Chemical Correlation Research Articles

Improved understanding of aqueous solubility modeling through topological data analysis

Topological data analysis is a family of recent mathematical techniques seeking to understand the ‘shape’ of data, and has been used to understand the structure of the descriptor space produced from a standard chemical informatics software from the point of view of solubility. We have used the mapper algorithm, a TDA method that creates low-dimensional representations of data, to create a network visualization of the solubility space. While descriptors with clear chemical implications are prominent features in this space, reflecting their importance to the chemical properties, an unexpected and interesting correlation between chlorine content and rings and their implication for solubility prediction is revealed. A parallel representation of the chemical space was generated using persistent homology applied to molecular graphs. Links between this chemical space and the descriptor space were shown to be in agreement with chemical heuristics. The use of persistent homology on molecular graphs, extended by the use of norms on the associated persistence landscapes allow the conversion of discrete shape descriptors to continuous ones, and a perspective of the application of these descriptors to quantitative structure property relations is presented.

Morphinandienone and aporphine alkaloids from Corydalis decumbens

Phytochemical examination of Corydalis decumbens has afforded two new morphinandienone alkaloids, namely, (-)-pallidine N-oxide (1) and (-)-salutaridine N-oxide (2), together with one known analogue, (-)-pallidine (3), and three known aporphine alkaloids (4−6). Their structures were elucidated via comprehensive spectroscopic analysis and chemical correlation. This study represents the first isolation of morphinandienone alkaloids from the title plant. All isolates were tested for their activities towards neuronal excitability in primary cultured neocortical neurons.

Secondary Metabolites from Peucedanum tauricum Fruits

From the essential oil of fruits of Peucedanum tauricum Bieb., two new guaiane type sesquiterpene hydrocarbons guaia-1(10),11-diene (1) and guaia-9,11-diene (2) were identified. The structures of 1 and 2 were assigned by 1D- and 2D-NMR analysis. The relative configurations of the new compounds were established by 2D-NOESY experiments while the absolute configurations were deduced through chemical correlations with (+)-g-gurjunene (9) and capillary GC analysis using modified cyclodextrins as the stationary phases. From the less volatile dichloromethane extract of the fruits, coumarins, viz. peucedanin (3), oxypeucedanin hydrate (4) and officinalin isobutyrate (5) were isolated. Compound 5 was confirmed to be 6- carbomethoxy-7-isobutyroxycoumarin by its 1D- and 2D-NMR data as well as by conversion into officinalin (7) by alkaline hydrolysis. Peuruthenicin, a positional isomer of officinalin, is assigned structure 8. Bergapten (6) was identified by its mass spectrum. This is the first report on the isolation of compounds 4 and 5 from P. tauricum. Keywords: Peucedanum tauricum Bieb.; Apiaceae; Essential oil; Guaia-1(10),11-diene; Guaia-9,11-diene; Coumarins; Peucedanin; Officinalin isobutyrate; Oxypeucedanin; Peuruthenicin; Bergapten.

Elucidation of Relative and Absolute Configurations of Highly Rearranged Diterpenoids and Evidence for a Putative Biosynthetic Intermediate from the Australian Nudibranch Goniobranchus geometricus.

A diterpene (1), previously isolated from a Japanese marine sponge, together with two undescribed (2, 3) diterpenes with highly rearranged carbon skeletons have been characterized from the Australian nudibranch species Goniobranchus geometricus. The structures and relative configuration were determined by spectroscopic analyses informed by detailed molecular modeling, as well as by DFT, DP4, and coupling constant predictions. A 13 R,14 R configuration was determined for secoshahamin (1) by chemical correlation with 12-desacetoxyshahamin C (4) and 12-desacetoxypolyrhaphin A (5); each metabolite (1, 4, and 5) was subjected to saponification and lactonization, yielding the same δ-lactone product (6). Secoshahamin has the same carbon skeleton as a putative precursor that may play a key role in the biosynthesis of highly rearranged diterpenoid scaffolds via C-9/C-11 cleavage of a spongian diterpene precursor.

