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Background: This study aimed to engineer and optimise a dysbiotic biofilm model to develop in vitro root caries for investigating microbial modulation strategies. The model involved growing complex biofilms from a saliva inoculum collected from four volunteers using two strategies. In the first strategy ("pre-treatment strategy"), bovine root slabs were used, and two natural compounds were incorporated at time 0 of the 10-day biofilm experiment, which included sucrose cycles mimicking the cariogenic environment. In the second strategy ("post-treatment strategy"), mature biofilms were grown in a modified Calgary biofilm device coated with collagen and hydroxyapatite for 7 days and then were exposed to the same natural compounds. The metatranscriptome of each biofilm was then determined and analysed. Collagenase activity was examined, and the biofilms and dentine were imaged using confocal and scanning electron microscopy (SEM). Mineral loss and lesion formation were confirmed through micro-computed tomography (μ-CT). Results: The pH confirmed the cariogenic condition. In the metatranscriptome, we achieved a biofilm compositional complexity, showing a great diversity of the metabolically active microbiome in both pre- and post-treatment strategies, including reads mapped to microorganisms other than bacteria, such as archaea and viruses. Carbohydrate esterases had increased expression in the post-treated biofilms and in samples without sugar cycles, while glucosyltransferases were highly expressed in the presence of sucrose cycles. Enrichment for functions related to nitrogen compound metabolism and organic cyclic component metabolism in groups without sucrose compared to the sucrose-treated group. Pre-treatment of the roots with cranberry reduced microbial viability and gelatinase (but not collagenase) activity (p < 0.05). SEM images showed the complexity of biofilms was maintained, with a thick extracellular polysaccharides layer. Conclusions: This root caries model was optimized to produce complex cariogenic biofilms and root caries-like lesions, and could be used to test microbial modulation in vitro. Pre-treatments before biofilm development and cariogenic challenges were more effective than post-treatments. The clinical significance lies in the potential to apply the findings to develop varnish products for post-professional tooth prophylaxis, aiming at implementing a strategy for dysbiosis reversal in translational research. 2cRgxuoMbmgt6TZPkgExXQ Video Abstract [ABSTRACT FROM AUTHOR]

Rapeseed (Brassica napus L.) holds significant commercial value as one of the leading oil crops, with its agronomic features and oil quality being crucial determinants. In this investigation, 73,226 single nucleotide polymorphisms (SNPs) across 95 rapeseed mutant lines induced by gamma rays, alongside the original cultivar ('Tamra'), using genotyping-by-sequencing (GBS) analysis were examined. This study encompassed gene ontology (GO) analysis and a genomewide association study (GWAS), thereby concentrating on agronomic traits (e.g., plant height, ear length, thousand-seed weight, and seed yield) and oil traits (including fatty acid composition and crude fat content). The GO analysis unveiled a multitude of genes with SNP variations associated with cellular processes, intracellular anatomical structures, and organic cyclic compound binding. Through GWAS, we detected 320 significant SNPs linked to both agronomic (104 SNPs) and oil traits (216 SNPs). Notably, two novel candidate genes, Bna.A05p02350D (SFGH) and Bna.C02p22490D (MDN1), are implicated in thousand-seed weight regulation. Additionally, Bna.C03p14350D (EXO70) and Bna.A09p05630D (PI4Kα1) emerged as novel candidate genes associated with erucic acid and crude fat content, respectively. These findings carry implications for identifying superior genotypes for the development of new cultivars. Association studies offer a cost-effective means of screening mutants and selecting elite rapeseed breeding lines, thereby enhancing the commercial viability of this pivotal oil crop. [ABSTRACT FROM AUTHOR]

Introduction: Heavy ion beam is a novel approach for crop mutagenesis with the advantage of high energy transfer line density and low repair effect after injury, however, little investigation on the biological effect on plant was performed. 50 Gy irradiation significantly stimulated the growth of Arabidopsis seedlings, as indicated byanincreasein root andbiomass, while200Gy irradiationsignificantly inhibitedthe growth of seedlings, causing a visible decrease in plant growth. Methods: The Arabidopsis seeds were irradiated by 12C6+. Monte Carlo simulations were used to calculate the damage to seeds and particle trajectories by ion implantation. The seed epidermis received SEM detection and changes in its organic composition were detected using FTIR. Evidence of ROS and antioxidant systems were analyzed. RNA-seq and qPCR were used to detect changes in seedling transcript levels. Results and discussion: MonteCarlo simulations revealed thathigh-doseirradiation causes various damage. Evidence of ROS and antioxidant systems implies that the emergence of phenotypes in plant cells may be associated with oxidative stress. Transcriptomic analysis of the seedlings demonstrated that 170DEGswere present in the 50 Gy and 200 Gy groups and GO enrichment indicated that they were mainly associated with stress resistance and cellwall homeostasis. FurtherGOenrichment of DEGsuniqueto 50Gyand200Gyrevealed 5850Gy-exclusiveDEGswere enriched in response to oxidative stress and jasmonic acid entries, while 435 200 Gy-exclusive DEGs were enriched in relation to oxidative stress, organic cyclic compounds, and salicylic acid. This investigation advancesour insight into thebiologicaleffects of heavy ion irradiation and the underlying mechanisms. [ABSTRACT FROM AUTHOR]

Organic cycles play an important role in chemistry, pharmacology and material science for their unique properties. Construction of organic cycles from thioalkynes attracted increasing attention due to the facile access of thioalkynes. 2H‐Azirines were synthesized successfully from thioalkynyl oxime ethers. Cyclobutanes were formed through chiral titanium catalyzed cycloaddition of thioalkynes. Cyclopentenes were afforded by annulation of thioalkynes. Thioalkynes could be also applied to synthesize thiophenes, oxazoles, benzo[b]thiophenes, 2H‐chromenes, 2‐phenylbenzothiazoles, diazacyclobutene, etc. In this review, construction of organic cycles from thioalkynes were highlighted. Firstly, the property and application of organic cyclic compounds were simply introduced. After presenting the general methods to access organic cycles, applications of thioalkynes as synthons to prepare organic cycles were classified and presented in detail. Based on different kinds of organic cycles obtained from thioalkynes, organic reactions for synthesis of three‐, four‐, five‐, six‐membered as well as fused cycles would be summarized and the plausible reaction mechanisms could be presented if available. [ABSTRACT FROM AUTHOR]

