The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer

PubMed Central

Zheng, Mingyue; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

2015-01-01

Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer. PMID:26047514

Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

PubMed Central

Jaspard, Emmanuel; Macherel, David; Hunault, Gilles

2012-01-01

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs. PMID:22615859

An Investigation of the Effects of Deposit Feeding Invertebrates on the Structural Properties of Clay Minerals.

DTIC Science & Technology

1981-07-01

Dennis M. Lavoie of NORDA for chemical analysis of clay minerals with the x-ray energy dispersive spectrometer. We thank Fred Bowles, Peter Fleischer...diffractograi of Nuculana acuta fecal pellet 11 residue (illite experiment). TABLES TABLE 1. X-ray energy dispersive spectrometer chemical 8 analysis for...inontmorillonite experiments. Counts for elements after background counts removed. TABLE 2. X-ray energy dispersive spectroneter chemical analysis 12 for

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beauchamp, R.O. Jr.

A preliminary examination of chemical-substructure analysis (CSA) demonstrates the effective use of the Chemical Abstracts compound connectivity file in conjunction with the bibliographic file for relating chemical structures to biological activity. The importance of considering the role of metabolic intermediates under a variety of conditions is illustrated, suggesting structures that should be examined that may exhibit potential activity. This CSA technique, which utilizes existing large files accessible with online personal computers, is recommended for use as another tool in examining chemicals in drugs. 2 refs., 4 figs.

Towards a nondestructive chemical characterization of biofilm matrix by Raman microscopy.

PubMed

Ivleva, Natalia P; Wagner, Michael; Horn, Harald; Niessner, Reinhard; Haisch, Christoph

2009-01-01

In this study, the applicability of Raman microscopy (RM) for nondestructive chemical analysis of biofilm matrix, including microbial constituents and extracellular polymeric substances (EPS), has been assessed. The examination of a wide range of reference samples such as biofilm-specific polysaccharides, proteins, microorganisms, and encapsulated bacteria revealed characteristic frequency regions and specific marker bands for different biofilm constituents. Based on received data, the assignment of Raman bands in spectra of multispecies biofilms was performed. The study of different multispecies biofilms showed that RM can correlate various structural appearances within the biofilm to variations in their chemical composition and provide chemical information about a complex biofilm matrix. The results of RM analysis of biofilms are in good agreement with data obtained by confocal laser scanning microscopy (CLSM). Thus, RM is a promising tool for a label-free chemical characterization of different biofilm constituents. Moreover, the combination of RM with CLSM analysis for the study of biofilms grown under different environmental conditions can provide new insights into the complex structure/function correlations in biofilms.

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

PubMed

Skinnider, Michael A; Dejong, Chris A; Franczak, Brian C; McNicholas, Paul D; Magarvey, Nathan A

2017-08-16

Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have been extensively optimized by natural selection. The large and structurally complex scaffolds of natural products distinguish their physical and chemical properties from those of synthetic compounds. However, no analysis of the performance of existing methods for molecular similarity calculation specific to natural products has been reported to date. Here, we present LEMONS, an algorithm for the enumeration of hypothetical modular natural product structures. We leverage this algorithm to conduct a comparative analysis of molecular similarity methods within the unique chemical space occupied by modular natural products using controlled synthetic data, and comprehensively investigate the impact of diverse biosynthetic parameters on similarity search. We additionally investigate a recently described algorithm for natural product retrobiosynthesis and alignment, and find that when rule-based retrobiosynthesis can be applied, this approach outperforms conventional two-dimensional fingerprints, suggesting it may represent a valuable approach for the targeted exploration of natural product chemical space and microbial genome mining. Our open-source algorithm is an extensible method of enumerating hypothetical natural product structures with diverse potential applications in bioinformatics.

NIR and Py-mbms coupled with multivariate data analysis as a high-throughput biomass characterization technique: a review

PubMed Central

Xiao, Li; Wei, Hui; Himmel, Michael E.; Jameel, Hasan; Kelley, Stephen S.

2014-01-01

Optimizing the use of lignocellulosic biomass as the feedstock for renewable energy production is currently being developed globally. Biomass is a complex mixture of cellulose, hemicelluloses, lignins, extractives, and proteins; as well as inorganic salts. Cell wall compositional analysis for biomass characterization is laborious and time consuming. In order to characterize biomass fast and efficiently, several high through-put technologies have been successfully developed. Among them, near infrared spectroscopy (NIR) and pyrolysis-molecular beam mass spectrometry (Py-mbms) are complementary tools and capable of evaluating a large number of raw or modified biomass in a short period of time. NIR shows vibrations associated with specific chemical structures whereas Py-mbms depicts the full range of fragments from the decomposition of biomass. Both NIR vibrations and Py-mbms peaks are assigned to possible chemical functional groups and molecular structures. They provide complementary information of chemical insight of biomaterials. However, it is challenging to interpret the informative results because of the large amount of overlapping bands or decomposition fragments contained in the spectra. In order to improve the efficiency of data analysis, multivariate analysis tools have been adapted to define the significant correlations among data variables, so that the large number of bands/peaks could be replaced by a small number of reconstructed variables representing original variation. Reconstructed data variables are used for sample comparison (principal component analysis) and for building regression models (partial least square regression) between biomass chemical structures and properties of interests. In this review, the important biomass chemical structures measured by NIR and Py-mbms are summarized. The advantages and disadvantages of conventional data analysis methods and multivariate data analysis methods are introduced, compared and evaluated. This review aims to serve as a guide for choosing the most effective data analysis methods for NIR and Py-mbms characterization of biomass. PMID:25147552

Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism

PubMed Central

Wildenhain, Jan; Spitzer, Michaela; Dolma, Sonam; Jarvik, Nick; White, Rachel; Roy, Marcia; Griffiths, Emma; Bellows, David S.; Wright, Gerard D.; Tyers, Mike

2016-01-01

The network structure of biological systems suggests that effective therapeutic intervention may require combinations of agents that act synergistically. However, a dearth of systematic chemical combination datasets have limited the development of predictive algorithms for chemical synergism. Here, we report two large datasets of linked chemical-genetic and chemical-chemical interactions in the budding yeast Saccharomyces cerevisiae. We screened 5,518 unique compounds against 242 diverse yeast gene deletion strains to generate an extended chemical-genetic matrix (CGM) of 492,126 chemical-gene interaction measurements. This CGM dataset contained 1,434 genotype-specific inhibitors, termed cryptagens. We selected 128 structurally diverse cryptagens and tested all pairwise combinations to generate a benchmark dataset of 8,128 pairwise chemical-chemical interaction tests for synergy prediction, termed the cryptagen matrix (CM). An accompanying database resource called ChemGRID was developed to enable analysis, visualisation and downloads of all data. The CGM and CM datasets will facilitate the benchmarking of computational approaches for synergy prediction, as well as chemical structure-activity relationship models for anti-fungal drug discovery. PMID:27874849

Recent advances in the in silico modelling of UDP glucuronosyltransferase substrates.

PubMed

Sorich, Michael J; Smith, Paul A; Miners, John O; Mackenzie, Peter I; McKinnon, Ross A

2008-01-01

UDP glucurononosyltransferases (UGT) are a superfamily of enzymes that catalyse the conjugation of a range of structurally diverse drugs, environmental and endogenous chemicals with glucuronic acid. This process plays a significant role in the clearance and detoxification of many chemicals. Over the last decade the regulation and substrate profiles of UGT isoforms have been increasingly characterised. The resulting data has facilitated the prototyping of ligand based in silico models capable of predicting, and gaining insights into, binding affinity and the substrate- and regio- selectivity of glucuronidation by UGT isoforms. Pharmacophore modelling has produced particularly insightful models and quantitative structure-activity relationships based on machine learning algorithms result in accurate predictions. Simple structural chemical descriptors were found to capture much of the chemical information relevant to UGT metabolism. However, quantum chemical properties of molecules and the nucleophilic atoms in the molecule can enhance both the predictivity and chemical intuitiveness of structure-activity models. Chemical diversity analysis of known substrates has shown some bias towards chemicals with aromatic and aliphatic hydroxyl groups. Future progress in in silico development will depend on larger and more diverse high quality metabolic datasets. Furthermore, improved protein structure data on UGTs will enable the application of structural modelling techniques likely leading to greater insight into the binding and reactive processes of UGT catalysed glucuronidation.

Structural analysis and anticoagulant activities of two sulfated polysaccharides from the sea cucumber Holothuria coluber.

PubMed

Yang, Wenjiao; Cai, Ying; Yin, Ronghua; Lin, Lisha; Li, Zhongkun; Wu, Mingyi; Zhao, Jinhua

2018-05-01

Sulfated polysaccharides such as fucosylated glycosaminoglycan and fucan sulfate from echinoderm possess complex chemical structure and various biological activities. The two sulfated polysaccharides were purified from the low-value sea cucumber Holothuria coluber. Their physicochemical properties and chemical structures were analyzed and characterized by chemical and instrumental methods. Structural analysis clarified that the sea cucumber fucosylated glycosaminoglycan contains a chondroitin sulfate-like backbone and fucosyl branches with four various sulfation patterns. The fucan sulfate with molecular weight of 64.6 kDa comprises a central core of regular α(1 → 4)-linked tetrasaccharide repeating units, each of which is linked by a 4-O-sulfated fucose residue. Anticoagulant assays indicated that these sulfated polysaccharides possessed strong APTT prolonging activities and intrinsic factor Xase inhibitory activities, both of which decreased with the reduction of their molecular weights. Our results expand knowledge on the structural types of sulfated polysaccharides from sea cucumbers and further illustrate their functionality. Copyright © 2018. Published by Elsevier B.V.

Supramolecular structures on silica surfaces and their adsorptive properties.

PubMed

Belyakov, Vladimir N; Belyakova, Lyudmila A; Varvarin, Anatoly M; Khora, Olexandra V; Vasilyuk, Sergei L; Kazdobin, Konstantin A; Maltseva, Tetyana V; Kotvitskyy, Alexey G; Danil de Namor, Angela F

2005-05-01

The study of adsorptive and chemical immobilization of beta-cyclodextrin on a surface of hydroxylated silicas with various porous structure is described. Using IR spectroscopy, thermal gravimetrical analysis with a programmed heating, and chemical analysis of the silica surface, it is shown that the process of adsorption-desorption of beta-cyclodextrin depends on the porous structure of the silica. The reaction of esterification was used for chemical grafting of beta-cyclodextrin on the surface of hydroxylated silicas. Hydrolytic stability of silicas chemically modified by beta-cyclodextrin apparently is explained by simultaneous formation of chemical and hydrogen bonds between surface silanol groups and hydroxyl groups of beta-cyclodextrin. The uptake of the cations Cu(II), Cd(II), and Pb(II) and the anions Cr(VI) and As(V) by silicas modified with beta-cyclodextrin is investigated as a function of equilibrium ion concentrations. The increase of ion uptake and selectivity of ion extraction in comparison with starting silicas is established. It is due to the formation of surface inclusion complexes of the "host-guest" type in which one molecule of beta-cyclodextrin interacts simultaneously with several ions.

Vibrational spectroscopic study of dehydroacetic acid and its cinnamoyl pyrone derivatives

NASA Astrophysics Data System (ADS)

Billes, Ferenc; Elečková, Lenka; Mikosch, Hans; Andruch, Vasil

2015-07-01

The infrared and Raman spectra of dehydroacetic acid and some of its derivatives were measured. The assignments of the vibrational bands were based on quantum chemical calculations and normal coordinate analysis. The optimized structures, atomic net charges and dipole moments of the investigated molecules were also results of our quantum chemical calculations. The analysis of the last properties made possible a deeper insight into the structure and substituent effect on the investigated molecules. One of them is presented in the graphical abstract.

The structure and function of fungal cells

NASA Technical Reports Server (NTRS)

Nozawa, Y.

1984-01-01

The structure and function of fungal cell walls were studied with particular emphasis on dermatophytes. Extraction, isolation, analysis, and observation of the cell wall structure and function were performed. The structure is described microscopically and chemically.

One Hundred False-Positive Amphetamine Specimens Characterized by Liquid Chromatography Time-of-Flight Mass Spectrometry.

PubMed

Marin, Stephanie J; Doyle, Kelly; Chang, Annie; Concheiro-Guisan, Marta; Huestis, Marilyn A; Johnson-Davis, Kamisha L

2016-01-01

Some amphetamine (AMP) and ecstacy (MDMA) urine immunoassay (IA) kits are prone to false-positive results due to poor specificity of the antibody. We employed two techniques, high-resolution mass spectrometry (HRMS) and an in silico structure search, to identify compounds likely to cause false-positive results. Hundred false-positive IA specimens for AMP and/or MDMA were analyzed by an Agilent 6230 time-of-flight (TOF) mass spectrometer. Separately, SciFinder (Chemical Abstracts) was used as an in silico structure search to generate a library of compounds that are known to cross-react with AMP/MDMA IAs. Chemical formulas and exact masses of 145 structures were then compared against masses identified by TOF. Compounds known to have cross-reactivity with the IAs were identified in the structure-based search. The chemical formulas and exact masses of 145 structures (of 20 chemical formulas) were compared against masses identified by TOF. Urine analysis by HRMS correlates accurate mass with chemical formulae, but provides little information regarding compound structure. Structural data of targeted antigens can be utilized to correlate HRMS-derived chemical formulas with structural analogs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

INVERSE QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP ANALYSIS FOR IMPROVING PREDICTIONS OF CHEMICAL TOXICITY

EPA Science Inventory

The toxic outcomes associated with environmental contaminants are often not due to the chemical form that was originally introduced into the environment, but rather to the chemical having undergone a transformation prior to reaching the vulnerable species. More importantly, the c...

Determinants of job stress in chemical process industry: A factor analysis approach.

PubMed

Menon, Balagopal G; Praveensal, C J; Madhu, G

2015-01-01

Job stress is one of the active research domains in industrial safety research. The job stress can result in accidents and health related issues in workers in chemical process industries. Hence it is important to measure the level of job stress in workers so as to mitigate the same to avoid the worker's safety related problems in the industries. The objective of this study is to determine the job stress factors in the chemical process industry in Kerala state, India. This study also aims to propose a comprehensive model and an instrument framework for measuring job stress levels in the chemical process industries in Kerala, India. The data is collected through a questionnaire survey conducted in chemical process industries in Kerala. The collected data out of 1197 surveys is subjected to principal component and confirmatory factor analysis to develop the job stress factor structure. The factor analysis revealed 8 factors that influence the job stress in process industries. It is also found that the job stress in employees is most influenced by role ambiguity and the least by work environment. The study has developed an instrument framework towards measuring job stress utilizing exploratory factor analysis and structural equation modeling.

Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order.

PubMed

Jindalertudomdee, Jira; Hayashida, Morihiro; Zhao, Yang; Akutsu, Tatsuya

2016-03-01

Drug discovery and design are important research fields in bioinformatics. Enumeration of chemical compounds is essential not only for the purpose, but also for analysis of chemical space and structure elucidation. In our previous study, we developed enumeration methods BfsSimEnum and BfsMulEnum for tree-like chemical compounds using a tree-structure to represent a chemical compound, which is limited to acyclic chemical compounds only. In this paper, we extend the methods, and develop BfsBenNaphEnum that can enumerate tree-like chemical compounds containing benzene rings and naphthalene rings, which include benzene isomers and naphthalene isomers such as ortho, meta, and para, by treating a benzene ring as an atom with valence six, instead of a ring of six carbon atoms, and treating a naphthalene ring as two benzene rings having a special bond. We compare our method with MOLGEN 5.0, which is a well-known general purpose structure generator, to enumerate chemical structures from a set of chemical formulas in terms of the number of enumerated structures and the computational time. The result suggests that our proposed method can reduce the computational time efficiently. We propose the enumeration method BfsBenNaphEnum for tree-like chemical compounds containing benzene rings and naphthalene rings as cyclic structures. BfsBenNaphEnum was from 50 times to 5,000,000 times faster than MOLGEN 5.0 for instances with 8 to 14 carbon atoms in our experiments.

Feasibility Analysis of Incorporating In-Vitro Toxicokinetic Data ...

EPA Pesticide Factsheets

The underlying principle of read-across is that biological activity is a function of physical and structural properties of chemicals. Analogs are typically identified on the basis of structural similarity and subsequently evaluated for their use in read-across on the basis of their bioavailability, reactivity and metabolic similarity. While the concept of similarity is the major tenet in grouping chemicals for read-across, a critical consideration is to evaluate if structural differences significantly impact toxicological activity. This is a key source of uncertainty in read-across predictions. We hypothesize that inclusion of toxicokinetic (TK) information will reduce the uncertainty in read-across predictions. TK information can help substantiate whether chemicals within a category have similar ADME properties and, hence, increase the likelihood of exhibiting similar toxicological properties. This current case study is part of a larger study aimed at performing a systematic assessment of the extent to which in-vitro TK data can obviate in-vivo TK data, while maintaining or increasing scientific confidence in read-across predictions. The analysis relied on a dataset of ~7k chemicals with predicted exposure data (chemical inventory), of which 819 chemicals had rat and/or human in-vitro TK data (analog inventory), and 33 chemicals had rat in-vivo TK data (target inventory). The set of chemicals with human in vitro TK data was investigated to determine whether str

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

PubMed Central

Hong, Mei

2016-01-01

We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ~94 % of the 13C NMR data and almost all 15N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided command-line Python script (PLUQin), which should be useful in protein structure determination. The refined chemical shift distributions are utilized in a simple quality test (SQAT) that should be applied to new protein NMR data before deposition in a databank, and they could benefit many other chemical-shift based tools. PMID:26787537

Microstructural characterization of multiphase chocolate using X-ray microtomography.

PubMed

Frisullo, Pierangelo; Licciardello, Fabio; Muratore, Giuseppe; Del Nobile, Matteo Alessandro

2010-09-01

In this study, X-ray microtomography (μCT) was used for the image analysis of the microstructure of 12 types of Italian aerated chocolate chosen to exhibit variability in terms of cocoa mass content. Appropriate quantitative 3-dimensional parameters describing the microstructure were calculated, for example, the structure thickness (ST), object structure volume ratio (OSVR), and the percentage object volume (POV). Chemical analysis was also performed to correlate the microstructural data to the chemical composition of the samples. Correlation between the μCT parameters acquired for the pore microstructure evaluation and the chemical analysis revealed that the sugar crystals content does not influence the pore structure and content. On the other hand, it revealed that there is a strong correlation between the POV and the sugar content obtained by chemical analysis. The results from this study show that μCT is a suitable technique for the microstructural analysis of confectionary products such as chocolates and not only does it provide an accurate analysis of the pores and microstructure but the data obtained could also be used to aid in the assessment of its composition and consistency with label specifications. X-ray microtomography (μCT) is a noninvasive and nondestructive 3-D imaging technique that has several advantages over other methods, including the ability to image low-moisture materials. Given the enormous success of μCT in medical applications, material science, chemical engineering, geology, and biology, it is not surprising that in recent years much attention has been focused on extending this imaging technique to food science as a useful technique to aid in the study of food microstructure. X-ray microtomography provides in-depth information on the microstructure of the food product being tested; therefore, a better understanding of the physical structure of the product and from an engineering perspective, knowledge about the microstructure of foods can be used to identify the important processing parameters that affect the quality of a product.

Occupational and Qualification Structures in the Field of Environmental Protection in the Metal and Chemical Industries in Italy.

ERIC Educational Resources Information Center

Stanzani, Claudio

This report provides an initial analysis of the occupational and qualification structures in the field of environmental protection in the Italian metal and chemical industries. The first two chapters review the legislative background, situation in industry, and provision of environmental education and training. The third chapter presents results…

Sulfur compounds in coal

NASA Technical Reports Server (NTRS)

Attar, A.; Corcoran, W. H.

1977-01-01

The literature on the chemical structure of the organic sulfur compounds (or functional groups) in coal is reviewed. Four methods were applied in the literature to study the sulfur compounds in coal: direct spectrometric and chemical analysis, depolymerization in drastic conditions, depolymerization in mild conditions, and studies on simulated coal. The data suggest that most of the organic sulfur in coal is in the form of thiophenic structures and aromatic and aliphatic sulfides. The relative abundance of the sulfur groups in bituminous coal is estimated as 50:30:20%, respectively. The ratio changes during processing and during the chemical analysis. The main effects are the transformation during processing of sulfides to the more stable thiophenic compounds and the elimination of hydrogen sulfide.

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective

NASA Technical Reports Server (NTRS)

Gutell, R. R.; Larsen, N.; Woese, C. R.

1994-01-01

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS).

Chemical structure of the Chromophoric Dissolved Organic Matter (CDOM) fluorescent matter.

NASA Astrophysics Data System (ADS)

Blough, N. V.; Del Vecchio, R.; Cartisano, C. M.; Bianca, M.

2017-12-01

The structure(s), distribution and dynamics of CDOM have been investigated over the last several decades largely through optical spectroscopy (including both absorption and fluorescence) due to the fairly inexpensive instrumentation and the easy-to-gather data (over thousands published papers from 1990-2016). Yet, the chemical structure(s) of the light absorbing and emitting species or constituents within CDOM has only recently being proposed and tested through chemical manipulation of selected functional groups (such as carbonyl and carboxylic/phenolic containing molecules) naturally occurring within the organic matter pool. Similarly, fitting models (among which the PArallel FACtor analysis, PARAFAC) have been developed to better understand the nature of a subset of DOM, the CDOM fluorescent matter (FDOM). Fluorescence spectroscopy coupled with chemical tests and PARAFAC analyses could potentially provide valuable insights on CDOM sources and chemical nature of the FDOM pool. However, despite that applications (and publications) of PARAFAC model to FDOM have grown exponentially since its first application/publication (2003), a large fraction of such publications has misinterpreted the chemical meaning of the delivered PARAFAC `components' leading to more confusion than clarification on the nature, distribution and dynamics of the FDOM pool. In this context, we employed chemical manipulation of selected functional groups to gain further insights on the chemical structure of the FDOM and we tested to what extent the PARAFAC `components' represent true fluorophores through a controlled chemical approach with the ultimate goal to provide insights on the chemical nature of such `components' (as well as on the chemical nature of the FDOM) along with the advantages and limitations of the PARAFAC application.

Structural analysis and biological activity of a highly regular glycosaminoglycan from Achatina fulica.

PubMed

Liu, Jie; Zhou, Lutan; He, Zhicheng; Gao, Na; Shang, Feineng; Xu, Jianping; Li, Zi; Yang, Zengming; Wu, Mingyi; Zhao, Jinhua

2018-02-01

Edible snails have been widely used as a health food and medicine in many countries. A unique glycosaminoglycan (AF-GAG) was purified from Achatina fulica. Its structure was analyzed and characterized by chemical and instrumental methods, such as Fourier transform infrared spectroscopy, analysis of monosaccharide composition, and 1D/2D nuclear magnetic resonance spectroscopy. Chemical composition analysis indicated that AF-GAG is composed of iduronic acid (IdoA) and N-acetyl-glucosamine (GlcNAc) and its average molecular weight is 118kDa. Structural analysis clarified that the uronic acid unit in glycosaminoglycan (GAG) is the fully epimerized and the sequence of AF-GAG is →4)-α-GlcNAc (1→4)-α-IdoA2S (1→. Although its structure with a uniform repeating disaccharide is similar to those of heparin and heparan sulfate, this GAG is structurally highly regular and homogeneous. Anticoagulant activity assays indicated that AF-GAG exhibits no anticoagulant activities, but considering its structural characteristic, other bioactivities such as heparanase inhibition may be worthy of further study. Copyright © 2017 Elsevier Ltd. All rights reserved.

Silicon sheet growth development for the large area silicon sheet task of the low cost solar array project. Quantitative analysis of defects in silicon

NASA Technical Reports Server (NTRS)

Natesh, R.

1978-01-01

The various steps involved in obtaining quantitative information of structural defects in crystalline silicon samples are described. Procedures discussed include: (1) chemical polishing; (2) chemical etching; and (3) automated image analysis of samples on the QTM 720 System.

Core-shell SrTiO3/graphene structure by chemical vapor deposition for enhanced photocatalytic performance

NASA Astrophysics Data System (ADS)

He, Chenye; Bu, Xiuming; Yang, Siwei; He, Peng; Ding, Guqiao; Xie, Xiaoming

2018-04-01

Direct growth of high quality graphene on the surface of SrTiO3 (STO) was realized through chemical vapor deposition (CVD), to construct few-layer 'graphene shell' on every STO nanoparticle. The STO/graphene composite shows significantly enhanced UV light photocatalytic activity compared with the STO/rGO reference. Mechanism analysis confirms the role of special core-shell structure and chemical bond (Tisbnd C) for rapid interfacial electron transfer and effective electron-hole separation.

Design and analysis of a silicon-based antiresonant reflecting optical waveguide chemical sensor

NASA Astrophysics Data System (ADS)

Remley, Kate A.; Weisshaar, Andreas

1996-08-01

The design of a silicon-based antiresonant reflecting optical waveguide (ARROW) chemical sensor is presented, and its theoretical performance is compared with that of a conventional structure. The use of an ARROW structure permits incorporation of a thick guiding region for efficient coupling to a single-mode fiber. A high-index overlay is added to fine tune the sensitivity of the ARROW chemical sensor. The sensitivity of the sensor is presented, and design trade-offs are discussed.

[Studies on chemical constituents from leaves and stems of Aconitum coreanum].

PubMed

Li, Yan; Liang, Shuai

2009-05-01

To study the chemical constituents in the leaves and stems of Aconitum coreanum. The isolation and purification of chemical constituents were carried out on silica gel and polyamide column chromatographic. Their structures were identified by physico-chemical properties and spectral analysis. Five compounds were obtained and their structures were identified as guan-fu base I (1), guan-fu base R (2), beta-sitosterol (3), D-mannitol (4), daucosterol (5). Compound 2 is a new compound. Compounds 1 and 3, 4 are isolated from the leaves and stems of A. coreanum for the first time.

PubChem atom environments.

PubMed

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many seemingly due to erroneous interpretation of structures from patent data. Compared to fragmentation statistics published 40 years ago, the exponential growth in chemistry is mirrored in a nearly eightfold increase in the number of unique chemical fragments; however, this result is clearly an upper bound estimate as earlier studies employed structure sampling approaches and this study shows that a relatively high rate of atom fragments are found in only a single chemical structure (singletons). In addition, the percentage of singletons grows as the size of the chemical fragment is increased. The observed growth of the numbers of unique fragments over time suggests that many chemically possible connections of atom types to larger fragments have yet to be explored by chemists. A dramatic drop in the relative rate of increase of atom environments from smaller to larger fragments shows that larger fragments mainly consist of diverse combinations of a limited subset of smaller fragments. This is further supported by the observed concomitant increase of singleton atom environments. Combined, these findings suggest that there is considerable opportunity for chemists to combine known fragments to novel chemical compounds. The comparison of PubChem to an older study of known chemical structures shows noticeable differences. The changes suggest advances in synthetic capabilities of chemists to combine atoms in new patterns. Log-log plots of fragment incidence show small numbers of fragments are found in many structures and that large numbers of fragments are found in very few structures, with nearly half being novel using the methods in this work. The relative decrease in the count of new fragments as a function of size further suggests considerable opportunity for more novel chemicals exists. Lastly, the differences in atom environment diversity between PubChem Substance and Compound showcase the effect of PubChem standardization protocols, but also indicate that a normalization procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information.

Quantum-mechanics-derived 13Cα chemical shift server (CheShift) for protein structure validation

PubMed Central

Vila, Jorge A.; Arnautova, Yelena A.; Martin, Osvaldo A.; Scheraga, Harold A.

2009-01-01

A server (CheShift) has been developed to predict 13Cα chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the φ, ψ, ω, χ1 and χ2 torsional angles for all 20 naturally occurring amino acids. Their 13Cα chemical shifts were computed at the DFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regression formula, to reproduce the values obtained with a larger basis set. Analysis of the accuracy and sensitivity of the CheShift predictions, in terms of both the correlation coefficient R and the conformational-averaged rmsd between the observed and predicted 13Cα chemical shifts, was carried out for 3 sets of conformations: (i) 36 x-ray-derived protein structures solved at 2.3 Å or better resolution, for which sets of 13Cα chemical shifts were available; (ii) 15 pairs of x-ray and NMR-derived sets of protein conformations; and (iii) a set of decoys for 3 proteins showing an rmsd with respect to the x-ray structure from which they were derived of up to 3 Å. Comparative analysis carried out with 4 popular servers, namely SHIFTS, SHIFTX, SPARTA, and PROSHIFT, for these 3 sets of conformations demonstrated that CheShift is the most sensitive server with which to detect subtle differences between protein models and, hence, to validate protein structures determined by either x-ray or NMR methods, if the observed 13Cα chemical shifts are available. CheShift is available as a web server. PMID:19805131

Integrated chemical and multi-scale structural analyses for the processes of acid pretreatment and enzymatic hydrolysis of corn stover.

PubMed

Chen, Longjian; Li, Junbao; Lu, Minsheng; Guo, Xiaomiao; Zhang, Haiyan; Han, Lujia

2016-05-05

Corn stover was pretreated with acid under moderate conditions (1.5%, w/w, 121°C, 60min), and kinetic enzymolysis experiments were performed on the pretreated substrate using a mixture of Celluclast 1.5L (20FPU/g dry substrate) and Novozyme 188 (40CBU/g dry substrate). Integrated chemical and multi-scale structural methods were then used to characterize both processes. Chemical analysis showed that acid pretreatment removed considerable hemicellulose (from 19.7% in native substrate to 9.28% in acid-pretreated substrate) and achieved a reasonably high conversion efficiency (58.63% of glucose yield) in the subsequent enzymatic hydrolysis. Multi-scale structural analysis indicated that acid pretreatment caused structural changes via cleaving acetyl linkages, solubilizing hemicellulose, relocating cell wall surfaces and enlarging substrate porosity (pore volume increased from 0.0067cm(3)/g in native substrate to 0.019cm(3)/g in acid-pretreated substrate), thereby improving the polysaccharide digestibility. Copyright © 2016 Elsevier Ltd. All rights reserved.

Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

PubMed Central

Shen, Yang; Bax, Ad

2015-01-01

Summary Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors and the artificial neural network based TALOS-N program has been trained to extract backbone and sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

An Analysis of Chemical Ingredients Network of Chinese Herbal Formulae for the Treatment of Coronary Heart Disease

PubMed Central

Ding, Fan; Zhang, Qianru; Ung, Carolina Oi Lam; Wang, Yitao; Han, Yifan; Hu, Yuanjia; Qi, Jin

2015-01-01

As a complex system, the complicated interactions between chemical ingredients, as well as the potential rules of interactive associations among chemical ingredients of traditional Chinese herbal formulae are not yet fully understood by modern science. On the other hand, network analysis is emerging as a powerful approach focusing on processing complex interactive data. By employing network approach in selected Chinese herbal formulae for the treatment of coronary heart disease (CHD), this article aims to construct and analyze chemical ingredients network of herbal formulae, and provide candidate herbs, chemical constituents, and ingredient groups for further investigation. As a result, chemical ingredients network composed of 1588 ingredients from 36 herbs used in 8 core formulae for the treatment of CHD was produced based on combination associations in herbal formulae. In this network, 9 communities with relative dense internal connections are significantly associated with 14 kinds of chemical structures with P<0.001. Moreover, chemical structural fingerprints of network communities were detected, while specific centralities of chemical ingredients indicating different levels of importance in the network were also measured. Finally, several distinct herbs, chemical ingredients, and ingredient groups with essential position in the network or high centrality value are recommended for further pharmacology study in the context of new drug development. PMID:25658855

Toxmatch-a new software tool to aid in the development and evaluation of chemically similar groups.

PubMed

Patlewicz, G; Jeliazkova, N; Gallegos Saliner, A; Worth, A P

2008-01-01

Chemical similarity is a widely used concept in toxicology, and is based on the hypothesis that similar compounds should have similar biological activities. This forms the underlying basis for performing read-across, forming chemical groups and developing (Quantitative) Structure-Activity Relationships ((Q)SARs). Chemical similarity is often perceived as structural similarity but in fact there are a number of other approaches that can be used to assess similarity. A systematic similarity analysis usually comprises two main steps. Firstly the chemical structures to be compared need to be characterised in terms of relevant descriptors which encode their physicochemical, topological, geometrical and/or surface properties. A second step involves a quantitative comparison of those descriptors using similarity (or dissimilarity) indices. This work outlines the use of chemical similarity principles in the formation of endpoint specific chemical groupings. Examples are provided to illustrate the development and evaluation of chemical groupings using a new software application called Toxmatch that was recently commissioned by the European Chemicals Bureau (ECB), of the European Commission's Joint Research Centre. Insights from using this software are highlighted with specific focus on the prospective application of chemical groupings under the new chemicals legislation, REACH.

Investigating High-School Chemical Kinetics: The Greek Chemistry Textbook and Students' Difficulties

ERIC Educational Resources Information Center

Gegios, Theodoros; Salta, Katerina; Koinis, Spyros

2017-01-01

In this study we present an analysis of how the structure and content of the Greek school textbook approaches the concepts of chemical kinetics, and an investigation of the difficulties that 11th grade Greek students face regarding these concepts. Based on the structure and content of the Greek textbook, a tool was developed and applied to…

Nuclear magnetic resonance studies of phosphorus(v) pesticides. Part I. Chemical shifts of protons as a means of identification of pesticides

USGS Publications Warehouse

Babad, H.; Herbert, W.; Goldberg, M.C.

1968-01-01

Correlations of structural and proton chemical-hift data for 40 commercial phosphorus(V) pesticides are reported. Correlations of structure with the phosphorus coupling constants are discussed, and general trends are noted which aid in the use of NMR as a tool for identification and analysis of phosphorus(V) compounds. ?? 1968.

Dynamic mechanical analysis and organization/storage of data for polymetric materials

NASA Technical Reports Server (NTRS)

Rosenberg, M.; Buckley, W.

1982-01-01

Dynamic mechanical analysis was performed on a variety of temperature resistant polymers and composite resin matrices. Data on glass transition temperatures and degree of cure attained were derived. In addition a laboratory based computer system was installed and data base set up to allow entry of composite data. The laboratory CPU termed TYCHO is based on a DEC PDP 11/44 CPU with a Datatrieve relational data base. The function of TYCHO is integration of chemical laboratory analytical instrumentation and storage of chemical structures for modeling of new polymeric structures and compounds

Natural chemical shielding analysis of nuclear magnetic resonance shielding tensors from gauge-including atomic orbital calculations

NASA Astrophysics Data System (ADS)

Bohmann, Jonathan A.; Weinhold, Frank; Farrar, Thomas C.

1997-07-01

Nuclear magnetic shielding tensors computed by the gauge including atomic orbital (GIAO) method in the Hartree-Fock self-consistent-field (HF-SCF) framework are partitioned into magnetic contributions from chemical bonds and lone pairs by means of natural chemical shielding (NCS) analysis, an extension of natural bond orbital (NBO) analysis. NCS analysis complements the description provided by alternative localized orbital methods by directly calculating chemical shieldings due to delocalized features in the electronic structure, such as bond conjugation and hyperconjugation. Examples of NCS tensor decomposition are reported for CH4, CO, and H2CO, for which a graphical mnemonic due to Cornwell is used to illustrate the effect of hyperconjugative delocalization on the carbon shielding.

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

Understanding the NMR properties and conformational behavior of indole vs. azaindole group in protoberberines: NICS and NCS analysis

NASA Astrophysics Data System (ADS)

Kadam, Shivaji S.; Toušek, Jaromír; Maier, Lukáš; Pipíška, Matej; Sklenář, Vladimír; Marek, Radek

2012-11-01

We report here the preparation and the structural investigation into a series of 8-(indol-1-yl)-7,8-dihydroprotoberberine derivatives derived from berberine, palmatine, and coptisine. Structures of these new compounds were characterized mainly by 2D NMR spectroscopy and the conformational behavior was investigated by using methods of density-functional theory (DFT). PBE0/6-311+G** calculated NMR chemical shifts for selected derivatives correlate excellently with the experimental NMR data and support the structural conclusions drawn from the NMR experiments. An interesting role of the nitrogen atom in position N7' of the indole moiety in 8-(7-azaindol-1-yl)-7,8-dihydroprotoberberines as compared to other 8-indolyl derivatives is investigated in detail. The experimentally observed trends in NMR chemical shifts are rationalized by DFT calculations and analysis based on the nucleus-independent chemical shifts (NICS) and natural localized molecular orbitals (NLMOs).

Characterizing TPS Microstructure: A Review of Some techniques

NASA Technical Reports Server (NTRS)

Gasch, Matthew; Stackpole, Mairead; Agrawal, Parul; Chavez-Garcie, Jose

2011-01-01

I. When seeking to understand ablator microstructure and morphology there are several useful techniques A. SEM 1) Visual characteriza3on at various length scales. 2) Chemical mapping by backscatter or x-ray highlights areas of interest. 3) Combined with other techniques (density, weight change, chemical analysis) SEM is a powerful tool to aid in explaining thermo/structural data. B. ASAP. 1) Chemical characteriza3on at various length scales. 2) Chemical mapping of pore structure by gas adsorption. 3) Provides a map of pore size vs. pore volume. 4) Provided surface area of exposed TPS. II. Both methods help characterize and understand how ablators react with other chemical species and provides insight into how they oxidize.

High resolution Physio-chemical Tissue Analysis: Towards Non-invasive In Vivo Biopsy

NASA Astrophysics Data System (ADS)

Xu, Guan; Meng, Zhuo-Xian; Lin, Jian-Die; Deng, Cheri X.; Carson, Paul L.; Fowlkes, J. Brian; Tao, Chao; Liu, Xiaojun; Wang, Xueding

2016-02-01

Conventional gold standard histopathologic diagnosis requires information of both high resolution structural and chemical changes in tissue. Providing optical information at ultrasonic resolution, photoacoustic (PA) technique could provide highly sensitive and highly accurate tissue characterization noninvasively in the authentic in vivo environment, offering a replacement for histopathology. A two-dimensional (2D) physio-chemical spectrogram (PCS) combining micrometer to centimeter morphology and chemical composition simultaneously can be generated for each biological sample with PA measurements at multiple optical wavelengths. This spectrogram presents a unique 2D “physio-chemical signature” for any specific type of tissue. Comprehensive analysis of PCS, termed PA physio-chemical analysis (PAPCA), can lead to very rich diagnostic information, including the contents of all relevant molecular and chemical components along with their corresponding histological microfeatures, comparable to those accessible by conventional histology. PAPCA could contribute to the diagnosis of many diseases involving diffusive patterns such as fatty liver.

Conformational analysis, spectroscopic, structure-activity relations and quantum chemical simulation studies of 4-(trifluoromethyl)benzylamine

NASA Astrophysics Data System (ADS)

Arjunan, V.; Devi, L.; Mohan, S.

2018-05-01

The FT-IR and FT-Raman spectra of 4-trifluoromethylbenzylamine (TFMBA) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to attain stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers obtained theoretically from the B3LYP gradient calculations employing the standard high level 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra were also recorded. The electronic properties, highest occupied molecular orbital and lowest unoccupied molecular orbital energies are measured by DFT approach. The charges of the atoms by natural bond orbital (NBO) analysis are determined by B3LYP/cc-pVTZ method. The structure-chemical reactivity relations of the compound are determined through chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods.

Multivariate analysis of chromatographic retention data as a supplementary means for grouping structurally related compounds.

PubMed

Fasoula, S; Zisi, Ch; Sampsonidis, I; Virgiliou, Ch; Theodoridis, G; Gika, H; Nikitas, P; Pappa-Louisi, A

2015-03-27

In the present study a series of 45 metabolite standards belonging to four chemically similar metabolite classes (sugars, amino acids, nucleosides and nucleobases, and amines) was subjected to LC analysis on three HILIC columns under 21 different gradient conditions with the aim to explore whether the retention properties of these analytes are determined from the chemical group they belong. Two multivariate techniques, principal component analysis (PCA) and discriminant analysis (DA), were used for statistical evaluation of the chromatographic data and extraction similarities between chemically related compounds. The total variance explained by the first two principal components of PCA was found to be about 98%, whereas both statistical analyses indicated that all analytes are successfully grouped in four clusters of chemical structure based on the retention obtained in four or at least three chromatographic runs, which, however should be performed on two different HILIC columns. Moreover, leave-one-out cross-validation of the above retention data set showed that the chemical group in which an analyte belongs can be 95.6% correctly predicted when the analyte is subjected to LC analysis under the same four or three experimental conditions as the all set of analytes was run beforehand. That, in turn, may assist with disambiguation of analyte identification in complex biological extracts. Copyright © 2015 Elsevier B.V. All rights reserved.

Characterization of newly synthesized pyrimidine derivatives for corrosion inhibition as inferred from computational chemical analysis

NASA Astrophysics Data System (ADS)

El-Taib Heakal, F.; Rizk, S. A.; Elkholy, A. E.

2018-01-01

Corrosion of metallic constructions is a serious problem in most industries worldwide that can be controlled via addition of special chemicals having adsorption capability on metal surfaces and hence isolating it from the aggressive environment. These chemicals are characterized by being rich in functional groups containing free lone pairs of electrons and/or π-electrons. In the present study four newly imidazole-pyrimidine based ionic derivatives have been synthesized and their structures were characterized by means of elemental analysis and different spectroscopic techniques. Quantum chemical calculations were carried out to give insights into the structural and electronic characteristics of these fabricated compounds. Monte Carlo simulation was also applied to shed the light on our prepared corrosion inhibitor molecules by examining their aptitude to adsorb on iron surface. Our ultimate goal is to help industries in fighting corrosion by providing them with a cheap and efficient anti-corrosion molecules.

Combined use of computational chemistry and chemoinformatics methods for chemical discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugimoto, Manabu, E-mail: sugimoto@kumamoto-u.ac.jp; Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012

2015-12-31

Data analysis on numerical data by the computational chemistry calculations is carried out to obtain knowledge information of molecules. A molecular database is developed to systematically store chemical, electronic-structure, and knowledge-based information. The database is used to find molecules related to a keyword of “cancer”. Then the electronic-structure calculations are performed to quantitatively evaluate quantum chemical similarity of the molecules. Among the 377 compounds registered in the database, 24 molecules are found to be “cancer”-related. This set of molecules includes both carcinogens and anticancer drugs. The quantum chemical similarity analysis, which is carried out by using numerical results of themore » density-functional theory calculations, shows that, when some energy spectra are referred to, carcinogens are reasonably distinguished from the anticancer drugs. Therefore these spectral properties are considered of as important measures for classification.« less

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

PubMed

Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M; Weissman, Jonathan S; Rouskin, Silvi

2017-01-01

Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.

Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR) Methodology

PubMed Central

Wen, Jia-Long; Sun, Shao-Long; Xue, Bai-Liang; Sun, Run-Cang

2013-01-01

The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA), nitrobenzene oxidation (NBO), and derivatization followed by reductive cleavage (DFRC). Recent advances in nuclear magnetic resonance (NMR) technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (in situ), as well as their applications are reviewed. PMID:28809313

Direct and indirect influence of parental bedrock on streambed microbial community structure in forested streams.

PubMed

Mosher, Jennifer J; Findlay, Robert H

2011-11-01

A correlative study was performed to determine if variation in streambed microbial community structure in low-order forested streams can be directly or indirectly linked to the chemical nature of the parental bedrock of the environments through which the streams flow. Total microbial and photosynthetic biomass (phospholipid phosphate [PLP] and chlorophyll a), community structure (phospholipid fatty acid analysis), and physical and chemical parameters were measured in six streams, three located in sandstone and three in limestone regions of the Bankhead National Forest in northern Alabama. Although stream water flowing through the two different bedrock types differed significantly in chemical composition, there were no significant differences in total microbial and photosynthetic biomass in the sediments. In contrast, sedimentary microbial community structure differed between the bedrock types and was significantly correlated with stream water ion concentrations. A pattern of seasonal variation in microbial community structure was also observed. Further statistical analysis indicated dissolved organic matter (DOM) quality, which was previously shown to be influenced by geological variation, correlated with variation in bacterial community structure. These results indicate that the geology of underlying bedrock influences benthic microbial communities directly via changes in water chemistry and also indirectly via stream water DOM quality.

Oral LD50 toxicity modeling and prediction of per- and polyfluorinated chemicals on rat and mouse.

PubMed

Bhhatarai, Barun; Gramatica, Paola

2011-05-01

Quantitative structure-activity relationship (QSAR) analyses were performed using the LD(50) oral toxicity data of per- and polyfluorinated chemicals (PFCs) on rodents: rat and mouse. PFCs are studied under the EU project CADASTER which uses the available experimental data for prediction and prioritization of toxic chemicals for risk assessment by using the in silico tools. The methodology presented here applies chemometrical analysis on the existing experimental data and predicts the toxicity of new compounds. QSAR analyses were performed on the available 58 mouse and 50 rat LD(50) oral data using multiple linear regression (MLR) based on theoretical molecular descriptors selected by genetic algorithm (GA). Training and prediction sets were prepared a priori from available experimental datasets in terms of structure and response. These sets were used to derive statistically robust and predictive (both internally and externally) models. The structural applicability domain (AD) of the models were verified on 376 per- and polyfluorinated chemicals including those in REACH preregistration list. The rat and mouse endpoints were predicted by each model for the studied compounds, and finally 30 compounds, all perfluorinated, were prioritized as most important for experimental toxicity analysis under the project. In addition, cumulative study on compounds within the AD of all four models, including two earlier published models on LC(50) rodent analysis was studied and the cumulative toxicity trend was observed using principal component analysis (PCA). The similarities and the differences observed in terms of descriptors and chemical/mechanistic meaning encoded by descriptors to prioritize the most toxic compounds are highlighted.

Multi-component quantitation of meso/nanostructural surfaces and its application to local chemical compositions of copper meso/nanostructures self-organized on silica

NASA Astrophysics Data System (ADS)

Huang, Chun-Yi; Chang, Hsin-Wei; Chang, Che-Chen

2018-03-01

Knowledge about the chemical compositions of meso/nanomaterials is fundamental to development of their applications in advanced technologies. Auger electron spectroscopy (AES) is an effective analysis method for the characterization of meso/nanomaterial structures. Although a few studies have reported the use of AES for the analysis of the local composition of these structures, none have explored in detail the validity of the meso/nanoanalysis results generated by the AES instrument. This paper addresses the limitations of AES and the corrections necessary to offset them for this otherwise powerful meso/nanoanalysis tool. The results of corrections made to the AES multi-point analysis of high-density copper-based meso/nanostructures provides major insights into their local chemical compositions and technological prospects, which the primitive composition output of the AES instrument failed to provide.

Effect of mechanical activation on structure changes and reactivity in further chemical modification of lignin.

PubMed

Zhao, Xiaohong; Zhang, Yanjuan; Hu, Huayu; Huang, Zuqiang; Yang, Mei; Chen, Dong; Huang, Kai; Huang, Aimin; Qin, Xingzhen; Feng, Zhenfei

2016-10-01

Lignin was treated by mechanical activation (MA) in a customized stirring ball mill, and the structure and reactivity in further esterification were studied. The chemical structure and morphology of MA-treated lignin and the esterified products were analyzed by chemical analysis combined with UV/vis spectrometer, FTIR,NMR, SEM and particle size analyzer. The results showed that MA contributed to the increase of aliphatic hydroxyl, phenolic hydroxyl, carbonyl and carboxyl groups but the decrease of methoxyl groups. Moreover, MA led to the decrease of particle size and the increase of specific surface area and roughness of surface in lignin. The reactivity of lignin was enhanced significantly for the increase of hydroxyl content and the improvement of mass transfer in chemical reaction caused by the changes of molecular structure and morphological structure. The process of MA is green and simple, and is an effective method for enhancing the reactivity of lignin. Copyright © 2016 Elsevier B.V. All rights reserved.

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

PubMed Central

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; Sale, Kenneth L.; Yu, Eizadora T.

2016-01-01

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations. PMID:27507966

Density Functionals of Chemical Bonding

PubMed Central

Putz, Mihai V.

2008-01-01

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. PMID:19325846

The Pharmaceutical Industry in 2016. An Analysis of FDA Drug Approvals from a Perspective of the Molecule Type.

PubMed

Torre, Beatriz G de la; Albericio, Fernando

2017-02-27

This is an analysis from a chemical point of view of the 22 drugs accepted by the FDA during 2016. The different drugs from the 2016 "harvest" have been classified according to their chemical structure: antibodies; TIDES (oligonucleotides and peptides); amino acids and natural products; drug combination; and small molecules.

Structural analysis of an innate immunostimulant from broccoli, Brassica oleracea var. italica.

PubMed

Urai, Makoto; Kataoka, Keiko; Nishida, Satoshi; Sekimizu, Kazuhisa

2017-11-22

Vegetables are eaten as part of a healthy diet throughout the world, and some are also applied topically as a traditional medicine. We evaluated the innate immunostimulating activities of hot water extracts of various vegetables using the silkworm muscle contraction assay system, and found that broccoli, Brassica oleracea var. italica, contains a strong innate immunostimulant. We purified the innate immunostimulant from broccoli, and characterized the chemical structure by chemical analyses and NMR spectroscopy. The innate immunostimulant comprised galacturonic acid, galactose, glucose, arabinose, and rhamnose, and had a pectic-like polysaccharide structure. To determine the structural motif involved in the innate immunostimulating activity, we modified the structure by chemical and enzymatic treatment, and found that the activity was attenuated by pectinase digestion. These findings suggest that a pectic-like polysaccharide purified from broccoli has innate immune-stimulating activity, for which the polygalacturonic acid structure is necessary.

Composition analysis of a polymer electrolyte membrane fuel cell microporous layer using scanning transmission X-ray microscopy and near edge X-ray absorption fine structure analysis

NASA Astrophysics Data System (ADS)

George, Michael G.; Wang, Jian; Banerjee, Rupak; Bazylak, Aimy

2016-03-01

The novel application of scanning transmission X-ray microscopy (STXM) to the microporous layer (MPL) of a polymer electrolyte membrane fuel cell is investigated. A spatially resolved chemical component distribution map is obtained for the MPL of a commercially available SGL 25 BC sample. This is achieved with near edge X-ray absorption fine structure spectroscopic analysis. Prior to analysis the sample is embedded in non-reactive epoxy and ultra-microtomed to a thickness of 100 nm. Polytetrafluoroethylene (PTFE), carbon particle agglomerates, and supporting epoxy resin distributions are identified and reconstructed for a scanning area of 6 μm × 6 μm. It is observed that the spatial distribution of PTFE is strongly correlated to the carbon particle agglomerations. Additionally, agglomerate structures of PTFE are identified, possibly indicating the presence of a unique mesostructure in the MPL. STXM analysis is presented as a useful technique for the investigation of chemical species distributions in the MPL.

Elemental Analysis of Beryllium Samples Using a Microzond-EGP-10 Unit

NASA Astrophysics Data System (ADS)

Buzoverya, M. E.; Karpov, I. A.; Gorodnov, A. A.; Shishpor, I. V.; Kireycheva, V. I.

2017-12-01

Results concerning the structural and elemental analysis of beryllium samples obtained via different technologies using a Microzond-EGP-10 unit with the help of the PIXE and RBS methods are presented. As a result, the overall chemical composition and the nature of inclusions were determined. The mapping method made it possible to reveal the structural features of beryllium samples: to select the grains of the main substance having different size and chemical composition, to visualize the interfaces between the regions of different composition, and to describe the features of the distribution of impurities in the samples.

Determination of anisotropy and multimorphology in fly ash based geopolymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, M. Irfan, E-mail: mirfanwazir@gmail.com; Azizli, Khairun, E-mail: khairun-azizli@petronas.com.my; Sufian, Suriati, E-mail: suriati@petronas.com.my

2015-07-22

In this study, Malaysian coal fly ash-based geopolymers were investigated for its morphology and chemical composition using scanning electron microscopy coupled with energy dispersive X-rays (SEM-EDX). Geopolymer was synthesized using sodium hydroxide as activator. SEM studies revealed multiphasous structure of the material, composed of geopolymeric gel, partially reacted fly ashparticles and selectively leached particles. EDX analysis confirmed the chemical composition of different regions. Infra red spectroscopic studies supported the SEM-EDX analysis by confirming presence of unreacted quartzite and mullite in geopolymers. It is concluded that geopolymers possese a non uniform chemistry through out the structure.

Determination of anisotropy and multimorphology in fly ash based geopolymers

NASA Astrophysics Data System (ADS)

Khan, M. Irfan; Azizli, Khairun; Sufian, Suriati; Man, Zakaria; Siyal, Ahmer Ali; Ullah, Hafeez

2015-07-01

In this study, Malaysian coal fly ash-based geopolymers were investigated for its morphology and chemical composition using scanning electron microscopy coupled with energy dispersive X-rays (SEM-EDX). Geopolymer was synthesized using sodium hydroxide as activator. SEM studies revealed multiphasous structure of the material, composed of geopolymeric gel, partially reacted fly ashparticles and selectively leached particles. EDX analysis confirmed the chemical composition of different regions. Infra red spectroscopic studies supported the SEM-EDX analysis by confirming presence of unreacted quartzite and mullite in geopolymers. It is concluded that geopolymers possese a non uniform chemistry through out the structure.

Current Research into Chemical and Textual Information Retrieval at the Department of Information Studies, University of Sheffield.

ERIC Educational Resources Information Center

Lynch, Michael F.; Willett, Peter

1987-01-01

Discusses research into chemical information and document retrieval systems at the University of Sheffield. Highlights include the use of cluster analysis methods for document retrieval and drug design, representation and searching of files of generic chemical structures, and the application of parallel computer hardware to information retrieval.…

Interaction of ammonium with birnessite: Evidence of a chemical and structural transformation in alkaline aqueous medium

NASA Astrophysics Data System (ADS)

Boumaiza, Hella; Coustel, Romain; Despas, Christelle; Ruby, Christian; Bergaoui, Latifa

2018-02-01

The ammonium cation interaction with Na-birnessite in aqueous alkaline medium was studied. Solution and solid analysis give evidence that birnessite is not only acting as a cationic exchanger toward NH4+. The surface analysis performed by XPS showed that N1s spectra are characterized by the existence of two different environments: one assignable to an interlayer NH4+ and the second to a chemisorbed N-species. Structural and chemical transformations were observed on birnessite with nitrogen mass balance deficit. The monitoring of NH4+, Na+, Mn2+, NO3- and NO2- and solid changes (average oxidation state of Mn, cation exchange capacity, solid nitrogen content and symmetry evolution identified by XRD and FTIR) indicate unambiguously that NH4+ reacts chemically with the birnessite.

A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure.

PubMed

Hebels, Dennie G A J; Rasche, Axel; Herwig, Ralf; van Westen, Gerard J P; Jennen, Danyel G J; Kleinjans, Jos C S

2016-01-01

When evaluating compound similarity, addressing multiple sources of information to reach conclusions about common pharmaceutical and/or toxicological mechanisms of action is a crucial strategy. In this chapter, we describe a systems biology approach that incorporates analyses of hepatotoxicant data for 33 compounds from three different sources: a chemical structure similarity analysis based on the 3D Tanimoto coefficient, a chemical structure-based protein target prediction analysis, and a cross-study/cross-platform meta-analysis of in vitro and in vivo human and rat transcriptomics data derived from public resources (i.e., the diXa data warehouse). Hierarchical clustering of the outcome scores of the separate analyses did not result in a satisfactory grouping of compounds considering their known toxic mechanism as described in literature. However, a combined analysis of multiple data types may hypothetically compensate for missing or unreliable information in any of the single data types. We therefore performed an integrated clustering analysis of all three data sets using the R-based tool iClusterPlus. This indeed improved the grouping results. The compound clusters that were formed by means of iClusterPlus represent groups that show similar gene expression while simultaneously integrating a similarity in structure and protein targets, which corresponds much better with the known mechanism of action of these toxicants. Using an integrative systems biology approach may thus overcome the limitations of the separate analyses when grouping liver toxicants sharing a similar mechanism of toxicity.

Non-destructive analysis of the conformational differences among feedstock sources and their corresponding co-products from bioethanol production with molecular spectroscopy.

PubMed

Gamage, I H; Jonker, A; Zhang, X; Yu, P

2014-01-24

The objective of this study was to determine the possibility of using molecular spectroscopy with multivariate technique as a fast method to detect the source effects among original feedstock sources of wheat and their corresponding co-products, wheat DDGS, from bioethanol production. Different sources of the bioethanol feedstock and their corresponding bioethanol co-products, three samples per source, were collected from the same newly-built bioethanol plant with current bioethanol processing technology. Multivariate molecular spectral analyses were carried out using agglomerative hierarchical cluster analysis (AHCA) and principal component analysis (PCA). The molecular spectral data of different feedstock sources and their corresponding co-products were compared at four different regions of ca. 1800-1725 cm(-1) (carbonyl CO ester, mainly related to lipid structure conformation), ca. 1725-1482 cm(-1) (amide I and amide II region mainly related to protein structure conformation), ca. 1482-1180 cm(-1) (mainly associated with structural carbohydrate) and ca. 1180-800 cm(-1) (mainly related to carbohydrates) in complex plant-based system. The results showed that the molecular spectroscopy with multivariate technique could reveal the structural differences among the bioethanol feedstock sources and among their corresponding co-products. The AHCA and PCA analyses were able to distinguish the molecular structure differences associated with chemical functional groups among the different sources of the feedstock and their corresponding co-products. The molecular spectral differences indicated the differences in functional, biomolecular and biopolymer groups which were confirmed by wet chemical analysis. These biomolecular and biopolymer structural differences were associated with chemical and nutrient profiles and nutrient utilization and availability. Molecular spectral analyses had the potential to identify molecular structure difference among bioethanol feedstock sources and their corresponding co-products. Copyright © 2013 Elsevier B.V. All rights reserved.

Non-destructive analysis of the conformational differences among feedstock sources and their corresponding co-products from bioethanol production with molecular spectroscopy

NASA Astrophysics Data System (ADS)

Gamage, I. H.; Jonker, A.; Zhang, X.; Yu, P.

2014-01-01

The objective of this study was to determine the possibility of using molecular spectroscopy with multivariate technique as a fast method to detect the source effects among original feedstock sources of wheat and their corresponding co-products, wheat DDGS, from bioethanol production. Different sources of the bioethanol feedstock and their corresponding bioethanol co-products, three samples per source, were collected from the same newly-built bioethanol plant with current bioethanol processing technology. Multivariate molecular spectral analyses were carried out using agglomerative hierarchical cluster analysis (AHCA) and principal component analysis (PCA). The molecular spectral data of different feedstock sources and their corresponding co-products were compared at four different regions of ca. 1800-1725 cm-1 (carbonyl Cdbnd O ester, mainly related to lipid structure conformation), ca. 1725-1482 cm-1 (amide I and amide II region mainly related to protein structure conformation), ca. 1482-1180 cm-1 (mainly associated with structural carbohydrate) and ca. 1180-800 cm-1 (mainly related to carbohydrates) in complex plant-based system. The results showed that the molecular spectroscopy with multivariate technique could reveal the structural differences among the bioethanol feedstock sources and among their corresponding co-products. The AHCA and PCA analyses were able to distinguish the molecular structure differences associated with chemical functional groups among the different sources of the feedstock and their corresponding co-products. The molecular spectral differences indicated the differences in functional, biomolecular and biopolymer groups which were confirmed by wet chemical analysis. These biomolecular and biopolymer structural differences were associated with chemical and nutrient profiles and nutrient utilization and availability. Molecular spectral analyses had the potential to identify molecular structure difference among bioethanol feedstock sources and their corresponding co-products.

Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery.

PubMed

Perualila-Tan, Nolen Joy; Shkedy, Ziv; Talloen, Willem; Göhlmann, Hinrich W H; Moerbeke, Marijke Van; Kasim, Adetayo

2016-08-01

The modern process of discovering candidate molecules in early drug discovery phase includes a wide range of approaches to extract vital information from the intersection of biology and chemistry. A typical strategy in compound selection involves compound clustering based on chemical similarity to obtain representative chemically diverse compounds (not incorporating potency information). In this paper, we propose an integrative clustering approach that makes use of both biological (compound efficacy) and chemical (structural features) data sources for the purpose of discovering a subset of compounds with aligned structural and biological properties. The datasets are integrated at the similarity level by assigning complementary weights to produce a weighted similarity matrix, serving as a generic input in any clustering algorithm. This new analysis work flow is semi-supervised method since, after the determination of clusters, a secondary analysis is performed wherein it finds differentially expressed genes associated to the derived integrated cluster(s) to further explain the compound-induced biological effects inside the cell. In this paper, datasets from two drug development oncology projects are used to illustrate the usefulness of the weighted similarity-based clustering approach to integrate multi-source high-dimensional information to aid drug discovery. Compounds that are structurally and biologically similar to the reference compounds are discovered using this proposed integrative approach.

