Small Molecular Groups Research Articles

Click Chemistry in Detecting Protein Modification.

Click chemistry, also known as "link chemistry," is an important molecular connection method that can achieve simple and efficient connections between specific small molecular groups at the molecular level. Click chemistry offers several advantages, including high efficiency, good selectivity, mild conditions, and few side reactions. These features make it a valuable tool for in-depth analysis of various protein posttranslational modifications (PTMs) caused by changes in cell metabolism during viral infection. This chapter considers the palmitoylation, carbonylation, and alkylation of STING and presents detailed information and experimental procedures for measuring PTMs using click chemistry.

Synergistic Effect of Small Molecular Organic Matter and Functional Groups in Coal on Methane Adsorption.

Functional groups and small-molecule organic matter are two key parts of coal. To explore the microscopic mechanism underlying the synergistic effect of both parts on methane adsorption, the oxygen-containing (-OH, -COOH, and -C=O) and nitrogen-containing (-NH2) functional groups and two common small molecular organic matter methylbenzene and tetrahydrofuran-2-alcohol in coal are selected. The quantum chemical meta-GGA functional method is used to optimize all structures. The electrostatic potential analyses, weak interaction analyses, and theory of atoms in molecules have been used to delve further into the nature of this synergistic effect. Our results show that functional groups inhibit methane adsorption by coal molecules, and the inhibition effect is enhanced in the presence of methylbenzene. Interestingly, the synergistic effects between functional groups and small molecular organic matter are changed from inhibition to promotion after introducing tetrahydrofuran-2-alcohol, wherein -COOH has the best synergistic effect. This work not only offers a theoretical foundation for exploring the synergistic effect of small molecular organic matter and functional groups on methane adsorption by coal molecules but also lays a foundation for further research on gas prevention and extraction.

Searching for carriers of the diffuse interstellar bands across disciplines, using Natural Language Processing

The explosion of scientific publications overloads researchers with information. This is even more dramatic for interdisciplinary studies, where several fields need to be explored. A tool to help researchers overcome this is Natural Language Processing (NLP): a machine-learning (ML) technique that allows scientists to automatically synthesize information from many articles. As a practical example, we have used NLP to conduct an interdisciplinary search for compounds that could be carriers for Diffuse Interstellar Bands (DIBs), a long-standing open question in astrophysics. We have trained a NLP model on a corpus of 1.5 million cross-domain articles in open access, and fine-tuned this model with a corpus of astrophysical publications about DIBs. Our analysis points us toward several molecules, studied primarily in biology, having transitions at the wavelengths of several DIBs and composed of abundant interstellar atoms. Several of these molecules contain chromophores, small molecular groups responsible for the molecule's colour, could be promising candidate carriers. Identifying viable carriers demonstrates the value of using NLP to tackle open scientific questions, in an interdisciplinary manner.

Novel 1,3,4-oxadiazole sulfonate/carboxylate flavonoid derivatives: synthesis and biological activity.

With the long-term use of traditional bactericides and antiviral agents, drug resistance has become increasingly prominent, resulting in impaired crop growth and yields. Based on this, the introduction of small molecular active groups into natural products has become the direction of research for green pesticides. In this study, novel 1,3,4-oxadiazole sulfonate/carboxylate flavonoid derivatives were explored. Among them, D4 exhibited good inhibitory effects on plant bacteria. It is worth mentioning that D4 (15 μg ml-1 ) exhibited an excellent median effective concentration (EC50 ) value against Xanthomonas oryzae pv. oryzae (Xoo), which was better than bismerthiazol (73 μg ml-1 ) and thiodiazole copper (100 μg ml-1 ). The EC50 for D4 was much lower than the two positive controls (bismerthiazol, thiodiazole copper), making D4 more potent in this assay of bacterial growth inhibition. In addition, mechanism research using scanning electron microscopy revealed that D4 could cause deformation or rupture of the cell membranes of Xoo and Pseudomonas syringae pv. actinidiae. Moreover, D4 exhibited the best EC50 for in vivo curative (132 μg ml-1 ) and protective (101 μg ml-1 ) activities against tobacco mosaic virus, which were more effective than ningnanmycin. Microscale thermophoresis data suggested that D4 [dissociation constant(Kd ) = 0.038 ± 0.011 μmol L-1 ] exhibited a stronger binding capacity than the control agent ningnanmycin (Kd = 4.707 ± 2.176 μmol L-1 ). The biological activity data and mode of action demonstrated that D4 had the best antibacterial and antiviral effects. Compound D4 discovered in the current work may be a very promising agricultural drug. © 2022 Society of Chemical Industry.

