Molecular Structural Features Research Articles

Seventeen-Armed Star Polystyrenes in Various Molecular Weights: Structural Details and Chain Characteristics.

Star-shaped polymers are very attractive because of their potential application ability in various technological areas due to their unique molecular topology. Thus, information on the molecular structure and chain characteristics of star polymers is essential for gaining insights into their properties and finding better applications. In this study, we report molecular structure details and chain characteristics of 17-armed polystyrenes in various molecular weights: 17-Arm(2k)-PS, 17-Arm(6k)-PS, 17-Arm(10k)-PS, and 17-Arm(20k)-PS. Quantitative X-ray scattering analysis using synchrotron radiation sources was conducted for this series of star polymers in two different solvents (cyclohexane and tetrahydrofuran), providing a comprehensive set of three-dimensional structure parameters, including radial density profiles and chain characteristics. Some of the structural parameters were crosschecked by qualitative scattering analysis and dynamic light scattering. They all were found to have ellipsoidal shapes consisting of a core and a fuzzy shell; such ellipse nature is originated from the dendritic core. In particular, the fraction of the fuzzy shell part enabling to store desired chemicals or agents was confirmed to be exceptionally high in cyclohexane, ranging from 74 to 81%; higher-molecular-weight star polymer gives a larger fraction of the fuzzy shell. The largest fraction (81%) of the fuzzy shell was significantly reduced to 52% in tetrahydrofuran; in contrast, the lowest fraction (19%) of core was increased to 48%. These selective shell contraction and core expansion can be useful as a key mechanism in various applications. Overall, the 17-armed polystyrenes of this study are suitable for applications in various technological fields including smart deliveries of drugs, genes, biomedical imaging agents, and other desired chemicals.

Phosphorus fertilization alters complexity of paddy soil dissolved organic matter

The structural complexity of soil dissolved organic matter (DOM) may reflect soil biogeochemical processes due to its spectral characteristics. However, the features of DOM structural complexity in paddy soil amended with long-term chemical P fertilization are still unclear, which may limit understanding of nutrient-related soil C cycle. We collected soil samples from field experiments receiving application of 0, 30, 60, and 90 kg P ha−1 yr−1 to assess the effect of exogenous P on the complexity of soil DOM structure. Three-dimensional excitation-emission matrix fluorescence analysis and enzymatic activity assay were used to determine the features of soil DOM molecular structure and the associated microbial reactions. The results showed that P input increased the biodegradability of DOM, indicating by the increased lower molecular weight components and decreased humic degree in the DOM. P input also reduced the structural complexity of DOM with blue shifts of fluorescent signals. The fluorescence index and β/α index of DOM increased with increasing P application by 4–5% and 3–11%, respectively, while humification index decreased by 8–13%. The P input increased the abundance of bacteria and fungi by 34–167% and 159–964%, respectively, while 29–54% increments were found for the β-1,4-glucosidase activities. These results implicated that P fertilization accelerated the soil DOM cycle, although the structural complexity of DOM declined, which potentially benefits soil C sequestration in paddy fields and may be a C sequestration mechanism in the P-dependent paddy.

Hg(II) coordination compounds containing tridentate NNO Schiff-base ligand: synthesis, characterization, and crystal structure analysis

Hg(II) coordination complexes containing the tridentate N-(2-methoxyphenyl)-1-(pyridin-2-yl)methanimine ligand were synthesized by using template synthesis approach and characterized using spectroscopic techniques and single crystal X-ray crystallography. The molecular structure and supramolecular features of these compounds were investigated using geometrical, Hirshfeld surface analyses, and theoretical calculations. The supramolecular architecture of these coordination complexes is governed by a combination of π–π, C–H⋯π, and C–H⋯X–M hydrogen bonding interactions. This study may provide further insight into the understanding of the coordination chemistry of Hg(II) containing multidentate Schiff-base ligand and the role of weak non-covalent interactions in the solid-state structure of coordination compounds.