Advanced thermally stable jet fuels. Technical progress report, January 1995--March 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schobert, H.H.; Eser, S.; Song, C.

Quantitative structure-property relationships have been applied to study the thermal stability of pure hydrocarbons typical of jet fuel components. A simple method of chemical structure description in terms of Benson groups was tested in searching for structure-property relationships for the hydrocarbons tested experimentally in this program. Molecular connectivity as a structure-based approach to chemical structure-property relationship analysis was also tested. Further development of both the experimental data base and computational methods will be necessary. Thermal decomposition studies, using glass tube reactors, were extended to two additional model compounds: n-decane and n-dodecane. Efforts on refining the deposit growth measurement and characterizationmore » of suspended matter in stressed fuels have lead to improvements in the analysis of stressed fuels. Catalytic hydrogenation and dehydrogenation studies utilizing a molybdenum sulfide catalyst are also described.« less

Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.

PubMed

Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

2012-10-24

The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory.

Chemical synthesis and NMR characterization of structured polyunsaturated triacylglycerols.

PubMed

Fauconnot, Laëtitia; Robert, Fabien; Villard, Renaud; Dionisi, Fabiola

2006-02-01

The chemical synthesis of pure triacylglycerol (TAG) regioisomers, that contain long chain polyunsaturated fatty acids, such as arachidonic acid (AA) or docosahexaenoic acid (DHA), and saturated fatty acids, such as lauric acid (La) or palmitic acid (P), at defined positions, is described. A single step methodology using (benzotriazol-1-yloxy)-tripyrrolidinophosphonium hexafluorophosphate (PyBOP), an activator of carboxyl group commonly used in peptide synthesis and occasionally used in carboxylic acid esterification, has been developed for structured TAG synthesis. Identification of the fatty acyl chains for each TAG species was confirmed by atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) and fatty acid positional distribution was determined by (1)H and (13)C NMR spectra. The generic described procedures can be applied to a large variety of substrates and was used for the production of specific triacylglycerols of defined molecular structures, with high regioisomeric purity. Combination of MS and NMR was shown to be an efficient tool for structural analysis of TAG. In particular, some NMR signals were demonstrated to be regioisomer specific, allowing rapid positional analysis of LC-PUFA containing TAG.

Chemical structure of interfaces

NASA Technical Reports Server (NTRS)

Grunthaner, F. J.

1985-01-01

The interfacial structure of silicon/dielectric and silicon/metal systems is particularly amenable to analysis using a combination of surface spectroscopies together with a variety of chemical structures of Si/SiO2, Si/SiO2Si3N4, Si/Si2N2O, Si/SiO2/Al, and Si/Native Oxide interfaces using high resolution (0.350 eV FWHM) X ray photoelectron spectroscopy. The general structure of these dielectric interfaces entails a monolayer chemical transition layer at the Si/dielectric boundary. Amorphous Si substrates show a wide variety of hydrogenated Si and Si(OH) sub x states that are not observed in thermal oxidation of single crystal material. Extended SiO2 layers greater than 8 A in thickness are shown to be stoichiometric SiO2, but to exhibit a wide variety of local network structures. In the nitrogen containing systems, an approach to stoichiometric oxynitride compounds with interesting impurity and electron trapping properties are seen. In native oxides, substantial topographical nonuniformity in oxide thickness and composition are found. Analysis of metal/oxide interfacial layers is accomplished by analytical removal of the Si substrate by UHV XeF2 dry etching methods.

Persistent hydrogen bonding in polymorphic crystal structures.

PubMed

Galek, Peter T A; Fábián, László; Allen, Frank H

2009-02-01

The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability.

Photoelectron spectra and biological activity of cinnamic acid derivatives revisited

NASA Astrophysics Data System (ADS)

Novak, Igor; Klasinc, Leo; McGlynn, Sean P.

2018-01-01

The electronic structures of several derivatives of cinnamic acid have been studied by UV photoelectron spectroscopy (UPS) and Green's function quantum chemical calculations. The spectra reveal the presence of dimers in the gas phase for p-coumaric and ferulic acids. The electronic structure analysis has been related to the biological properties of these compounds through the analysis of some structure-activity relationships (SAR).

Development of a Searchable Metabolite Database and Simulator of Xenobiotic Metabolism

EPA Science Inventory

A computational tool (MetaPath) has been developed for storage and analysis of metabolic pathways and associated metadata. The system is capable of sophisticated text and chemical structure/substructure searching as well as rapid comparison of metabolites formed across chemicals,...

In vitro Cytotoxicity and Genotoxicity Analysis of Ten Tannery Chemicals Using SOS/umu Tests and High-content In vitro Micronucleus Tests.

PubMed

Huang, Zehao; Li, Na; Rao, Kaifeng; Liu, Cuiting; Wang, Zijian; Ma, Mei

2018-01-01

More than 2,000 chemicals have been used in the tannery industry. Although some tannery chemicals have been reported to have harmful effects on both human health and the environment, only a few have been subjected to genotoxicity and cytotoxicity evaluations. This study focused on cytotoxicity and genotoxicity of ten tannery chemicals widely used in China. DNA-damaging effects were measured using the SOS/umu test with Salmonella typhimurium TA1535/pSK1002. Chromosome-damaging and cytotoxic effects were determined with the high-content in vitro Micronucleus test (MN test) using the human-derived cell lines MGC-803 and A549. The cytotoxicity of the ten tannery chemicals differed somewhat between the two cell assays, with A549 cells being more sensitive than MGC-803 cells. None of the chemicals induced DNA damage before metabolism, but one was found to have DNA-damaging effects on metabolism. Four of the chemicals, DY64, SB1, DB71 and RR120, were found to have chromosome-damaging effects. A Quantitative Structure-Activity Relationship (QSAR) analysis indicated that one structural feature favouring chemical genotoxicity, Hacceptor-path3-Hacceptor, may contribute to the chromosome-damaging effects of the four MN-test-positive chemicals. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Advancements in mass spectrometry for biological samples: Protein chemical cross-linking and metabolite analysis of plant tissues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klein, Adam

2015-01-01

This thesis presents work on advancements and applications of methodology for the analysis of biological samples using mass spectrometry. Included in this work are improvements to chemical cross-linking mass spectrometry (CXMS) for the study of protein structures and mass spectrometry imaging and quantitative analysis to study plant metabolites. Applications include using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to further explore metabolic heterogeneity in plant tissues and chemical interactions at the interface between plants and pests. Additional work was focused on developing liquid chromatography-mass spectrometry (LC-MS) methods to investigate metabolites associated with plant-pest interactions.

[Studies on chemical constituents from Elaeocarpus sylvestris].

PubMed

Zhang, Hong-Chao; Shi, Hai-Ming

2008-10-01

To study the chemical constituents of Elaeocarpus sylvestris. The compounds were isolated by chromatographic methods and their structures were elucidated by physico-chemical properties and spectral analysis. Six compounds were isolated and identified as: 2-hydroxy-benzaldehyde (1), coniferyl alcohol (2), umbelliferone (3), scopoletin (4), beta-sitosterol (5), daucosterol (6). All above compounds are isolated from Elaeocarpus Genus for the first time.

Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gasparotto, Piero; Ceriotti, Michele, E-mail: michele.ceriotti@epfl.ch

The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogenmore » bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.« less

Recognizing molecular patterns by machine learning: an agnostic structural definition of the hydrogen bond.

PubMed

Gasparotto, Piero; Ceriotti, Michele

2014-11-07

The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding--a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

Structural landscape of base pairs containing post-transcriptional modifications in RNA

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. PMID:28341704

Cross-Linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path through the Maze

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merkley, Eric D.; Cort, John R.; Adkins, Joshua N.

2013-09-01

Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature.more » These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.« less

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE PAGES

Foston, Marcus B.; Samuel, Reichel; He, Jian; ...

2016-01-19

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foston, Marcus B.; Samuel, Reichel; He, Jian

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

Structural and Mössbauer analysis of pure and Ce-Dy doped cobalt ferrite nanoparticles

NASA Astrophysics Data System (ADS)

Hashim, Mohd.; Meena, Sher Singh; Kumar, Shalendra; Ahmed, Ateeq; Bhatt, Pramod

2018-05-01

Ce and Dy doped Cobalt ferrites with the chemical composition CoCexDyxFe2-2xO4 (x = 0.00 and 0.04) were synthesized via the chemical route using citrate-gel auto-combustion method. The structural analysis has been carried out with the help of x-ray diffraction (XRD). Formation of spinel cubic structure of the ferrites was confirmed by XRD analysis. Mössbauer spectra were recorded for both samples at room temperature. Presence of the well resolved sextet spectra corresponding to A and B sub-lattice clearly shows that both the samples have ferrimagnetic ordering at room temperature. Isomer shift observed from fitting of the Mössbauer spectra infers that Fe3+ ions are in high valence state. The decrease in the hyperfine field due to the doping of Ce and Dy clearly showed that magnetic interactions diluted due to the doping of Ce and Dy ions.

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

PubMed Central

Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M.; Weissman, Jonathan S.; Rouskin, Silvi

2017-01-01

Coupling structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structural studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduces biases and necessitates population-average assessments of RNA structure. Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in non-canonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs to their mature isoforms. These applications illustrate DMS-MaPseq’s capacity to dramatically expand in vivo analysis of RNA structure. PMID:27819661

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid.

PubMed

Stevens, Joanna S; Gainar, Adrian; Suljoti, Edlira; Xiao, Jie; Golnak, Ronny; Aziz, Emad F; Schroeder, Sven L M

2015-05-04

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO-LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute-solvent interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p -Aminobenzoic Acid

DOE PAGES

Stevens, Joanna S.; Gainar, Adrian; Suljoti, Edlira; ...

2015-03-18

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs andmore » σ* shape resonances in the NEXAFS spectra. Finally, this provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.« less

A new stilbenoid from Arundina graminifolia.

PubMed

Liu, Mei-Feng; Han, Yun; Xing, Dong-Ming; Shi, Yue; Xu, Li-Zhen; Du, Li-Jun; Ding, Yi

2004-09-01

A chemical investigation of the Orchidaceae Arundina gramnifolia has led to the isolation of a novel stilbenoid, named arundinan (1). The structure of 1 has been elucidated as 2-(p-hydroxybenzyl)-3-hydroxy-5-methoxybibenzyl on the basis of physical and chemical evidence and spectral analysis.

Factors affecting the use of 13Cα chemical shifts to determine, refine, and validate protein structures

PubMed Central

Vila, Jorge A.; Scheraga, Harold A.

2008-01-01

Interest centers here on the analysis of two different, but related, phenomena that affect side-chain conformations and consequently 13Cα chemical shifts and their applications to determine, refine, and validate protein structures. The first is whether 13Cα chemical shifts, computed at the DFT level of approximation with charged residues is a better approximation of observed 13Cα chemical shifts than those computed with neutral residues for proteins in solution. Accurate computation of 13Cα chemical shifts requires a proper representation of the charges, which might not take on integral values. For this analysis, the charges for 139 conformations of the protein ubiquitin were determined by explicit consideration of protein binding equilibria, at a given pH, that is, by exploring the 2ξ possible ionization states of the whole molecule, with ξ being the number of ionizable groups. The results of this analysis, as revealed by the shielding/deshield-ing of the 13Cα nucleus, indicated that: (i) there is a significant difference in the computed 13Cα chemical shifts, between basic and acidic groups, as a function of the degree of charge of the side chain; (ii) this difference is attributed to the distance between the ionizable groups and the 13Cα nucleus, which is shorter for the acidic Asp and Glu groups as compared with that for the basic Lys and Arg groups; and (iii) the use of neutral, rather than charged, basic and acidic groups is a better approximation of the observed 13Cα chemical shifts of a protein in solution. The second is how side-chain flexibility influences computed 13Cα chemical shifts in an additional set of ubiquitin conformations, in which the side chains are generated from an NMR-derived structure with the backbone conformation assumed to be fixed. The 13Cα chemical shift of a given amino acid residue in a protein is determined, mainly, by its own backbone and side-chain torsional angles, independent of the neighboring residues; the conformation of a given residue itself, however, depends on the environment of this residue and, hence, on the whole protein structure. As a consequence, this analysis reveals the role and impact of an accurate side-chain computation in the determination and refinement of protein conformation. The results of this analysis are: (i) a lower error between computed and observed 13Cα chemical shifts (by up to 3.7 ppm), was found for ~68% and ~63% of all ionizable residues and all non-Ala/Pro/Gly residues, respectively, in the additional set of conformations, compared with results for the model from which the set was derived; and (ii) all the additional conformations exhibit a lower root-mean-square-deviation (1.97 ppm ≤ rmsd ≤ 2.13 ppm), between computed and observed 13Cα chemical shifts, than the rmsd (2.32 ppm) computed for the starting conformation from which this additional set was derived. As a validation test, an analysis of the additional set of ubiquitin conformations, comparing computed and observed values of both 13Cα chemical shifts and χ1 torsional angles (given by the vicinal coupling constants, 3JN–Cγ and 3JC′–Cγ, is discussed. PMID:17975838

Thai students' mental model of chemical bonding

NASA Astrophysics Data System (ADS)

Sarawan, Supawadee; Yuenyong, Chokchai

2018-01-01

This Research was finding the viewing about concept of chemical bonding is fundamental to subsequent learning of various other topics related to this concept in chemistry. Any conceptions about atomic structures that students have will be shown their further learning. The purpose of this study is to interviews conceptions held by high school chemistry students about metallic bonding and to reveal mental model of atomic structures show according to the educational level. With this aim, the questionnaire prepared making use of the literature and administered for analysis about mental model of chemical bonding. It was determined from the analysis of answers of questionnaire the 10th grade, 11th grade and 12th grade students. Finally, each was shown prompts in the form of focus cards derived from curriculum material that showed ways in which the bonding in specific metallic substances had been depicted. Students' responses revealed that learners across all three levels prefer simple, realistic mental models for metallic bonding and reveal to chemical bonding.

Predominant information quality scheme for the essential amino acids: an information-theoretical analysis.

PubMed

Esquivel, Rodolfo O; Molina-Espíritu, Moyocoyani; López-Rosa, Sheila; Soriano-Correa, Catalina; Barrientos-Salcedo, Carolina; Kohout, Miroslav; Dehesa, Jesús S

2015-08-24

In this work we undertake a pioneer information-theoretical analysis of 18 selected amino acids extracted from a natural protein, bacteriorhodopsin (1C3W). The conformational structures of each amino acid are analyzed by use of various quantum chemistry methodologies at high levels of theory: HF, M062X and CISD(Full). The Shannon entropy, Fisher information and disequilibrium are determined to grasp the spatial spreading features of delocalizability, order and uniformity of the optimized structures. These three entropic measures uniquely characterize all amino acids through a predominant information-theoretic quality scheme (PIQS), which gathers all chemical families by means of three major spreading features: delocalization, narrowness and uniformity. This scheme recognizes four major chemical families: aliphatic (delocalized), aromatic (delocalized), electro-attractive (narrowed) and tiny (uniform). All chemical families recognized by the existing energy-based classifications are embraced by this entropic scheme. Finally, novel chemical patterns are shown in the information planes associated with the PIQS entropic measures. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical structure, biosynthesis and synthesis of free and glycosylated pyridinolines formed by cross-link of bone and synovium collagen.

PubMed

Anastasia, Luigi; Rota, Paola; Anastasia, Mario; Allevi, Pietro

2013-09-21

This review focuses on the chemical structure, biosynthesis and synthesis of free and glycosylated pyridinolines (Pyds), fluorescent collagen cross-links, with a pyridinium salt structure. Pyds derive from the degradation of bone collagen and have attracted attention for their use as biochemical markers of bone resorption and to assess fracture risk prediction in persons suffering from osteoporosis, bone cancer and other bone or collagen diseases. We consider and critically discuss all reported syntheses of free and glycosylated Pyds evidencing an unrevised chemistry, original and of general utility, analysis of which allows us to also support a previously suggested non-enzymatic formation of Pyds in collagen better rationalizing and justifying the chemical events.

Chemical Dynamics of nano-Aluminum and Iodine Based Oxidizers

NASA Astrophysics Data System (ADS)

Little, Brian; Ridge, Claron; Overdeep, Kyle; Slizewski, Dylan; Lindsay, Michael

2017-06-01

As observed in previous studies of nanoenergetic powder composites, micro/nano-structural features such as particle morphology and/or reactant spatial distance are expected to strongly influence properties that govern the combustion behavior of energetic materials (EM). In this study, highly reactive composites containing crystalline iodine (V) oxide or iodate salts with nano-sized aluminum (nAl) were blended by two different processing techniques and then collected as a powder for characterization. Physiochemical techniques such as thermal gravimetric analysis, calorimetry, X-ray diffraction, electron microscopy, high speed photography, pressure profile analysis, temperature programmed reactions, and spectroscopy were employed to characterize these EM with emphasis on correlating the chemical reactivity with inherent structural features and variations in stoichiometry. This work is a continuation of efforts to probe the chemical dynamics of nAl-iodine based composites.

Structural characterization and mechanical performance of calcium phosphate scaffolds and natural bones: a comparative study.

PubMed

Fuentes, Elena; Sáenz de Viteri, Virginia; Igartua, Amaya; Martinetti, Roberta; Dolcini, Laura; Barandika, Gotzone

2010-01-01

The knowledge of the mechanical response of bones and their substitutes is pertinent to numerous medical problems. Understanding the effects of mechanical influence on the body is the first step toward developing innovative treatment and rehabilitation concepts for orthopedic disorders. This was a comparative study of 5 synthetic scaffolds based on porous calcium phosphates and natural bones, with regard to their microstructural, chemical, and mechanical characterizations. The structural and chemical characterizations of the scaffolds were examined by means of X-ray diffraction, scanning electron microscopy, and X-ray spectroscopy analysis. The mechanical characterization of bones and bone graft biomaterials was carried out through compression tests using samples with noncomplex geometry. Analysis of the chemical composition, surface features, porosity, and compressive strength indicates that hydroxyapatite-based materials and trabecular bone have similar properties.

Cheminformatic comparison of approved drugs from natural product versus synthetic origins.

PubMed

Stratton, Christopher F; Newman, David J; Tan, Derek S

2015-11-01

Despite the recent decline of natural product discovery programs in the pharmaceutical industry, approximately half of all new drug approvals still trace their structural origins to a natural product. Herein, we use principal component analysis to compare the structural and physicochemical features of drugs from natural product-based versus completely synthetic origins that were approved between 1981 and 2010. Drugs based on natural product structures display greater chemical diversity and occupy larger regions of chemical space than drugs from completely synthetic origins. Notably, synthetic drugs based on natural product pharmacophores also exhibit lower hydrophobicity and greater stereochemical content than drugs from completely synthetic origins. These results illustrate that structural features found in natural products can be successfully incorporated into synthetic drugs, thereby increasing the chemical diversity available for small-molecule drug discovery. Copyright © 2015 Elsevier Ltd. All rights reserved.

Self-organizing ontology of biochemically relevant small molecules

PubMed Central

2012-01-01

Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology can ease the burden of chemical data annotators and dramatically increase their productivity. We anticipate that the use of formal logic in our proposed framework will make chemical classification criteria more transparent to humans and machines alike and will thus facilitate predictive and integrative bioactivity model development. PMID:22221313

Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction

NASA Astrophysics Data System (ADS)

Minitti, M. P.; Budarz, J. M.; Kirrander, A.; Robinson, J. S.; Ratner, D.; Lane, T. J.; Zhu, D.; Glownia, J. M.; Kozina, M.; Lemke, H. T.; Sikorski, M.; Feng, Y.; Nelson, S.; Saita, K.; Stankus, B.; Northey, T.; Hastings, J. B.; Weber, P. M.

2015-06-01

Structural rearrangements within single molecules occur on ultrafast time scales. Many aspects of molecular dynamics, such as the energy flow through excited states, have been studied using spectroscopic techniques, yet the goal to watch molecules evolve their geometrical structure in real time remains challenging. By mapping nuclear motions using femtosecond x-ray pulses, we have created real-space representations of the evolving dynamics during a well-known chemical reaction and show a series of time-sorted structural snapshots produced by ultrafast time-resolved hard x-ray scattering. A computational analysis optimally matches the series of scattering patterns produced by the x rays to a multitude of potential reaction paths. In so doing, we have made a critical step toward the goal of viewing chemical reactions on femtosecond time scales, opening a new direction in studies of ultrafast chemical reactions in the gas phase.

Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction.

PubMed

Minitti, M P; Budarz, J M; Kirrander, A; Robinson, J S; Ratner, D; Lane, T J; Zhu, D; Glownia, J M; Kozina, M; Lemke, H T; Sikorski, M; Feng, Y; Nelson, S; Saita, K; Stankus, B; Northey, T; Hastings, J B; Weber, P M

2015-06-26

Structural rearrangements within single molecules occur on ultrafast time scales. Many aspects of molecular dynamics, such as the energy flow through excited states, have been studied using spectroscopic techniques, yet the goal to watch molecules evolve their geometrical structure in real time remains challenging. By mapping nuclear motions using femtosecond x-ray pulses, we have created real-space representations of the evolving dynamics during a well-known chemical reaction and show a series of time-sorted structural snapshots produced by ultrafast time-resolved hard x-ray scattering. A computational analysis optimally matches the series of scattering patterns produced by the x rays to a multitude of potential reaction paths. In so doing, we have made a critical step toward the goal of viewing chemical reactions on femtosecond time scales, opening a new direction in studies of ultrafast chemical reactions in the gas phase.

Chemical imaging of molecular changes in a hydrated single cell by dynamic secondary ion mass spectrometry and super-resolution microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hua, Xin; Szymanski, Craig; Wang, Zhaoying

2016-01-01

Chemical imaging of single cells is important in capturing biological dynamics. Single cell correlative imaging is realized between structured illumination microscopy (SIM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) using System for Analysis at the Liquid Vacuum Interface (SALVI), a multimodal microreactor. SIM characterized cells and guided subsequent ToF-SIMS analysis. Dynamic ToF-SIMS provided time- and space-resolved cell molecular mapping. Lipid fragments were identified in the hydrated cell membrane. Principal component analysis was used to elucidate chemical component differences among mouse lung cells that uptake zinc oxide nanoparticles. Our results provided submicron chemical spatial mapping for investigations of cell dynamics atmore » the molecular level.« less

A new chalcone structure of (E)-1-(4-Bromophenyl)-3-(napthalen-2-yl)prop-2-en-1-one: Synthesis, structural characterizations, quantum chemical investigations and biological evaluations.

PubMed

Thanigaimani, Kaliyaperumal; Arshad, Suhana; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Arunagiri, C; Subashini, A; Sulaiman, Shaida Fariza; Hashim, Nurul Shafiqah; Ooi, Kheng Leong

2015-01-01

The structure of (E)-1-(4-Bromophenyl)-3-(napthalen-2-yl)prop-2-en-1-one (C19H13BrO) crystallized in the triclinic system of P-1 space group. The unit cell dimensions are: a=5.8944 (9)Å, b=7.8190 (12)Å, c=16.320 (2)Å, α=102.4364 (19)°, β=95.943 (2)°, γ=96.274 (2)° and Z=2. The physical properties of this compound was determined by the spectroscopic methods (FTIR and (1)H and (13)C NMR). Quantum chemical investigations have been employed to investigate the structural and spectral properties. The molecular structure, vibrational assignments, (1)H and (13)C NMR chemical shift values, non-linear optical (NLO) effect, HOMO-LUMO analysis and natural bonding orbital (NBO) analysis were calculated using HF and DFT/B3LYP methods with 6-311++G(d,p) basis set in the ground state. The results show that the theoretical calculation of the geometrical parameters, vibrational frequencies and chemical shifts are comparable with the experimental data. The crystal structure is influenced and stabilized by weak C-H⋯π interactions connecting the molecules into infinite supramolecular one dimensional ladder-like arrangement. Additionally, this compound is evaluated for their antibacterial activities against gram positive and gram negative strains using a micro dilution procedure and shows activities against a panel of microorganisms. Copyright © 2015 Elsevier B.V. All rights reserved.

The Use of Bayesian Methods for Uncertainty Analysis and Evaluation of Biological Hypotheses in PBPK Models

EPA Science Inventory

Physiologically based pharmacokinetic (PBPK) models are compartmental models that describe the uptake and distribution of drugs and chemicals throughout the body. They can be structured so that model parameters (i.e., physiological and chemical-specific) reflect biological charac...

Precise structural analysis of α-helical polypeptide by quantum-chemical calculation related to reciprocal side-chain combination of two L-phenylalanine residues

NASA Astrophysics Data System (ADS)

Niimura, Subaru; Kurosu, Hiromichi; Shoji, Akira

2010-04-01

To clarify the positive role of side-chain conformation in the stability of protein secondary structure (main-chain conformation), we successfully calculated the optimization structure of a series of well-defined α-helical octadecapeptides composed of two L-phenylalanine (Phe) and 16 L-alanine (Ala) residues, based on the molecular orbital calculation with density functional theory (DFT/B3LYP/6-31G(d)). From the total energy calculation and the precise secondary structural analysis, we found that the conformational stability of the α-helix is closely related to the reciprocal side-chain combinations (such as positional relation and side-chain conformation) of two Phe residues in this system. Furthermore, we demonstrated that the 1H, 13C, 15N and 17O isotropic chemical shifts of each Phe residue depend on the respective side-chain conformations of the Phe residue.

[n-Butyl Alcohol-soluble Chemical Constituents of Psidium guajava Leaves].

PubMed

Chen, Gang; Wan, Kai-hua; Fu, Hui-zheng; Yan, Qing-wei

2015-03-01

To study the chemical constituents of the leaves of Psidium guajava. The chemical constituents were isolated by column chromatography on silica gel, Sephadex LH-20 and MPLC. Their chemical structures were elucidated on the basis of special analysis. Seven compounds were isolated from n-butyl alcohol fraction, whose structures were elucidated as morin-3-O-α-L-arabopyranoside (1), morin-3-O-α-L-iyxopyranoside (2), 2,6-dihydroxy-4-O-β-D-glucopyranosyl-benzophenone (3), casuarictin (4),2,6-dihydroxy-3,5-dimethyl-4-O-(6"-O-galloyl-β-D-glucopyranosyl)-benzophenone(5), globulusin A(6), and kaempferol-3-O-β-D-(6"-galloyl) galactopyranoside (7). Compounds 3 and 5 ~ 7 are isolated from this plant for the first time.

Simulation and analysis of chemical release in the ionosphere

NASA Astrophysics Data System (ADS)

Gao, Jing-Fan; Guo, Li-Xin; Xu, Zheng-Wen; Zhao, Hai-Sheng; Feng, Jie

2018-05-01

Ionospheric inhomogeneous plasma produced by single point chemical release has simple space-time structure, and cannot impact radio wave frequencies higher than Very High Frequency (VHF) band. In order to produce more complicated ionospheric plasma perturbation structure and trigger instabilities phenomena, multiple-point chemical release scheme is presented in this paper. The effects of chemical release on low latitude ionospheric plasma are estimated by linear instability growth rate theory that high growth rate represents high irregularities, ionospheric scintillation occurrence probability and high scintillation intension in scintillation duration. The amplitude scintillations and the phase scintillations of 150 MHz, 400 MHz, and 1000 MHz are calculated based on the theory of multiple phase screen (MPS), when they propagate through the disturbed area.

Surface characterization and chemical analysis of bamboo substrates pretreated by alkali hydrogen peroxide.

PubMed

Song, Xueping; Jiang, Yan; Rong, Xianjian; Wei, Wei; Wang, Shuangfei; Nie, Shuangxi

2016-09-01

The surface characterization and chemical analysis of bamboo substrates by alkali hydrogen peroxide pretreatment (AHPP) were investigated in this study. The results tended to manifest that AHPP prior to enzymatic and chemical treatment was potential for improving accessibility and reactivity of bamboo substrates. The inorganic components, organic solvent extractives and acid-soluble lignin were effectively removed by AHPP. X-ray photoelectron spectroscopy (XPS) analysis indicated that the surface of bamboo chips had less lignin but more carbohydrate after pre-treatment. Fiber surfaces became etched and collapsed, and more pores and debris on the substrate surface were observed with Scanning Electron Microscopy (SEM). Brenauer-Emmett-Teller (BET) results showed that both of pore volume and surface area were increased after AHPP. Although XRD analysis showed that AHPP led to relatively higher crystallinity, pre-extraction could overall enhance the accessibility of enzymes and chemicals into the bamboo structure. Copyright © 2016. Published by Elsevier Ltd.

Scanning probe microscopy in mineralogical studies: about origin of the observed roughness of natural silica-rich glasses

NASA Astrophysics Data System (ADS)

Golubev, Ye A.; Isaenko, S. I.

2017-10-01

We have studied different mineralogical objects: natural glasses of impact (tektites, impactites) and volcanic (obsidians) origin, using atomic force microscopy, X-ray microanalysis, infrared and Raman spectroscopy. The spectroscopy showed the difference in the structure and chemical composition of the glasses of different origin. The analysis of the dependence of nanoscale heterogeneity of the glasses, revealed by the atomic force microscopy, on their structural and chemical features was carried out.

Conformational analysis of α-helical polypeptide included L-proline residue by high-resolution solid-state NMR measurement and quantum chemical calculation

NASA Astrophysics Data System (ADS)

Souma, Hiroyuki; Shoji, Akira; Kurosu, Hiromichi

2008-10-01

We challenged the problem about the stabilization mechanism of an α-helix formation for polypeptides containing L-proline (Pro) residue. We computed the optimized structure of α-helical poly( L-alanine) molecules including a Pro residue, H-(Ala) 8-Pro-(Ala) 9-OH, based on the molecular orbital calculation with density functional theory, B3LYP/6-31G(d) and the 13C and 15N chemical shift values based on the GIAO-CHF method with B3LYP/6-311G(d,p), respectively. It was found that two kinds of optimized structures, 'Bent structure' and 'Included α-helix structure', were preferred structures in H-(Ala) 8-Pro-(Ala) 9-OH. In addition, based on the precise 13C and 15N chemical shift data of the simple model, we successfully analyzed the secondary structure of well-defined synthetic polypeptide H-(Phe-Leu-Ala) 3-Phe C-Pro-Ala N-(Phe-Leu-Ala) 2-OH (FLA-11P), the secondary structure of which was proven to the 'Included α-helix structure'.