Comprehensive investigation of the mechanisms for pyrolyzing macromolecular networks in Hecaogou subbituminous coal by comparing the ethanolysis and flash pyrolysis

The organic macromolecular networks (MMNs) from Hecaogou subbituminous coal (HSBC) were investigated by multiple technical strategies, including SEM, 1H and 13C NMR, FTIR, XPS, TG/DTG, and flash pyrolysis (FP) technology. The pyrolysis mechanisms of MMNs were effectively investigated to release organic volatile species between ethanolyzed (E) inextractable portion (IEPE) and FP of IEP (IEPFP) at molecular level. In detail, solid-state 13C NMR analysis shows that carbon skeleton of IEP mainly consists of aliphatic (59.6%) and aromatic carbons (39.3%). XPS analysis shows that the >C–OH groups, pyrrolic, and sulfonic sulfurs in IEP surface are the most abundant O-, N-, and S-containing species. FTIR analysis proves that the weak- and medium >Cal-X (X denotes Cal<, H, O-, N<, and S-) in IEP could be cleaved during ethanolysis. Based on the destructive analysis with TG/DTG, the structure of MMNs in IEP features dissociating small molecular groups with different types >Cal-X bridge bonds, which facilitates the release of organic volatile species and then prevents the thermal condensation during pyrolysis process. Additionally, the relative content (RC) in IEPE of various organic species are as follows: chain alkanes (CAs, 18.5%), alkenes (0.9%), arenes (11.9%), and oxygen-containing organic compounds (OCOCs, 58.4%), while the RC of CAs (46.8%), alkenes (17.5%), arenes (16.8%), and OCOCs (13.8%) in IEPFP. Comprehensive investigation and detailed analysis the distribution of organic species further prove that the active hydrogen (H‧) cleave the >Cal-X of MMNs at different positions during the pyrolysis process to obtain more CAs, alkenes, alkanols, and phenols at molecular level.

Study on the molecular structure evolution of long-term-operation XLPE cable insulation materials

Crosslinked polyethylene (XLPE) insulation is widely used in power systems because of its excellent properties. During long-term operation, the aging of insulating materials will lead to cable failure and threaten the safe operation of the power system. The molecular structure evolution of XLPE cable insulation materials was studied by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), differential scanning calorimetry (DSC) and thermogravimetric (TG) methods. The results show that the crystallinity and melting temperature of 0 year sample are the highest, which are 24% and 105.52 °C, respectively. The carbonyl index is small, and the proportion of TG in the first stage is small. After 15 and 30 years of operation, the crystallinity of the cable decreased by 16.7% and 25.0% respectively, the carbonyl index increased first and then slightly decreased, the melting temperature decreased first and then slightly increased, and the proportion of TG in the first stage increased. The results show that the microstructure of the 0 year old sample is relatively complete, and it has good thermal stability and oxidation resistance. After a long period of operation, the crystal region of the sample is destroyed, and the thermal-oxygen reaction takes place, resulting in thermal-oxygen cracking of macromolecules, generating more volatile small molecular groups, and reducing the insulation performance of the cable.

Probing Ligand Effects on the Ultrafast Dynamics of Copper Complexes via Midinfrared Pump-Probe and 2DIR Spectroscopies.