Chemistry of floral rewards: intra‐ and interspecific variability of nectar and pollen secondary metabolites across taxa

AbstractFloral chemistry mediates plant interactions with pollinators, pathogens, and herbivores, with major consequences for fitness of both plants and flower visitors. The outcome of such interactions often depends on compound dose and chemical context. However, chemical diversity and intraspecific variation of nectar and pollen secondary chemistry are known for very few species, precluding general statements about their composition. We analyzed methanol extracts of flowers, nectar, and pollen from 31 cultivated and wild plant species, including multiple sites and cultivars, by liquid‐chromatography–mass‐spectrometry. To depict the chemical niche of each tissue type, we analyzed differences in nectar and pollen chemical richness, absolute and proportional concentrations, and intraspecific variability. We hypothesized that pollen would have higher concentrations and more compounds than nectar, consistent with Optimal Defense Theory and pollen's importance as a male gamete. To investigate chemical correlations across and within tissues, which could reflect physiological constraints, we quantified chemical overlap between conspecific nectar and pollen, and phenotypic integration of individual compounds within tissue types. Nectar and pollen were chemically differentiated both across and within species. Of 102 compounds identified, most occurred in only one species. Machine‐learning algorithms assigned samples to the correct species and tissue type with 98.6% accuracy. Consistent with our hypothesis, pollen had 23.8‐ to 235‐fold higher secondary chemical concentrations and 63% higher chemical richness than nectar. The most common secondary compound classes were flavonoids, alkaloids, terpenoids, and phenolics (primarily phenylpropanoids including chlorogenic acid). The most common specific compound types were quercetin and kaempferol glycosides, known to mediate biotic and abiotic effects. Pollens were distinguished from nectar by high concentrations of hydroxycinnamoyl‐spermidine conjugates, which affect plant development, abiotic stress tolerance, and herbivore resistance. Although chemistry was qualitatively consistent within species and tissue types, concentrations varied across cultivars and sites, which could influence pollination, herbivory, and disease in wild and agricultural plants. Analyses of multivariate trait space showed greater overlap across sites and cultivars in nectar than pollen chemistry; this overlap reflected greater within‐site and within‐cultivar variability of nectar. Our analyses suggest different ecological roles of nectar and pollen mediated by chemical concentration, composition, and variability.

Further new eunicellin-based diterpenoids from the Guangxi Weizhou soft coral Cladiella krempfi

Three new polyoxygenated diterpenes (1, 3 and 4) of eunicellin-type, namely, 8-n-butyryl-litophynol A, 6-keto-litophynol B and 6-epi-litophynol B, respectively, together with two related known ones (2 and 5), were isolated from the soft coral Cladiella krempfi collected off the Weizhou island, Guangxi Zhuang Autonomous Region, China. The structures of the new compounds were elucidated by extensive spectroscopic analysis and chemical correlation. In bioassay, all the new compounds displayed moderate anti-inflammatory effects.

Isolation of 3,4-seco-27-norlanostane triterpenoids from cultivated fruiting bodies of Ganoderma orbiforme

Four new 3,4-seco-27-norlanostane triterpenoids, ganoboninketals E (1) and F (2), and ganoboninones G (3) and H (4), and two known derivatives (5 and 6), a new C30 lanostane, (24Z)-3β,27-dihydroxylanosta-7,9(11),24-triene (7), and twelve known lanostanes (8–19), together with three known meroterpenoids, fornicin A (20) and ganomycins B (21) and I (22), were isolated from cultivated fruiting bodies of the basidiomycete Ganoderma orbiforme. The structures were elucidated on the basis of NMR spectroscopic and mass spectrometry data and chemical correlations. Biological activities of all new compounds and some selected known compounds were evaluated. Ganomycin I showed moderate activity against Gram-positive bacteria.

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.

BackgroundKnowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.MethodsWe used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.ResultsSoil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, várzea, igapó and campina) than between substrates (soil and litter).DiscussionIn spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world’s largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity.

Three Lycopodium alkaloids from Thai club mosses

Phytochemical constituents in alkaloid extracts from three Thai club mosses Huperzia squarrosa, Huperzia phlegmaria and Phlegmariurus nummularifolius were investigated. Squarrosinoxide was an undescribed Lycopodium alkaloid from H. squarrosa possessing an unprecedented 6/5/7 tricyclic spiro system. Acetyllycophlegmarianol was an undescribed N-oxide lycopodine-type alkaloid isolated from H. phlegmaria. 4-Epilycopodine, an undescribed epimer of lycopodine, was first isolated from P. nummularifolius. The structural assignments were established through comprehensive spectroscopic techniques and chemical correlations. All compounds were assayed for their anti-acetylcholinesterase activity in vitro.

CLASSIFICATION OF OILS. SULFUR CONTENT AS GENETIC CLASSIFICATION SIGN

In the article we considered the following variants of oil classification: technological, chemical, and geochemical (genetic). Applicability of the classification indicators (hydrocarbon composition, fractional composition of oils, asphaltic-resinous components, sulfur content, metal content) is discussed to separate oils to different chemical types Stable direct correlations between sulfur concentration in oils and diverse characteristics of oils allow to consider the sulfur content as an indicator of genetic nature.

Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy.