Auto-grading, as an instruction tool, could reduce teachers’ workload, provide students with instant feedback and support highly personalized learning. Therefore, this topic attracts considerable attentions from researchers recently. To realize the automatic grading of handwritten chemistry assignments, the problem of chemical notations recognition should be solved first. The recent handwritten chemical notations recognition solutions belonging to the end-to-end trainable category suffered from the problem of lacking the accurate alignment information between the input and output. They serve the aim of reading notations into electrical devices to better prepare relevant e-documents instead of auto-grading handwritten assignments. To tackle this limitation to enable the auto-grading of handwritten chemistry assignments at a fine-grained level. In this work, we propose a component-detectionbased approach for recognizing off-line handwritten Organic Cyclic Compound Structure Formulas (OCCSFs). Specifically, we define different components of OCCSFs as objects (including graphical objects and text objects), and adopt the deep learning detector to detect them. Then, regarding the detected text objects, we introduce an improved attention-based encoder-decoder model for text recognition. Finally, with these detection results and the geometric relationships of detected objects, this article designs a holistic algorithm for interpreting the spatial structure of handwritten OCCSFs. The proposed method is evaluated on a self-collected data set consisting of 3000 samples and achieves promising results. [ABSTRACT FROM AUTHOR]

The mycotoxin citrinin, which can contaminate food, is a major global concern. Citrinin is regarded as an inevitable pollutant in foods and feed since fungi are widely present in the environment. To identify contentious toxicity and lessen its severity by understanding the targets of citrinin in the human body and the impacted biosynthetic pathways, we analyzed the production of citrinin from Aspergillus flavus and Penicillium notatum and used a thorough bioinformatics analysis to characterize the toxicity and predict genes and protein targets for it. The predicted median fatal dosage (LD50) for citrinin was 105 mg/kg weight, and it belonged to toxicity class 3 (toxic if swallowed). Citrinin was found to be well absorbed by human intestinal epithelium and was a Pgp nonsubstrate (permeability glycoprotein), which means that once it is absorbed, it cannot be pumped out, hence leading to bioconcentration or biomagnification in the human body. The main targets of toxicity were casp3, TNF, IL10, IL1B, BAG3, CCNB1, CCNE1, and CDC25A, and the biological pathways implicated were signal transduction involved in DNA damage checkpoints, cellular and chemical responses to oxidative stress, DNA damage response signal transduction by P53, stress-activated protein kinase signaling cascade, netrin–UNC5B signaling, PTEN gene regulation, and immune response. Citrinin was linked to neutrophilia, squamous cell carcinoma, Fanconi anemia, leukemia, hepatoblastoma, and fatty liver diseases. The transcription factors E2F1, HSF1, SIRT1, RELA, NFKB, JUN, and MYC were found to be responsible. When data mining was performed on citrinin targets, the top five functional descriptions were a cell's response to an organic cyclic compound, the netrin–UNC5B signaling pathway, lipids and atherosclerosis, thyroid cancer, and controlling the transcription of the PTEN gene. [ABSTRACT FROM AUTHOR]

Asymmetric cycloaddition/annulation reactions have contributed greatly to the synthesis of a variety of novel cyclic compounds used in organic synthesis, natural product synthesis, material science, and chemical biology. Thus, chiral phosphoric acid‐catalyzed asymmetric cycloaddition reactions have received the attention of the synthetic community to design new vital asymmetric reactions and synthesize complex molecules for the past two decades. Although several review articles on organocatalyzed asymmetric cycloaddition reactions can be found in the literature, there has been no specific review on CPA‐catalyzed asymmetric cycloaddition/annulation reactions. Herein, the most recent research progress on chiral phosphoric acid catalyzed asymmetric [3+2], [4+2], [2+2], [3+3], [4+3], [4+1] annulation, and 1,3‐dipolar cycloadditions have been compiled and analyzed to demonstrate the importance of chiral phosphoric acid catalysis in asymmetric cycloaddition or annulation reactions. [ABSTRACT FROM AUTHOR]

Protoporphyrins are organic compounds with cyclic structure that are synthesised by a wide variety of organisms. In humans, these compounds are detected in blood and urine, with significantly higher levels in blood. Their potential as biomarkers of anemia and other diseases is currently being investigated, as their levels change according to the biochemical processes associated with the disease. The most widely used biomarker of anemia is serum ferritin, but it is unreliable in patients with inflammatory bowel disease (IBD) because its levels can be altered by acute inflammation and/or infections. There is therefore a need to look for new markers to help diagnose anemia in IBD patients. This work develops and validates a method for the determination of three protoporphyrins in human urine: protoporphyrin IX (PPIX), protoporphyrin IX complex with Zn (ZnPPIX) and protoporphyrin IX complex with Fe (II) (FePPIX), the latter also known as heme. The aim is to evaluate their potential as biomarkers of anemic disease in patients diagnosed with IBD. The proposed analytical method is based on high performance liquid chromatography (HPLC) with dual detection based on photodiode array (PDA) and fluorescence (FD). Quantification of the analytes at very low concentrations is possible due to the efficient preconcentration provided by dispersive liquid-liquid microextraction (DLLME) and the sensitivity of the detection systems. The method was validated by evaluating linearity (25–1000 ng mL−1), matrix effect, sensitivity (limits of quantification were between 5 and 11 ng mL−1), selectivity, accuracy, carry-over, dilution integrity, stability and precision (< 12.1 %). Finally, statistical analyses applied to the sample quantification results showed these three markers, together with five clinical markers, were significantly different between anemic and non-anemic IBD patients. [Display omitted] • Heme, PPIX and ZnPPIX are determined in human urine by HPLC with dual detection. • DLLME with chloroform efficiently preconcentrates protoporphyrins. • Anemic and non-anemic IBD patients show different protoporphyrins urinary levels. • Protoporphyrins are promising biomarkers to diagnose anemia in IBD patients. [ABSTRACT FROM AUTHOR]