Occurrence forms and molecular structural characteristics of the organic nitrogen in lignite

The occurrence forms of organic nitrogen in Xianfeng lignite (XL), Xiaolongtan lignite (XLT) and Shengli lignite (SL) as well as their extraction residues were characterized by X-ray photoelectron spectroscopy (XPS). The results show that the content distributions of organic nitrogen in the three extraction residues are different, but all are mainly dominated by pyrrolic nitrogen. The NaOH-catalyzed supercritical methanolysis of lignite extraction residues at 300°C was then investigated, which indicates that the yields of petroleum ether soluble portions from supercritical methanolysis of extraction residues derived from XL, XLT and SL are 46.0%, 43.8%, and 47.6%, respectively. The characterization of nitrogen-containing compounds (NCCs) in petroleum ether soluble portions by Fourier transform ion cyclotron resonance mass spectrometry (FTICR/MS) indicates that NCCs are mainly composed of N1, N1O1-N1O5, N2, N2O1-N2O4, N3O2 and N5O2-N5O4 class species. The molecular structural characteristics of NCCs were speculated according to the distributions of double bond equivalent values and carbon numbers, which shows that most of NCCs contain oxygen-functional groups like hydroxyl and carboxyl groups, and the nitrogen atoms are mainly present in aromatic structures (mainly 1–3 aromatic rings) in the forms of pyrrolic, pyridinic and amino groups. The cleavage of C-O bridged bonds in lignite is an important pathway for producing NCCs.

Yeni Koronavirüsün (Covid-19) Moleküler Yapısı ve Genomik Karakterizasyonu

SARS-CoV-2, transmitted from person to person and associated with the outbreak of atypical pneumonia, first emerged in Wuhan, China. Although bats, SARS-CoV and MERS-CoV are the primary reservoirs for COVID-19, it turns out that SARS-CoV may have been transmitted from the civet in China, MERS-CoV from camels in the Middle East, and COVID-19 from the bat to humans via the pangolin (scaly anteater). SARS-CoV, MERS-CoV and SARS-CoV-2 are coronaviruses belonging to the Coronaviridae family and Betacoronavirus genus, which cause epidemiological outbreaks, are enveloped viruses with approximately 32 Kb long positive sense, ssRNA, and play a role in the pathogenesis of proinflammatory responses with high mortality rates associated with infection. The 2019-nCoV genome has 89% nucleotide identity with bat SARS-like CoVZXC21 and 82% with human SARS-CoV. ACE2 is the receptor of this severe acute respiratory syndrome coronavirus. The aim of this review is to reveal the molecular structure and genetic features of the SARS-CoV-2 virus and the clinical effects of the disease, which causes COVID-19 acute respiratory disease, and to compare it to SARS and MERS. Clarifying the specific molecular details of COVID-19 will guide researchers to the discovery of its treatment. Thus, the development of the molecular genetic methods for COVID-19 will increase our control measures against the virus in the future.

Predicting Binding from Screening Assays with Transformer Network Embeddings.

Cheminformatics aims to assist in chemistry applications that depend on molecular interactions, structural characteristics, and functional properties. The arrival of deep learning and the abundance of easily accessible chemical data from repositories like PubChem have enabled advancements in computer-aided drug discovery. Virtual high-throughput screening (vHTS) is one such technique that integrates chemical domain knowledge to perform in silico biomolecular simulations, but prediction of binding affinity is restricted due to limited availability of ground-truth binding assay results. Here, text representations of 83 000 000 molecules are leveraged to perform single-target binding affinity prediction directly on the outcome of screening assays. The embedding of an end-to-end transformer neural network, trained to encode the structural characteristics of a molecule via a text-based translation task, is repurposed through transfer learning to classify binding affinity to single targets with few known binding compounds. We quantify the observed increase in AUC on binding prediction tasks between classifiers trained on the translation embedding versus those using an untrained embedding. Visualization of the embedding space reveals organization of structural and functional properties that aid binding prediction. The pretrained transformer, data, and associated software to extract embeddings are made publicly available at https://github.com/mpcrlab/MolecularTransformerEmbeddings.