The effects of ligand structural variation on the ultrafast dynamics of a series of copper coordination complexes were investigated using polarization-dependent mid-IR pump-probe spectroscopy and two-dimensional infrared (2DIR) spectroscopy. The series consists of three copper complexes [(R3P3tren)CuIIN3]BAr4F (1PR3, R3P3tren = tris[2-(phosphiniminato)ethyl]amine, BAr4F = tetrakis(pentafluorophenyl)borate) where the number of methyl and phenyl groups in the PR3 ligand are systematically varied across the series (PR3 = PMe3, PMe2Ph, PMePh2). The asymmetric stretching mode of azide in the 1PR3 series is used as a vibrational probe of the small-molecule binding site. The results of the pump-probe measurements indicate that the vibrational energy of azide dissipates through intramolecular pathways and that the bulkier phenyl groups lead to an increase in the spatial restriction of the diffusive reorientation of bound azide. From 2DIR experiments, we characterize the spectral diffusion of the azide group and find that an increase in the number of phenyl groups maps to a broader inhomogeneous frequency distribution (Δ2). This indicates that an increase in the steric bulk of the secondary coordination sphere acts to create more distinct configurations in the local environment that are accessible to the azide group. This work demonstrates how ligand structural variation affects the ultrafast dynamics of a small molecular group bound to the metal center, which could provide insight into the structure-function relationship of the copper coordination complexes and transition-metal coordination complexes in general.

Application Analysis of 124I-PPMN for Enhanced Retention in Tumors of Prostate Cancer Xenograft Mice.

BackgroundIn recent years, nuclear medicine imaging and therapy for prostate cancer have radically changed through the introduction of radiolabeled prostate-specific membrane antigen (PSMA)-binding peptides. However, these small molecular probes have some inherent limitations, including high nephrotoxicity and short circulation time, which limits their utility in biological systems.Methods and ResultsIn this study, organic melanin nanoparticles were used to directly label the long half-life radionuclide 124I (t1/2=100.8 h), and PSMA small molecular groups were efficiently bonded on the surface of nanoparticles to construct the PSMA-targeted long-retention nanoprobe 124I-PPMN, which has the potential to increase tumor uptake and prolong residence time. The results showed that the nanoprobe could substantially aggregate in the tumors of prostate cancer xenograft mice and was visible for more than 72 h. Positron Emission Computed Tomography (PET) imaging showed that the nanoprobe could be used for precise imaging of prostate cancer with high expression of PSMA. In addition, organic melanin nanoparticles labeled with an elemental radionuclide achieved a stable, metal-free structure. Cell experiments and mouse toxicity experiments indicated that the nanoprobe has high safety.ConclusionThe new nanoprobe constructed in this study has high specificity and biocompatibility. In the future, combined with the multifunctional potential of melanin nanoparticles, this nanoprobe is expected to be used in the integrated theranostics of prostate cancer.

Remdesivir interactions with sulphobutylether-β-cyclodextrins: A case study using selected substitution patterns

Modified cyclodextrins (CDs) consist of a distribution of different structures with different number and location of the substituted groups. Among the most important applications of these molecules is their use as an enabling excipient in pharmaceutical formulations to provide the necessary solubility, stability and bioavailability for a drug to be effectively used. The most typical interaction mechanism of small molecular groups with CDs is the formation of host–guest inclusion complexes. The thermodynamic affinity constant between CDs and drugs should not be too strong, since then the biological activity could be negated by the formation of the complex. In the opposite scenario, if the affinity constant is too weak, the complex is barely formed and the amount of CD required in the formulation may become too great. Thus, a balance between the affinity of the CD and the drug is necessary for an optimal formulation. Additionally in the case of modified CDs and specific drug complexes there are further questions concerning the effect that the locations and number of substitutions plays in complexation. In the present work, this question is explored by using sulphobutylether-β-cyclodextrin and remdesivir, the only antiviral medication currently approved by the United States Food and Drug Administration for treating COVID-19, as a case study. This paper presents results from an orthogonal study using isothermal titration calorimetry measurements and biased molecular dynamics simulations that provide complementary information. Isothermal titration calorimetry delves into the global impact of the species distribution while molecular dynamics simulations deals with specific chemical structures. The goal is to provide useful information to optimize pharmaceutical formulations based on modified CDs, specifically in the case of remdesivir, used to treat SARS-CoV-2 infection, although the main conclusions could be extended to the interaction of other drugs with modified cyclodextrins.