This paper presents a model, which we have designed to get insight into the development of electro-induced instability of a thin toluene emulsion film in contact with the saline aqueous phase. Molecular dynamics (MD) simulations demonstrate the role of charge accumulation in the toluene-film rupture induced by a DC electric field. Two ensembles--NVT and NPT--are used to determine the critical value of the external field at which the film ruptures, the charge distribution and capacitance of the thin film, number densities, and the film structure. The rupture mechanism as seen from this model is the following: in both NVT and NPT ensembles, condenser plates, where the charge density is maximal, are situated at the very border between the bulk aqueous (water) phase and the mixed layer. No ion penetration is observed within the toluene core, thus leaving all the distribution of charges within the mixed zone and the bulk phase that could be attributed to the formation of hydration shells. When the critical electric field is reached within a certain time after the field application, electric discharge occurs indicating the beginning of the rupturing process. The MD simulations indicate that the NPT ensemble predicts a value of the critical field that is closer to the experimental finding. [ABSTRACT FROM AUTHOR]

OBJECTIVE: To explore the potential active ingredients and possible mechanism of Renshen Guben oral liquid in the treatment of breast cancer by network pharmacology and molecular docking technology . METHODS: The active ingredients and potential targets in Renshen Guben oral liquid were obtained by Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, BATMAN-TCM and other databases. Related disease targets of breast cancer were obtained from databases such as Human Mendelian Inheritance Omnibus and DigSee. The intersection targets of potential targets and related disease targets were imported into the STRING website for protein - protein interaction analysis, and the obtained data were imported into Cytoscape 3. 8. 2 software for module analysis by using the MCODE plug-in. And the representative targets were screened for gene ontology functional enrichment analysis (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis by Metascape and other software. Cytoscape 3. 8. 2 software was used to construct "compound-target" " traditional Chinese medicine compound-target-pathway" and other networks. The core target was extracted for molecular docking with corresponding compounds. RESULTS: 448 common targets of Renshen Guben oral liquid and breast cancer were screened. The key targets included SRC, STAT3, HSP90AA1, PIK3Rl, Aktl, EGFR and ESRl. GO and KEGG enrichment analysis showed that the treatment of breast cancer by Renshen Guben oral liquid was mainly related to biological processes such as cellular response to nitrogen compound, cellular response to organic cyclic compound and MAPK cascade. Molecular docking results showed that the minimum binding energy between the core target and the corresponding compounds was <-20 929. 26 J/mol. CONCLUSIONS: The mechanism of Renshen Guben oral liquid in the treatment of breast cancer may be closely related to neuroactive ligand-receptor interaction, SRC, HSP90AA1, PIK3Rl, Aktl, EGFR and ESRl. [ABSTRACT FROM AUTHOR]

Objective: We reported the differentially methylated genes in patients with subarachnoid hemorrhage (SAH) using bioinformatics analyses to explore the biological characteristics of the development of delayed cerebral ischemia (DCI). Methods: DNA methylation profiles obtained from 40 SAH patients from an epigenome-wide association study were analyzed. Functional enrichment analysis, protein-protein interaction (PPI) network, and module analyses were carried out. Results: A total of 13 patients (32.5%) experienced DCI during the follow-up. In total, we categorized the genes into the two groups of hypermethylation (n=910) and hypomethylation (n=870). The hypermethylated genes referred to biological processes of organic cyclic compound biosynthesis, nucleobase-containing compound biosynthesis, heterocycle biosynthesis, aromatic compound biosynthesis and cellular nitrogen compound biosynthesis. The hypomethylated genes referred to biological processes of carbohydrate metabolism, the regulation of cell size, and the detection of a stimulus, and molecular functions of amylase activity, and hydrolase activity. Based on PPI network and module analysis, three hypermethylation modules were mainly associated with antigen-processing, Golgi-to-ER retrograde transport, and G alpha (i) signaling events, and two hypomethylation modules were associated with post-translational protein phosphorylation and the regulation of natural killer cell chemotaxis. VHL, KIF3A, KIFAP3, RACGAP1, and OPRM1 were identified as hub genes for hypermethylation, and ALB and IL5 as hub genes for hypomethylation. Conclusion: This study provided novel insights into DCI pathogenesis following SAH. Differently methylated hub genes can be useful biomarkers for the accurate DCI diagnosis. [ABSTRACT FROM AUTHOR]

Background. Young patients with type 2 diabetes mellitus (DM) and acute myocardial infarction (AMI) have high long-term all-cause and cardiovascular mortality rates. We aimed to investigate the differentially expressed genes (DEGs) that might be potential targets for DM patients with AMI. Methods. Gene datasets GSE775, GSE19322, and GSE97494 were meta-analyzed to obtain DEGs of the left ventricle myocardium in infarcted mice. Gene datasets including GSE3313, GSE10617, and GSE136948 were meta-analyzed to identify DEGs in diabetes mice. A Venn diagram was used to obtain the overlapping DEGs. KEGG and GO pathway analyses were performed, and hub genes were obtained. Pivotal miRNAs were predicted and validated using the miRNA dataset in GSE114695. To investigate the cardiac function of the screened genes, a MI mouse model was constructed; echocardiogram, qPCR, and ELISA of hub genes were performed; ELISA of hub genes in human blood samples was also utilized. Results. A total of 67 DEGs were identified, which may be potential biomarkers for patients with DM and AMI. GO and KEGG pathway analyses were performed, which were mainly enriched in response to organic cyclic compound and PI3K-Akt signaling pathway. The expression of PIK3R1 and SPNB2 increased in the MI group and was negatively correlated to left ventricular ejection fraction (LVEF), whereas that of CRYAB decreased and was positively correlated to LVEF. Patients with high CRYAB expression demonstrated a short hospital stay and the area under the curves of the three protein levels before and after treatment were 0.964, 0.982, and 0.918, suggesting that PIK3R1, SPNB2, and CRYAB may be diagnostic and prognostic biomarkers for the diabetes patients with AMI. Conclusion. The screened hub genes, PIK3R1, SPNB2, and CRYAB, were validated as credible molecular biomarkers and may provide a novel therapy for diabetic cardiac diseases with increased proteotoxic stress. [ABSTRACT FROM AUTHOR]