Synthesis, characterisation and biocompatibility of graphene–L-methionine nanomaterial

The article presents data on synthesis, identification, computer modelling and biocompatibility of graphene oxide functionalised with L-methionine (GFM). In the framework of our research, graphene oxide synthesised using Hammers' method was modified through amidation reaction. The characterisation of the compound was performed using various physicochemical techniques, such as X-ray diffraction, X-ray photoelectron spectroscopy, infrared, Raman spectroscopy, thermogravimetric analysis, scanning electron microscopy, and high-resolution transmission electron microscopy. Investigation of biocompatibility included experiments on erythrocytes haemolysis, platelet aggregation, photodynamic and antiradical activity studies, binding to human serum albumin, geno- and cytotoxicity. Moreover, using density functional theory and molecular dynamics approaches, structural and dynamic characteristics of a GFM–water binary system were obtained.

Molecular structure features and lactic acid fermentation behaviors of water- and alkali-soluble polysaccharides from Dendrobium officinale.

One water-soluble polysaccharide (WDOP) and three alkali-soluble polysaccharides (ADOP1, ADOP2 and ADOP3) were successfully obtained from Dendrobium officinale. Molecular structure of the polysaccharides was analyzed, and in vitro lactic acid fermentation of the polysaccharides by lactic acid bacteria (LAB) and bifidobacteria was performed. All the polysaccharides exerted proliferative effect on the LAB and bifidobacteria. ADOP2 was the most effective one, followed by WDOP. This could be attributed to their molecular structure features, such as a high level of total sugar, uronic acid and reducing sugar, an abundance of glucose and mannose, and a low and middle weight-average molecular weight. ADOP2 and WDOP produced more short-chain fatty acids (SCFAs) than ADOP1 and ADOP3 did during lactic acid fermentation. Propionic and acetic acids were the main SCFAs produced. These findings are useful for understanding the structure-activity relationship of D. officinale polysaccharides in lactic acid fermentation, and for developing new functional foods and beverages from D. officinale.

Disruption of the CD Loop by Enzymatic Cleavage Promotes the Formation of Toxic Transthyretin Oligomers through a Common Transthyretin Misfolding Pathway.

Amyloid formation of full-length TTR involves dissociation of the native tetramers into misfolded monomers that self-assemble into amyloid. In addition to the full-length TTR, C-terminal fragments including residues 49-127 were also observed in vivo, implying the presence of additional misfolding pathways. It was previously proposed that a proteolytic cleavage might lead to the formation of the C-terminal fragment TTR amyloid. Here, we report mechanistic studies of misfolding and aggregation of a TTR variant (G53A) in the absence and presence of a serine protease. A proteolytic cleavage of G53A in the CD loop (K48 and T49) with agitation promoted TTR misfolding and aggregation, suggesting that the proteolytic cleavage may lead to the aggregation of the C-terminal fragment (residues 49-127). To gain more detailed insights into TTR misfolding promoted by proteolytic cleavage, we investigated structural changes in G53A TTR in the presence and absence of trypsin. Our combined biophysical analyses revealed that the proteolytic cleavage accelerated the formation of spherical small oligomers, which exhibited cytotoxic activities. However, the truncated TTR appeared to maintain native-like structures, rather than the C-terminal fragment (residues 49-127) being released and unfolded from the native state. In addition, our solid-state nuclear magnetic resonance and Fourier transform infrared structural studies showed that the two aggregates derived from the full-length and cleaved TTR exhibited nearly identical molecular structural features, suggesting that the proteolytic cleavage in the CD loop destabilizes the native tetrameric structure and accelerates oligomer formation through a common TTR misfolding and aggregation mechanism rather than through a distinct molecular mechanism.