Protein-protein interactions (PPIs) regulate a plethora of cellular processes and NMR spectroscopy has been a leading technique for characterizing them at the atomic resolution. Technically, however, PPIs characterization has been challenging due to multiple samples required to characterize the hot spots at the protein interface. In this paper, we review our recently developed methods that greatly simplify PPI studies, which minimize the number of samples required to fully characterize residues involved in the protein-protein binding interface. This original strategy combines asymmetric labeling of two binding partners and the carbonyl-carbon label selective (CCLS) pulse sequence element implemented into the heteronuclear single quantum correlation (1H-15N HSQC) spectra. The CCLS scheme removes signals of the J-coupled 15N–13C resonances and records simultaneously two individual amide fingerprints for each binding partner. We show the application to the measurements of chemical shift correlations, residual dipolar couplings (RDCs), and paramagnetic relaxation enhancements (PRE). These experiments open an avenue for further modifications of existing experiments facilitating the NMR analysis of PPIs.

Theoretical investigation of C-(A)-S-H(I) cement hydrates

The atomic-level understanding of the correlation of chemical, electronic and bonding behavior to mechanical properties of complex multi-component calcium (alumino)silicate hydrates [C-(A)-S-H] (The Cement Chemist Notation heavily used in this manuscript refers to C=CaO; A=Al2O3; S=SiO2; H=H2O or –OH), which is among the main binding phases of concrete could provide a point of departure for the study of cement behavior. In this paper, models of highly ordered C-(A)-S-H(I) are proposed and investigated. These models have been optimized and constructed in close relation and guidance of relevant experiments. The focus of the work is on illuminating the effect of Al substitution on chemical and mechanical properties of highly ordered synthetic cement phases. Furthermore, we show the importance of hydrogen bonds to mechanical properties in cements. We show, for the first time, that in the absence of vacancies in Dreierketten chains, the Al substitution in bridging sites reduces the mechanical anisotropy of C-(A)-S-H(I) cement. The study also shows the average partial charge of O, H, Si of different structural units are effectively independent of the chemical environment. This finding could have profound implications upon relevant classical molecular dynamics force fields for cements and could lead to further improvements in the modeling capabilities.

Cytotoxic macrocyclic diterpenoids from Jatropha multifida

Nine new macrocyclic diterpenoids (1–9), jatromultones A-I, along with eight known analogues (10–17) were isolated from the trunks of Jatropha multifida. The structures of the new compounds, including their absolute configurations, were elucidated by combination of spectroscopic analysis, single crystal X-ray diffraction, Rh2(OCOCF3)4-induced CD method, and chemical correlations. All compounds were screened for the cytotoxicity against five cancer cell lines, including one drug-resistant cell line, and seven compounds exhibited significant activity with IC50 values less than 10 μM. Compound 4 with IC50 values ranging from 2.69 to 6.44 μM toward all cell lines was selected for further mechanistic study, which showed that 4 could arrest cell cycle at G2/M phase and induce apoptosis. The brief structure-activity relationships (SARs) of these macrocyclic diterpenoids were also discussed.

Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics.

A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide remains a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate. We present here an efficient search algorithm, GlycoNMRSearch, which matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus, searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics. The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.nmrhub.eu. Supplementary data are available at Bioinformatics online.

Application of Magnetic Nanoparticles with Structure of Core-shell, as Bactericidal

Initially, magnetic nanoparticles (MNP) Fe3O4 are synthesized by a chemical correlation method and its core / shell structure is detected using SEM, FT-IR analysis. The purpose of this production was to use the nanoparticle performance level in the absorption of antibiotics, namely, ampicillin (amp). Absorption sampling was analyzed by UV-Vis spectrophotometer and the results indicate that the absorbance of the ampere increases to 85%. The bond between these two is electrostatic bonding, which was confirmed by EDX analysis. Ultimately, this compound was used for the antibacterial process. In this case, the MNP-amp compound was added in a natural amount of 20 μl a bacterial culture pattern overnight (In-vitro). The results showed that 95% of the bacteria were killed (confirmation of antibacterial properties of MNP). Therefore, it can be transmitted intentionally by controlling the magnetic field into living cells for the destruction of pathogenic bacteria.

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba.

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.