Background: Tetraploid cotton plants serve as prime natural fiber source for the textile industry. Although various omics studies have revealed molecular basis for fiber development, a better understanding of transcriptional regulation mechanism regulating lint fiber initiation is necessary to meet global natural fiber demand. Results: Here, we aimed to perform transcriptome sequencing to identify DEGs (differentially expressed genes) in ovules of the cotton variety Xu142 and its fibreless mutant Xu142fl during early lint fiber initiation period. Totally, 5516 DEGs including 1840 upregulated and 3676 downregulated were identified. GO enrichment analysis revealed that the downregulated DEGs were mainly associated with biological processes such as transcription related biosynthesis and metabolism, organic cyclic compound biosynthesis and metabolism, photosynthesis, and plant cell wall organization, with molecular functions involving transcription related binding, organic cyclic compound binding, and dioxygenase activity, while the upregulated DEGs were associated with DNA replication and phospholipid biosynthetic related processes. Among the 490 DEGs annotated as transcription factor genes, 86.5% were downregulated in the mutant including the Malvaceae-specific MMLs, expression patterns of which were confirmed during the central period of lint fiber initiation. Investigation of the 16 genes enriched in the cell wall organization revealed that 15 were EXPA coding genes. Conclusions: Overall, our data indicate that lint fiber initiation is a complicated process involving cooperation of multiple transcription factor families, which might ultimately lead to the reorganization of the cell wall and terminated cell division of the differentiating fiber initials. [ABSTRACT FROM AUTHOR]

Saturated heterocycles are found in numerous therapeutics and bioactive natural products and are abundant in many medicinal and agrochemical compound libraries. To access new chemical space and function, many methods for functionalization on the periphery of these structures have been developed. Comparatively fewer methods are known for restructuring their core framework. Herein, we describe a visible lightÐmediated ring contraction of a-acylated saturated heterocycles. This unconventional transformation is orthogonal to traditional ring contractions, challenging the paradigm for diversification of heterocycles including piperidine, morpholine, thiane, tetrahydropyran, and tetrahydroisoquinoline derivatives. The success of this Norrish type II variant rests on reactivity differences between photoreactive ketone groups in specific chemical environments. This strategy was applied to late-stage remodeling of pharmaceutical derivatives, peptides, and sugars. [ABSTRACT FROM AUTHOR]

Educational games can be used as an effective means of transferring knowledge in a fun way to complement education and training. The aim of the study was to develop a game and get students' opinions on the game that can be played in Organic Chemistry courses in order to teach the names of commonly used organic compounds with cyclic and aromatic structure. The game, which is called OrgChemGame can be played with at least 3 individuals, one of whom is the referee. The game set includes 48 pcs of 3 cm diameter styrofoam balls with structural formulas of organic compounds identified. OrgChemGame was played by 20 students taking the organic chemistry lecture and studying in the 2nd grade of the Science Education program at a state university in Turkey. The opinions of the students about the game were taken with the opinion form prepared by the researchers. As a result of the research, it was determined that the sizes and colors of the balls and cubes used in the game were appropriate, and the texts used were readable. As a result, OrgChemGame has been designed as an educational game having a purpose and rules. It aims to acquire target behaviors and appropriate to the level of the students, allowing the students to learn with fun, and having sufficient duration and comprehensibility. [ABSTRACT FROM AUTHOR]

While the vast number of DNA and RNA viruses participate in biogeochemical cycles in natural systems, little is known about virome in river ecosystems. Here, we analyzed the DNA viral composition and its metabolic potential in the Yangtze River, including freshwater (FW) and freshwater sediments (FWS). A total of 1237 river-derived virus contigs (RVCs) were obtained following de novo assembly from 62 metagenomics. We found that the viral diversity is significantly positively correlated longitudinally. Moreover, FW exhibited a greater viral variety and significantly different composition than FWS. The viral co-occurrence network suggested that positive correlations predominate between RVCs. Lastly, 1657 viral functions were predicted by gene ontology. Notably, 96 of 150 RVCs with higher weights identified by random-forest classier were more abundant in FW, which most engage organic cyclic compound metabolic processes and hydrolase activity. Together, this study highlights the previously unrecognized viruses and the importance of their distributions and functions in major river systems. • A total of 1237 river-derived virus contigs (RVCs) were obtained from 62 metagenomics. • DNA viral diversity significant correlated with longitude and spatial distances. • Compared to sediments, freshwater has more complicated viral co-occurrence and diversity. • 1.28% of viral genes could be classified as functions including macromolecular recycling. [ABSTRACT FROM AUTHOR]

Metal-mediated [2+2+2] cycloadditions of unsaturated molecules to cyclic and polycyclic organic compounds are a versatile synthetic route affording good yields and selectivity under mild conditions. In the last two decades, in silico investigations have unveiled important details about the mechanism and the energetics of the whole catalytic cycle. Particularly, a number of computational studies address the topic of half-sandwich catalysts which, due to their structural fluxionality, have been widely employed, since the 1980s. In these organometallic species, the metal is coordinated to an aromatic ring, typically the ubiquitous cyclopentadienyl anion, C5 H5– (Cp) or to the Cp moiety of a larger polycyclic aromatic ligand (Cp′). During the catalytic process, the metal continuously 'slips' on the ring, changing its hapticity. This phenomenon of metal slippage and its implications for the catalyst's performance are discussed in this work, referring to the most important computational mechanistic studies reported in literature for Rh(I) half-metallocenes, with the purpose of providing hints for a rational design of this class of compounds. 1 Introduction 2 Mechanism of Metal-Catalyzed Acetylene [2+2+2] Cycloaddition to Benzene and the Problem of the Indenyl Effect 2.1 Acetylene-Acetonitrile [2+2+2] Co-cycloaddition to 2-Methylpyridine: Evidence of the Indenyl Effect 2.2 Heteroaromatic Catalysts and the Evidence of a Reverse Indenyl Effect 2.3 Booth's Mechanistic Hypothesis and the Evidence of the Indenyl Effect 3 Structure–Reactivity Correlation: The Slippage-Span Model 4 Conclusions and Perspectives [ABSTRACT FROM AUTHOR]