Metal Complexes of π-Expanded Ligand (7): Syntheses, Structures and Properties of Pt(II) Complexes Containing the Isomeric 1- and 2-Alkyliminomethyl Pyrene Ligands

A [O,N] bidentate π-expanded ligand system, (E)-1-(n-octylimino)methylpyren-2-ol (2), was newly synthesized via a six-step synthesis from pyrene. The ligand 2 reacts with [PtCl2(PhCN)2] in chlorobenzene and the presence of a base at reflux for 2 h under the formation of (2(Pt)) complex with a yield of 70%. The molecular structure of (2(Pt)), studied by common spectroscopic methods and X-ray diffraction, shows a square planar geometry with a trans-configuration of the ligands. The molecular structure, absorption spectra, electrochemical properties, and phosphorescence characteristics of the (2(Pt)) complex are discussed, emphasizing the comparison with those of the previously reported Pt complex (1(Pt)) containing the isomeric ligands of 2, (E)-2-(n-octylimino)methylpyren-1-ol. The DFT calculations of the two Pt complexes are carried out and exhibit a clear explanation of the relationship between their physico-chemical characteristics.

4094 Structural Determinants of Immunogenicity for Peptide-Based Immunotherapy

OBJECTIVES/GOALS: Neoantigen vaccine immunotherapies have shown promise in clinical trials, but identifying which peptides to include in a vaccine remains a challenge. We aim to establish that molecular structural features can help predict which neoantigens to target to achieve tumor regression. METHODS/STUDY POPULATION: Proteins were prepared by recombinant expression in E. coli followed by in vitro refolding. Correctly folded proteins were purified by chromatography. Affinities of protein-protein interactions were measured by surface plasmon resonance (SPR) and thermal stabilities of proteins were determined by differential scanning fluorimetry. All experiments were performed at least in triplicate. Protein crystals were obtained by hanging drop vapor diffusion. The protein crystal structures were solved by molecular replacement and underwent several rounds of automated refinement. Molecular dynamics simulations were performed using the AMBER molecular dynamics package. RESULTS/ANTICIPATED RESULTS: A T cell receptor (TCR) expressed by tumor-infiltrating T cells exhibited a 20-fold stronger binding affinity to the neoantigen peptide compared to the self-peptide. X-ray crystal structures of the peptides with the major histocompatibility complex (MHC) protein demonstrated that a non-mutated residue in the peptide samples different positions with the mutation. The difference in conformations of the non-mutated residue was supported by molecular dynamics simulations. Crystal structures of the TCR engaging both peptide/MHCs suggested that the conformation favored by the mutant peptide was crucial for TCR binding. The TCR bound the neoantigen/MHC with faster binding kinetics. DISCUSSION/SIGNIFICANCE OF IMPACT: Our results suggest that the mutation impacts the conformation of another residue in the peptide, and this alteration allows for more favorable T cell receptor binding to the neoantigen. This highlights the potential of non-mutated residues in contributing to neoantigen recognition.

Structure characteristics and association behavior of coal and petroleum C7-asphaltenes

The structural characteristics and differences of coal tar and petroleum C7-asphaltenes were studied, such as chemical composition, functional groups and molecular structure, using nuclear magnetic resonance (NMR), small angle X-ray scattering (SAXS), X-ray photoelectron spectroscopy (XPS), improved B-L method and other methods. Furthermore, the association behavior and aggregation size of two different types of asphaltenes as well as the hydrogen bonds and acidic-basic interaction were analyzed by asphaltenes solubility parameters in polar solvents. The experiment results showed that the coal tar asphaltenes (CT-asp) was mainly composed of less aromatic rings with short alkyl branched chains and possessed a high aromaticity degree. The higher content oxygen heteroatoms of CT-asp were mostly presented as aromatic ether bonds and phenolic hydroxyl groups. The aromatic nucleus size and the average relative molecular weight of petroleum asphaltenes (M-asp) were larger than that of CT-asp. The M-asp consisted primarily of more aromatic rings with long alkyl branched chains and possessed a low aromaticity degree. The association and aggregation degree between CT-asp and M-asp was associated with the amount of substance ratio (nCT-asp/nM-asp) and their molecular structure characteristics. The association force of two types mainly was the hydrogen bonds and the acidic-basic interaction from heteroatomic functional groups.