Identification of specific sources of airborne particles emitted from within a complex industrial (steelworks) site

A case study is provided of the development and application of methods to identify and quantify specific sources of emissions from within a large complex industrial site. Methods include directional analysis of concentrations, chemical source tracers and correlations with gaseous emissions. Extensive measurements of PM10, PM2.5, trace gases, particulate elements and single particle mass spectra were made at sites around the Port Talbot steelworks in 2012. By using wind direction data in conjunction with real-time or hourly-average pollutant concentration measurements, it has been possible to locate areas within the steelworks associated with enhanced pollutant emissions. Directional analysis highlights the Slag Handling area of the works as the most substantial source of elevated PM10 concentrations during the measurement period. Chemical analyses of air sampled from relevant wind directions is consistent with the anticipated composition of slags, as are single particle mass spectra. Elevated concentrations of PM10 are related to inverse distance from the Slag Handling area, and concentrations increase with increased wind speed, consistent with a wind-driven resuspension source. There also appears to be a lesser source associated with Sinter Plant emissions affecting PM10 concentrations at the Fire Station monitoring site. The results are compared with a ME2 study using some of the same data, and shown to give a clearer view of the location and characteristics of emission sources, including fugitive dusts.

Alkaloids from Corydalis decumbens suppress neuronal excitability in primary cultures of mouse neocortical neurons

Eight previously undescribed alkaloids, named corydemine, dihydrocorydemine, corydedine, 8,13-dioxo-14-hydroxytetrahydropalmatine, egenine-α-N-oxide, egenine-β-N-oxide, 7′-O-ethylegenine-α-N-oxide, and 7′-O-ethylegenine-β-N-oxide, together with three known ones, muramine, l-tetrahydropalmatine, and (+)-egenine, were isolated from the bulbs of Corydalis decumbens. Their structures were elucidated by comprehensive spectroscopic analysis and chemical correlation. The isolated compounds were tested for their ability to modulate neuronal excitability in primary cultured neocortical neurons. Four of the compounds, corydemine, dihydrocorydemine, muramine, and l-tetrahydropalmatine, inhibited neuronal excitability with IC50 values of 3.6, 16.7, 13.5 and 14.0 μM, respectively.

Comparative Ascaroside Profiling of Caenorhabditis Exometabolomes Reveals Species-Specific (ω) and (ω – 2)-Hydroxylation Downstream of Peroxisomal β-Oxidation

Chemical communication in nematodes such as the model organism Caenorhabditis elegans is modulated by a variety of glycosides based on the dideoxysugar l-ascarylose. Comparative ascaroside profiling of nematode exometabolome extracts using a GC-EIMS screen reveals that several basic components including ascr#1 (asc-C7), ascr#2 (asc-C6-MK), ascr#3 (asc-ΔC9), ascr#5 (asc-ωC3), and ascr#10 (asc-C9) are highly conserved among the Caenorhabditis. Three novel side chain hydroxylated ascaroside derivatives were exclusively detected in the distantly related C. nigoni and C. afra. Molecular structures of these species-specific putative signaling molecules were elucidated by NMR spectroscopy and confirmed by total synthesis and chemical correlations. Biological activities were evaluated using attraction assays. The identification of (ω)- and (ω - 2)-hydroxyacyl ascarosides demonstrates how GC-EIMS-based ascaroside profiling facilitates the detection of novel ascaroside components and exemplifies how species-specific hydroxylation of ascaroside aglycones downstream of peroxisomal β-oxidation increases the structural diversity of this highly conserved class of nematode signaling molecules.

Chemical Perturbation Two-Dimensional Correlation Ultraviolet Visible Spectroscopy for Quality Control of Chinese Liquor

ABSTRACTIn this work, a new method of two-dimensional correlation ultraviolet visible spectroscopy of Chinese liquor system was constructed with chemical reaction as an external perturbation. It has the advantages of easy to implement, simple operation, and abundant spectral signals. Using the Hai-Zhi-Lan liquor as the main research sample, this study found that the two-dimensional correlation ultraviolet visible spectrum of Hai-Zhi-Lan liquor exhibited two auto peaks and six cross peaks. Quantitative analysis using the correlation coefficient method showed that there were high correlations among different batches of Hai-Zhi-Lan liquor (≥0.99). Furthermore, the two-dimensional correlation ultraviolet visible spectra of Tian-Zhi-Lan liquor and Meng-Zhi-Lan liquor were obtained under the same conditions, which were produced in the same factory as Hai-Zhi-Lan liquor (Yang-He Company). The results showed that these liquors from the same manufacturer have certain correlations, but there were also differences in spectral intensities and regions, and, as a result, the correlation coefficients showed a downward trend. Finally, the two-dimensional correlation ultraviolet visible spectra of different brands of Chinese liquor produced by other manufactures were investigated and compared with the Hai-Zhi-Lan liquor. The results showed that there were some differences among the liquors, and the correlation coefficients were lower. Hence, through the use of the two-dimensional correlation ultraviolet visible spectroscopy, the characteristics of Chinese liquor can be obtained in three-dimensional space. This method can be applied to brand discrimination of quality control of Chinese liquor with high potential application value. Additionally, this strategy can provide a reference for quality discrimination research of other food systems.