A circular compound is a chemical compound that consists of a series of atoms that are periodically bound together. The majority of cyclic compounds are organic compounds, but there is a small percentage of inorganic cyclic compounds, including: sulfur, silicon, which forms silicon, and phosphorous, which forms phosphorous compounds. Some types of heterocyclic compounds are aromatic, such as pyridine. The concept of a polycyclic compound is used when one molecule consists of more than one ring, such as a compound naphthalene, and the concept of a massive cyclic compound is used when it contains more than ten atoms. The object in this study is preparation of chalcone-heterocyclic compounds (Five, Six, Seven)-membered ring by cyclization step via reaction with amine derivatives like (semicarbazide, thisemicarbazide, hydrazine, thio amide derivative,....). All new synthesized compounds identified through types of instrumental methods like (FT.IR, H.NMR, Mass)-spectrophotometric, other chemical investigations, with evaluation of prepared compounds as antimicrobial compounds. [ABSTRACT FROM AUTHOR]

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Photocyclization, irrespective of whether multiple steps (e.g. Norrish–Yang cyclization) or a single concerted step (e.g. 6π photocyclization) are involved, is an intramolecular photochemical process resulting in the formation of one new single bond to afford a ring system. In particular, visible‐light‐induced photocyclization offers a green and sustainable route to organic cyclic compounds that are difficult to access by thermal reactions. Herein, we describe the ambient light‐induced intramolecular photocyclization of a series of donor/acceptor chromophores 1 d–3 d containing two types of photoresponsive motifs, namely an electron‐deficient BF2‐chelated ketone fused with an electron‐rich thiophene, and probe the solution‐phase and solid‐state photochromic performance of these compounds. The results reveal that simple variation of R substituents on the diaryl moiety allows one to control the intramolecular photocyclization mechanism with high photochemical selectivity, e.g. under ambient light, methyl‐substituted 1 d and 2 d undergo reversible 6π photocyclization, whereas ethyl‐substituted 3 d exclusively undergoes irreversible Norrish–Yang photocyclization. Single‐crystal X‐ray analysis of Norrish–Yang cyclization products reveals the formation of four pairs of conformational enantiomers differing in the dihedral angle between benzothiophene and the BF2 core, namely (±)N‐3 d@68°, (±)N‐3 d@‐77°, (±)N‐3 d@‐78°, and (±)N‐3 d@‐102°. The UV/Vis absorption spectra of 1 d–3 d cover a broad visible‐light region (380–572 nm), while DFT and TD‐DFT calculations reveal that absorption in this region is dominated by the charge‐transfer (CT) transition from the thiophene‐centered HOMO to the LUMO of the electron‐deficient π‐conjugated BF2‐chelated unit and the n→π* and π→π* transitions within the latter unit. The spatial separation of the HOMO and LUMO of these dyes promotes triplet‐state generation and self‐photosensitizes intramolecular photocyclization in the visible‐light region. Three‐dimensional time‐resolved and steady‐state emission spectra of 3 d show that the Norrish–Yang photocyclization takes place within milliseconds with excellent conversion efficiency (96 %). [ABSTRACT FROM AUTHOR]

Iron, an essential element for all organisms, acts as a cofactor of enzymes in bacterial degradation of recalcitrant aromatic compounds. The bacterial family, Sphingomonadaceae comprises various degraders of recalcitrant aromatic compounds; however, little is known about their iron acquisition system. Here, we investigated the iron acquisition system in a model bacterium capable of degrading lignin-derived aromatics, Sphingobium sp. strain SYK-6. Analyses of SYK-6 mutants revealed that FiuA (SLG_34550), a TonB-dependent receptor (TBDR), was the major outer membrane iron transporter. Three other TBDRs encoded by SLG_04340, SLG_04380, and SLG_10860 also participated in iron uptake, and tonB2 (SLG_34540), one of the six tonB comprising the Ton complex which enables TBDR-mediated transport was critical for iron uptake. The ferrous iron transporter FeoB (SLG_36840) played an important role in iron uptake across the inner membrane. The promoter activities of most of the iron uptake genes were induced under iron-limited conditions, and their regulation is controlled by SLG_29410 encoding the ferric uptake regulator, Fur. Although feoB, among all the iron uptake genes identified is highly conserved in Sphingomonad strains, the outer membrane transporters seem to be diversified. Elucidation of the iron acquisition system promises better understanding of the bacterial degradation mechanisms of aromatic compounds. [ABSTRACT FROM AUTHOR]

In recent decades, organocatalysis by N-heterocyclic carbenes (NHCs) has emerged as a versatile and powerful method in organic synthesis. As a result of the power of NHC organocatalysis to produce cyclic compounds, polysubstituted benzenes, which are among the most important cyclic compounds in organic chemistry, can be synthesized efficiently and selectively. This article briefly summarizes the history of NHC organocatalysis, including recent developments in benzene-formation methods, and highlights our recent work in atroposelective arene formation by carbene-catalyzed formal [4+2] cyclo-additions. We expect that more NHC-catalyzed methods for the synthesis of asymmetric arenes will be developed in the near future, providing shortcuts to syntheses of sophisticated chiral functional molecules with polysubstituted benzene nuclei. [ABSTRACT FROM AUTHOR]

A study of the electrodeposition of silver from 2 different types of electrolytes; (1) neutral pyrophosphatecyanide electrolyte and (2) alkaline high concentrated cyanide electrolyte in the presence of a variety of additives such as 2-mercaptobenzothiazole, potassium selenocyanate, and potassium antimony tartrate was performed. Influence of additives and cyanide concentration on microstructure and kinetics of the cathodic processes were studied. A brightener couple, 2-mercaptobenzothiazole and potassium antimony tartrate, were combined within this investigation and detected to be highly effective for silver electrodeposition. The rapid increase in current density at the same potential interval related to grain refinement effect of potassium antimony tartrate was shown. The cyclic organic compound, 2-mercaptobenzothiazole, polarizes the reduction to high cathodic potential in pyrophosphate electrolyte. However, the sufficient levelling effect required for the mirror-bright appearance seems to be related to the high polarizing effect of the high concentration cyanide content. In the case of pyrophosphate electrolytes, sufficient levelling cannot be achieved, so semigloss coatings are obtained. The low cathodic potential electrodeposition of silver in pyrophosphate electrolyte, which is found to proceed by 3D instantaneous nucleation, is polarized to high cathodic potentials and grows into 3D progressive nucleation and diffusion-controlled growth in high concentration cyanide electrolyte. [ABSTRACT FROM AUTHOR]