Characterization of Ionic Liquid Lignins Isolated from Spruce Wood with 1-Butyl-3-methylimidazolium Acetate and Methyl Sulfate and Their Binary Mixtures with DMSO.

Ionic liquids (ILs) based on 1-butyl-3-methylimidazolium (bmim) cation have proved to be promising solvents for the fractionation of plant biomass with the production of cellulose and lignin. This study deals with the characterization of lignins isolated from coniferous (spruce) wood using [bmim]OAc and [bmim]MeSO4 ionic liquids and their binary mixtures with DMSO (80:20). Molecular weight distributions, functional composition, and structural features of IL lignins were studied by size-exclusion chromatography, NMR spectroscopy (1D and 2D) and atmospheric pressure photoionization high-resolution mass spectrometry. It was shown that the interaction of ILs with lignin leads to significant chemical changes in the biopolymer; a decrease in the degree of polymerization and in the content of free phenolic hydroxyl groups due to alkylation, the disappearance (in the case of [bmim]OAc) of carbonyl groups and a significant destruction of β-O-4 bonds. The chemical reactions between lignin and 1-butyl-3-methylidazolium cation with covalent binding of ionic liquids or products of their decomposition is evidenced by the presence of a large number of nitrogen-containing oligomers in IL lignins.

Quantitative structure-activity relationship models for predicting singlet oxygen reaction rate constants of dissociating organic compounds

As singlet oxygen (1O2) is ubiquitous in the environment, 1O2-involved oxidation may play an important role in the transformation and fate of organic pollutants. Accordingly, the reaction rate constants (k1O2) of organic compounds with 1O2 are important to determine the environmental fate and persistence assessment of organic pollutants. However, currently there are limited k1O2 data available, especially for organic chemicals with different charged (deprotonated/protonated) forms. Herein three quantitative structure-activity relationship (QSAR) models (one comprehensive model and two models for neutral and deprotonated molecules) were created for predicting aqueous k1O2 values for diversely dissociating molecules. The models include larger datasets (180 chemicals) and have wider applicability domain than previous ones. Molecular structural characteristics (only half-wave potential is present in both models) determining the 1O2 reaction rate of neutral and deprotonated molecules vary greatly. The comparison results of predicting k1O2 values of organic compounds at certain pH conditions show that the combination of the QSAR models for neutral and deprotonated molecules has advantages over the comprehensive QSAR model. This work is the first study to predict k1O2 for a wide variety of neutral and deprotonated molecules and provides an important tool for assessing the fate of organic pollutants in aquatic environments.

Synthesis and structure of pyrido[1,2-a]quinazoline condensed derivatives

Present manuscript describes the synthesis and molecular structure features of novel condensed pyrido[1,2-a]quinazolines. The above-mentioned compounds were synthesized via condensation of 2-[azolyl-(аzinyl-)]anilines with 5-oxohexanoic acid. The tandem condensation intermediates were isolated and cyclized under various conditions. The structures of synthesized compounds were confirmed by LC-MS and NMR-spectroscopy. The existence of the substituted pyrido[1,2-a][1,2,4]triazolo[1,5-c]quinazolines molecules as superposition of two resonance structures was detected by the X-Ray analysis.

Overview of Asphaltene Nanostructures and Thermodynamic Applications

Previously, asphaltene science had been hindered by many significant uncertainties regarding molecular weight, molecular structure, and nanocolloidal characteristics in laboratory solvents and crud...

Two-Step Solvent-Free Synthesis of Poly(hydroxybutyrate)-Based Photocurable Resin with Potential Application in Stereolithography.