Study on covalent coupling process and flow characteristics of antibody on the surface of immunoassay microfluidic chip

The immune response system of immunoassay microfluidic chips is a dynamic reaction process that continuously sends reactants to the surface of a solid carrier. Signal acquisition results from the heterogeneous immune reactions and reactant transport. Antibody immobilization is the most important part of heterogeneous immune reactions, and reactant transport is reflected in the form of fluid velocity. Here, we reported several surface modification processes on polystyrene substrates that are employed to study the relationship between the antibody immobilization and flow behavior in heterogeneous immune response processes. The antibody was immobilized using covalent grafting. Based on the mechanism of sandwich enzyme linked immunosorbent assay, a fluorescence quantitative detection method was used to evaluate the immune response process. The effects of different surface modification processes on immune response and flow behavior were studied. We identified an optimal flow velocity in the dynamic immune response system in the microfluidic chip. The immune response signal was the strongest when the average flow velocity was approximately 0.2 mm/s in the procalcitonin detection system. Compared with the amino and aldehyde group substrates, the epoxy group substrate has the highest antibody immobilization efficiency; compared with the surface modified by small molecular groups, the introduction of Poly-L-Lysine can increase the amount of antibody immobilization.

STUDY ON MAGNETIZATION TREATMENT AND CUTTING PERFORMANCE OF A NEW-TYPE OF TRIETHANOLAMINE BORATE CUTTING FLUID

The composition of water-based cutting fluid and emulsion is different, and it has not been reported whether the magnetization treatment will affect the performance of water-based cutting fluid. In this study, a newly developed triethanolamine borate water-based cutting fluid is used as the research object to study the magnetization treatment technology and the law of its influence on cutting performance systematically. The cutting fluid magnetization experimental system was set up based on the principle of magnetization and the influence of magnetization parameters (magnetic field strength, magnetization duration) on the results of magnetization was further studied. The experimental results are measured by force measuring instrument, temperature measuring instrument, roughness measuring instrument and scanning electron microscope, and the parameters such as milling force, milling temperature, surface roughness, cutting specific energy, friction coefficient and workpiece surface morphology are comprehensively analyzed through data processing; the performance of cutting fluid before and after magnetization is also compared. The test results show that the magnetization effect is best when the magnetic field strength is 10000GS and the magnetization time is 40 minutes. The mechanism of magnetization treatment is to change the macromolecular group into a small molecular group, and the disordered array of molecules becomes ordered.

Activation of Humic Acid in Lignite Using Molybdate-Phosphorus Hierarchical Hollow Nanosphere Catalyst Oxidation: Molecular Characterization and Rice Seed Germination-Promoting Performances.

Although solid-phase activation of lignite using a nanocatalyst has great potential in producing low-cost and sustainable humic acid, the large-scale application of this technology still faces challenges because of the high price and toxicity of the nanocatalyst. Additionally, the specific molecular components of humic acid in activated lignite remain unknown. In this work, a multifunctional molybdate-phosphorus hierarchical hollow nanosphere (Mo-P-HH) catalyst was successfully manufactured by a simple way followed by phosphorization. In comparison with a commercial Pd/C catalyst, the multifunctional Mo-P-HH catalyst was more effective in producing water-soluble humic acid with small molecular functional groups from lignite via solid-phase activation. Moreover, Fourier transform ion cyclotron resonance mass spectrometry revealed the molecular compositions of humic acid in activated lignite. Compared with that from raw lignite, the humic acid after Mo-P-HH activation had less aromatic structure but higher content of lipids, proteins, amino sugar, and carbohydrates. In addition, the activated humic acid simulated seed germination and seedling growth. Therefore, this study provided a high-performance hierarchical hollow nanocatalyst for activation of humic acid and also offered the theoretical basis for the application of humic acid in agriculture.