An accurate and sensitive liquid chromatography-electrospray ionisation/multi stage mass spectrometry (LC–ESI–MS/MS) method has been developed for the characterization and quantitation of nine heterocyclic amine (HCA) compounds. We were identified 2-Amino-3-methyl-3H-imidazo[4,5-F]quinoline (IQ), 2-Amino-3-methyl-3H-imidazo[4,5-f]quinoxaline (IQx), 2-Amino-3,4-dimethyl-3H-imidazo[4,5-f]quinoline (MeIQ), 2-Amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), 2-Amino-3,7,8-trimethyl-3H-imidazo[4,5-f]quinoxaline (7,8-DiMeIQx), 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine as polar molecules, and they were eluted accordingly at the beginning of the analysis. However, Norharman, Harman and AαC were identified as a non-polar molecules and were eluted last. The excellent selectivity and sensitivity achieved by the selected reaction monitoring mode permitted satisfactory quantitation and confirmation of the injected HCA compounds with limit of detection and quantitation ranges from 0.17 to 1.44 pg and 0.53 to 4.57 pg, respectively. The recoveries ranged from 74 to 108%, with an interday and intraday precision of 1.6–1.9% and 0.1–0.9%, respectively. The method was successfully applied to identify and quantify the studied HCAs in fried and grilled chicken. [ABSTRACT FROM AUTHOR]

Adaptations to low temperature play a critical role in restricting the geographical distribution of insects. Decreasing day lengths and temperatures trigger seasonal cold adaptations in insects. These adaptions include changes in expression at the miRNA, mRNA and protein levels. The rice water weevil (RWW), Lissorhoptrus oryzophilus , introduced from the Mississippi River, is a globally invasive pest of wetland rice that can survive at the northern border of China. To investigate the changes in expression at the protein level in overwintering female RWW adults, 6-plex tandem mass tags (TMTs) were used in overwintering and summer adults. By using a proteome database available for Curculionidae, 1077 proteins were quantified, 183 of which differed significantly between the overwintering and summer samples. To further understand these differentially expressed proteins (DEPs), bioinformatics analyses such as gene ontology (GO) enrichment analyses were performed. DEPs associated with the terms binding, structural molecule activity, catalytic activity, multicellular organismal process, extracellular region, chitin binding, metabolic process, intracellular part and organic cyclic compound binding were altered by selection during winter. The changes in the expression of these proteins suggest that the proteins are important for RWW survival in winter. [ABSTRACT FROM AUTHOR]

The synthesis of chemotherapeutic agents derived from 1,2,4-triazino indoles, condensed or fused, or bearing heterocyclic moieties are reported. Herein we emphasized its potential biological, pharmacological, and medicinal properties. This review covers the most remarkable compounds of this class in the literature. [ABSTRACT FROM AUTHOR]

Thiophene molecule selectively binds to the adjacent adatom-rest atom pair on the Si(111)-(7×7) surface through its α-carbon atoms, leading to the covalent attachment of a C–S–C linkage and remaining C==C (β-carbon) bond onto the surface. Photoemission studies show that Cu atom readily adsorbs onto the S atom of the functional group to form the Cu–S molecular anchor in two forms: one points away from the thiophene C==C group; the other points toward the C==C group. [ABSTRACT FROM AUTHOR]

Optical physical properties of neutral and charged quinquethiophene monomer, and neutral and cationic π-dimeric quinquethiophenes were investigated with density functional theory as well as the two dimensional (2D) site (transition density matrix) and three dimensional (3D) cube (transition density and charge difference density) representations, stimulated by the recent experimental report [T. Sakai et al., J. Am. Chem. Soc. 127, 8082 (2005)]. Transition density shows the orientation and strength of the transition dipole moment of neutral and charged quinquethiophene monomer, and charge difference density reveals the orientation and result of the charge transfer in neutral and charged quinquethiophene monomer. To study if coupling exciton and oscillation of electron-hole pair exist in neutral and cationic π-dimeric quinquethiophenes, the coupling constants J (coupling exciton of electron-hole pair) and K (coupling oscillation of electron-hole pair) were introduced to the exciton coordinate and momentum operators, respectively, and the 2D and 3D analysis methods were further developed by extending our previous theoretical methods [M. T. Sun, J. Chem. Phys. 124, 054903 (2006)]. With the new developed 2D and 3D analysis methods, we investigated the excited state properties of neutral and cationic π-dimeric quinquethiophenes, especially on the coupling exciton and oscillation of electron-hole pair between monomers. The 2D results show that there is neither coupling exciton (J=0) nor oscillation (K=0) of electron-hole pair in neutral π-dimeric quinquethiophenes. For some excited states of cationic π-dimeric quinquethiophenes, there is no coupling exciton (J=0), but there is coupling oscillation (K≠0); while for some excited states, there are both coupling exciton and coupling oscillator simultaneously (J≠0 and K≠0). The strength of transition dipole moments of π-dimeric quinquethiophenes were interpreted with 3D transition density, which reveals the orientations of their two subtransition dipole moments. The 3D charge transition density reveals the orientation and result of intermonomer and/or intramonomer charge transfer. The calculated results reveal that excited state properties of neutral π-dimeric quinquethiophene are significantly different from those of the cationic π-dimeric quinquethiophenes. [ABSTRACT FROM AUTHOR]

The spectrally narrowed emissions (SNE) from a flat single crystal of a thiophene/phenylene co-oligomer were investigated in a series of polarized measurements. The SNE spectra comprise of two major lines occurring at 507 and 514 nm. Of these, the former line effectively causes the emission gain narrowing by the pulse laser excitation polarized along the c axis. The intensity of the SNE is nearly isotropic with the radial directions along the flat crystal plane paralleling the bc plane. The SNE is strongly polarized along the a axis with its emission polarization ratio of the a axis to the b axis being 16.7. These polarized SNEs can be understood by the upright configuration of the molecular long axis paralleling the a axis. [ABSTRACT FROM AUTHOR]