Profiling and multivariate statistical analysis of Panax ginseng based on ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry.

PubMed

Wu, Wei; Sun, Le; Zhang, Zhe; Guo, Yingying; Liu, Shuying

2015-03-25

An ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) method was developed for the detection and structural analysis of ginsenosides in white ginseng and related processed products (red ginseng). Original neutral, malonyl, and chemically transformed ginsenosides were identified in white and red ginseng samples. The aglycone types of ginsenosides were determined by MS/MS as PPD (m/z 459), PPT (m/z 475), C-24, -25 hydrated-PPD or PPT (m/z 477 or m/z 493), and Δ20(21)-or Δ20(22)-dehydrated-PPD or PPT (m/z 441 or m/z 457). Following the structural determination, the UHPLC-Q-TOF-MS-based chemical profiling coupled with multivariate statistical analysis method was applied for global analysis of white and processed ginseng samples. The chemical markers present between the processed products red ginseng and white ginseng could be assigned. Process-mediated chemical changes were recognized as the hydrolysis of ginsenosides with large molecular weight, chemical transformations of ginsenosides, changes in malonyl-ginsenosides, and generation of 20-(R)-ginsenoside enantiomers. The relative contents of compounds classified as PPD, PPT, malonyl, and transformed ginsenosides were calculated based on peak areas in ginseng before and after processing. This study provides possibility to monitor multiple components for the quality control and global evaluation of ginseng products during processing. Copyright © 2014 Elsevier B.V. All rights reserved.

Impact of Tropopause Structures on Deep Convective Transport Observed during MACPEX

NASA Astrophysics Data System (ADS)

Mullendore, G. L.; Bigelbach, B. C.; Christensen, L. E.; Maddox, E.; Pinkney, K.; Wagner, S.

2016-12-01

Deep convection is the most efficient method of transporting boundary layer mass to the upper troposphere and stratosphere (UTLS). The Mid-latitude Airborne Cirrus Properties Experiment (MACPEX) was conducted during April of 2011 over the central U.S. With a focus on cirrus clouds, the campaign flights often sampled large cirrus anvils downstream from deep convection and included an extensive observational suite of chemical measurements on a high altitude aircraft. As double-tropopause structures are a common feature in the central U.S. during the springtime, the MACPEX campaign provides a good opportunity to gather cases of deep convective transport in the context of both single and double tropopause structures. Sampling of chemical plumes well downstream from convection allows for sampling in relatively quiescent conditions and analysis of irreversible transport. The analysis presented includes multiple methods to assess air mass source and possible convective processing, including back trajectories and ratios of chemical concentrations. Although missions were flown downstream of deep convection, recent processing by convection does not seem likely in all cases that high altitude carbon monoxide plumes were observed. Additionally, the impact of single and double tropopause structures on deep convective transport is shown to be strongly dependent on high stability layers.

Durability and degradation analysis of hydrocarbon ionomer membranes in polymer electrolyte fuel cells accelerated stress evaluation

NASA Astrophysics Data System (ADS)

Shimizu, Ryo; Tsuji, Junichi; Sato, Nobuyuki; Takano, Jun; Itami, Shunsuke; Kusakabe, Masato; Miyatake, Kenji; Iiyama, Akihiro; Uchida, Makoto

2017-11-01

The chemical durabilities of two proton-conducting hydrocarbon polymer electrolyte membranes, sulfonated benzophenone poly(arylene ether ketone) (SPK) semiblock copolymer and sulfonated phenylene poly(arylene ether ketone) (SPP) semiblock copolymer are evaluated under accelerated open circuit voltage (OCV) conditions in a polymer electrolyte fuel cell (PEFC). Post-test characterization of the membrane electrodes assemblies (MEAs) is carried out via gel permeation chromatography (GPC) and nuclear magnetic resonance (NMR) spectroscopy. These results are compared with those of the initial MEAs. The SPP cell shows the highest OCV at 1000 h, and, in the post-test analysis, the SPP membrane retains up to 80% of the original molecular weight, based on the GPC results, and 90% of the hydrophilic structure, based on the NMR results. The hydrophilic structure of the SPP membrane is more stable after the durability evaluation than that of the SPK. From these results, the SPP membrane, with its simple hydrophilic structure, which does not include ketone groups, is seen to be significantly more resistant to radical attack. This structure leads to high chemical durability and thus impedes the chemical decomposition of the membrane.

There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order".

PubMed

Nielsen, Jakob T; Mulder, Frans A A

2016-01-01

The protein universe consists of a continuum of structures ranging from full order to complete disorder. As the structured part of the proteome has been intensively studied, stably folded proteins are increasingly well documented and understood. However, proteins that are fully, or in large part, disordered are much less well characterized. Here we collected NMR chemical shifts in a small database for 117 protein sequences that are known to contain disorder. We demonstrate that NMR chemical shift data can be brought to bear as an exquisite judge of protein disorder at the residue level, and help in validation. With the help of secondary chemical shift analysis we demonstrate that the proteins in the database span the full spectrum of disorder, but still, largely segregate into two classes; disordered with small segments of order scattered along the sequence, and structured with small segments of disorder inserted between the different structured regions. A detailed analysis reveals that the distribution of order/disorder along the sequence shows a complex and asymmetric distribution, that is highly protein-dependent. Access to ratified training data further suggests an avenue to improving prediction of disorder from sequence.

Identification of helix capping and β-turn motifs from NMR chemical shifts

PubMed Central

Shen, Yang; Bax, Ad

2012-01-01

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13Cβ chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7–0.9 for the Matthews correlation coefficient of its predictions far exceed that attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures. PMID:22314702

Theoretical NMR correlations based Structure Discussion.

PubMed

Junker, Jochen

2011-07-28

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction.

Crystal structure and theoretical studies of derivative of imidazo-1,2,4-triazine

NASA Astrophysics Data System (ADS)

Dybała, Izabela; Sztanke, Krzysztof

2016-09-01

In this study, we present the result of X-ray structure analysis of methyl [8-(3-chlorophenyl)-4-oxo-2,3,4,6,7,8-heksahydroimidazo[2,1-c][1,2,4]triazin-3-yl]acetate (1). The molecule conformation is flat, with a chlorophenyl substituent and the ester moiety lying in the plain of the heterobicyclic scaffold. Its conformation is stabilized by an intramolecular Nsbnd H…O hydrogen bond. Within the crystalline structure of 1, molecules associate with one another by weak Csbnd H…O, Csbnd H…Cl and Csbnd H…π bonds. The molecular and crystal structure of 1 was compared with the previously described structurally similar compound possessing the same bicyclic rigid core and similar chemical nature of the functional ester moiety. Very interesting differences in molecules geometry and association were observed. Non-covalent bonds within the crystals are additionally visualized by determination of Hirshfeld surfaces. Moreover, the quantum chemical calculation for 1 in the gas phase were carried out. The DFT calculation methods was used to optimize of molecule geometry and obtain molecular energy profiles with respect to selected torsion angles. The quantum chemical conformational analysis that was carried out for compound 1 in the gas phase suggests that in the solid state the molecules adopt the minimum energy conformation.

Structure elucidation of metabolite x17299 by interpretation of mass spectrometric data.

PubMed

Zhang, Qibo; Ford, Lisa A; Evans, Anne M; Toal, Douglas R

2017-01-01

A major bottleneck in metabolomic studies is metabolite identification from accurate mass spectrometric data. Metabolite x17299 was identified in plasma as an unknown in a metabolomic study using a compound-centric approach where the associated ion features of the compound were used to determine the true molecular mass. The aim of this work is to elucidate the chemical structure of x17299, a new compound by de novo interpretation of mass spectrometric data. An Orbitrap Elite mass spectrometer was used for acquisition of mass spectra up to MS 4 at high resolution. Synthetic standards of N,N,N -trimethyl-l-alanyl-l-proline betaine (l,l-TMAP), a diastereomer, and an enantiomer were chemically prepared. The planar structure of x17299 was successfully proposed by de novo mechanistic interpretation of mass spectrometric data without any laborious purification and nuclear magnetic resonance spectroscopic analysis. The proposed structure was verified by deuterium exchanged mass spectrometric analysis and confirmed by comparison to a synthetic standard. Relative configuration of x17299 was determined by direct chromatographic comparison to a pair of synthetic diastereomers. Absolute configuration was assigned after derivatization of x17299 with a chiral auxiliary group followed by its chromatographic comparison to a pair of synthetic standards. The chemical structure of metabolite x17299 was determined to be l,l-TMAP.

Predicting hepatotoxicity using ToxCast in vitro bioactivity and ...

EPA Pesticide Factsheets

Background: The U.S. EPA ToxCastTM program is screening thousands of environmental chemicals for bioactivity using hundreds of high-throughput in vitro assays to build predictive models of toxicity. We represented chemicals based on bioactivity and chemical structure descriptors then used supervised machine learning to predict their hepatotoxic effects.Results: A set of 677 chemicals were represented by 711 in vitro bioactivity descriptors (from ToxCast assays), 4,376 chemical structure descriptors (from QikProp, OpenBabel, PADEL, and PubChem), and three hepatotoxicity categories (from animal studies). Hepatotoxicants were defined by rat liver histopathology observed after chronic chemical testing and grouped into hypertrophy (161), injury (101) and proliferative lesions (99). Classifiers were built using six machine learning algorithms: linear discriminant analysis (LDA), Naïve Bayes (NB), support vector classification (SVM), classification and regression trees (CART), k-nearest neighbors (KNN) and an ensemble of classifiers (ENSMB). Classifiers of hepatotoxicity were built using chemical structure, ToxCast bioactivity, and a hybrid representation. Predictive performance was evaluated using 10-fold cross-validation testing and in-loop, filter-based, feature subset selection. Hybrid classifiers had the best balanced accuracy for predicting hypertrophy (0.78±0.08), injury (0.73±0.10) and proliferative lesions (0.72±0.09). Though chemical and bioactivity class

Architecture of dermatophyte cell Walls: Electron microscopic and biochemical analysis

NASA Technical Reports Server (NTRS)

Nozawa, Y.; Kitajima, Y.

1984-01-01

A review with 83 references on the cell wall structure of dermatophytes is presented. Topics discussed include separation and preparation of cell walls; microstructure of cell walls by electron microscopy; chemical composition of cell walls; structural model of cell walls; and morphological structure of cell walls.

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

DOE PAGES

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; ...

2016-07-26

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations.« less

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations.« less

PHYSICOCHEMICAL PROPERTIES AS PREDICTORS OF ORGANIC CHEMICAL EFFECTS ON SOIL MICROBIAL RESPIRATION

EPA Science Inventory

Structure-activity analysis was used to evaluate the effects of 19 hazardous organic chemicals on microbial respiration in two slightly acidic soils (a Captina silt loam from Roane County Tennessee, and a McLaurin sandy loam from Stone County, Mississippi), both low in organic ca...

Photoelectron spectra and biological activity of cinnamic acid derivatives revisited.

PubMed

Novak, Igor; Klasinc, Leo; McGlynn, Sean P

2018-01-15

The electronic structures of several derivatives of cinnamic acid have been studied by UV photoelectron spectroscopy (UPS) and Green's function quantum chemical calculations. The spectra reveal the presence of dimers in the gas phase for p-coumaric and ferulic acids. The electronic structure analysis has been related to the biological properties of these compounds through the analysis of some structure-activity relationships (SAR). Copyright © 2017 Elsevier B.V. All rights reserved.

[Studies on chemical constituents of leaves of Psidium guajava].

PubMed

Fu, Huizheng; Luo, Yongming; Zhang, Dongming

2009-03-01

To study the chemical constituents of the leaves of Psidium guajava. The chemical constituents were isolated by column chromatography on silica gel, Sephadex LH-20 and MPLC. Their structures were elucidated on the basis of spectral analysis. Nine compounds were isolated from this plant, and the structure of them were identified as ursolic acid (1), 2alpha-hydroxyursolic acid (2), 2alpha-hydroxyoleanolic acid (3), morin-3-O-alpha-L-arabopyranoside (4), quercetin (5), hyperin (6), myricetin-3-O-beta-D-glucoside (7), quercetin-3-O-beta-D-glucuronopyranoside (8), 1-O-galloyl-beta-D-glucose (9). Compounds 3, 7-9 were isolated from this plant for the first time.

Inclusion compound of vitamin B6 in β-CD. Physico-chemical and structural investigations

NASA Astrophysics Data System (ADS)

Borodi, Gheorghe; Kacso, Irina; Farcaş, Sorin I.; Bratu, Ioan

2009-08-01

Structural and physico-chemical characterization of supramolecular assembly of vitamin B6 with β-cyclodextrin (β-CD) prepared by different methods (kneading, co-precipitation and freeze-drying) has been performed by using several spectroscopic techniques (FTIR, 1H NMR, UV-Vis), powder X-ray diffraction and DSC in order to evidence the inclusion compound formation. An analysis of the chemical shifts observed in the 1H-NMR spectra and of the vibrational frequency shifts led to the tentative conclusion that the vitamin B6 probably enters the cyclodextrin torus when forming the β-CD-vitamin B6 inclusion complex.

[Drug Dependence and Cytotoxicity of Law-evading Drugs: Their Identities Explored from Basic Research].

PubMed

Funada, Masahiko

2016-01-01

  Cases of people experiencing disturbed consciousness or dyspnea, causing traffic accidents, or requiring ambulance transport to hospital due to abuse of law-evading chemical substances have become a serious social problem in Japan. Most law-evading herbal products are marketed as incense or herbs and consist of finely chopped, dry vegetative matter mixed with chemical substances (drugs). Analysis of the chemical substances in these herbal products has demonstrated that they contain synthetic cannabinoids. Because there are many cannabinoid compounds, even if a particular drug is regulated, similar compounds that differ only slightly in structure may be added in their place. Therefore a cat-and-mouse game exists between regulations on chemical substances and their propagation. This paper summarizes the pharmacological actions and dangers of chemical substances contained in law-evading herbal products by focusing on synthetic cannabinoids, as a group of chemical substances contained in these products. Furthermore, comprehensive designations of synthetic cannabinoids have been introduced as a new method of regulation that emphasizes the similarity of chemical structures; this paper also outlines the comprehensive designations. We established a psychic-dependence liability and cytotoxicity screening system for synthetic cannabinoids using animals (behavioral analysis in vivo) and cell cultures (cytotoxicity analysis in vitro). With our drug-screening system, we were able rapidly to evaluate and quantify psychic-dependence liabilities and cytotoxicity of synthetic cannabinoids contained in law-evading herbal products. These scientific data using our screening system contributed to the establishment of legislation for comprehensive designations of synthetic cannabinoids.

Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action.

PubMed

Papamokos, George; Silins, Ilona

2016-01-01

There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens.

Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action

PubMed Central

Papamokos, George; Silins, Ilona

2016-01-01

There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens. PMID:27625608

Application of Spectroscopic Methods for Structural Analysis of Chitin and Chitosan

PubMed Central

Kumirska, Jolanta; Czerwicka, Małgorzata; Kaczyński, Zbigniew; Bychowska, Anna; Brzozowski, Krzysztof; Thöming, Jorg; Stepnowski, Piotr

2010-01-01

Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds. PMID:20559489

Determination of the oxidative stability of perfluoropolyalkyl ethers and correlation with chemical structure

NASA Technical Reports Server (NTRS)

Helmick, Larry S.; Jones, William R., Jr.

1992-01-01

The oxidative stabilities of several perfluoropolyalkyl ethers (PFPAE) with related chemical structures were determined by thermal gravimetric analysis and correlated with their chemical structures. These results show that oxidative stability increases as the number of difluoroformal groups decreases and as trifluoromethyl substituents are added. They are also consistent with a recently proposed intramolecular disproportionation reaction mechanism involving coordination of successive ether oxygens to a Lewis acid. Since polytetrafluoroethylene contains no oxygen, it provides an indication of the upper limit to oxidative stability of PFPAE fluids. These results also show that oxidative decomposition of PFPAE fluids requires the presence of an active metal as well as air. Consequently, it may be possible to minimize decomposition and thus improve oxidative stability by passivating reactive metal surfaces.

The angular structure of ONC201, a TRAIL pathway-inducing compound, determines its potent anti-cancer activity

PubMed Central

Wagner, Jessica; Kline, Christina Leah; Pottorf, Richard S.; Nallaganchu, Bhaskara Rao; Olson, Gary L.; Dicker, David T.; Allen, Joshua E.; El-Deiry, Wafik S.

2014-01-01

We previously identified TRAIL-inducing compound 10 (TIC10), also known as NSC350625 or ONC201, from a NCI chemical library screen as a small molecule that has potent anti-tumor efficacy and a benign safety profile in preclinical cancer models. The chemical structure that was originally published by Stahle, et. al. in the patent literature was described as an imidazo[1,2-a]pyrido[4,3-d]pyrimidine derivative. The NCI and others generally accepted this as the correct structure, which was consistent with the mass spectrometry analysis outlined in the publication by Allen et. al. that first reported the molecule's anticancer properties. A recent publication demonstrated that the chemical structure of ONC201 material from the NCI is an angular [3,4-e] isomer of the originally disclosed, linear [4,3-d] structure. Here we confirm by NMR and X-ray structural analysis of the dihydrochloride salt form that the ONC201 material produced by Oncoceutics is the angular [3,4-e] structure and not the linear structure originally depicted in the patent literature and by the NCI. Similarly, in accordance with our biological evaluation, the previously disclosed anti-cancer activity is associated with the angular structure and not the linear isomer. Together these studies confirm that ONC201, produced by Oncoceutics or obtained from the NCI, possesses an angular [3,4-e] structure that represents the highly active anti-cancer compound utilized in prior preclinical studies and now entering clinical trials in advanced cancers. PMID:25587031

The angular structure of ONC201, a TRAIL pathway-inducing compound, determines its potent anti-cancer activity.

PubMed

Wagner, Jessica; Kline, Christina Leah; Pottorf, Richard S; Nallaganchu, Bhaskara Rao; Olson, Gary L; Dicker, David T; Allen, Joshua E; El-Deiry, Wafik S

2014-12-30

We previously identified TRAIL-inducing compound 10 (TIC10), also known as NSC350625 or ONC201, from a NCI chemical library screen as a small molecule that has potent anti-tumor efficacy and a benign safety profile in preclinical cancer models. The chemical structure that was originally published by Stahle, et. al. in the patent literature was described as an imidazo[1,2-a]pyrido[4,3-d]pyrimidine derivative. The NCI and others generally accepted this as the correct structure, which was consistent with the mass spectrometry analysis outlined in the publication by Allen et. al. that first reported the molecule's anticancer properties. A recent publication demonstrated that the chemical structure of ONC201 material from the NCI is an angular [3,4-e] isomer of the originally disclosed, linear [4,3-d] structure. Here we confirm by NMR and X-ray structural analysis of the dihydrochloride salt form that the ONC201 material produced by Oncoceutics is the angular [3,4-e] structure and not the linear structure originally depicted in the patent literature and by the NCI. Similarly, in accordance with our biological evaluation, the previously disclosed anti-cancer activity is associated with the angular structure and not the linear isomer. Together these studies confirm that ONC201, produced by Oncoceutics or obtained from the NCI, possesses an angular [3,4-e] structure that represents the highly active anti-cancer compound utilized in prior preclinical studies and now entering clinical trials in advanced cancers.

Trust, but verify: On the importance of chemical structure curation in cheminformatics and QSAR modeling research

PubMed Central

Fourches, Denis; Muratov, Eugene; Tropsha, Alexander

2010-01-01

Molecular modelers and cheminformaticians typically analyze experimental data generated by other scientists. Consequently, when it comes to data accuracy, cheminformaticians are always at the mercy of data providers who may inadvertently publish (partially) erroneous data. Thus, dataset curation is crucial for any cheminformatics analysis such as similarity searching, clustering, QSAR modeling, virtual screening, etc., especially nowadays when the availability of chemical datasets in public domain has skyrocketed in recent years. Despite the obvious importance of this preliminary step in the computational analysis of any dataset, there appears to be no commonly accepted guidance or set of procedures for chemical data curation. The main objective of this paper is to emphasize the need for a standardized chemical data curation strategy that should be followed at the onset of any molecular modeling investigation. Herein, we discuss several simple but important steps for cleaning chemical records in a database including the removal of a fraction of the data that cannot be appropriately handled by conventional cheminformatics techniques. Such steps include the removal of inorganic and organometallic compounds, counterions, salts and mixtures; structure validation; ring aromatization; normalization of specific chemotypes; curation of tautomeric forms; and the deletion of duplicates. To emphasize the importance of data curation as a mandatory step in data analysis, we discuss several case studies where chemical curation of the original “raw” database enabled the successful modeling study (specifically, QSAR analysis) or resulted in a significant improvement of model's prediction accuracy. We also demonstrate that in some cases rigorously developed QSAR models could be even used to correct erroneous biological data associated with chemical compounds. We believe that good practices for curation of chemical records outlined in this paper will be of value to all scientists working in the fields of molecular modeling, cheminformatics, and QSAR studies. PMID:20572635

[Studies on the chemical constituents of the root and rhizoma of Ligusticum jeholense].

PubMed

Zhang, Bo; Sun, Jia-Ming; Chang, Ren-Long; Zhang, Hui

2009-05-01

To study the chemical constituents of the root and rhizoma of Ligusticum jeholense. The constituents were isolated by silica gel column chromatography, Sephadex LH-20 column chromatography and their structures were elucidated through spectral analysis. Seven compounds were separated from the EtOH extracts. Their structures were identified as levistolide A (1), xiongterpene (2), linoleic acid (3), sucrose (4), daucosterol (5), ferulic acid (6) and beta-sitosterol (7). Compounds 1-5 are isolated from the genus for the first time.

USU Center of Excellence in Theory and Analysis of the Geo-Plasma Environment

DTIC Science & Technology

1992-05-25

AFM CN AOR9002 B. ADORE=S ICRYi. Stei md ZIP Codej 10. SOURCE OF FUNOING NOS. BuildPng 410 PROGRAM PROJECT TASK WORK UNIT.- Buling 410D..203 ELEMENT ...OTH radars, communications, and orbiting space structures. The overall goal of the research is to obtain a better understanding of the basic chemical...and orbiting space structures. The overall goal of the research is to obtain a better understanding of the basic chemical and physical processes

Advances in single-molecule magnet surface patterning through microcontact printing.

PubMed

Mannini, Matteo; Bonacchi, Daniele; Zobbi, Laura; Piras, Federica M; Speets, Emiel A; Caneschi, Andrea; Cornia, Andrea; Magnani, Agnese; Ravoo, Bart Jan; Reinhoudt, David N; Sessoli, Roberta; Gatteschi, Dante

2005-07-01

We present an implementation of strategies to deposit single-molecule magnets (SMMs) using microcontact printing microCP). We describe different approaches of microCP to print stripes of a sulfur-functionalized dodecamanganese (III, IV) cluster on gold surfaces. Comparison by atomic force microscopy profile analysis of the patterned structures confirms the formation of a chemically stable single layer of SMMs. Images based on chemical contrast, obtained by time-of-flight secondary ion mass spectrometry, confirm the patterned structure.

High-performance liquid chromatography-mass spectrometry for mapping and sequencing glycosaminoglycan-derived oligosaccharides

PubMed Central

Volpi, Nicola; Linhardt, Robert J

2012-01-01

Glycosaminoglycans (GAGs) have proven to be very difficult to analyze and characterize because of their high negative charge density, polydispersity and sequence heterogeneity. As the specificity of the interactions between GAGs and proteins results from the structure of these polysaccharides, an understanding of GAG structure is essential for developing a structure–activity relationship. Electrospray ionization (ESI) mass spectrometry (MS) is particularly promising for the analysis of oligosaccharides chemically or enzymatically generated by GAGs because of its relatively soft ionization capacity. Furthermore, on-line high-performance liquid chromatography (HPLC)-MS greatly enhances the characterization of complex mixtures of GAG-derived oligosaccharides, providing important structural information and affording their disaccharide composition. A detailed protocol for producing oligosaccharides from various GAGs, using controlled, specific enzymatic or chemical depolymerization, is presented, together with their HPLC separation, using volatile reversed-phase ion-pairing reagents and on-line ESI-MS structural identification. This analysis provides an oligosaccharide map together with sequence information from a reading frame beginning at the nonreducing end of the GAG chains. The preparation of oligosaccharides can be carried out in 10 h, with subsequent HPLC analysis in 1–2 h and HPLC-MS analysis taking another 2 h. PMID:20448545

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

PubMed

Chavez, Juan D; Eng, Jimmy K; Schweppe, Devin K; Cilia, Michelle; Rivera, Keith; Zhong, Xuefei; Wu, Xia; Allen, Terrence; Khurgel, Moshe; Kumar, Akhilesh; Lampropoulos, Athanasios; Larsson, Mårten; Maity, Shuvadeep; Morozov, Yaroslav; Pathmasiri, Wimal; Perez-Neut, Mathew; Pineyro-Ruiz, Coriness; Polina, Elizabeth; Post, Stephanie; Rider, Mark; Tokmina-Roszyk, Dorota; Tyson, Katherine; Vieira Parrine Sant'Ana, Debora; Bruce, James E

2016-01-01

Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.

A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding.

PubMed

Lin, Ying-Ting

2013-04-30

A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from the bulk of a cell; the second part is the actual detection of the important identities. To identify the key structural modifications around ligand binding, the present study aims to develop a counterpart of tandem technique for cheminformatics. A statistical regression and its outliers act as a computational technique for separation. A PPARγ (peroxisome proliferator-activated receptor gamma) agonist cellular system was subjected to such an investigation. Results show that this tandem regression-outlier analysis, or the prioritization of the context equations tagged with features of the outliers, is an effective regression technique of cheminformatics to detect key structural modifications, as well as their tendency of impact to ligand binding. The key structural modifications around ligand binding are effectively extracted or characterized out of cellular reactions. This is because molecular binding is the paramount factor in such ligand cellular system and key structural modifications around ligand binding are expected to create outliers. Therefore, such outliers can be captured by this tandem regression-outlier analysis.

Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

DOE PAGES

Yu, Peiqiang

2006-01-01

Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advancedmore » synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in biological tissues at ultraspatial resolutions.« less

Local Fine Structural Insight into Mechanism of Electrochemical Passivation of Titanium.

PubMed

Wang, Lu; Yu, Hongying; Wang, Ke; Xu, Haisong; Wang, Shaoyang; Sun, Dongbai

2016-07-20

Electrochemically formed passive film on titanium in 1.0 M H2SO4 solution and its thickness, composition, chemical state, and local fine structure are examined by Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), and X-ray absorption fine structure. AES analysis reveals that the thickness and composition of oxide film are proportional to the reciprocal of current density in potentiodynamic polarization. XPS depth profiles of the chemical states of titanium exhibit the coexistence of various valences cations in the surface. Quantitative X-ray absorption near edge structure analysis of the local electronic structure of the topmost surface (∼5.0 nm) shows that the ratio of [TiO2]/[Ti2O3] is consistent with that of passivation/dissolution of electrochemical activity. Theoretical calculation and analysis of extended X-ray absorption fine structure spectra at Ti K-edge indicate that both the structures of passivation and dissolution are distorted caused by the appearance of two different sites of Ti-O and Ti-Ti. And the bound water in the topmost surface plays a vital role in structural disorder confirmed by XPS. Overall, the increase of average Ti-O coordination causes the electrochemical passivation, and the dissolution is due to the decrease of average Ti-Ti coordination. The structural variations of passivation in coordination number and interatomic distance are in good agreement with the prediction of point defect model.

Differential Dynamic Engagement within 24 SH3 Domain: Peptide Complexes Revealed by Co-Linear Chemical Shift Perturbation Analysis

PubMed Central

Stollar, Elliott J.; Lin, Hong; Davidson, Alan R.; Forman-Kay, Julie D.

2012-01-01

There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP) behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences. PMID:23251481

Combining density functional theory (DFT) and pair distribution function (PDF) analysis to solve the structure of metastable materials: the case of metakaolin.

PubMed

White, Claire E; Provis, John L; Proffen, Thomas; Riley, Daniel P; van Deventer, Jannie S J

2010-04-07

Understanding the atomic structure of complex metastable (including glassy) materials is of great importance in research and industry, however, such materials resist solution by most standard techniques. Here, a novel technique combining thermodynamics and local structure is presented to solve the structure of the metastable aluminosilicate material metakaolin (calcined kaolinite) without the use of chemical constraints. The structure is elucidated by iterating between least-squares real-space refinement using neutron pair distribution function data, and geometry optimisation using density functional modelling. The resulting structural representation is both energetically feasible and in excellent agreement with experimental data. This accurate structural representation of metakaolin provides new insight into the local environment of the aluminium atoms, with evidence of the existence of tri-coordinated aluminium. By the availability of this detailed chemically feasible atomic description, without the need to artificially impose constraints during the refinement process, there exists the opportunity to tailor chemical and mechanical processes involving metakaolin and other complex metastable materials at the atomic level to obtain optimal performance at the macro-scale.

Collision-induced dissociative chemical cross-linking reagents and methodology: Applications to protein structural characterization using tandem mass spectrometry analysis.

PubMed

Soderblom, Erik J; Goshe, Michael B

2006-12-01

Chemical cross-linking combined with mass spectrometry is a viable approach to study the low-resolution structure of protein and protein complexes. However, unambiguous identification of the residues involved in a cross-link remains analytically challenging. To enable a more effective analysis across various MS platforms, we have developed a novel set of collision-induced dissociative cross-linking reagents and methodology for chemical cross-linking experiments using tandem mass spectrometry (CID-CXL-MS/MS). These reagents incorporate a single gas-phase cleavable bond within their linker region that can be selectively fragmented within the in-source region of the mass spectrometer, enabling independent MS/MS analysis for each peptide. Initial design concepts were characterized using a synthesized cross-linked peptide complex. Following verification and subsequent optimization of cross-linked peptide complex dissociation, our reagents were applied to homodimeric glutathione S-transferase and monomeric bovine serum albumin. Cross-linked residues identified by our CID-CXL-MS/MS method were in agreement with published crystal structures and previous cross-linking studies using conventional approaches. Common LC/MS/MS acquisition approaches such as data-dependent acquisition experiments using ion trap mass spectrometers and product ion spectral analysis using SEQUEST were shown to be compatible with our CID-CXL-MS/MS reagents, obviating the requirement for high resolution and high mass accuracy measurements to identify both intra- and interpeptide cross-links.