Research progress in protein post-translational modification in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignant tumors, which is prone to tumor recurrence and metastasis. At present, surgery combined with radiotherapy and chemotherapy is the conventional modality for HNSCC patients, but for patients who have tumor relapse or metastasis, the treatment outcome is not ideal and the prognosis is pretty poor. Thus, to deepen the understanding of tumor mechanism will be very crucial. Post-translational modification (PTM) refer to covalent binding of small chemical molecular groups on the amino acid side chain of proteins, which is an important way of protein function regulation as well as a research hotspot of epigenetics. In recent years, it has been found that the occurrence of tumor is often accompanied by the abnormality of PTM. The abnormality plays an important role in the development of tumor and can be used as a target of tumor diagnosis and treatment. Many types of protein PTM involve in the development of HNSCC. This paper reviews the relationship between HNSCC and several major protein PTM types, including acetylation, methylation, glycosylation, in order to provide clues for the clinicians in diagnosis and treatment of HNSCC.

Protein Post-translational Modifications in Head and Neck Cancer.

Head and neck cancer (HNC) is one of the most common malignant tumors worldwide, and is prone to tumor recurrence and metastasis. At present, surgery combined with radiotherapy and chemotherapy is still the conventional treatment modality for patients with HNC. However, for patients with relapse or metastasis of HNC, the treatment outcome is not ideal, and the prognosis is poor. Thus, it is crucial to deepen the understand of tumor mechanisms. Post-translational modifications (PTMs) refer to covalent binding of small chemical molecular groups to amino-acid side-chain of proteins. Post-translational modification is an important regulator of protein function, and as such, a current research hotspot of epigenetics. In recent years, it has been found that tumor occurrence is often accompanied by the abnormality of PTMs. Indeed, the abnormality play an important role in tumor development, and can be used as a target for tumor diagnosis and treatment. To date, several types of protein PTMs involved in the development of HNC have been reported. This paper reviews the relationship between HNC and several major protein PTMs, including acetylation, methylation, and glycosylation, in order to provide clues for the future application about PTMs in diagnosis and treatment of HNC.

Nanoscaled Characteristics of Recovered Asphalt Binders from Weathered Asphalt Mixtures

Abstract The nanoscaled properties including morphology and mechanics of recovered asphalt binders from open-graded friction course (OGFC) asphalt mixtures weathered in a laboratory were measured by atomic force microscopy. In addition, specific functional groups and molecular size distributions of the recovered binders were tested by Fourier infrared spectroscopy and gel permeation chromatography (GPC), respectively. The OGFC mixtures were weathered in an accelerated weathering machine for various durations of 0, 1,000, 2,000, and 3,000 h. The results showed that (1) as the weathering degree increased, the root mean square of morphology increased, and both the number of the “bee-structures” and the adhesion decreased; (2) as the weathering degree increased, the carbonyl and sulfoxide indexes increased, whereas the butadiene-based index decreased; and (3) the large molecular size groups from GPC tests increased, whereas the small molecular size groups decreased, as the weathering time increased. The changes of the molecular size groups had fairly good linear correlations with the weathering time.

Multifunctional Slow-Release Fertilizer Prepared from Lignite Activated by a 3D-Molybdate-Sulfur Hierarchical Hollow Nanosphere Catalyst

To improve fertilizer use efficiency, reduce irrigation requirement, and minimize negative environmental impact, a novel large-grained-activated-lignite-slow-release fertilizer (LAF) with good water retention was developed by mechanical extrusion of activated lignite and conventional fertilizer. A 3D molybdate-sulfur hierarchical hollow nanosphere (3D-MoS2–HN) catalyst was successfully fabricated via a simple route, and the lignite was activated by 3D-MoS2–HN to increase its water-soluble humic acid content and nutrient adsorption ability. After activation, the amounts of small molecular active groups and water-soluble humic acid of activated lignite were significantly higher than those of raw lignite. The activation also increased adsorption ability of the activated lignite for nutrients. LAF prepared from the activated lignite had a preferable slow-release property and good water-holding capacity in soil. Moreover, a pot trial further demonstrated that LAF effectively improved the growth of an apple pla...