In a three-component system containing dibenzo-24-crown-8 (1), diamino-dibenzo-24-crown-8 (2), and 1,2-bis(4,4′-dipyridyl)ethane (32+), axle 32+ can shuttle between wheels 1 and 2 by acid-base control, accompanying color changes from yellow to red. This system could not only be taken as a chromophoric supramolecular switch, but also exhibit a function as INHIBIT logic gate. [ABSTRACT FROM AUTHOR]

• Donor-acceptor cyclopropane. • Three-membered ring. • Cycloaddition. • Lewis acid. • Organic synthesis. Donor-acceptor cyclopropanes are known as a versatile carbon-based building block in organic synthesis. Due to their unique characteristics, 2-substituted d-A cyclopropanes easily undergo annulation and cycloaddition with diverse substrates for the construction of hetero-, and carbocyclic compounds. Ring-opening of d-A cyclopropanes in the presence of Lewis acids is one of the powerful tools for the synthesis of various acyclic and cyclic compounds. The current review highlights recent developments in the application of 2-substituted d-A cyclopropanes in organic transformations since 2015. Donor-acceptor cyclopropanes, owing to their exceptional reactivity can act as 1,3-dipoles and undergo annulation and cycloaddition with a diverse range of substrates under acid catalysis conditions. d-A cyclopropanes have been recognized as powerful tools for the construction of diverse carbo-, and heterocyclic compounds. Accordingly, the synthesis of various cyclic and acyclic organic compounds starting from d-A cyclopropanes through ring-opening, rearrangements, and (3 + n) cycloadditions is highlighted in this review. [Display omitted] [ABSTRACT FROM AUTHOR]

A quinoidal thiophene molecule which is a prototype of the repeated unit of s-trans-cis-polyacetylene was studied by sub-5 fs spectroscopy. A breatherlike mode modulation of both the amplitude and frequency of the C==C stretching was observed for the first time. It generates two sidebands of 2238 and 700 cm-1 with a separation of 769 cm-1 corresponding to the modulation frequency. The latter mode is very close to the C–S–C ring deformation, which indicate that this mode mediates coupling between the breather mode and the Cβ–Cβ stretching mode. It was also found that the breather-type excitation has a longer lifetime (2–3 ps) than in all-trans-polyacetylene (50 fs) due to its confinement. [ABSTRACT FROM AUTHOR]

This paper reports on a combined spectroscopic and density functional theory study on a series of cyclo(diacetylenes-oligothiophenes) with different shapes and dimensions. The case of a macrocycle fragmented by the insertion of Pt metallic atoms is illustrated as well. The analysis covers the neutral and oxidized samples. A full assignment of the spectra has been proposed, supported by BP86/cc-pVDZ theoretical calculations. Ring shape and molecular dimension have been related with the C==C/C–C structural parameters and Raman wave numbers. Platinum atom insertion within the acetylene spacer seems to soften ring strain owing to the rupture of the strained circular shape. Oxidation causes an overall downshift of the Raman wave numbers likely due to the skeletal relaxation of CC conjugated path, while the ring shape of each macrocycle is conserved upon oxidation. [ABSTRACT FROM AUTHOR]

A route for generating arrays of printable polythiophene-based gas sensor materials suitable for low-cost manufacturing is demonstrated. Materials with complementary sensor responses are synthesized by incorporating functional groups into the molecule, either along the polymer backbone or as end-capping groups. Using these materials as printable sensor inks, a functional, integrated gas sensor array chip is fabricated using additive deposition techniques. The sensor array shows sensitivity to a range of volatile organic compounds down to concentrations of 10 ppm. A three-terminal thin film transistor structure is used, allowing the extraction of multiple parameters that help to elucidate the mechanisms responsible for sensor response and the role of the functional groups in this response. [ABSTRACT FROM AUTHOR]

The polarized absorption spectra of single crystals of oligothiophenes in a wide spectral range are reported. The experimental procedure is discussed, underlying several details which are relevant to obtain reliable spectra particularly for samples of increasing thickness. On the basis of these considerations, it has been possible to fully detect the transition to the upper Davydov exciton originating from the first molecular state. The position and shape of the main exciton peak in these materials are compared and discussed, taking into consideration the molecular arrangement and the longitudinal contribution which depends on the transition moment orientation. The Davydov splitting values as deduced from the experimental data at room temperature are also reported either for the first vibronic replica or for the electronic transition as a whole. The difference between the purely transverse and the measured Davydov splitting is discussed. [ABSTRACT FROM AUTHOR]

We report a detailed quantum-chemical investigation of donor-acceptor substituted dipolar nonlinear optical chromophores incorporating the 4-(dimethylamino)phenyl donor end group and a variety of strong heterocyclic acceptor end groups, including tricyanofurans and tricyanopyrroles. In particular, we study the variation of the molecular second-order polarizability (β) with the acceptor end group and when inserting auxiliary donors (thiophene) and acceptors (thiazole) into the π bridge. Both finite-field calculations (in the context of local contributions) and sum-over-states calculations were carried out in order to probe the relationship between β and the chemical structure of the various chromophores. The trends obtained with these two methods are fully consistent. The large β values (up to 700×10-30 esu) as well as the observed tunability of the optical absorption maximum (λmax) make the chromophores investigated here interesting candidates for use in electro-optic applications at telecommunications wavelengths. [ABSTRACT FROM AUTHOR]

Photoluminescence (PL) and optical gain measurements have been performed for single crystals of thiophene/phenylene co-oligomer at room and low temperatures. Broad PL bands are transformed to be an ensemble of several spectrally narrower vibronic peaks with decreasing temperature. Very sharp lines as narrow as ∼3 meV are observed at 10 K under weak excitation. Intensities of sharp emission lines superlinearly increased at 10 K under intense excitation, showing the amplified spontaneous emission (ASE). The ASE bands were clearly identified to the sidebands of B1 and A1+B1 vibronic modes. The ASE is also observed at room temperature under the intense excitation. Spectroscopic investigation at varied temperatures enabled us to identify the origin of the ASE band to the vibronic sidebands of the electronic transition of the thiophene/phenylene co-oligomer crystals. In addition, highly polarized optical gains ∼50 cm-1 were obtained for the two ASE bands at room temperature. [ABSTRACT FROM AUTHOR]