Chemical structural analysis of diamondlike carbon films: II. Raman analysis

NASA Astrophysics Data System (ADS)

Takabayashi, Susumu; Ješko, Radek; Shinohara, Masanori; Hayashi, Hiroyuki; Sugimoto, Rintaro; Ogawa, Shuichi; Takakuwa, Yuji

2018-02-01

The chemical structure of diamondlike carbon (DLC) films, synthesized by photoemission-assisted glow discharge, has been analyzed by Raman spectroscopy. Raman analysis in conjunction with the sp2 cluster model clarified the film structure. The sp2 clusters in DLC films synthesized at low temperature preferred various aliphatic structures. Sufficient argon-ion assist allowed for formation of less strained DLC films containing large amounts of hydrogen. As the synthesis temperature was increased, thermal desorption of hydrogen left carbon dangling bonds with active unpaired electrons in the films, and the reactions that followed created strained films containing aromatic sp2 clusters. In parallel, the desorption of methane molecules from the growing surface by chemisorption of hydrogen radicals prevented the action of argon ions, promoting internal strain of the films. However, in synthesis at very high temperature, where sp2 clusters are sufficiently dominant, the strain was dissolved gradually. In contrast, the DLC films synthesized at low temperature were more stable than other films synthesized at the same temperature because of stable hydrogen-carbon bonds in the films.

Gas Chromatography-Tandem Mass Spectrometry of Lignin Pyrolyzates with Dopant-Assisted Atmospheric Pressure Chemical Ionization and Molecular Structure Search with CSI:FingerID

NASA Astrophysics Data System (ADS)

Larson, Evan A.; Hutchinson, Carolyn P.; Lee, Young Jin

2018-06-01

Dopant-assisted atmospheric pressure chemical ionization (dAPCI) is a soft ionization method rarely used for gas chromatography-mass spectrometry (GC-MS). The current study combines GC-dAPCI with tandem mass spectrometry (MS/MS) for analysis of a complex mixture such as lignin pyrolysis analysis. To identify the structures of volatile lignin pyrolysis products, collision-induced dissociation (CID) MS/MS using a quadrupole time-of-flight mass spectrometer (QTOFMS) and pseudo MS/MS through in-source collision-induced dissociation (ISCID) using a single stage TOFMS are utilized. To overcome the lack of MS/MS database, Compound Structure Identification (CSI):FingerID is used to interpret CID spectra and predict best matched structures from PubChem library. With this approach, a total of 59 compounds were positively identified in comparison to only 22 in NIST database search of GC-EI-MS dataset. This study demonstrates the effectiveness of GC-dAPCI-MS/MS to overcome the limitations of traditional GC-EI-MS analysis when EI-MS database is not sufficient. [Figure not available: see fulltext.

MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

EPA Science Inventory

Abstract
One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants.

PubMed

Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

2014-01-01

The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure-activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein-ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. © The Author(s) 2014. Published by Oxford University Press.

Ryan M. Ness | NREL

Science.gov Websites

Interests Ryan M. Ness is a research technician in the Biomass Analysis group within the National Renewable , wet chemical analysis, and instrumental analysis of lignocellulosic biomass feedstocks. Bench-scale Publications "The Effect of Biomass Densification on Structural Sugar Release and Yield in Biofuel

Variability of chemical analysis of reinforcing bar produced in Saudi Arabia

NASA Astrophysics Data System (ADS)

Salman, A.; Djavanroodi, F.

2018-04-01

In view of the importance and demanding roles of steel rebar’s in the reinforced concrete structures, accurate information on the properties of the steels is important at the design stage. In the steelmaking process, production variations in chemical composition are unavoidable. The aim of this work is to study the variability of the chemical composition of reinforcing steel produced throughout the Saudi Arabia and asses the quality of steel rebar’s acoording to ASTM A615. 68 samples of ASTM A615 Grade 60 from different manufacturers were collected and tested using the Spectrometer test to obtain Chemical Compositions. EasyFit (5.6) software is utilized to conducted statistical analysis. Chemical compositions distributions and, control charts are generated for the compositions. Results showed that some compositions are above the upper line of the control chart. Finally, the analyses show that less than 3% of the steel failed to meet minimum ASTM standards for chemical composition.

Propulsion Technology Lifecycle Operational Analysis

NASA Technical Reports Server (NTRS)

Robinson, John W.; Rhodes, Russell E.

2010-01-01

The paper presents the results of a focused effort performed by the members of the Space Propulsion Synergy Team (SPST) Functional Requirements Sub-team to develop propulsion data to support Advanced Technology Lifecycle Analysis System (ATLAS). This is a spreadsheet application to analyze the impact of technology decisions at a system-of-systems level. Results are summarized in an Excel workbook we call the Technology Tool Box (TTB). The TTB provides data for technology performance, operations, and programmatic parameters in the form of a library of technical information to support analysis tools and/or models. The lifecycle of technologies can be analyzed from this data and particularly useful for system operations involving long running missions. The propulsion technologies in this paper are listed against Chemical Rocket Engines in a Work Breakdown Structure (WBS) format. The overall effort involved establishing four elements: (1) A general purpose Functional System Breakdown Structure (FSBS). (2) Operational Requirements for Rocket Engines. (3) Technology Metric Values associated with Operating Systems (4) Work Breakdown Structure (WBS) of Chemical Rocket Engines The list of Chemical Rocket Engines identified in the WBS is by no means complete. It is planned to update the TTB with a more complete list of available Chemical Rocket Engines for United States (US) engines and add the Foreign rocket engines to the WBS which are available to NASA and the Aerospace Industry. The Operational Technology Metric Values were derived by the SPST Sub-team in the form of the TTB and establishes a database for users to help evaluate and establish the technology level of each Chemical Rocket Engine in the database. The Technology Metric Values will serve as a guide to help determine which rocket engine to invest technology money in for future development.

Soil microcosm for testing the effects of chemical pollutants on soil fauna communities and trophic structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parmelee, R.W.; Wentsel, R.S.; Phillips, C.T.

1993-08-01

A microcosm technique is presented that uses community and trophic-level analysis of soil nematodes and microarthropods to determine the effects of chemicals on soil systems. Forest soil was treated with either copper, p-nitrophenol, or trinitrotoluene. Nematodes were sorted into bacterivore, fungivore, herbivore, and omnivore-predator trophic groups, and a hatchling category. Microarthropods were sorted to the acarine suborders Prostigmata, Mesostigmata, and Oribatida; the insectan order Collembola; and a miscellaneous group. Omnivore-predator nematodes and meso-stigmatid and oribatid mites were the groups most sensitive to copper and were significantly reduced at levels as low as 100 [mu]g g[sup [minus]1] copper. Total nematode andmore » microarthropod numbers declined above 200 [mu]g g[sup [minus]1] copper. Trophic structure analysis suggested that high sensitivity of nematode predators to intermediate levels of copper reduced predation on herbivore nematodes and resulted in greater numbers of nematodes compared to controls. p-Nitrophenol was very toxic to the nematode community, and all trophic groups were significantly reduced above 20 [mu]g g[sup [minus]1]. However, there was no effect of p-nitrophenol on microarthropods. Trinitrotoluene had no significant negative effect on total abundance of either groups of soil fauna, but oribatids were significantly reduced at 200 [mu]g g[sup [minus]1]. The results demonstrated that soil nematodes and microarthropods were sensitive indicators of environmental contaminants and that trophic-structure and community analysis has the potential to detect more subtle indirect effects of chemicals on soil food-web structure. The authors conclude that microcosms with field communities of soil microfauna offer high resolution of the ecotoxicological effects of chemicals in complex soil systems.« less

Analysis of Publically Available Skin Sensitization Data from REACH Registrations 2008–2014

PubMed Central

Luechtefeld, Thomas; Maertens, Alexandra; Russo, Daniel P.; Rovida, Costanza; Zhu, Hao; Hartung, Thomas

2017-01-01

Summary The public data on skin sensitization from REACH registrations already included 19,111 studies on skin sensitization in December 2014, making it the largest repository of such data so far (1,470 substances with mouse LLNA, 2,787 with GPMT, 762 with both in vivo and in vitro and 139 with only in vitro data). 21% were classified as sensitizers. The extracted skin sensitization data was analyzed to identify relationships in skin sensitization guidelines, visualize structural relationships of sensitizers, and build models to predict sensitization. A chemical with molecular weight > 500 Da is generally considered non-sensitizing owing to low bioavailability, but 49 sensitizing chemicals with a molecular weight > 500 Da were found. A chemical similarity map was produced using PubChem’s 2D Tanimoto similarity metric and Gephi force layout visualization. Nine clusters of chemicals were identified by Blondel’s module recognition algorithm revealing wide module-dependent variation. Approximately 31% of mapped chemicals are Michael’s acceptors but alone this does not imply skin sensitization. A simple sensitization model using molecular weight and five ToxTree structural alerts showed a balanced accuracy of 65.8% (specificity 80.4%, sensitivity 51.4%), demonstrating that structural alerts have information value. A simple variant of k-nearest neighbors outperformed the ToxTree approach even at 75% similarity threshold (82% balanced accuracy at 0.95 threshold). At higher thresholds, the balanced accuracy increased. Lower similarity thresholds decrease sensitivity faster than specificity. This analysis scopes the landscape of chemical skin sensitization, demonstrating the value of large public datasets for health hazard prediction. PMID:26863411

Characterization of a defective PbWO4 crystal cut along the a-c crystallographic plane: structural assessment and a novel photoelastic stress analysis

NASA Astrophysics Data System (ADS)

Montalto, L.; Natali, P. P.; Daví, F.; Mengucci., P.; Paone, N.; Rinaldi, D.

2017-12-01

Among scintillators, the PWO is one of the most widely used, for instance in CMS calorimeter at CERN and PANDA project. Crystallographic structure and chemical composition as well as residual stress condition, are indicators of homogeneity and good quality of the crystal. In this paper, structural characterization of a defective PbWO4 (PWO) crystal has been performed by X-ray Diffraction (XRD), Energy Dispersive Spectroscopy (EDS) and Photoelasticity in the unusual (a, c) crystallographic plane. XRD and EDS analysis have been used to investigate crystallographic orientation and chemical composition, while stress distribution, which indicates macroscopic inhomogeneities and defects, has been obtained by photoelastic approaches, in Conoscopic and Sphenoscopic configuration. Since the sample is cut along the (a, c) crystallographic plane, a new method is proposed for the interpretation of the fringe pattern. The structural analysis has detected odds from the nominal lattice dimension, which can be attributed to the strong presence of Pb and W. A strong inhomogeneity over the crystal sample has been revealed by the photoelastic inspection. The results give reliability to the proposed procedure which is exploitable in crystals with other structures.

Macromolecular structure of coals. 6. Mass spectroscopic analysis of coal-derived liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hooker, D.T.; Lucht, L.M.; Peppas, N.A.

1986-02-01

The macromolecular structure of coal networks was analyzed by depolymerizing coal samples using the Sternberg reductive alkylation and the Miyake alkylation techniques. Electron impact mass spectra showed peaks of greater abundance of 125-132, 252-260, 383-391, and 511-520 m/z ratios. Based on analysis of the patterns of the spectra, the cluster size of the cross-linked structure of bituminous coals was determined as 126-130. Various chemical species were identified.

TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants

PubMed Central

Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

2014-01-01

The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure–activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein–ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. PMID:24930145

Using novel descriptor accounting for ligand-receptor interactions to define and visually explore biologically relevant chemical space.

PubMed

Rabal, Obdulia; Oyarzabal, Julen

2012-05-25

The definition and pragmatic implementation of biologically relevant chemical space is critical in addressing navigation strategies in the overlapping regions where chemistry and therapeutically relevant targets reside and, therefore, also key to performing an efficient drug discovery project. Here, we describe the development and implementation of a simple and robust method for representing biologically relevant chemical space as a general reference according to current knowledge, independently of any reference space, and analyzing chemical structures accordingly. Underlying our method is the generation of a novel descriptor (LiRIf) that converts structural information into a one-dimensional string accounting for the plausible ligand-receptor interactions as well as for topological information. Capitalizing on ligand-receptor interactions as a descriptor enables the clustering, profiling, and comparison of libraries of compounds from a chemical biology and medicinal chemistry perspective. In addition, as a case study, R-groups analysis is performed to identify the most populated ligand-receptor interactions according to different target families (GPCR, kinases, etc.), as well as to evaluate the coverage of biologically relevant chemical space by structures annotated in different databases (ChEMBL, Glida, etc.).

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

An improved synthesis, spectroscopic (FT-IR, NMR) study and DFT computational analysis (IR, NMR, UV-Vis, MEP diagrams, NBO, NLO, FMO) of the 1,5-methanoazocino[4,3-b]indole core structure

NASA Astrophysics Data System (ADS)

Uludağ, Nesimi; Serdaroğlu, Goncagül

2018-03-01

This study examines the synthesis of azocino[4,3-b]indole structure, which constitutes the tetracyclic framework of uleine, dasycarpidoneand tubifolidineas well as ABDE substructure of the strychnosalkaloid family. It has been synthesized by Fischer indolization of 2 and through the cylization of 4 by 2,3-dichlor-5-6-dicyanobenzoquinone (DDQ). 1H and 1C NMR chemical shifts have been predicted with GIAO approach and the calculated chemical shifts show very good agreement with observed shifts. FT-IR spectroscopy is important for the analysis of functional groups of synthesized compounds and we also supported FT-IR vibrational analysis with computational IR analysis. The vibrational spectral analysis was performed at B3LYP level of the theory in both the gas and the water phases and it was compared with the observed IR values for the important functional groups. The DFT calculations have been conducted to determine the most stable structure of the 1,2,3,4,5,6,7-Hexahydro-1,5-methanoazocino [4,3-b] indole (5). The Frontier Molecular Orbital Analysis, quantum chemical parameters, physicochemical properties have been predicted by using the same theory of level in both gas phase and the water phase, at 631 + g** and 6311++g** basis sets. TD- DFT calculations have been performed to predict the UV- Vis spectral analysis for this synthesized molecule. The Natural Bond Orbital (NBO) analysis have been performed at B3LYP level of theory to elucidate the intra-molecular interactions such as electron delocalization and conjugative interactions. NLO calculations were conducted to obtain the electric dipole moment and polarizability of the title compound.

Carpatizine, a novel bridged oxazine derivative generated by non-enzymatic reactions.

PubMed

Fu, Peng; MacMillan, John B

2017-06-27

Carpatizine (1), a new bridged oxazine derivative, was isolated from a marine-derived Streptomyces strain SNE-011. The structure was fully determined by spectroscopic analysis, ECD calculations and chemical methods. A plausible non-enzymatic reaction mechanism from daryamide D leading to carpatizine was presented, which was confirmed by chemical transformation.

DIFFERENCES IN THE STRUCTURE AND FUNCTION OF FATHEAD MINNOW AND HUMAN ERA: IMPLICATIONS FOR IN VITRO TESTING OF ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

Mammalian receptors and assay systems are generally used for in vitro analysis of endocrine disrupting chemicals (EDC) with the assumption that minor differences in amino acid sequences among species do not translate into significant differences in receptor function. We have fou...

In vivo chemical and structural analysis of plant cuticular waxes using stimulated Raman scattering microscopy.

PubMed

Littlejohn, George R; Mansfield, Jessica C; Parker, David; Lind, Rob; Perfect, Sarah; Seymour, Mark; Smirnoff, Nicholas; Love, John; Moger, Julian

2015-05-01

The cuticle is a ubiquitous, predominantly waxy layer on the aerial parts of higher plants that fulfils a number of essential physiological roles, including regulating evapotranspiration, light reflection, and heat tolerance, control of development, and providing an essential barrier between the organism and environmental agents such as chemicals or some pathogens. The structure and composition of the cuticle are closely associated but are typically investigated separately using a combination of structural imaging and biochemical analysis of extracted waxes. Recently, techniques that combine stain-free imaging and biochemical analysis, including Fourier transform infrared spectroscopy microscopy and coherent anti-Stokes Raman spectroscopy microscopy, have been used to investigate the cuticle, but the detection sensitivity is severely limited by the background signals from plant pigments. We present a new method for label-free, in vivo structural and biochemical analysis of plant cuticles based on stimulated Raman scattering (SRS) microscopy. As a proof of principle, we used SRS microscopy to analyze the cuticles from a variety of plants at different times in development. We demonstrate that the SRS virtually eliminates the background interference compared with coherent anti-Stokes Raman spectroscopy imaging and results in label-free, chemically specific confocal images of cuticle architecture with simultaneous characterization of cuticle composition. This innovative use of the SRS spectroscopy may find applications in agrochemical research and development or in studies of wax deposition during leaf development and, as such, represents an important step in the study of higher plant cuticles. © 2015 American Society of Plant Biologists. All Rights Reserved.

Mechanical-chemical analyses and sub-chronic systemic toxicity of chemical treated organic bovine bone.

PubMed

Lee, Kwang-il; Lee, Jung-soo; Lee, Keun-soo; Jung, Hong-hee; Ahn, Chan-min; Kim, Young-sik; Shim, Young-bock; Jang, Ju-woong

2015-12-01

Sequentially chemical-treated bovine bone was not only evaluated by mechanical and chemical analyses but also implanted into the gluteal muscles of rats for 12 weeks to investigate potential local pathological effects and systemic toxicities. The test (chemical treated bone) and control (heat treated bone) materials were compared using scanning electron microscope (SEM), x-ray diffraction pattern, inductively coupled plasma analysis, and bending strength test. In the SEM images, the micro-porous structure of heat-treated bone was changed to sintered ceramic-like structure. The structure of bone mineral from test and control materials was analyzed as100% hydroxyapatite. The ratio of calcium (Ca) to potassium (P), the main inorganic elements, was same even though the Ca and P percentages of the control material was relatively higher than the test material. No death or critical symptoms arose from implantation of the test (chemical treated bone) and control (physiological saline) materials during 12 weeks. The implanted sites were macroscopically examined, with all the groups showing non-irritant results. Our results indicate that chemical processed bovine bone has a better mechanical property than the heat treated bone and the implantation of this material does not produce systemic or pathological toxicity. Copyright © 2015 Elsevier Inc. All rights reserved.

20180318 - Using the US EPA's CompTox Chemistry Dashboard for structure identification and non-targeted analyses (ACS Spring)

EPA Science Inventory

The CompTox Chemistry Dashboard provides access to data for ~760,000 chemicals. High quality curated data and rich metadata facilitates mass spec analysis. “MS-Ready” processed data enables structure identification.

X-ray absorption fine structure (XAFS) analysis of titanium-implanted soft tissue.

PubMed

Uo, Motohiro; Asakura, Kiyotaka; Yokoyama, Atsuro; Ishikawa, Makoto; Tamura, Kazuchika; Totsuka, Yasunori; Akasaka, Tsukasa; Watari, Fumio

2007-03-01

Tissues contacting Ti dental implants were subjected to X-ray absorption fine structure (XAFS) analysis to examine the chemical state of Ti transferred from the placed implant into the surrounding tissue. Nine tissues that contacted pure Ti cover screws for several months were excised in a second surgery whereby healing abutments were set. Six tissues that surrounded implants retrieved due to their failure were also excised. Ti distributions in the excised specimens were confirmed by X-ray scanning analytical microscopy (XSAM), and the specimens were subjected to fluorescence XAFS analysis to determine the chemical states of the low concentrations of Ti in the tissues surrounding Ti dental implants. Ti mostly existed in the metallic state and was considered to be debris derived from the abrasion of implant pieces during implant surgery. Oxidized forms of Ti, such as anatase and rutile, were also detected in a few specimens-and existed in either a pure state or mixed state with metallic Ti. It was concluded that the existence of Ti in the tissue did not cause implant failure. Moreover, the usefulness of XAFS for analysis of the chemical states of rarely contained elements in biological tissue was demonstrated.

Qualitative and quantitative analysis of lignocellulosic biomass using infrared techniques: A mini-review

USDA-ARS?s Scientific Manuscript database

Current wet chemical methods for biomass composition analysis using two-step sulfuric acid hydrolysis are time-consuming, labor-intensive, and unable to provide structural information about biomass. Infrared techniques provide fast, low-cost analysis, are non-destructive, and have shown promising re...

Analysis and prediction of structure-reactive toxicity relationships of substituted aromatic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Z.T.; Wang, L.S.; Chen, S.P.

1996-12-31

The fundamental differentiation of toxicity is between reactive and nonreactive toxicity. Reactive toxicity is associated with a specific mechanism for the reaction with an enzyme or inhibition of a metabolic pathway, and nonreactive toxicity is related directly to the quantity of toxicant acting upon the cell. The quantitative structure-activity relationships (QSARs) have been successfully used in the nonreactive toxicity, such as prediction of the toxicity of nonreactive compounds based on their solubility in the lipids of organisms. The elements of molecular structure that are most closely related to nonreactive toxicity are those that describe the partitioning of the toxicant intomore » the organism, while QSARs for the reactive toxicity are less common in the environmental toxicology literature. With the recent increase in the use of synthetic substituted benzenes as industrial chemicals, the accurate analysis of the effect of reactive toxic chemicals has become recognized with QSAR. For this purpose, we selected the fish (Carassias auratus) as the test organism, measured the acute toxicity of 50% lethal concentration (LC{sub 50}) of the chemicals and the adenosine triphosphate (ATP) content of the liver cells for the organism. These determined the relationships of the acute toxicity of some substituted benzenes with their physicochemical structural parameters. The effects on the ATP content was also compared to predict biological reactivities of the chemicals, so as to find some clues to explain the mode of mechanism of the toxicity. 17 refs., 1 tab.« less

Characterization of iron-phosphate-silicate chemical garden structures.

PubMed

Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

2012-02-28

Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life. © 2011 American Chemical Society

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Conformational, structural, vibrational and quantum chemical analysis on 4-aminobenzohydrazide and 4-hydroxybenzohydrazide--a comparative study.

PubMed

Arjunan, V; Jayaprakash, A; Carthigayan, K; Periandy, S; Mohan, S

2013-05-01

Experimental and theoretical quantum chemical studies were carried out on 4-hydroxybenzohydrazide (4HBH) and 4-aminobenzohydrazide (4ABH) using FTIR and FT-Raman spectral data. The structural characteristics and vibrational spectroscopic analysis were carried performed by quantum chemical methods with the hybrid exchange-correlation functional B3LYP using 6-31G(**), 6-311++G(**) and aug-cc-pVDZ basis sets. The most stable conformer of the title compounds have been determined from the analysis of potential energy surface. The stable molecular geometries, electronic and thermodynamic parameters, IR intensities, harmonic vibrational frequencies, depolarisation ratio and Raman intensities have been computed. Molecular electrostatic potential and frontier molecular orbitals were constructed to understand the electronic properties. The potential energy distributions (PEDs) were calculated to explain the mixing of fundamental modes. The theoretical geometrical parameters and the fundamental frequencies were compared with the experimental. The interactions of hydroxy and amino group substitutions on the characteristic vibrations of the ring and hydrazide group have been analysed. Copyright © 2013 Elsevier B.V. All rights reserved.

Composite structural materials

NASA Technical Reports Server (NTRS)

Loewy, Robert G.; Wiberley, Stephen E.

1988-01-01

A decade long program to develop critical advanced composite technology in the areas of physical properties, structural concept and analysis, manufacturing, reliability, and life predictions is reviewed. Specific goals are discussed. The status of the chemical vapor deposition effects on carbon fiber properties; inelastic deformation of metal matrix laminates; fatigue damage in fibrous MMC laminates; delamination fracture toughness in thermoplastic matrix composites; and numerical analysis of composite micromechanical behavior are presented.

Sesterterpenes as tubulin tyrosine ligase inhibitors. First insight of structure-activity relationships and discovery of new lead.

PubMed

Dal Piaz, Fabrizio; Vassallo, Antonio; Lepore, Laura; Tosco, Alessandra; Bader, Ammar; De Tommasi, Nunziatina

2009-06-25

Twenty-four new sesterterpenes, compounds 1-24, were isolated from the aerial parts of Salvia dominica. Their structures were elucidated by 1D and 2D NMR experiments as well as ESIMS analysis and chemical methods. The evaluation of the biological activity of Salvia dominica sesterterpenes by means of a panel of chemical and biological approaches, including chemical proteomics, surface plasmon resonance (SPR) measurements, and biochemical assays were realized. Obtained results showed that 18 out of the 24 sesterterpene lactones isolated from Salvia dominica interact with tubulin-tyrosine ligase (TTL) an enzyme involved in the tyrosination cycle of the C-terminal of tubulin, and inhibit TTL activity in cancer cells. Besides, results of our studies provided an activity/structure relationship that can be used to design effective TTL inhibitors.

Essential Parameters for Structural Analysis and Dereplication by 1H NMR Spectroscopy

PubMed Central

2015-01-01

The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain 1H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1–1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen (1H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms. PMID:24895010

Biogeographical Analysis of Chemical Co-Occurrence Data to ...

EPA Pesticide Factsheets

A challenge with multiple chemical risk assessment is the need to consider the joint behavior of chemicals in mixtures. To address this need, pharmacologists and toxicologists have developed methods over the years to evaluate and test chemical interaction. In practice, however, testing of chemical interaction more often comprises ad hoc binary combinations and rarely examines higher order combinations. One explanation for this practice is the belief that there are simply too many possible combinations of chemicals to consider. Indeed, under stochastic conditions the possible number of chemical combinations scales geometrically as the pool of chemicals increases. However, the occurrence of chemicals in the environment is determined by factors, economic in part, which favor some chemicals over others. We investigate methods from the field of biogeography, originally developed to study avian species co-occurrence patterns, and adapt these approaches to examine chemical co-occurrence. These methods were applied to a national survey of pesticide residues in 168 child care centers from across the country. Our findings show that pesticide co-occurrence in the child care center was not random but highly structured, leading to the co-occurrence of specific pesticide combinations. Thus, ecological studies of species co-occurrence parallel the issue of chemical co-occurrence at specific locations. Both are driven by processes that introduce structure in the pattern of co-o

Pump-probe imaging of pigmented cutaneous melanoma primary lesions gives insight into metastatic potential

PubMed Central

Robles, Francisco E.; Deb, Sanghamitra; Wilson, Jesse W.; Gainey, Christina S.; Selim, M. Angelica; Mosca, Paul J.; Tyler, Douglas S.; Fischer, Martin C.; Warren, Warren S.

2015-01-01

Metastatic melanoma is associated with a poor prognosis, but no method reliably predicts which melanomas of a given stage will ultimately metastasize and which will not. While sentinel lymph node biopsy (SLNB) has emerged as the most powerful predictor of metastatic disease, the majority of people dying from metastatic melanoma still have a negative SLNB. Here we analyze pump-probe microscopy images of thin biopsy slides of primary melanomas to assess their metastatic potential. Pump-probe microscopy reveals detailed chemical information of melanin with subcellular spatial resolution. Quantification of the molecular signatures without reference standards is achieved using a geometrical representation of principal component analysis. Melanin structure is analyzed in unison with the chemical information by applying principles of mathematical morphology. Results show that melanin in metastatic primary lesions has lower chemical diversity than non-metastatic primary lesions, and contains two distinct phenotypes that are indicative of aggressive disease. Further, the mathematical morphology analysis reveals melanin in metastatic primary lesions has a distinct “dusty” quality. Finally, a statistical analysis shows that the combination of the chemical information with spatial structures predicts metastatic potential with much better sensitivity than SLNB and high specificity, suggesting pump-probe microscopy can be an important tool to help predict the metastatic potential of melanomas. PMID:26417529

Structural, chemical and optical evaluation of Cu-doped ZnO nanoparticles synthesized by an aqueous solution method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iribarren, A., E-mail: augusto@imre.oc.uh.cu; Hernández-Rodríguez, E.; Maqueira, L.

Highlights: • Cu-doped ZnO nanoparticles obtained by chemical synthesis. • Substitutional or interstitial Cu into ZnO lead specific structural, chemical, and optical changes. • Incorporation efficiency of Cu atoms in ZnO as a function of the Cu concentration in the precursor dissolution. - Abstract: In this work a study of ZnO and Cu-doped ZnO nanoparticles obtained by chemical synthesis in aqueous media was carried out. Structural analysis gave the dominant presence of wurtzite ZnO phase forming a solid solution Zn{sub 1−x}Cu{sub x}O. For high Cu doping CuO phase is also present. For low Cu concentration the lattice shrinks due tomore » Cu atoms substitute Zn atoms. For high Cu concentration the lattice enlarges due to predominance of interstitial Cu. From elemental analysis we determined and analyzed the incorporation efficiency of Cu atoms in Zn{sub 1−x}Cu{sub x}O as a function of the Cu concentration in the precursor dissolution. Combining structural and chemical results we described the Cu/Zn precursor concentrations r{sub w} in which the solid solution of Cu in ZnO is predominant. In the region located at r{sub w} ≈ 0.2–0.3 it is no longer valid. For Cu/Zn precursor concentration r{sub w} > 0.3 interstitial Cu dominates, and some amount of copper oxide appears. As the Cu concentration increases, the effective size of nanoparticles decreases. Photoluminescence (PL) measurements of the Cu-doped ZnO nanoparticles were carried out and analyzed.« less

Christopher Chang | NREL

Science.gov Websites

transition metal systems, macromolecular dynamics, comparative chemical bonding analysis, electron transfer . Research Interests Dynamics and control on discrete structures, including excited-state transition metal

X-ray photoemission analysis of chemically modified TlBr surfaces for improved radiation detectors

DOE PAGES

Nelson, A. J.; Voss, L. F.; Beck, P. R.; ...