Theoretical Structural Stability of Small Molecules Water

It has been found that small molecules of water are fully consistent with our requirements for healthy drinking through the study of various types of water microstructure. And we also found that long-term consumption of small molecules of water can improve some lifestyle-related diseases. The current structure of small molecules of water drawing people most acceptable, The most stable structure of a water mass having n=2 to 5, which is more than two water molecules linked by a hydrogen bond, is ring-shaped and its basic building block is a water molecule containing a proton donor and a proton acceptor. It has been predicted almost like there are several low energy continuum energy of two or three dimensional when n=6, This is a cage-type three-dimensional structure of small molecules between groups and macromolecules turning point. Based on the principle of primary principle, this paper analyzes the structural stability of small molecular group water from the electronic level, and gives the optimal small molecular structure model.

Value-Added Humic Acid Derived from Lignite Using Novel Solid-Phase Activation Process with Pd/CeO2 Nanocatalyst: A Physiochemical Study

Soil, air, and water pollution caused by lignite is considered a serious environmental problem. Activation methods thus have been developed to extract humic acid from lignite to support the agricultural production as the soil amendment or fertilizer synergist. The traditional activation methods of humic acid from lignite, however, are not environmentally friendly. As the first study, this work developed a novel solid-phase activation method with a Pd/CeO2 nanocatalyst for lignite-derived humic acid. This study analyzed the morphology and structures of the as-synthesized Pd/CeO2 nanocatalyst with various characterization tools. The mechanisms of the Pd/CeO2 nanocatalyst for lignite activation were determined. The Pd/CeO2 catalyst effectively promoted the production of water-soluble humic acids from lignite via KOH solid-phase activation at room temperature. It increased the amount of small molecular active groups and the corresponding small molecules of humic acid. The existence of a strong synergistic eff...

Preparation of Conjugated Polymer Grafted with H2O2-Sensitive Prodrug for Cell Imaging and Tumor Cell Killing.

In this work, a new conjugated polymer poly(fluorene-co-phenylene) derivative containing pendent quaternized chlormethine (PFP-Chl) was synthesized by covalent linking small molecular prodrug groups onto conjugated polymer side chains. H2O2-sensitive prodrug with an eight-member-cyclic boronate ester structure could suffer from H2O2-triggered nitrogen mustard release and further DNA cross-linking and alkylation. PFP-Chl combines therapeutic characteristic with excellent optical property of conjugated polymers. It is found that PFP-Chl could enter into cells by endocytosis to simultaneously exhibit abilities of fluorescent imaging and tumor cell inhibition.

Gaussian process model for extrapolation of scattering observables for complex molecules: From benzene to benzonitrile.

We consider a problem of extrapolating the collision properties of a large polyatomic molecule A-H to make predictions of the dynamical properties for another molecule related to A-H by the substitution of the H atom with a small molecular group X, without explicitly computing the potential energy surface for A-X. We assume that the effect of the -H →-X substitution is embodied in a multidimensional function with unknown parameters characterizing the change of the potential energy surface. We propose to apply the Gaussian Process model to determine the dependence of the dynamical observables on the unknown parameters. This can be used to produce an interval of the observable values which corresponds to physical variations of the potential parameters. We show that the Gaussian Process model combined with classical trajectory calculations can be used to obtain the dependence of the cross sections for collisions of C6H5CN with He on the unknown parameters describing the interaction of the He atom with the CN fragment of the molecule. The unknown parameters are then varied within physically reasonable ranges to produce a prediction uncertainty of the cross sections. The results are normalized to the cross sections for He - C6H6 collisions obtained from quantum scattering calculations in order to provide a prediction interval of the thermally averaged cross sections for collisions of C6H5CN with He.