The vibronic profiles of one-photon absorption spectra of dioxaborine heterocycles in gas phase and solution have been calculated at the Hartree-Fock and density-functional-theory levels. The polarizable continuum model has been applied to simulate the solvent effect, while the linear coupling model is used to compute the Franck-Condon and Herzberg-Teller contributions. It is found that a good agreement between theory and experiment can be achieved when the solvent effect and electron correlation are taken into account simultaneously. For the first excited charge-transfer state, the maximum of its Herzberg-Teller profile is blueshifted from that of the Franck-Condon profile. The shifted energy is found to be around 0.2 eV, which agrees well with the measured energy difference between two- and one-photon absorptions of the first excited state. [ABSTRACT FROM AUTHOR]

The molecular structures and electron affinities of eight radicals derived from the halide benzene by removing a hydrogen atom have been determined using seven hybrid Hartree-Fock/density-functional methods. The basis set used in this work is of double-ζ plus polarization quality with additional diffuse s- and p-type functions, denoted as DZP++. These methods have been carefully calibrated [J. C. Rienstra-Kiracofe, G. S. Tschumper, H. F. Schaefer, S. Nandi, and G. B. Ellison, Chem. Rev. (Washington, D. C.) 102, 231 (2002)]. The geometries are fully optimized with each density-functional theory method and discussed, respectively. The three different types of the neutral-anion energy separations reported in this work are the adiabatic electron affinity, the vertical electron affinity, and the vertical detachment energy. The most reliable adiabatic electron affinities (with zero-point vibrational energy correction), obtained at the DZP++ B3LYP level of theory, are 1.74 eV (o-C6H4F·), 1.39 eV (m-C6H4F·), 1.34 eV (p-C6H4F·), 1.78 eV (o-C6H4Cl·), 1.53 eV (m-C6H4Cl·), 1.45 eV (p-C6H4Cl·), 2.06 eV (o-C6H3F2·), and 2.04 eV (p-C6H3F2·), respectively. Compared with the experimental values, the average absolute error of the B3LYP method is 0.03 eV. The BLYP, BP86, and BPW91 functionals also gave excellent predictions, with average absolute errors of 0.05, 0.08, and 0.08 eV, respectively. [ABSTRACT FROM AUTHOR]

The influence of full deuteration on the T1[functional_relationship]S0 intersystem crossing in benzene is studied by a phase space approach. A full treatment of all the vibrational modes in the molecule leads to a ratio of the rate between the two isotopomers which is very close to the experimental value. Several aspects of the results are compared to previous estimates, and the effects of anharmonicity on the rates and accepting modes are examined. This first successful application of the method to a real physical system encourages the possibility of establishing a routine procedure for simple calculations of tranistion rates even for relatively large molecules. [ABSTRACT FROM AUTHOR]

We report on the relationship between optical and morphological properties of thin films of a blend of thiophene-based monomer and a diamine derivative. This system is of interest as it gives rise to white emission, due to the formation of exciplex energy levels in the solid state. The photoluminescence emission has been collected for different relative concentrations of the two blend components, and the film topography has been mapped correspondingly by means of atomic force microscopy. Along with a complex evolution of the film surface morphology, a significant variation of the emission properties has been observed upon change of the blend composition. In particular, the intensity of the broad low-energy exciplex band turns out to be affected by a balance of two factors, namely, the extension of homogeneous blend film areas, and their effective concentration. [ABSTRACT FROM AUTHOR]

The present work investigates the structure of large polystyrene (PS) chains in solutions of small poly(ethyl methacrylate) (PEMA) microgel particles in toluene. Toluene is a good solvent for the PS chains. The PEMA colloids have an outer radius of R=11 nm which is much smaller in size than the radius of gyration Rg=58 nm of the PS chains. The system is considered to represent the protein limit of polymer-colloid mixtures. Structural investigation is performed by small-angle neutron scattering (SANS) using an appropriate contrast matching. This could be achieved by dissolving fully deuterated PS chains (D8-PS) in solutions of hydrogenated PEMA colloids in hydrogenated toluene (H-toluene). It is first demonstrated that PEMA colloids are satisfactorily contrast matched for SANS in H-toluene if the PEMA concentration does not exceed 200 g/l. Based on these findings, D8-PS is investigated by SANS in pure H-toluene and three different PEMA concentrations in H-toluene. The results indicate a drastic shrinking of D8-PS chain dimensions with increasing PEMA content. Comparison with model curves of star-branched Gaussian chains and Gaussian rings suggest a striking similarity of the respective density–density correlation of those models with the shrunken D8-PS chains. Along with this, a shrinking as large as 0.5 was estimated when the PEMA content reached 200 g/l. [ABSTRACT FROM AUTHOR]

The structure and microscopic dynamics of liquid mixtures of benzene and hexafluorobenzene at room temperature and several compositions have been studied by molecular-dynamics simulations. In this implementation we have rescaled the intermolecular H–F cross potential parameters obtained from the Lorentz–Berthelot combining rules, in order to avoid the substantial overestimation of the energy of mixing predicted by the model when the usual rules are employed. We found that a reduction in the strength of cross H–F interactions by 50% relative to the geometric mean is required in order to get a good agreement with experiments. Radial-angular pair-correlation functions between like and unlike species have been computed and analyzed, by comparing them with the correlations in the corresponding neat liquids. We have also studied the microscopic intermolecular momentum transfer, by computing the time correlation function between the initial velocity of a central molecule and later velocities of neighboring molecules. Structural and dynamical information extracted from the mentioned functions seem to be consistent with the picture of relatively long-lived benzene–hexafluorobenzene (Bz–Hf) complexes present in the mixtures, which would be responsible for the considerable perturbation of the structure in the first shell of like species, and would be moving within the liquid in a parallel face-to-face configuration. Using the tools developed originally to estimate hydrogen-bond lifetimes in liquids, we have computed the lifetimes of the Bz–Hf complexes as a function of the mixture composition, by two different methods: the direct time-averaging scheme and from the autocorrelation function of bond occupation numbers. The obtained lifetimes are strongly dependent on the scheme chosen to compute the characteristic times. We have obtained for the Bz–Hf dimer in solution, at room temperature, lifetimes in the range of 30–40 ps from averaging schemes and around 60–120 ps from autocorrelation function methods. In the latter case, the longest times correspond to the equimolar mixture. [ABSTRACT FROM AUTHOR]