2013-01-12

We subjected device-grade TlBr to various chemical treatments used in room temperature radiation detector fabrication to determine the resulting surface composition and electronic structure. As-polished TlBr was treated separately with HCl, SOCl 2, Br:MeOH and HF solutions. High-resolution photoemission measurements on the valence band electronic structure and Tl 4f, Br 3d, Cl 2p and S 2p core lines were used to evaluate surface chemistry and shallow heterojunction formation. Surface chemistry and valence band electronic structure were correlated with the goal of optimizing the long-term stability and radiation response.

X-ray photoemission analysis of chemically modified TlBr surfaces for improved radiation detectors

NASA Astrophysics Data System (ADS)

Nelson, A. J.; Voss, L. F.; Beck, P. R.; Graff, R. T.; Conway, A. M.; Nikolic, R. J.; Payne, S. A.; Lee, J.-S.; Kim, H.; Cirignano, L.; Shah, K.

2013-04-01

Device-grade TlBr was subjected to various chemical treatments used in room temperature radiation detector fabrication to determine the resulting surface composition and electronic structure. As-polished TlBr was treated separately with HCl, SOCl2, Br:MeOH, and HF solutions. High-resolution photoemission measurements on the valence band electronic structure and Tl 4f, Br 3d, Cl 2p, and S 2p core lines were used to evaluate surface chemistry and shallow heterojunction formation. Surface chemistry and valence band electronic structure were correlated with the goal of optimizing the long-term stability and radiation response.

[Studies on chemical constituents from seeds of Euryale ferox].

PubMed

Sun, Hai-lin; Zhang, Ya-qiong; Xie, Xiao-yan; Che, Yan-yun

2014-11-01

To study the chemical constituents from the seeds of Euryale ferox. The chemical constituents were isolated by silica gel column, Sephadex LH-20 and their structures were identified by physico-chemical and spectral analysis. Seven compounds were purified from the 95% ethanol extract. These constituents were elucidated as protocatechuic acid (1), gallic acid (2), gallic acid ethyl ester(3),5 ,7-dihydroxychromone(4), β-sitosterol(5), daucosterol(6), and 5,7-dihydroxy-6,4'-dimethoxyflavone(7), respectively. All compounds are isolated from this plant for the first time.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

PubMed Central

Hafsa, Noor E.; Arndt, David; Wishart, David S.

2015-01-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

Compositional depth profile of a native oxide LPCVD MNOS structure using X-ray photoelectron spectroscopy and chemical etching

NASA Technical Reports Server (NTRS)

Wurzbach, J. A.; Grunthaner, F. J.

1983-01-01

It is pointed out that there is no report of an unambiguous analysis of the composition and interfacial structure of MNOS (metal-nitride oxide semiconductor) systems, despite the technological importance of these systems. The present investigation is concerned with a study of an MNOS structure on the basis of a technique involving the use of X-ray photoelectron spectroscopy (XPS) with a controlled stopped-flow chemical-etching procedure. XPS is sensitive to the structure of surface layers, while stopped-flow etching permits the controlled removal of overlying material on a scale of atomic layers, to expose new surface layers as a function of thickness. Therefore, with careful analysis of observed intensities at measured depths, this combination of techniques provides depth resolution between 5 and 10 A. According to the obtained data there is intact SiO2 at the substrate interface. There appears to be a thin layer containing excess bonds to silicon on top of the SiO2.

Synthesis of zinc sulfide nanoparticles and their incorporation into poly(hydroxybutyrate) matrix in the formation of a novel nanocomposite

NASA Astrophysics Data System (ADS)

Riaz, Shahina; Raza, Zulfiqar Ali; Majeed, Muhammad Irfan; Jan, Tariq

2018-05-01

In the present study, zinc sulfide (ZnS) nanoparticles (NPs) were successfully synthesized through a modified chemical precipitation protocol and then mediated into poly(hydroxybutyrate) (PHB) matrix to get ZnS/PHB nanocomposite. Mean diameter and zeta potential of ZnS NPs, as determined using dynamic light scattering technique (DLS), were observed to be 53 nm and ‑89 mV, respectively. The structural investigations performed using x-ray diffraction (XRD) technique depicted the phase purity of ZnS NPs exhibiting cubic crystal structure. Fourier transform infrared (FTIR) spectroscopic analysis was conducted to identify the presence or absence of bonding vibrational modes on the surface of synthesized single phase ZnS NPs. The FTIR analysis confirmed the metal to sulphur bond formation by showing the characteristic band at 1123 cm‑1. The UV–vis absorption spectra of ZnS NPs confirmed the synthesis of particles in nanoscale regime showing a λ max of 302 nm. These NPs were then successfully incorporated into PHB matrix to synthesize ZnS/PHB nanocomposite. The synthesis of nanocomposite was confirmed by EDX analysis. The chemical bonding and structural properties of ZnS/PHB nanocomposite were determined by FTIR and XRD analysis, respectively. The FTIR analysis confirmed the synthesis of ZnS/PHB nanocomposite. Moreover, XRD analysis showed that structure of nanocomposite was completely controlled by ZnS NPs as pure PHB exhibited orthorhombic crystal structure while the nanocomposite demonstrated cubic crystal structure of ZnS. Thermal properties of nanocomposite were studied through thermogravimetric analysis revealing that the incorporation of ZnS NPs into PHB matrix lead to enhance heat resistance properties of PHB.

Comparative study of A-site order in the lead-free bismuth titanates M{sub 1/2}Bi{sub 1/2}TiO{sub 3} (M=Li, Na, K, Rb, Cs, Ag, Tl) from first-principles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gröting, Melanie, E-mail: groeting@mm.tu-darmstadt.de; Albe, Karsten, E-mail: albe@mm.tu-darmstadt.de

2014-05-01

We investigate the possibility of enhancing chemical order in the relaxor ferroelectric Na{sub 1/2}Bi{sub 1/2}TiO{sub 3} upon substitution of Na{sup +} by other monovalent cations M{sup +} using total energy calculations based on density functional theory. All chemically available monovalent cations M{sup +}, which are Li, Na, Ag, K, Tl, Rb and Cs, are considered and an analysis of the structurally relaxed structures in terms of symmetry-adapted distortion modes is given in order to quantify the chemically induced structural distortions. We demonstrate that the replacement of Na{sup +} by other monovalent cations can hardly alter the tendency of chemical ordermore » with respect to Na{sub 1/2}Bi{sub 1/2}TiO{sub 3}. Only Tl{sub 1/2}Bi{sub 1/2}TiO{sub 3} and Ag{sub 1/2}Bi{sub 1/2}TiO{sub 3} show enhanced tendency for chemical ordering. Both heavy metals behave similar to the light alkali metals in terms of structural relaxations and relative stabilities of the ordered configurations. Although a comparison of the Goldschmidt factors of components (M TiO{sub 3}){sup −} reveals for Tl a value above the upper stability limit for perovskites, the additional lone-pair effect of Tl{sup +} stabilizes the ordered structure. - Graphical abstract: Amplitudes of chemically induced distortion modes in different ordered perovskites M{sub 1/2}Bi{sub 1/2}TiO{sub 3} and visualisation of atomic displacements associated with distortion mode X{sup +}{sub 1} in the 001-ordered compounds Li{sub 1/2}Bi{sub 1/2}TiO{sub 3} and Cs{sub 1/2}Bi{sub 1/2}TiO{sub 3}. Due to a substantial size mismatch between bismuth (green) and caesium (dark blue), incorporation of the latter leads to enhanced displacements of oxygen atoms (red) and suppresses displacements of titanium (silver) as compared to lithium (light blue) or other smaller monovalent cations. - Highlights: • Lead-free A-site mixed bismuth titanates M{sub 1/2}Bi{sub 1/2}TiO{sub 3} are studied by first-principles calculations. • Investigation of chemical ordering tendency for M=Li, Na, K, Rb, Cs, Ag, and Tl. • Group theoretical analysis of different ordered structures. • Ag and Tl compounds are the most promising candidates for study of chemical order dependent ferroelectric properties.« less

Fractionation and physicochemical characterization of lignin from waste jute bags: Effect of process parameters on yield and thermal degradation.

PubMed

Ahuja, Dheeraj; Kaushik, Anupama; Chauhan, Ghanshyam S

2017-04-01

In this work lignin was extracted from waste jute bags using soda cooking method and effect of varying alkali concentration and pH on yield, purity, structure and thermal degradation of lignin were studied. The Lignin yield, chemical composition and purity were assessed using TAPPI method and UV-vis spectroscopy. Yield and purity of lignin ranged from 27 to 58% and 50-94%, respectively for all the samples and was maximum for 8% alkali concentration and at pH 2 giving higher thermal stability. Chemical structure, thermal stability and elementary analysis of lignin were studied using FTIR, H NMR, thermo gravimetric analysis (TGA) and Elemental analyzer. FTIR and H NMR results showed that core structure of lignin starts breaking beyond 10% alkali concentration. S/G ratio shows the dominance of Syringyl unit over guaiacyl unit. Copyright © 2017 Elsevier B.V. All rights reserved.

Using in Vitro Evolution and Whole Genome Analysis To Discover Next Generation Targets for Antimalarial Drug Discovery

PubMed Central

2018-01-01

Although many new anti-infectives have been discovered and developed solely using phenotypic cellular screening and assay optimization, most researchers recognize that structure-guided drug design is more practical and less costly. In addition, a greater chemical space can be interrogated with structure-guided drug design. The practicality of structure-guided drug design has launched a search for the targets of compounds discovered in phenotypic screens. One method that has been used extensively in malaria parasites for target discovery and chemical validation is in vitro evolution and whole genome analysis (IVIEWGA). Here, small molecules from phenotypic screens with demonstrated antiparasitic activity are used in genome-based target discovery methods. In this Review, we discuss the newest, most promising druggable targets discovered or further validated by evolution-based methods, as well as some exceptions. PMID:29451780

The Chemistry and Pharmacology of Citrus Limonoids.

PubMed

Gualdani, Roberta; Cavalluzzi, Maria Maddalena; Lentini, Giovanni; Habtemariam, Solomon

2016-11-13

Citrus limonoids (CLs) are a group of highly oxygenated terpenoid secondary metabolites found mostly in the seeds, fruits and peel tissues of citrus fruits such as lemons, limes, oranges, pumellos, grapefruits, bergamots, and mandarins. Represented by limonin, the aglycones and glycosides of CLs have shown to display numerous pharmacological activities including anticancer, antimicrobial, antioxidant, antidiabetic and insecticidal among others. In this review, the chemistry and pharmacology of CLs are systematically scrutinised through the use of medicinal chemistry tools and structure-activity relationship approach. Synthetic derivatives and other structurally-related limonoids from other sources are include in the analysis. With the focus on literature in the past decade, the chemical classification of CLs, their physico-chemical properties as drugs, their biosynthesis and enzymatic modifications, possible ways of enhancing their biological activities through structural modifications, their ligand efficiency metrics and systematic graphical radar plot analysis to assess their developability as drugs are among those discussed in detail.

Breaking free from chemical spreadsheets.

PubMed

Segall, Matthew; Champness, Ed; Leeding, Chris; Chisholm, James; Hunt, Peter; Elliott, Alex; Garcia-Martinez, Hector; Foster, Nick; Dowling, Samuel

2015-09-01

Drug discovery scientists often consider compounds and data in terms of groups, such as chemical series, and relationships, representing similarity or structural transformations, to aid compound optimisation. This is often supported by chemoinformatics algorithms, for example clustering and matched molecular pair analysis. However, chemistry software packages commonly present these data as spreadsheets or form views that make it hard to find relevant patterns or compare related compounds conveniently. Here, we review common data visualisation and analysis methods used to extract information from chemistry data. We introduce a new framework that enables scientists to work flexibly with drug discovery data to reflect their thought processes and interact with the output of algorithms to identify key structure-activity relationships and guide further optimisation intuitively. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterization of dermal plates from armored catfish Pterygoplichthys pardalis reveals sandwich-like nanocomposite structure.

PubMed

Ebenstein, Donna; Calderon, Carlos; Troncoso, Omar P; Torres, Fernando G

2015-05-01

Dermal plates from armored catfish are bony structures that cover their body. In this paper we characterized structural, chemical, and nanomechanical properties of the dermal plates from the Amazonian fish Pterygoplichthys pardalis. Analysis of the morphology of the plates using scanning electron microscopy (SEM) revealed that the dermal plates have a sandwich-like structure composed of an inner porous matrix surrounded by two external dense layers. This is different from the plywood-like laminated structure of elasmoid fish scales but similar to the structure of osteoderms found in the dermal armour of some reptiles and mammals. Chemical analysis performed using Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and X-ray diffraction (XRD) results revealed similarities between the composition of P. pardalis plates and the elasmoid fish scales of Arapaima gigas. Reduced moduli of P. pardalis plates measured using nanoindentation were also consistent with reported values for A. gigas scales, but further revealed that the dermal plate is an anisotropic and heterogeneous material, similar to many other fish scales and osteoderms. It is postulated that the sandwich-like structure of the dermal plates provides a lightweight and tough protective layer. Copyright © 2015 Elsevier Ltd. All rights reserved.

Consistent global structures of complex RNA states through multidimensional chemical mapping

PubMed Central

Cheng, Clarence Yu; Chou, Fang-Chieh; Kladwang, Wipapat; Tian, Siqi; Cordero, Pablo; Das, Rhiju

2015-01-01

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states. DOI: http://dx.doi.org/10.7554/eLife.07600.001 PMID:26035425

Interactive Design Strategy for a Multi-Functional PAMAM Dendrimer-Based Nano-Therapeutic Using Computational Models and Experimental Analysis

PubMed Central

Lee, Inhan; Williams, Christopher R.; Athey, Brian D.; Baker, James R.

2010-01-01

Molecular dynamics simulations of nano-therapeutics as a final product and of all intermediates in the process of generating a multi-functional nano-therapeutic based on a poly(amidoamine) (PAMAM) dendrimer were performed along with chemical analyses of each of them. The actual structures of the dendrimers were predicted, based on potentiometric titration, gel permeation chromatography, and NMR. The chemical analyses determined the numbers of functional molecules, based on the actual structure of the dendrimer. Molecular dynamics simulations calculated the configurations of the intermediates and the radial distributions of functional molecules, based on their numbers. This interactive process between the simulation results and the chemical analyses provided a further strategy to design the next reaction steps and to gain insight into the products at each chemical reaction step. PMID:20700476

[Chemical constituents of Pileostegia viburnoides var. glabrescens].

PubMed

Zou, Ju-ying; Chen, Sheng-huang; Li, Qin-wen; Ou, Yang-wen; Chen, Han-jun; Wang, Wei

2012-05-01

To study the chemical constituents of Pileostegia viburnoides var. glabrescens. The compounds were isolated and purified by various techniques. Their structures were determined by physicochemical properties and spectral analysis. Five compounds were isolated and identified as friedelin (1), beta-sitosterol (2), umbelliferone (3), daucosterol (4) and skimmin (5). All the compounds were isolated from this genus for the first time.

Tropical sea snail shells: Possible exotic sources for ceramic biomaterial synthesis

NASA Astrophysics Data System (ADS)

Oktar, F. N.; Kiyici, I. A.; Gökçe, H.; Aǧaogulları, D.; Kayali, E. S.

2013-12-01

In this study, chemical and structural properties of sea snail shell based bioceramic materials (i.e. hydroxyapatite, whitlockite and other phases) are produced by using mechano-chemical (ultrasonic) conversion method. For this purpose, differential thermal and gravimetric analysis (DTA/TG), X-ray diffraction, infra-red (IR) and scanning electron microscope (SEM) studies are performed.

[Chemical constituents from Ajuga nipponensis].

PubMed

He, Gui-xia; Liang, Xiao-lan; Ouyang, Wen; Yi, Gang-qiang; Li, Yun-yao; Zhao, Jian-ping; Ikhlas, Khan

2013-12-01

To study the chemical constituents of Ajuga nipponensis. The chemical constituents were isolated by repeated silica gel column chromatography and their structures were elucidated by phyisochemical properties and spectral analysis. Ten compounds were isolated and identified as:hexadecanoic acid(1), ajuforrestin A(2), beta-sitosterol(3), acacetin(4), apigenin(5), ajugamacrin B(6), ursolic acid(7), beta-ecdysone(8), 8-acetylharpagide(9) and daucosterol(10). Compounds 1-7 and 10 are isolated from this plant for the first time.

Computational study of some fluoroquinolones: Structural, spectral and docking investigations

NASA Astrophysics Data System (ADS)

Sayin, Koray; Karakaş, Duran; Kariper, Sultan Erkan; Sayin, Tuba Alagöz

2018-03-01

Quantum chemical calculations are performed over norfloxacin, tosufloxacin and levofloxacin. The most stable structures for each molecule are determined by thermodynamic parameters. Then the best level for calculations is determined by benchmark analysis. M062X/6-31 + G(d) level is used in calculations. IR, UV-VIS and NMR spectrum are calculated and examined in detail. Some quantum chemical parameters are calculated and the tendency of activity is recommended. Additionally, molecular docking calculations are performed between related compounds and a protein (ID: 2J9N).

Structural Elucidation and Biological Activity of a Highly Regular Fucosylated Glycosaminoglycan from the Edible Sea Cucumber Stichopus herrmanni.

PubMed

Li, Xiaomei; Luo, Lan; Cai, Ying; Yang, Wenjiao; Lin, Lisha; Li, Zi; Gao, Na; Purcell, Steven W; Wu, Mingyi; Zhao, Jinhua

2017-10-25

Edible sea cucumbers are widely used as a health food and medicine. A fucosylated glycosaminoglycan (FG) was purified from the high-value sea cucumber Stichopus herrmanni. Its physicochemical properties and structure were analyzed and characterized by chemical and instrumental methods. Chemical analysis indicated that this FG with a molecular weight of ∼64 kDa is composed of N-acetyl-d-galactosamine, d-glucuronic acid (GlcA), and l-fucose. Structural analysis clarified that the FG contains the chondroitin sulfate E-like backbone, with mostly 2,4-di-O-sulfated (85%) and some 3,4-di-O-sulfated (10%) and 4-O-sulfated (5%) fucose side chains that link to the C3 position of GlcA. This FG is structurally highly regular and homogeneous, differing from the FGs of other sea cucumbers, for its sulfation patterns are simpler. Biological activity assays indicated that it is a strong anticoagulant, inhibiting thrombin and intrinsic factor Xase. Our results expand the knowledge on structural types of FG and illustrate its biological activity as a functional food material.

Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard

EPA Science Inventory

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...

Structural analysis of pyrolytic lignins isolated from switchgrass fast pyrolysis oil

USDA-ARS?s Scientific Manuscript database

Structural characterization of lignin extracted from the bio-oil produced by fast pyrolysis of switchgrass (Panicum virgatum) is reported. This new information is important to understanding the utility of lignin as a chemical feedstock in a pyrolysis based biorefinery. Pyrolysis induces a variety of...

Molecular cloning, sequence and structural analysis of dehairing Mn(2+) dependent alkaline serine protease (MASPT) of Bacillus pumilus TMS55.

PubMed

Ibrahim, Kalibulla Syed; Muniyandi, Jeyaraj; Pandian, Shunmugiah Karutha

2011-10-01

Leather industries release a large amount of pollution-causing chemicals which creates one of the major industrial pollutions. The development of enzyme based processes as a potent alternative to pollution-causing chemicals is useful to overcome this issue. Proteases are enzymes which have extensive applications in leather processing and in several bioremediation processes due to their high alkaline protease activity and dehairing efficacy. In the present study, we report cloning, characterization of a Mn2+ dependent alkaline serine protease gene (MASPT) of Bacillus pumilus TMS55. The gene encoding the protease from B. pumilus TMS55 was cloned and its nucleotide sequence was determined. This gene has an open reading frame (ORF) of 1,149 bp that encodes a polypeptide of 383 amino acid residues. Our analysis showed that this polypeptide is composed of 29 residues N-terminal signal peptide, a propeptide of 79 residues and a mature protein of 275 amino acids. We performed bioinformatics analysis to compare MASPT enzyme with other proteases. Homology modeling was employed to model three dimensional structure for MASPT. Structural analysis showed that MASPT structure is composed of nine α-helices and nine β-strands. It has 3 catalytic residues and 14 metal binding residues. Docking analysis showed that residues S223, A260, N263, T328 and S329 interact with Mn2+. This study allows initial inferences about the structure of the protease and will allow the rational design of its derivatives for structure-function studies and also for further improvement of the enzyme.

Hekate: Software Suite for the Mass Spectrometric Analysis and Three-Dimensional Visualization of Cross-Linked Protein Samples

PubMed Central

2013-01-01

Chemical cross-linking of proteins combined with mass spectrometry provides an attractive and novel method for the analysis of native protein structures and protein complexes. Analysis of the data however is complex. Only a small number of cross-linked peptides are produced during sample preparation and must be identified against a background of more abundant native peptides. To facilitate the search and identification of cross-linked peptides, we have developed a novel software suite, named Hekate. Hekate is a suite of tools that address the challenges involved in analyzing protein cross-linking experiments when combined with mass spectrometry. The software is an integrated pipeline for the automation of the data analysis workflow and provides a novel scoring system based on principles of linear peptide analysis. In addition, it provides a tool for the visualization of identified cross-links using three-dimensional models, which is particularly useful when combining chemical cross-linking with other structural techniques. Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight into the previously uncharacterized C-terminal domain of the protein. PMID:24010795

Chemoinformatic expedition of the chemical space of fungal products.

PubMed

González-Medina, Mariana; Prieto-Martínez, Fernando D; Naveja, J Jesús; Méndez-Lucio, Oscar; El-Elimat, Tamam; Pearce, Cedric J; Oberlies, Nicholas H; Figueroa, Mario; Medina-Franco, José L

2016-08-01

Fungi are valuable resources for bioactive secondary metabolites. However, the chemical space of fungal secondary metabolites has been studied only on a limited basis. Herein, we report a comprehensive chemoinformatic analysis of a unique set of 207 fungal metabolites isolated and characterized in a USA National Cancer Institute funded drug discovery project. Comparison of the molecular complexity of the 207 fungal metabolites with approved anticancer and nonanticancer drugs, compounds in clinical studies, general screening compounds and molecules Generally Recognized as Safe revealed that fungal metabolites have high degree of complexity. Molecular fingerprints showed that fungal metabolites are as structurally diverse as other natural products and have, in general, drug-like physicochemical properties. Fungal products represent promising candidates to expand the medicinally relevant chemical space. This work is a significant expansion of an analysis reported years ago for a smaller set of compounds (less than half of the ones included in the present work) from filamentous fungi using different structural properties.

QSAR modeling and chemical space analysis of antimalarial compounds

NASA Astrophysics Data System (ADS)

Sidorov, Pavel; Viira, Birgit; Davioud-Charvet, Elisabeth; Maran, Uko; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

2017-05-01

Generative topographic mapping (GTM) has been used to visualize and analyze the chemical space of antimalarial compounds as well as to build predictive models linking structure of molecules with their antimalarial activity. For this, a database, including 3000 molecules tested in one or several of 17 anti- Plasmodium activity assessment protocols, has been compiled by assembling experimental data from in-house and ChEMBL databases. GTM classification models built on subsets corresponding to individual bioassays perform similarly to the earlier reported SVM models. Zones preferentially populated by active and inactive molecules, respectively, clearly emerge in the class landscapes supported by the GTM model. Their analysis resulted in identification of privileged structural motifs of potential antimalarial compounds. Projection of marketed antimalarial drugs on this map allowed us to delineate several areas in the chemical space corresponding to different mechanisms of antimalarial activity. This helped us to make a suggestion about the mode of action of the molecules populating these zones.

QSAR modeling and chemical space analysis of antimalarial compounds.

PubMed

Sidorov, Pavel; Viira, Birgit; Davioud-Charvet, Elisabeth; Maran, Uko; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

2017-05-01

Generative topographic mapping (GTM) has been used to visualize and analyze the chemical space of antimalarial compounds as well as to build predictive models linking structure of molecules with their antimalarial activity. For this, a database, including ~3000 molecules tested in one or several of 17 anti-Plasmodium activity assessment protocols, has been compiled by assembling experimental data from in-house and ChEMBL databases. GTM classification models built on subsets corresponding to individual bioassays perform similarly to the earlier reported SVM models. Zones preferentially populated by active and inactive molecules, respectively, clearly emerge in the class landscapes supported by the GTM model. Their analysis resulted in identification of privileged structural motifs of potential antimalarial compounds. Projection of marketed antimalarial drugs on this map allowed us to delineate several areas in the chemical space corresponding to different mechanisms of antimalarial activity. This helped us to make a suggestion about the mode of action of the molecules populating these zones.

Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine

NASA Astrophysics Data System (ADS)

Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing

2016-12-01

Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.

Structure-activity relationships and prediction of the phototoxicity and phototoxic potential of new drugs.

PubMed

Barratt, Martin D

2004-11-01

Relationships between the structure and properties of chemicals can be programmed into knowledge-based systems such as DEREK for Windows (DEREK is an acronym for "Deductive Estimation of Risk from Existing Knowledge"). The DEREK for Windows computer system contains a subset of over 60 rules describing chemical substructures (toxophores) responsible for skin sensitisation. As part of the European Phototox Project, the rule base was supplemented by a number of rules for the prospective identification of photoallergens, either by extension of the scope of existing rules or by the generation of new rules where a sound mechanistic rationale for the biological activity could be established. The scope of the rules for photoallergenicity was then further refined by assessment against a list of chemicals identified as photosensitisers by the Centro de Farmacovigilancia de la Comunidad Valenciana, Valencia, Spain. This paper contains an analysis of the mechanistic bases of activity for eight important groups of photoallergens and phototoxins, together with rules for the prospective identification of the photobiological activity of new or untested chemicals belonging to those classes. The mechanism of action of one additional chemical, nitrofurantoin, is well established; however, it was deemed inappropriate to write a rule on the basis of a single chemical structure.

The Architecture of Chemical Alternatives Assessment.

PubMed

Geiser, Kenneth; Tickner, Joel; Edwards, Sally; Rossi, Mark

2015-12-01

Chemical alternatives assessment is a method rapidly developing for use by businesses, governments, and nongovernment organizations seeking to substitute chemicals of concern in production processes and products. Chemical alternatives assessment is defined as a process for identifying, comparing, and selecting safer alternatives to chemicals of concern (including those in materials, processes, or technologies) on the basis of their hazards, performance, and economic viability. The process is intended to provide guidance for assuring that chemicals of concern are replaced with safer alternatives that are not likely to be later regretted. Conceptually, the assessment methods are developed from a set of three foundational pillars and five common principles. Based on a number of emerging alternatives assessment initiatives, in this commentary, we outline a chemical alternatives assessment blueprint structured around three broad steps: Scope, Assessment, and Selection and Implementation. Specific tasks and tools are identified for each of these three steps. While it is recognized that on-going practice will further refine and develop the method and tools, it is important that the structure of the assessment process remain flexible, adaptive, and focused on the substitution of chemicals of concern with safer alternatives. © 2015 Society for Risk Analysis.

Implementation of an ADME enabling selection and visualization tool for drug discovery.

PubMed

Stoner, Chad L; Gifford, Eric; Stankovic, Charles; Lepsy, Christopher S; Brodfuehrer, Joanne; Prasad, J V N Vara; Surendran, Narayanan

2004-05-01

The pharmaceutical industry has large investments in compound library enrichment, high throughput biological screening, and biopharmaceutical (ADME) screening. As the number of compounds submitted for in vitro ADME screens increases, data analysis, interpretation, and reporting will become rate limiting in providing ADME-structure-activity relationship information to guide the synthetic strategy for chemical series. To meet these challenges, a software tool was developed and implemented that enables scientists to explore in vitro and in silico ADME and chemistry data in a multidimensional framework. The present work integrates physicochemical and ADME data, encompassing results for Caco-2 permeability, human liver microsomal half-life, rat liver microsomal half-life, kinetic solubility, measured log P, rule of 5 descriptors (molecular weight, hydrogen bond acceptors, hydrogen bond donors, calculated log P), polar surface area, chemical stability, and CYP450 3A4 inhibition. To facilitate interpretation of this data, a semicustomized software solution using Spotfire was designed that allows for multidimensional data analysis and visualization. The solution also enables simultaneous viewing and export of chemical structures with the corresponding ADME properties, enabling a more facile analysis of ADME-structure-activity relationship. In vitro and in silico ADME data were generated for 358 compounds from a series of human immunodeficiency virus protease inhibitors, resulting in a data set of 5370 experimental values which were subsequently analyzed and visualized using the customized Spotfire application. Implementation of this analysis and visualization tool has accelerated the selection of molecules for further development based on optimum ADME characteristics, and provided medicinal chemistry with specific, data driven structural recommendations for improvements in the ADME profile. Copyright 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93: 1131-1141, 2004

Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

PubMed Central

Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

2016-01-01

Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

From genomics to chemical genomics: new developments in KEGG

PubMed Central

Kanehisa, Minoru; Goto, Susumu; Hattori, Masahiro; Aoki-Kinoshita, Kiyoko F.; Itoh, Masumi; Kawashima, Shuichi; Katayama, Toshiaki; Araki, Michihiro; Hirakawa, Mika

2006-01-01

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource () provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps. PMID:16381885

Microscopy and Chemical Inversing Techniques to Determine the Photonic Crystal Structure of Iridescent Beetle Scales in the Cerambycidae Family

NASA Astrophysics Data System (ADS)

Richey, Lauren; Gardner, John; Standing, Michael; Jorgensen, Matthew; Bartl, Michael

2010-10-01

Photonic crystals (PCs) are periodic structures that manipulate electromagnetic waves by defining allowed and forbidden frequency bands known as photonic band gaps. Despite production of PC structures operating at infrared wavelengths, visible counterparts are difficult to fabricate because periodicities must satisfy the diffraction criteria. As part of an ongoing search for naturally occurring PCs [1], a three-dimensional array of nanoscopic spheres in the iridescent scales of the Cerambycidae insects A. elegans and G. celestis has been found. Such arrays are similar to opal gemstones and self-assembled colloidal spheres which can be chemically inverted to create a lattice-like PC. Through a chemical replication process [2], scanning electron microscopy analysis, sequential focused ion beam slicing and three-dimensional modeling, we analyzed the structural arrangement of the nanoscopic spheres. The study of naturally occurring structures and their inversing techniques into PCs allows for diversity in optical PC fabrication. [1] J.W. Galusha et al., Phys. Rev. E 77 (2008) 050904. [2] J.W. Galusha et al., J. Mater. Chem. 20 (2010) 1277.

