, analysed and employed as bipolar redox active materials for a total organic symmetric redox flow battery. Cyclic voltammetry studies show three redox couples, two anodic one electron transfer and one cathodic two electrons transfer redox transitions which are electrochemically reversible. The potential difference between the cathodic peak and the inner and outer anodic peaks leads to a promising cell voltage of 1.51V and 2.22V respectively in redox flow battery application. This work suggests an alternative way to design a multielectron redox active materials for symmetric batteries.Figure 1: Cyclic voltammogram of 0.002M diimide based molecule in 0.1M tetrabutylammonium hexafluorophosphate in dimethylformamide recorded on a glassy carbon working electrode with a scan rate of 50 mV/s. Acknowledgement The work described in this paper was fully supported by a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (Project No. T23-601/17-R) References [1] P. Alotto, M. Guarnieri, F. Moro, Renewable and Sustainable Energy Reviews. 29 (2014) 325-335.[2] J. Luo, B. Hu, M. Hu, Y. Zhao, T.L. Liu, ACS Energy Letters. 4 (2019) 2220-2240.[3] S. Shin, S. Yun, S. Moon, Rsc Advances. 3 (2013) 9095-9116.[4] W. Wang, V. Sprenkle, Nature Chemistry. 8 (2016) 204-206.[5] M. Hayyan, F.S. Mjalli, M.A. Hashim, I.M. AlNashef, T.X. Mei, Journal of Industrial and Engineering Chemistry. 19 (2013) 106-112. Figure 1

Extraction of Pectin from Satsuma Mandarin Orange Peels by Combining Pressurized Carbon Dioxide and Deionized Water: a Green Chemistry Method

Pectic oligosaccharides have vital properties that are dependent on their molecular assemblies, such as the degree of esterification (DE) and branched side chains. The molecular structures are affected by the extraction solvents and conditions. In this study, we used pressurized carbon dioxide treatment (CT) as a novel method for pectin extraction from fresh and ripe orange peels and compared the total yield, DE, molecular weight, and monosaccharide compositions of the product obtained with those of products obtained using conventional extraction methods, such as heating with HCl or chelating with sodium hexametaphosphate (SHMP). CT provided a yield of approximately 3.8%, which was less than that of HCl (9.9%/dry weight). However, DE in the CT extract was approximately 94%, which was higher than that of HCl (75%) and SHMP (59%). The molecular weights of pectins in the CT extract appeared to be higher than that of HCl, except at a pressure of 2 MPa. β-Galacturonic acid was the major monosaccharide in pectin extracted by HCl and SHMP, whereas that was decreased in CT extract from fresh oranges. The results showed that extraction with CT contributed to a high DE pectin yield and diverse pectin molecular structures compared to conventional methods, although its application resulted in a lower overall pectin yield. These findings suggest the possibility of manufacturing oligosaccharides with novel properties.

Ultrasonics induced variations in molecular structure and tensile properties of silk fibers in a chemical free environment

AbstractUltrasonics can be used as an alternative energy supply for a green silk wet processing and for enhancement of some chemical/physical properties of bio‐polymers. In this work, ultrasonically treated silk fabric were compared with that of untreated and were investigated for the changes in fiber conformation structure and subsequent tensile property. Experiments were conducted under different time duration in a chemical free environment. Fiber surface energy distribution and transformation of silk secondary structure were analyzed using X‐ray photoelectron spectroscopy (XPS), energy dispersive spectroscopy (EDS), and Fourier transform infrared spectrum (FITR). Results showed that subject to treatment time, a surface oxidation effect and a light transformation of random coil to β‐sheet can be induced from ultrasonic irradiation. Tensile testing showed that under certain treatment time, ultrasonics can lead to silk fibers with a slightly increased strength and reduced extensibility, as a result of the transition of fiber secondary structure.

Ganglioside isomer analysis using ion polarity switching liquid chromatography-tandem mass spectrometry.

Gangliosides are ubiquitously present on cell surface. They are more abundantly expressed in nerve cells and tissues and involved in pathology of various diseases. Diversity of molecular structures in the carbohydrate head group, fatty acyl, and long chain base increases the complexity of analyzing gangliosides. In this study, an ultrahigh-performance liquid chromatography-tandem mass spectrometry method is developed for analysis of the co-eluting ganglioside isomers, which uses ion polarity switching to integrate glycan head isomer identification, ceramide isomer differentiation, and quantification of ganglioside into one analysis. The method is facilitated with an extensive ganglioside target list by combining the various glycan head groups, long chain bases, and the experimentally determined fatty acyls. Correlation between the retention time of ganglioside and its ceramide total carbon number is experimentally validated and used to predict retention time of ganglioside target list for scheduling the final multiple reaction monitoring method. This method was validated according to the FDA guidelines: 96.5% of gangliosides with good accuracy (80-120%), precision (< 15%), and linearity R2 > 0.99. The authenticated gangliosides were quantified from mouse brain by isotope dilution. Overall, 165 gangliosides were quantified using 10mg mouse brain tissue, including 100 isomers of GM1, GM2, GM3, GD1a, GD1b, GD2, GD3, and GT1b.

The liberating force of ultrasound.

Sophisticated drug delivery systems are as essential to modern medicine as drugs themselves. Now, polymer mechanochemistry in sonicated solutions has been used to activate drugs in three different systems. These results offer a promising approach that can be tailored to diverse molecular structures of modern pharmaceuticals.