A bio-based polymeric ink for stereolithography developed through a two-step solvent-free process is herein proposed. Specifically, low-molecular-weight poly(hydroxybutyrate) (PHB)-diol oligomers are prepared via molten transesterification of bacterial PHB with 1,4-butanediol. Transesterification conditions such as diol concentration, catalyst amount, and reaction time are studied for optimizing the final oligomers' molecular weight and structural features. In the second step, the oligomeric hydroxyl terminals are converted into methacrylate moieties through a solvent-free end-capping reaction and diluted in propylene carbonate in order to obtain a photo-polymerizable ink with suitable viscosity. The ink is UV-cured, and the obtained material properties are investigated by FT-IR and differential scanning calorimetry measurements. The proposed method provides a valuable and environmentally friendly alternative to currently available synthetic routes, overcoming their typical disadvantages related to the used solvents and harsh conditions. Moreover, it opens up a sustainable route for converting polyesters into functionalized oligomeric derivatives, which can potentially find application in 3D printing of customized biomedical devices.

Study of the solvation process of some pyrazole derivatives in three different solvents by solution calorimetry and IR spectroscopy: Unravelling solute-solvent interactions

The study of the relationship between intermolecular interactions present in the solvation process and the magnitude of thermodynamic properties is extended from imidazole to pyrazole derivatives. The enthalpies of solution of pyrazole, 3,5-dimethylpyrazole and 3,4,5-trimethylpyrazole were calorimetrically determined in the solvents water, methanol and acetonitrile. The enthalpy of solution values for the three compounds in the three solvents are endothermic and spontaneous with an increase in entropy. As in the case with imidazole derivatives, the formation of a solution of pyrazole derivatives creates liquids that are more structured thermodynamically. The enthalpy of sublimation for 3,4,5-trimethylpyrazole, which is not available in the literature, was determined by the Knudsen effusion method. The combination of these thermodynamic properties has allowed the corresponding enthalpies of solvation to be obtained for the three pyrazole derivatives in the three selected solvents. With the use of the Pierotti equations and the enthalpies of solvation, the enthalpies of cavity formation were calculated along with the corresponding solute-solvent enthalpies of interaction. The infrared spectra and molecular volumes, as estimated through the electronic density, were used to obtain molecular insights into the solvation sensible sites within the studied solute molecules. The discussion of the solvation process and enthalpies of interaction of the pyrazole derivatives is based on the molecular structural features of solutes, specific intermolecular interactions and protic or aprotic nature of the solvents. The use of any empirical parameters in the discussion of the results was avoided.

Effect of gamma irradiation on industrial-grade nitrile butadiene rubber

Effect of gamma irradiation on molecular weight distribution and structural characteristics of unsaturated nitrile butadiene rubber (NBR) NBR-8 (copolymer containing 8% acrylonitrile) was studied by sol-gel analysis combined with size exclusion chromatography (SEC) and IR spectroscopy. This approach was shown to give a good understanding of radiation-induced cross-linking and following processes in cross-linked polymers.

Structural, pasting and thermal properties of common buckwheat (Fagopyrum esculentum Moench) starches affected by molecular structure

Common buckwheat starch (CBS) has extensive using value in the human diet. In this study, the molecular structure and physicochemical properties of CBS isolated from five cultivars collected from three regions of China were studied. Variations in molecular structure, crystalline structure, complexity, water solubility (WS), swelling power (SP), pasting properties, and thermal characteristics were recorded among the starches. The CBS had both similarities and differences in its properties by comparison with maize starch (MS) and potato starch (PS). The average molecular weight (MW) and amylopectin average chain length (ACL) of CBS ranged from 3.86 × 107 g/mol to 4.68 × 107 g/mol and from 21.29% to 22.68%, respectively. CBS and MS were divided into one subgroup and showed typical A diffraction patterns, while PS was divided into two subgroups and exhibited a typical B polymorphic pattern. The WS and SP of all the starches significantly increased with increasing temperature and had great variation at 70 °C and 90 °C. Pearson's correlation analysis showed that the molecular structure of starches greatly affected the physicochemical properties. This study revealed that the physicochemical properties of CBS could be affected by the molecular structures.