The Vertex Version of Weighted Wiener Number for Bicyclic Molecular Structures

PubMed Central

Gao, Wei

2015-01-01

Graphs are used to model chemical compounds and drugs. In the graphs, each vertex represents an atom of molecule and edges between the corresponding vertices are used to represent covalent bounds between atoms. We call such a graph, which is derived from a chemical compound, a molecular graph. Evidence shows that the vertex-weighted Wiener number, which is defined over this molecular graph, is strongly correlated to both the melting point and boiling point of the compounds. In this paper, we report the extremal vertex-weighted Wiener number of bicyclic molecular graph in terms of molecular structural analysis and graph transformations. The promising prospects of the application for the chemical and pharmacy engineering are illustrated by theoretical results achieved in this paper. PMID:26640513

Impact of physical and chemical parameters on the hydroxyapatite nanopowder synthesized by chemical precipitation method

NASA Astrophysics Data System (ADS)

Thu Trang Pham, Thi; Phuong Nguyen, Thu; Pham, Thi Nam; Phuong Vu, Thi; Tran, Dai Lam; Thai, Hoang; Thanh Dinh, Thi Mai

2013-09-01

In this paper, the synthesis of hydroxyapatite (HAp) nanopowder was studied by chemical precipitation method at different values of reaction temperature, settling time, Ca/P ratio, calcination temperature, (NH4)2HPO4 addition rate, initial concentration of Ca(NO3)2 and (NH4)2HPO4. Analysis results of properties, morphology, structure of HAp powder from infrared (IR) spectra, x-ray diffraction (XRD), energy dispersive x-ray (EDX) spectra and scanning electron microscopy (SEM) indicated that the synthesized HAp powder had cylinder crystal shape with size less than 100 nm, single-phase structure. The variation of the synthesis conditions did not affect the morphology but affected the size of HAp crystals.

Deep ultraviolet scanning near-field optical microscopy for the structural analysis of organic and biological materials

NASA Astrophysics Data System (ADS)

Aoki, Hiroyuki; Hamamatsu, Toyohiro; Ito, Shinzaburo

2004-01-01

Scanning near-field optical microscopy (SNOM) using a deep ultraviolet (DUV) light source was developed for in situ imaging of a variety of chemical species without staining. Numerous kinds of chemical species have a carbon-carbon double bond or aromatic group in their chemical structure, which can be excited at the wavelength below 300 nm. In this study, the wavelength range available for SNOM imaging was extended to the DUV region. DUV-SNOM allowed the direct imaging of polymer thin films with high detection sensitivity and spatial resolution of several tens of nanometers. In addition to the polymer materials, we demonstrated the near-field imaging of a cell without using a fluorescence label.

Characteristics of HgS nanoparticles formed in hair by a chemical reaction

NASA Astrophysics Data System (ADS)

Patriarche, G.; Walter, P.; Van Elslande, E.; Ayache, J.; Castaing, J.

2013-01-01

A chemical reaction, derived from an ancient recipe for hair dyeing, is used to precipitate nanoparticles of mercury sulphide in hair by the simple process of immersion in a water solution of Ca(OH)2 and HgO. After several days, HgS nanoparticles appear throughout the hair and are particularly numerous in the various interfaces. The formation of these nanoparticles has been studied by analytical and atomic resolution electron microscopy. High resolution quantitative analysis allowed the determination of two varieties of HgS precipitate crystal structures formed: a hexagonal cinnabar and a cubic metacinnabar structure. This very simple process of a chemical reaction in hair is a particularly inexpensive way to fabricate semiconductor sulphide nanoparticles with specific properties.

Methods for spectral image analysis by exploiting spatial simplicity

DOEpatents

Keenan, Michael R.

2010-05-25

Several full-spectrum imaging techniques have been introduced in recent years that promise to provide rapid and comprehensive chemical characterization of complex samples. One of the remaining obstacles to adopting these techniques for routine use is the difficulty of reducing the vast quantities of raw spectral data to meaningful chemical information. Multivariate factor analysis techniques, such as Principal Component Analysis and Alternating Least Squares-based Multivariate Curve Resolution, have proven effective for extracting the essential chemical information from high dimensional spectral image data sets into a limited number of components that describe the spectral characteristics and spatial distributions of the chemical species comprising the sample. There are many cases, however, in which those constraints are not effective and where alternative approaches may provide new analytical insights. For many cases of practical importance, imaged samples are "simple" in the sense that they consist of relatively discrete chemical phases. That is, at any given location, only one or a few of the chemical species comprising the entire sample have non-zero concentrations. The methods of spectral image analysis of the present invention exploit this simplicity in the spatial domain to make the resulting factor models more realistic. Therefore, more physically accurate and interpretable spectral and abundance components can be extracted from spectral images that have spatially simple structure.

Methods for spectral image analysis by exploiting spatial simplicity

DOEpatents

Keenan, Michael R.

2010-11-23

Several full-spectrum imaging techniques have been introduced in recent years that promise to provide rapid and comprehensive chemical characterization of complex samples. One of the remaining obstacles to adopting these techniques for routine use is the difficulty of reducing the vast quantities of raw spectral data to meaningful chemical information. Multivariate factor analysis techniques, such as Principal Component Analysis and Alternating Least Squares-based Multivariate Curve Resolution, have proven effective for extracting the essential chemical information from high dimensional spectral image data sets into a limited number of components that describe the spectral characteristics and spatial distributions of the chemical species comprising the sample. There are many cases, however, in which those constraints are not effective and where alternative approaches may provide new analytical insights. For many cases of practical importance, imaged samples are "simple" in the sense that they consist of relatively discrete chemical phases. That is, at any given location, only one or a few of the chemical species comprising the entire sample have non-zero concentrations. The methods of spectral image analysis of the present invention exploit this simplicity in the spatial domain to make the resulting factor models more realistic. Therefore, more physically accurate and interpretable spectral and abundance components can be extracted from spectral images that have spatially simple structure.

Exposomics research using suspect screening and non ...

EPA Pesticide Factsheets

High-resolution mass spectrometry (HRMS) is used for suspect screening (SSA) and non-targeted analysis (NTA) in an attempt to characterize xenobiotic chemicals in various samples broadly and efficiently. These important techniques aid characterization of the exposome, the totality of human exposures, and provide critical information on thousands of chemicals in commerce for which exposure data are lacking. The Environmental Protection Agency (EPA) SSA and NTA capabilities consist of analytical instrumentation [liquid chromatography (LC) with time of flight (TOF) and quadrupole-TOF (Q-TOF) HRMS], workflows (feature extraction, formula generation, structure prediction, spectral matching, chemical confirmation), and tools (databases; models for predicting retention time, functional use, media occurrence, and media concentration; and schemes for ranking features and chemicals). Suspect screening (SSA) and non-targeted analysis (NTA) are used to characterize xenobiotic chemicals in various samples and aid characterization of the exposome, the totality of human exposures, and provide critical information on thousands of chemicals in commerce for which exposure data are lacking.

Molybdenum X-Ray Absorption Edges from 200 – 20,000 eV, The Benefits of Soft X-Ray Spectroscopy for Chemical Speciation

PubMed Central

George, Simon J.; Drury, Owen B.; Fu, Juxia; Friedrich, Stephan; Doonan, Christian J.; George, Graham N.; White, Jonathan M.; Young, Charles G.; Cramer, Stephen P.

2009-01-01

We have surveyed the chemical utility of the near-edge structure of molybdenum x-ray absorption edges from the hard x-ray K-edge at 20,000 eV down to the soft x-ray M4,5-edges at ~230 eV. We compared, for each edge, the spectra of two tetrahedral anions, MoO4 and MoS42-. We used three criteria for assessing near-edge structure of each edge: (i) the ratio of the observed chemical shift between MoO42- and MoS42- and the linewidth, (ii) the chemical information from analysis of the near-edge structure and (iii) the ease of measurement using fluorescence detection. Not surprisingly, the K-edge was by far the easiest to measure, but it contained the least information. The L2,3-edges, although harder to measure, had benefits with regard to selection rules and chemical speciation in that they had both a greater chemical shift as well as detailed lineshapes which could be theoretically analyzed in terms of Mo ligand field, symmetry, and covalency. The soft x-ray M2,3-edges were perhaps the least useful, in that they were difficult to measure using fluorescence detection and had very similar information content to the corresponding L2,3-edges. Interestingly, the soft x-ray, low energy (~230 eV) M4,5-edges had greatest potential chemical sensitivity and using our high resolution superconducting tunnel junction (STJ) fluorescence detector they appear to be straightforward to measure. The spectra were amenable to analysis using both the TT-multiplet approach and FEFF. The results using FEFF indicate that the sharp near-edge peaks arise from 3d → 5p transitions, while the broad edge structure has predominately 3d → 4f character. A proper understanding of the dependence of these soft x-ray spectra on ligand field and site geometry is necessary before a complete assessment of the utility of the Mo M4,5-edges can be made. This work includes crystallographic characterization of sodium tetrathiomolybdate. PMID:19041140

Applications of Mass Spectrometry to Structural Analysis of Marine Oligosaccharides

PubMed Central

Lang, Yinzhi; Zhao, Xia; Liu, Lili; Yu, Guangli

2014-01-01

Marine oligosaccharides have attracted increasing attention recently in developing potential drugs and biomaterials for their particular physical and chemical properties. However, the composition and sequence analysis of marine oligosaccharides are very challenging for their structural complexity and heterogeneity. Mass spectrometry (MS) has become an important technique for carbohydrate analysis by providing more detailed structural information, including molecular mass, sugar constituent, sequence, inter-residue linkage position and substitution pattern. This paper provides an overview of the structural analysis based on MS approaches in marine oligosaccharides, which are derived from some biologically important marine polysaccharides, including agaran, carrageenan, alginate, sulfated fucan, chitosan, glycosaminoglycan (GAG) and GAG-like polysaccharides. Applications of electrospray ionization mass spectrometry (ESI-MS) are mainly presented and the general applications of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) are also outlined. Some technical challenges in the structural analysis of marine oligosaccharides by MS have also been pointed out. PMID:24983643

Abuse of guaifenesin-containing medications generates an excess of a carboxylate salt of beta-(2-methoxyphenoxy)-lactic acid, a guaifenesin metabolite, and results in urolithiasis.

PubMed

Pickens, C L; Milliron, A R; Fussner, A L; Dversdall, B C; Langenstroer, P; Ferguson, S; Fu, X; Schmitz, F J; Poole, E C

1999-07-01

Several urinary calculi were submitted to our institution for compositional analysis. The typical techniques of analysis, polarized light microscopy, electron microprobe analysis, and infrared spectroscopy proved inadequate for a definitive identification. As a result, a more detailed organic analysis was conducted to determine the exact chemical structure of the material. Infrared spectroscopy and mass spectrometric analysis were carried out on the solid material, providing information concerning the functional groups and the molecular mass of the organic constituent and its components. The stone was solubilized in deuterated solvents and analyzed by nuclear magnetic resonance spectroscopy, which resulted in a definitive chemical structure. The spectroscopic analysis indicated that the stones were composed of a calcium salt of beta-(2-methoxyphenoxy)-lactic acid, a metabolite of the pharmaceutical guaifenesin, which is used as an expectorant. Guaifenesin, an expectorant common in over-the-counter cold and allergy remedies, can cause urolithiasis if taken in excess. Discussions with physicians and their patients confirmed that most patients admitted to taking large doses of guaifenesin-containing medications.

20180318 - Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard (ACS Spring)

EPA Science Inventory

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...

Tailoring physical properties of transglutaminase-modified gelatin films by varying drying temperature

USDA-ARS?s Scientific Manuscript database

Gelatin films prepared with or without transglutaminase (TGase) and dried at 15, 25 and 35 °C were analyzed for polymeric network structure, chemical composition and physical properties. Differences in protein network structure were observed by optical microscopy analysis in freeze-dried film-formin...

Quantitative structure-activity relationships for primary aerobic biodegradation of organic chemicals in pristine surface waters: starting points for predicting biodegradation under acclimatization.

PubMed

Nolte, Tom M; Pinto-Gil, Kevin; Hendriks, A Jan; Ragas, Ad M J; Pastor, Manuel

2018-01-24

Microbial biomass and acclimation can affect the removal of organic chemicals in natural surface waters. In order to account for these effects and develop more robust models for biodegradation, we have compiled and curated removal data for un-acclimated (pristine) surface waters on which we developed quantitative structure-activity relationships (QSARs). Global analysis of the very heterogeneous dataset including neutral, anionic, cationic and zwitterionic chemicals (N = 233) using a random forest algorithm showed that useful predictions were possible (Q ext 2 = 0.4-0.5) though relatively large standard errors were associated (SDEP ∼0.7). Classification of the chemicals based on speciation state and metabolic pathway showed that biodegradation is influenced by the two, and that the dependence of biodegradation on chemical characteristics is non-linear. Class-specific QSAR analysis indicated that shape and charge distribution determine the biodegradation of neutral chemicals (R 2 ∼ 0.6), e.g. through membrane permeation or binding to P450 enzymes, whereas the average biodegradation of charged chemicals is 1 to 2 orders of magnitude lower, for which degradation depends more directly on cellular uptake (R 2 ∼ 0.6). Further analysis showed that specific chemical classes such as peptides and organic halogens are relatively less biodegradable in pristine surface waters, resulting in the need for the microbial consortia to acclimate. Additional literature data was used to verify an acclimation model (based on Monod-type kinetics) capable of extrapolating QSAR predictions to acclimating conditions such as in water treatment, downstream lakes and large rivers under μg L -1 to mg L -1 concentrations. The framework developed, despite being based on multiple assumptions, is promising and needs further validation using experimentation with more standardised and homogenised conditions as well as adequate characterization of the inoculum used.

Structures of Hydrated Alkali Metal Cations, M+(H2O)nAr (m = Li, Na, K, rb and Cs, n = 3-5), Using Infrared Photodissociation Spectroscopy and Thermodynamic Analysis

NASA Astrophysics Data System (ADS)

Ke, Haochen; van der Linde, Christian; Lisy, James M.

2014-06-01

Alkali metal cations play vital roles in chemical and biochemical systems. Lithium is widely used in psychiatric treatment of manic states and bipolar disorder; Sodium and potassium are essential elements, having major biological roles as electrolytes, balancing osmotic pressure on body cells and assisting the electroneurographic signal transmission; Rubidium has seen increasing usage as a supplementation for manic depression and depression treatment; Cesium doped compounds are used as essential catalysts in chemical production and organic synthesis. Since hydrated alkali metal cations are ubiquitous and the basic form of the alkali metal cations in chemical and biochemical systems, their structural and thermodynamic properties serve as the foundation for modeling more complex chemical and biochemical processes, such as ion transport and ion size-selectivity of ionophores and protein channels. By combining mass spectrometry and infrared photodissociation spectroscopy, we have characterized the structures and thermodynamic properties of the hydrated alkali metal cations, i.e. M+(H2O)nAr, (M = Li, Na, K, Rb and Cs, n = 3-5). Ab initio calculations and RRKM-EE (evaporative ensemble) calculations were used to assist in the spectral assignments and thermodynamic analysis. Results showed that the structures of hydrated alkali metal cations were determined predominantly by the competition between non-covalent interactions, i.e. the water---water hydrogen bonding interactions and the water---cation electrostatic interactions. This balance, however, is very delicate and small changes, i.e. different cations, different levels of hydration and different effective temperatures clearly impact the balance.

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile.

PubMed

Arjunan, V; Thillai Govindaraja, S; Jose, Sujin P; Mohan, S

2014-07-15

The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm(-1) respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G(**), high level 6-311++G(**) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The (1)H (400 MHz; CDCl3) and (13)C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors. Copyright © 2014 Elsevier B.V. All rights reserved.

[Studies on the chemical constituents from the roots of Kalopanax septemlobus].

PubMed

Yao, Huan-Kai; Duan, Jing-Yu; Li, Yan; Wang, Jian-Hui; Yin, Xiao-Xing; Duan, Hong-Quan

2011-05-01

To investigate the chemical constituents of Kalopanax septemlobus. Chromatographic techniques including silica gel, gel, semi-preparative HPLC and PTLC as well as recrystallization were employed in the isolation and purification, and the structures were elucidated by spectral analysis and physical and chemical properties. 6 compounds were identified as liriodendrin (1), (-) -syringarenol (2), trans-coniferyl aldehyde (3), trans-caffeic acid (4), beta-daucosterol (5), beta-sitosterol (6). Compounds 2 -5 are obtained from this genus for the first time.

[Studies on chemical constituents of Heterosmilax yunnanensis].

PubMed

Qin, Wen-jie; Wang, Gang-li; Lin, Rui-chao

2007-08-01

To study the chemical constituents of Heterosmilax yunianensis. The compounds were isolated and repeatedly purified with chromatograph and the structures were elucidated by physico-chemical properties and spectral analysis. Eight compounds were obtained and elucidated as beta-sitosterol (I), glycerol monopalmitate (II), daucosterol (IIl), hexacosanoic acid (IV), 5-hydroxymethyl furaldehyde (V), hergapen (VI), ursolic acid (VII), liquiritigenin (VIII). They have been isolated from this plant for the first time, and IV - VIII are obtained from the plants of Heterosmilax for the first time.

Symposium II: Mechanochemistry in Materials Science, MRS Fall Meeting, Nov 30-Dec 4, 2009, Boston, MA

DTIC Science & Technology

2010-09-02

Dynamic Mechanical Analysis (DMA). The fracture behavior of the mechanophore-linked polymer is also examined through the Double Cleavage Drilled ...multinary complex structures. Structural, microstructural, and chemical characterizations were explored by metrological tools to support this...simple hydrocarbons in order to quantitatively define structure-property relationships for reacting materials under shock compression. Embedded gauge

Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates.

PubMed

Southan, Christopher; Williams, Antony J; Ekins, Sean

2013-01-01

There is an expanding amount of interest directed at the repurposing and repositioning of drugs, as well as how in silico methods can assist these endeavors. Recent repurposing project tendering calls by the National Center for Advancing Translational Sciences (USA) and the Medical Research Council (UK) have included compound information and pharmacological data. However, none of the internal company development code names were assigned to chemical structures in the official documentation. This not only abrogates in silico analysis to support repurposing but consequently necessitates data gathering and curation to assign structures. Here, we describe the approaches, results and major challenges associated with this. Copyright © 2012 Elsevier Ltd. All rights reserved.

Photoemission analysis of chemically modified TlBr surfaces for improved radiation detectors

NASA Astrophysics Data System (ADS)

Nelson, A. J.; Lee, J.-S.; Stanford, J. A.; Grant, W. K.; Voss, L. F.; Beck, P. R.; Graff, R. T.; Swanberg, E. L.; Conway, A. M.; Nikolic, R. J.; Payne, S. A.; Kim, H.; Cirignano, L. J.; Shah, K.

2013-09-01

Device-grade TlBr was subjected to various chemical treatments used in room temperature radiation detector fabrication to determine the resulting surface composition and electronic structure. Samples of as polished TlBr were treated separately with 2%Br:MeOH, 10%HF, 10%HCl and 96%SOCl2 solutions. High-resolution photoemission measurements on the valence band electronic structure and Tl 4f, Br 3d, Cl 2p and S 2p core lines were used to evaluate surface chemistry. Results suggest anion substitution at the surface with subsequent shallow heterojunction formation. Surface chemistry and valence band electronic structure were further correlated with the goal of optimizing the long-term stability and radiation response.

An FT-raman study of softwood, hardwood, and chemically modified black spruce MWLS

Treesearch

Umesh P. Agarwal; James D. McSweeny; Sally A. Ralph

1999-01-01

Raman spectroscopy is being increasingly used to carry out in situ analysis of wood and other lignocellulosics. To obtain useful information from the spectra, the vibrational bands need to be assigned in terms of contributions from various chemical components and component sub-structures. In additional, so that the technique can be better applied as an analytical...

Cheminformatics Analysis of EPA ToxCast Chemical Libraries to Identify Domains of Applicability for Predictive Toxicity Models and Prioritize Compounds for Toxicity Testing

EPA Science Inventory

An important goal of toxicology research is the development of robust methods that use in vitro and chemical structure information to predict in vivo toxicity endpoints. The US EPA ToxCast program is addressing this goal using ~600 in vitro assays to create bioactivity profiles o...

[Studies on alkaloids of Asteropyrum cavaleriei (Lévl. et Vant.) Drumm. et Hutch].

PubMed

Xu, H L

2000-08-01

To investigate the chemical constituents in the plant of Asteropyrum cavaleriei. The Chemical constituents were extracted with cation exchange resin 732 and separated by column chromatography, and the structures were identified by spectral analysis. Four compounds were isolated and identified as berberine, berberrabine, palmatine and magnoflorine. All compounds were separated from A. Cavaleriei for the first time.

Gene-Transformation-Induced Changes in Chemical Functional Group Features and Molecular Structure Conformation in Alfalfa Plants Co-Expressing Lc-bHLH and C1-MYB Transcriptive Flavanoid Regulatory Genes: Effects of Single-Gene and Two-Gene Insertion.

PubMed

Heendeniya, Ravindra G; Yu, Peiqiang

2017-03-20

Alfalfa ( Medicago sativa L.) genotypes transformed with Lc-bHLH and Lc transcription genes were developed with the intention of stimulating proanthocyanidin synthesis in the aerial parts of the plant. To our knowledge, there are no studies on the effect of single-gene and two-gene transformation on chemical functional groups and molecular structure changes in these plants. The objective of this study was to use advanced molecular spectroscopy with multivariate chemometrics to determine chemical functional group intensity and molecular structure changes in alfalfa plants when co-expressing Lc-bHLH and C1-MYB transcriptive flavanoid regulatory genes in comparison with non-transgenic (NT) and AC Grazeland (ACGL) genotypes. The results showed that compared to NT genotype, the presence of double genes ( Lc and C1 ) increased ratios of both the area and peak height of protein structural Amide I/II and the height ratio of α-helix to β-sheet. In carbohydrate-related spectral analysis, the double gene-transformed alfalfa genotypes exhibited lower peak heights at 1370, 1240, 1153, and 1020 cm -1 compared to the NT genotype. Furthermore, the effect of double gene transformation on carbohydrate molecular structure was clearly revealed in the principal component analysis of the spectra. In conclusion, single or double transformation of Lc and C1 genes resulted in changing functional groups and molecular structure related to proteins and carbohydrates compared to the NT alfalfa genotype. The current study provided molecular structural information on the transgenic alfalfa plants and provided an insight into the impact of transgenes on protein and carbohydrate properties and their molecular structure's changes.

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

PubMed

Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

2018-05-10

Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products and Molecular Libraries Small Molecule Repository

PubMed Central

Singh, Narender; Guha, Rajarshi; Giulianotti, Marc; Pinilla, Clemencia; Houghten, Richard; Medina-Franco, Jose L.

2009-01-01

A multiple criteria approach is presented, that is used to perform a comparative analysis of four recently developed combinatorial libraries to drugs, Molecular Libraries Small Molecule Repository (MLSMR) and natural products. The compound databases were assessed in terms of physicochemical properties, scaffolds and fingerprints. The approach enables the analysis of property space coverage, degree of overlap between collections, scaffold and structural diversity and overall structural novelty. The degree of overlap between combinatorial libraries and drugs was assessed using the R-NN curve methodology, which measures the density of chemical space around a query molecule embedded in the chemical space of a target collection. The combinatorial libraries studied in this work exhibit scaffolds that were not observed in the drug, MLSMR and natural products collections. The fingerprint-based comparisons indicate that these combinatorial libraries are structurally different to current drugs. The R-NN curve methodology revealed that a proportion of molecules in the combinatorial libraries are located within the property space of the drugs. However, the R-NN analysis also showed that there are a significant number of molecules in several combinatorial libraries that are located in sparse regions of the drug space. PMID:19301827

Graph wavelet alignment kernels for drug virtual screening.

PubMed

Smalter, Aaron; Huan, Jun; Lushington, Gerald

2009-06-01

In this paper, we introduce a novel statistical modeling technique for target property prediction, with applications to virtual screening and drug design. In our method, we use graphs to model chemical structures and apply a wavelet analysis of graphs to summarize features capturing graph local topology. We design a novel graph kernel function to utilize the topology features to build predictive models for chemicals via Support Vector Machine classifier. We call the new graph kernel a graph wavelet-alignment kernel. We have evaluated the efficacy of the wavelet-alignment kernel using a set of chemical structure-activity prediction benchmarks. Our results indicate that the use of the kernel function yields performance profiles comparable to, and sometimes exceeding that of the existing state-of-the-art chemical classification approaches. In addition, our results also show that the use of wavelet functions significantly decreases the computational costs for graph kernel computation with more than ten fold speedup.

Ketide Synthase (KS) Domain Prediction and Analysis of Iterative Type II PKS Gene in Marine Sponge-Associated Actinobacteria Producing Biosurfactants and Antimicrobial Agents

PubMed Central

Selvin, Joseph; Sathiyanarayanan, Ganesan; Lipton, Anuj N.; Al-Dhabi, Naif Abdullah; Valan Arasu, Mariadhas; Kiran, George S.

2016-01-01

The important biological macromolecules, such as lipopeptide and glycolipid biosurfactant producing marine actinobacteria were analyzed and their potential linkage between type II polyketide synthase (PKS) genes was explored. A unique feature of type II PKS genes is their high amino acid (AA) sequence homology and conserved gene organization. These enzymes mediate the biosynthesis of polyketide natural products with enormous structural complexity and chemical nature by combinatorial use of various domains. Therefore, deciphering the order of AA sequence encoded by PKS domains tailored the chemical structure of polyketide analogs still remains a great challenge. The present work deals with an in vitro and in silico analysis of PKS type II genes from five actinobacterial species to correlate KS domain architecture and structural features. Our present analysis reveals the unique protein domain organization of iterative type II PKS and KS domain of marine actinobacteria. The findings of this study would have implications in metabolic pathway reconstruction and design of semi-synthetic genomes to achieve rational design of novel natural products. PMID:26903957

Experimental verification, and domain definition, of structural alerts for protein binding: epoxides, lactones, nitroso, nitros, aldehydes and ketones.

PubMed

Nelms, M D; Cronin, M T D; Schultz, T W; Enoch, S J

2013-01-01

This study outlines how a combination of in chemico and Tetrahymena pyriformis data can be used to define the applicability domain of selected structural alerts within the profilers of the OECD QSAR Toolbox. Thirty-three chemicals were profiled using the OECD and OASIS profilers, enabling the applicability domain of six structural alerts to be defined, the alerts being: epoxides, lactones, nitrosos, nitros, aldehydes and ketones. Analysis of the experimental data showed the applicability domains for the epoxide, nitroso, aldehyde and ketone structural alerts to be well defined. In contrast, the data showed the applicability domains for the lactone and nitro structural alerts needed modifying. The accurate definition of the applicability domain for structural alerts within in silico profilers is important due to their use in the chemical category in predictive and regulatory toxicology. This study highlights the importance of utilizing multiple profilers in category formation.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

PubMed

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

CheS-Mapper - Chemical Space Mapping and Visualization in 3D.

PubMed

Gütlein, Martin; Karwath, Andreas; Kramer, Stefan

2012-03-17

Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis.

CheS-Mapper - Chemical Space Mapping and Visualization in 3D

PubMed Central

2012-01-01

Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis. PMID:22424447

Structural analysis of the industrial grade calcite

NASA Astrophysics Data System (ADS)

Shah, Rajiv P.; Raval, Kamlesh G.

2017-05-01

The chemical, optical and structural characterization of the industrial grade Calcite by EDAX, FT-IR and XRD. EDAX is a widely used technique to analyze the chemical components in a material, FT-IR stands for Fourier Transform Infra-Red, the preferred method of infrared spectroscopy. The resultant spectrum represents the molecular absorption and transmission, creating a molecular fingerprint of the sample, The atomic planes of a crystal cause an incident beam of X-rays to interfere with one another as they leave the crystal. The phenomenon is called X ray diffraction.(XRD). Data analysis of EDAX, FT-IR and XRD has been carried out with help of various instruments and software and find out the results of the these industrial grade materials which are mostly used in ceramics industries

Chemical analysis of a polysaccharide of unripe (green) tomato (Lycopersicon esculentum).

PubMed

Chandra, Krishnendu; Ghosh, Kaushik; Ojha, Arnab K; Islam, Syed S

2009-11-02

A polysaccharide (PS-I) isolated from the aqueous extract of the unripe (green) tomatoes (Lycopersicon esculentum) consists of D-galactose, D-methyl galacturonate, D-arabinose, L-arabinose, and L-rhamnose. Structural investigation of the polysaccharide was carried out using total acid hydrolysis, methylation analysis, periodate oxidation study, and NMR studies ((1)H, (13)C, DQF-COSY, TOCSY, NOESY, ROESY, HMQC, and HMBC). On the basis of above-mentioned experiments the structure of the repeating unit of the polysaccharide (PS-I) was established as: [structure: see text].

Chemical structure-based predictive model for methanogenic anaerobic biodegradation potential.

PubMed

Meylan, William; Boethling, Robert; Aronson, Dallas; Howard, Philip; Tunkel, Jay

2007-09-01

Many screening-level models exist for predicting aerobic biodegradation potential from chemical structure, but anaerobic biodegradation generally has been ignored by modelers. We used a fragment contribution approach to develop a model for predicting biodegradation potential under methanogenic anaerobic conditions. The new model has 37 fragments (substructures) and classifies a substance as either fast or slow, relative to the potential to be biodegraded in the "serum bottle" anaerobic biodegradation screening test (Organization for Economic Cooperation and Development Guideline 311). The model correctly classified 90, 77, and 91% of the chemicals in the training set (n = 169) and two independent validation sets (n = 35 and 23), respectively. Accuracy of predictions of fast and slow degradation was equal for training-set chemicals, but fast-degradation predictions were less accurate than slow-degradation predictions for the validation sets. Analysis of the signs of the fragment coefficients for this and the other (aerobic) Biowin models suggests that in the context of simple group contribution models, the majority of positive and negative structural influences on ultimate degradation are the same for aerobic and methanogenic anaerobic biodegradation.

Identification of Chemical Features Linked to Thyroperoxidase ...

EPA Pesticide Factsheets

Disruption of maternal serum thyroid hormone (TH) adversely affects fetal neurodevelopment. Therefore, assay development within the US EPA ToxCast program is ongoing to enable screening for chemicals that may disrupt TH, in support of the Endocrine Disruption Screening Program (EDSP21). The AUR-TPO assay was recently developed to screen >1,000 ToxCast chemicals for potential thyroperoxidase (TPO) inhibition activity. TPO is critical for TH synthesis and is a known target of thyroid-disrupting chemicals. The bioactivity results from the AUR-TPO assay were used to identify chemical substructures associated with in vitro TPO inhibition. Substructure profiles were generated for each chemical in the ToxCast test set using the publicly-available ToxPrint 2.0 chemotypes. Chemotypes enriched among the putative TPO inhibitors were identified using a cumulative hypergeometric probability (p < 0.01). Of the total 729 chemotypes evaluated, 31 were overrepresented among TPO inhibitors. Examination of those 31 chemotypes revealed four basic pharmacophores that accounted for 70% of the ToxCast chemicals active in the AUR-TPO assay: aromatic alcohols, aromatic amines, thiocarbonyls and phosphothioates. Chemico-structural analysis of AUR-TPO screening results enabled the identification of chemical features that likely drive TPO inhibition in the AUR-TPO assay. This highlights the potential to identify thyroid-disrupting chemicals in silico using structural alerts identified by

Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artefacts of the electric field on the NMR chemical shift.

PubMed

Kukić, Predrag; Farrell, Damien; Søndergaard, Chresten R; Bjarnadottir, Una; Bradley, John; Pollastri, Gianluca; Nielsen, Jens Erik

2010-03-01

pH-induced chemical shift perturbations (CSPs) can be used to study pH-dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH-dependent structural transitions in bovine beta-lactoglobulin (betaLG) by analyzing its NMR pH-titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in betaLG. The results show that around 20% of the amide nuclei CSPs in betaLG originate exclusively from "through-space" electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH-dependent structural transitions in betaLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH-dependent conformational change. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Structure-based classification and ontology in chemistry

PubMed Central

2012-01-01

Background Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures), while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. Results We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Conclusion Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational utilities including algorithmic, statistical and logic-based tools. For the task of automatic structure-based classification of chemical entities, essential to managing the vast swathes of chemical data being brought online, systems which are capable of hybrid reasoning combining several different approaches are crucial. We provide a thorough review of the available tools and methodologies, and identify areas of open research. PMID:22480202

Sea urchin skeleton: Structure, composition, and application as a template for biomimetic materials

NASA Astrophysics Data System (ADS)

Shapkin, Nikolay P.; Khalchenko, Irina G.; Panasenko, Alexander E.; Drozdov, Anatoly L.

2017-07-01

SEM and optical microscopy, chemical and EDX analysis, XRD, and FT-IR spectroscopy of three sea urchins skeletons (tests) show that the test is a spongy stereom, consisting of calcite with high content of magnesium. The tests are composed of mineral-organic composite of calcite-magnesite crystals, coated with organic film, containing silicon in form of polyphenylsiloxane. In the test of sea urchin pore spaces are linked into united system of regular structure with structure motive period about 20 um. This developed three-dimensional structure was used as a template for polymer material based on polyferrofenilsiloxane [OSiC6H5OH]x[OSiC6H5O]y[OFeO]z, which is chemically similar to the native film, coating sea urchins skeleton.

The presence of cutan limits the interpretation of cuticular chemistry and structure: Ficus elastica leaf as an example.

PubMed

Guzmán-Delgado, Paula; Graça, José; Cabral, Vanessa; Gil, Luis; Fernández, Victoria

2016-06-01

Plant cuticles have been traditionally classified on the basis of their ultrastructure, with certain chemical composition assumptions. However, the nature of the plant cuticle may be misinterpreted in the prevailing model, which was established more than 150 years ago. Using the adaxial leaf cuticle of Ficus elastica, a study was conducted with the aim of analyzing cuticular ultrastructure, chemical composition and the potential relationship between structure and chemistry. Gradual chemical extractions and diverse analytical and microscopic techniques were performed on isolated leaf cuticles of two different stages of development (i.e. young and mature leaves). Evidence for the presence of cutan in F. elastica leaf cuticles has been gained after chemical treatments and tissue analysis by infrared spectroscopy and electron microscopy. Significant calcium, boron and silicon concentrations were also measured in the cuticle of this species. Such mineral elements which are often found in plant cell walls may play a structural role and their presence in isolated cuticles further supports the interpretation of the cuticle as the most external region of the epidermal cell wall. The complex and heterogeneous nature of the cuticle, and constraints associated with current analytical procedures may limit the chance for establishing a relationship between cuticle chemical composition and structure also in relation to organ ontogeny. © 2016 Scandinavian Plant Physiology Society.

RBAP, a rhodamine B-based derivative: synthesis, crystal structure analysis, molecular simulation, and its application as a selective fluorescent chemical sensor for Sn2+.

PubMed

Bao, Xiaofeng; Cao, Xiaowei; Nie, Xuemei; Jin, Yanyan; Zhou, Baojing

2014-06-11

A new fluorescent chemosensor based on a Rhodamine B and a benzyl 3-aminopropanoate conjugate (RBAP) was designed, synthesized, and structurally characterized. Its single crystal structure was obtained and analyzed by X-ray analysis. In a MeOH/H2O (2:3, v/v, pH 5.95) solution RBAP exhibits a high selectivity and excellent sensitivity for Sn2+ ions in the presence of many other metal cations. The binding analysis using the Job's plot suggested the RBAP formed a 1:1 complex with Sn2+.

Studies on densification, mechanical, micro-structural and structure–properties relationship of magnesium aluminate spinel refractory aggregates prepared from Indian magnesite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, Chandrima; Ghosh, Arup; Haldar, Manas Kamal, E-mail: manashaldar@cgcri.res.in

The present work intends to study the development of magnesium aluminate spinel aggregates from Indian magnesite in a single firing stage. The raw magnesite has been evaluated in terms of chemical analysis, differential thermal analysis, thermogravimetric analysis, infrared spectroscopy, and X-ray diffraction. The experimental batch containing Indian magnesite and calcined alumina has been sintered in the temperature range of 1550 °C–1700 °C. The sintered material has been characterized in terms of physico-chemical properties like bulk density, apparent porosity, true density, relative density and thermo-mechanical/mechanical properties like hot modulus of rupture, thermal shock resistance, cold modulus of rupture and structural propertiesmore » by X-ray diffraction in terms of phase identification and evaluation of crystal structure parameters of corresponding phases by Rietveld analysis. The microstructures developed at different temperatures have been analyzed by field emission scanning electron microscope study and compositional analysis of the developed phase has been carried out by energy dispersive X-ray study. - Highlights: • The studies have been done to characterize the developed magnesium aluminate spinel. • The studies reveal correlation between refractory behavior of spinel and developed microstructures. • The studies show the values of lattice parameters of developed phases.« less

Comparative NMR Analysis of an 80-Residue G Protein-Coupled Receptor Fragment in Two Membrane Mimetic Environments

PubMed Central

LS, Cohen; B, Arshava; A, Neumoin; JM, Becker; P, Güntert; O, Zerbe; Naider, F

2011-01-01

Fragments of integral membrane proteins have been used to study the physical chemical properties of regions of transporters and receptors. Ste2p(G31-T110) is an 80-residue polypeptide which contains a portion of the N-terminal domain, transmembrane domain 1 (TM1), intracellular loop 1, TM2 and part of extracellular loop 2 of the α-factor receptor (Ste2p) from Saccharomyces cerevisiae. The structure of this peptide was previously determined to form a helical hairpin in lyso-palmitoylphosphatidyl-glycerol micelles (LPPG)[1]. Herein, we perform a systematic comparison of the structure of this protein fragment in micelles and trifluoroethanol(TFE):water in order to understand whether spectra recorded in organic:aqueous medium can facilitate the structure determination in a micellar environment. Using uniformly labeled peptide and peptide selectively protonated on Ile, Val and Leu methyl groups in a perdeuterated background and a broad set of 3D NMR experiments we assigned 89% of the observable atoms. NOEs and chemical shift analysis were used to define the helical regions of the fragment. Together with constraints from paramagnetic spin labeling, NOEs were used to calculate a transiently folded helical hairpin structure for this peptide in TFE:water. Correlation of chemical shifts was insufficient to transfer assignments from TFE:water to LPPG spectra in the absence of further information. PMID:21791199

Chemical analysis of extracting transition metal oxides from polymetallic ore by sulphate process

NASA Astrophysics Data System (ADS)

Enkh-Uyanga, Otgon-Uul; Munkhtsetseg, Baatar; Urangoo, Urtnasan; Tserendulam, Enkhtur; Agiimaa, Davaadorj

2017-06-01

In this research work we attempt to improve the purity of polymetallic ores in Mongolia whilst developing practical applications of its refinement processes and this paper presents the results of chemical research of extracting transition metal titanium oxides, ferrous oxide and rare earth oxides from polymetallic ore. Thereby, chemical and mineral analysis of polymetallic ore is carried out basis of responses to the support process at various degrees of water whereas transition metal sulphates solubility differ. As a result of sulphate and resulphurization process we have extracted anatase with 62.5 percent titanium dioxide and brookite mineral with 89.6 percent of titanium dioxide as well as mineral with 83.8 percent of ferrous oxide hematite and rare earth oxides with 57.6 percent of cerium oxide. These oxides are identified under various conditions in the thermal processing. The morphology structure and chemical content compound of the mineral has been verified as a result of the XRF, XRD, SEM-EDX analysis.

Critical considerations for the qualitative and quantitative determination of process-induced disorder in crystalline solids.

PubMed

Newman, Ann; Zografi, George

2014-09-01

Solid-state instabilities in crystalline solids arise during processing primarily because a certain level of structural disorder has been introduced into the crystal. Many physical instabilities appear to be associated with the recrystallization of molecules from these disordered regions, while chemical instabilities arise from sufficient molecular mobility to allow solid-state chemical reactivity. In this Commentary we discuss the various forms of structural disorder, processing which can produce disorder, the quantitative analysis of process-induced order, and strategies to limit disorder and its effects. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

The structure and photochemical transformation of cyclopropylacetylene radical cation as revealed by matrix EPR and quantum chemical study

NASA Astrophysics Data System (ADS)

Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

2012-05-01

The primary radical cation of cyclopropylacetylene was first characterized by EPR spectroscopy in low-temperature freon matrices. The assignment was confirmed by specific deuteration and quantum-chemical calculations at PBE0 and CCSD(T) levels. Photolysis with visible light led to irreversible transformation of the initial species to a ring-open structure. Detailed computational analysis of energy and magnetic resonance parameters of possible reaction products justified formation of pent-3-en-1-yne radical cation (presumably, a (Z)-isomer). This conclusion was also supported by the effect of specific deuteration.

Tug-of-war between classical and multicenter bonds in H-(Be)n-H species

NASA Astrophysics Data System (ADS)

Lundell, Katie A.; Boldyrev, Alexander I.

2018-05-01

Quantum chemical calculations were performed for beryllium homocatenated compounds [H-(Be)n-H]. Global minimum structures were found using machine searches (Coalescence Kick method) with density functional theory. Chemical bonding analysis was performed with the Adaptive Natural Density Partitioning method. It was found that H-(Be)2-H and H-(Be)3-H clusters are linear with classical two-center two-electron bonds, while for n > 3, three-dimensional structures are more stable with multicenter bonding. Thus, at n = 4, multicenter bonding wins the tug-of-war vs. the classical bonding.

[Chemical constituents from the rhizoma of Arundina graminifolia].

PubMed

Liu, Mei-feng; Han, Yun; Xing, Dong-ming; Wang, Wei; Xu, Li-zhen; Du, Li-jun; Ding, Yi

2004-02-01

To isolate and elucidate the chemical constituents from the tuber of Arundina graminifolia. The compounds were extracted by 95% alcohol and isolated by column chromatography on silica gel, SephedaxLH-20 and ODS. The structures were determined by UV, IR, NMR and MS spectral analysis. Five compounds were isolated, and their structures were identified as (2E)-, 2-propenoic acid, 3-(4-hydroxy-3-methoxyphenyl)-decosyl ester (I), p-hydroxybenzyl alcohol (II), triacontanol (III) and p-hydroxybenzylethyl ether (IV), 3-hydroxy-5-methoxybibenzyl (V), respectively. All compounds were isolated from the genus of Arundina for the first time.

Predicting physical properties of emerging compounds with limited physical and chemical data: QSAR model uncertainty and applicability to military munitions.

PubMed

Bennett, Erin R; Clausen, Jay; Linkov, Eugene; Linkov, Igor

2009-11-01

Reliable, up-front information on physical and biological properties of emerging materials is essential before making a decision and investment to formulate, synthesize, scale-up, test, and manufacture a new material for use in both military and civilian applications. Multiple quantitative structure-activity relationships (QSARs) software tools are available for predicting a material's physical/chemical properties and environmental effects. Even though information on emerging materials is often limited, QSAR software output is treated without sufficient uncertainty analysis. We hypothesize that uncertainty and variability in material properties and uncertainty in model prediction can be too large to provide meaningful results. To test this hypothesis, we predicted octanol water partitioning coefficients (logP) for multiple, similar compounds with limited physical-chemical properties using six different commercial logP calculators (KOWWIN, MarvinSketch, ACD/Labs, ALogP, CLogP, SPARC). Analysis was done for materials with largely uncertain properties that were similar, based on molecular formula, to military compounds (RDX, BTTN, TNT) and pharmaceuticals (Carbamazepine, Gemfibrizol). We have also compared QSAR modeling results for a well-studied pesticide and pesticide breakdown product (Atrazine, DDE). Our analysis shows variability due to structural variations of the emerging chemicals may be several orders of magnitude. The model uncertainty across six software packages was very high (10 orders of magnitude) for emerging materials while it was low for traditional chemicals (e.g. Atrazine). Thus the use of QSAR models for emerging materials screening requires extensive model validation and coupling QSAR output with available empirical data and other relevant information.

Structural analysis of a homogeneous polysaccharide from Achatina fulica.

PubMed

Liu, Jie; Shang, Feineng; Yang, Zengming; Wu, Mingyi; Zhao, Jinhua

2017-05-01

Edible snails have been widely used as a health food and medicine in many countries. In our study, a water-soluble polysaccharide (AF-1) was isolated and purified from Achatina fulica by papain enzymolysis, alcohol precipitation and strong anion exchange chromatography. Structureof the polysaccharide was analyzed and characterized by chemical and instrumental methods, such as Fourier transform infrared spectroscopy, high performance liquid chromatography, analysis of monosaccharide composition, methylation analysis, and nuclear magnetic resonance (NMR) spectroscopy ( 1 H, 13 C, COSY, TOCSY, NOESY, HSQC and HMBC). Chemical composition analysis indicated that AF-1 is composed of glucose (Glc) and its average molecular weight is 1710kDa. Structural analysis suggested that AF-1 is mainly consisted of a linear repeating backbone of (1→4) linked α-d-Glc p residues with one branch, α-d-Glc p, attached to the main chain by (1→6) glycosidic bonds at every five main-chain units. Further studies on biological activities of the polysaccharide are currently in progress. Copyright © 2017 Elsevier B.V. All rights reserved.

77 FR 66149 - Significant New Use Rules on Certain Chemical Substances

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-02

... ecological structural activity relationship (EcoSAR) analysis of test data on analogous esters, EPA predicts... milligram/cubic meter (mg/m\\3\\) as an 8-hour time-weighted average. In addition, based on EcoSAR analysis of... the PMN substance via the inhalation route. In addition, based on EcoSAR analysis of test data on...

The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets.

PubMed

Karapetyan, Karen; Batchelor, Colin; Sharpe, David; Tkachenko, Valery; Williams, Antony J

2015-01-01

There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there are a myriad of issues that can exist with chemical structure representations online. In order to help facilitate validation and standardization of chemical structure datasets from various sources we have delivered a freely available internet-based platform to the community for the processing of chemical compound datasets. The chemical validation and standardization platform (CVSP) both validates and standardizes chemical structure representations according to sets of systematic rules. The chemical validation algorithms detect issues with submitted molecular representations using pre-defined or user-defined dictionary-based molecular patterns that are chemically suspicious or potentially requiring manual review. Each identified issue is assigned one of three levels of severity - Information, Warning, and Error - in order to conveniently inform the user of the need to browse and review subsets of their data. The validation process includes validation of atoms and bonds (e.g., making aware of query atoms and bonds), valences, and stereo. The standard form of submission of collections of data, the SDF file, allows the user to map the data fields to predefined CVSP fields for the purpose of cross-validating associated SMILES and InChIs with the connection tables contained within the SDF file. This platform has been applied to the analysis of a large number of data sets prepared for deposition to our ChemSpider database and in preparation of data for the Open PHACTS project. In this work we review the results of the automated validation of the DrugBank dataset, a popular drug and drug target database utilized by the community, and ChEMBL 17 data set. CVSP web site is located at http://cvsp.chemspider.com/. A platform for the validation and standardization of chemical structure representations of various formats has been developed and made available to the community to assist and encourage the processing of chemical structure files to produce more homogeneous compound representations for exchange and interchange between online databases. While the CVSP platform is designed with flexibility inherent to the rules that can be used for processing the data we have produced a recommended rule set based on our own experiences with the large data sets such as DrugBank, ChEMBL, and data sets from ChemSpider.

Mutagen Structure and Transcriptional Response: Induction of Distinct Transcriptional Profiles in Salmonella TA100 by the Drinking-Water Mutagen MX and Its Homologues

EPA Science Inventory

The relationship between chemical structure and biological activity has been examined for various compounds and endpoints for decades. To explore this question relative to global gene expression, we performed microarray analysis of Salmonella TA100 after treatment under condition...

Structural analysis and taste evaluation of γ-glutamyl peptides comprising sulfur-containing amino acids.

PubMed

Amino, Yusuke; Wakabayashi, Hidehiko; Akashi, Satoko; Ishiwatari, Yutaka

2018-03-01

The structures, flavor-modifying effects, and CaSR activities of γ-glutamyl peptides comprising sulfur-containing amino acids were investigated. The chemical structures, including the linkage mode of the N-terminal glutamic acid, of γ-L-glutamyl-S-(2-propenyl)-L-cysteine (γ-L-glutamyl-S-allyl-L-cysteine) and its sulfoxide isolated from garlic were established by comparing their NMR spectra with those of authentic peptides prepared using chemical methods. Mass spectrometric analysis also enabled determination of the linkage modes in the glutamyl dipeptides by their characteristic fragmentation. In sensory evaluation, these peptides exhibited flavor-modifying effects (continuity) in umami solutions less pronounced but similar to that of glutathione. Furthermore, the peptides exhibited intrinsic flavor due to the sulfur-containing structure, which may be partially responsible for their flavor-modifying effects. In CaSR assays, γ-L-glutamyl-S-methyl-L-cysteinylglycine was most active, which indicates that the presence of a medium-sized aliphatic substituent at the second amino acid residue in γ-glutamyl peptides enhances CaSR activity.

Precession technique and electron diffractometry as new tools for crystal structure analysis and chemical bonding determination.

PubMed

Avilov, A; Kuligin, K; Nicolopoulos, S; Nickolskiy, M; Boulahya, K; Portillo, J; Lepeshov, G; Sobolev, B; Collette, J P; Martin, N; Robins, A C; Fischione, P

2007-01-01

We have developed a new fast electron diffractometer working with high dynamic range and linearity for crystal structure determinations. Electron diffraction (ED) patterns can be scanned serially in front of a Faraday cage detector; the total measurement time for several hundred ED reflections can be tens of seconds having high statistical accuracy for all measured intensities (1-2%). This new tool can be installed to any type of TEM without any column modification and is linked to a specially developed electron beam precession "Spinning Star" system. Precession of the electron beam (Vincent-Midgley technique) reduces dynamical effects allowing also use of accurate intensities for crystal structure analysis. We describe the technical characteristics of this new tool together with the first experimental results. Accurate measurement of electron diffraction intensities by electron diffractometer opens new possibilities not only for revealing unknown structures, but also for electrostatic potential determination and chemical bonding investigation. As an example, we present detailed atomic bonding information of CaF(2) as revealed for the first time by precise electron diffractometry.

Accelerated detection of brown-rot decay : comparison of soil block test, chemical analysis, mechanical properties, and immunodetection

Treesearch

C. A. Clausen; S. N. Kartal

2003-01-01

Early detection of wood decay is critical because decay fungi can cause rapid structural failure. The objective of this study was to compare the sensitivity of different methods purported to detect brown-rot decay in the early stages of development. The immunodiagnostic wood decay (IWD)test, soil block test/cake pan test, mechanical property tests, and chemical...

Finding Chemical Structures Corresponding to a Set of Coordinates in Chemical Descriptor Space.

PubMed

Miyao, Tomoyuki; Funatsu, Kimito

2017-08-01

When chemical structures are searched based on descriptor values, or descriptors are interpreted based on values, it is important that corresponding chemical structures actually exist. In order to consider the existence of chemical structures located in a specific region in the chemical space, we propose to search them inside training data domains (TDDs), which are dense areas of a training dataset in the chemical space. We investigated TDDs' features using diverse and local datasets, assuming that GDB11 is the chemical universe. These two analyses showed that considering TDDs gives higher chance of finding chemical structures than a random search-based method, and that novel chemical structures actually exist inside TDDs. In addition to those findings, we tested the hypothesis that chemical structures were distributed on the limited areas of chemical space. This hypothesis was confirmed by the fact that distances among chemical structures in several descriptor spaces were much shorter than those among randomly generated coordinates in the training data range. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relationship between chemical structure of soil organic matter and intra-aggregate pore structure: evidence from X-ray computed micro-tomography

NASA Astrophysics Data System (ADS)

Kravchenko, Alexandra; Grandy, Stuart A.

2014-05-01

Understanding chemical structure of soil organic matter (SOM) and factors that affect it are vital for gaining understanding of mechanisms of C sequestration by soil. Physical protection of C by adsorption to mineral particles and physical disconnection between C sources and microbial decomposers is now regarded as the key component of soil C sequestration. Both of the processes are greatly influenced by micro-scale structure and distribution of soil pores. However, because SOM chemical structure is typically studied in disturbed (ground and sieved) soil samples the experimental evidence of the relationships between soil pore structure and chemical structure of SOM are still scarce. Our study takes advantage of the X-ray computed micro-tomography (µ-CT) tools that enable non-destructive analysis of pore structure in intact soil samples. The objective of this study is to examine the relationship between SOM chemical structure and pore-characteristics in intact soil macro-aggregates from two contrasting long-term land uses. The two studied land use treatments are a conventionally tilled corn-soybean-wheat rotation treatment and a native succession vegetation treatment removed from agricultural use >20 years ago. The study is located in southwest Michigan, USA, on sandy-loam Typic Hapludalfs. For this study we used soil macro-aggregates 4-6 mm in size collected at 0-15 cm depth. The aggregate size was selected so as both to enable high resolution of µ-CT and to provide sufficient amount of soil for C measurements. X-ray µ-CT scanning was conducted at APS Argonne at a scanning resolution of 14 µm. Two scanned aggregates (1 per treatment) were used in this preliminary study. Each aggregate was cut into 7 "geo-referenced" sections. Analyses of pore characteristics in each section were conducted using 3DMA and ImageJ image analysis tools. SOM chemistry was analyzed using pyrolysis/gas chromatography-mass spectroscopy. Results demonstrated that the relationships between SOM chemical structure and pore characteristics differed in the aggregates of the two treatments. For example, in the agricultural treatment, the aggregate sections with prevalence of small pores had lower relative lignin abundance, while higher lignin abundances occurred in aggregate sections with more large pores. This relationship could be reflecting the low accessibility of the sections dominated by small pores to plant roots. It is interesting to note that no relationship between pores and lignin were observed in the aggregate from the native succession treatment. In the native succession aggregate we found that a larger presence of protein and N-bearing compounds was associated with sections with greater presence of 35-90 µm pores. This could be a result of fungal activities, as pores of this size constitute a primary fungal habitat and fungi are known for secreting proteins. Fewer fungi in the soil under agricultural management are likely the reason that no such relationship was observed in the aggregate from the agricultural treatment. Our preliminary results indicate that substantial spatial variability patterns in SOM chemical structure can exist even within a single macro-aggregate and that pores are likely a main driver of intra-aggregate SOM chemistry.

Comparative study of Ni and Cu doped ZnO nanoparticles: Structural and optical properties

NASA Astrophysics Data System (ADS)

Thakur, Shaveta; Thakur, Samita; Sharma, Jyoti; Kumar, Sanjay

2018-05-01

Nanoparticles of undoped and doped (0.1 M Ni2+ and Cu2+) ZnO are synthesized using chemical precipitation method. The crystallite size, morphology, chemical bonding and optical properties of as prepared nanoparticles are determined by X-ray diffraction (XRD), Scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and UV-visible spectra. XRD analysis shows that the prepared samples are single phase and have hexagonal wurtzite structure. The crystallite size of the doped and undoped nanoparticles is determined using Scherrer method. The crystallite size is found to be increased with concentration of nickel and copper. All stretching and vibrational bands are observed at their specific positions through FTIR. The increase in band gap can be attributed to the different chemical nature of dopant and host cation.

Molecular similarity measures.

PubMed

Maggiora, Gerald M; Shanmugasundaram, Veerabahu

2011-01-01

Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

Clinical and laboratory evaluation of microstructural changes in the physical, mechanical and chemical properties of dental filling materials under the influence of an electromagnetic field.

PubMed

Moiseeva, Natalia S; Kunin, Anatoly A

2018-03-01

Restorative filling materials used for dental caries prevention and treatment consist of various components including monomers or oligomers, which play a significant role in forming the main structure of these materials, as well as in characterising their physical, mechanical and chemical properties. The necessity for the development and improvement of structural characteristics of polymeric dental filling materials intended for caries prevention and their life duration increase served as the initiating factor of our research. According to the research purpose and challenges, we studied the changes in the physical, mechanical and chemical properties of composite filling materials with and without electromagnetic field influence. The investigations in vivo include the study of microstructural features of polymeric filling materials by scanning electron microscopy (SEM) and the investigations in vitro include the study of sealed and extracted human teeth chips by using X-ray spectral analysis. We also evaluated the changes in the strength characteristics of dental filling materials with and without electromagnetic field influence. The analysis of the obtained data indicates the presence of structural changes in polymeric dental filling materials, including the material microstructure condensation confirmed by the SEM results, an increase in the strength and adhesion characteristics and certain regularities of the chemical elemental composition concentration change in the area of hard tooth tissue and dental filling material. These scientific data will provide tooth caries prevention and promote the increase of treatment quality.

Combined TEM and NanoSIMS Analysis of Subgrains in a SiC AB Grain

NASA Astrophysics Data System (ADS)

Hynes, K. M.; Amari, S.; Bernatowicz, T. J.; Lebsack, E.; Gyngard, F.; Nittler, L. R.

2011-03-01

We report the results of NanoSIMS and TEM analysis, including isotopic, structural, chemical, and subgrain data, on a SiC AB grain. This grain contains the first oldhamite subgrains observed in a presolar grain, as well as TiC- and Fe-rich subgrains.

Spatially resolved chemical analysis of cicada wings using laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS).

PubMed

Román, Jessica K; Walsh, Callee M; Oh, Junho; Dana, Catherine E; Hong, Sungmin; Jo, Kyoo D; Alleyne, Marianne; Miljkovic, Nenad; Cropek, Donald M

2018-03-01

Laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS) is an emerging bioanalytical tool for direct imaging and analysis of biological tissues. Performing ionization in an ambient environment, this technique requires little sample preparation and no additional matrix, and can be performed on natural, uneven surfaces. When combined with optical microscopy, the investigation of biological samples by LAESI allows for spatially resolved compositional analysis. We demonstrate here the applicability of LAESI-IMS for the chemical analysis of thin, desiccated biological samples, specifically Neotibicen pruinosus cicada wings. Positive-ion LAESI-IMS accurate ion-map data was acquired from several wing cells and superimposed onto optical images allowing for compositional comparisons across areas of the wing. Various putative chemical identifications were made indicating the presence of hydrocarbons, lipids/esters, amines/amides, and sulfonated/phosphorylated compounds. With the spatial resolution capability, surprising chemical distribution patterns were observed across the cicada wing, which may assist in correlating trends in surface properties with chemical distribution. Observed ions were either (1) equally dispersed across the wing, (2) more concentrated closer to the body of the insect (proximal end), or (3) more concentrated toward the tip of the wing (distal end). These findings demonstrate LAESI-IMS as a tool for the acquisition of spatially resolved chemical information from fragile, dried insect wings. This LAESI-IMS technique has important implications for the study of functional biomaterials, where understanding the correlation between chemical composition, physical structure, and biological function is critical. Graphical abstract Positive-ion laser-ablation electrospray ionization mass spectrometry coupled with optical imaging provides a powerful tool for the spatially resolved chemical analysis of cicada wings.

Effects of haze pollution on microbial community changes and correlation with chemical components in atmospheric particulate matter.

PubMed

Sun, Yujiao; Xu, Shangwei; Zheng, Danyang; Li, Jie; Tian, Hezhong; Wang, Yong

2018-05-10

In this study, particulate matter (PM) with aerodynamic diameters of ≤2.5 and ≤10 μm (PM 2.5 and PM 10 , respectively), which was found at different concentrations in spring, was collected in Beijing. The chemical composition and bacterial community diversity of PM were determined, and the relationship between them was studied by 16S rRNA sequencing and mathematical statistics. Chemical composition analysis revealed greater relative percentages of total organic compounds (TOC) and secondary ions (NO 3 - , SO 4 2- , and NH 4 + ). The concentrations of Ca 2+ , Na + , Mg 2+ , K + and SO 4 2- increased in high-concentration PM, which was associated with the contribution of soil, dust and soot. Microbiological analysis revealed 1191 operational taxonomic units. Microbial community structure was stable at the phylum level. The most abundant phyla were Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Community clustering analysis at the genus level showed that the difference in bacterial community structure between different PM concentrations (clean air vs. smog) was greater than that between different particle sizes. The dominant genera varied in different concentrations of PM. An unclassified genus of Cyanobacteria and Comamonadaceae were most abundant in low- and high-concentration PM, respectively. The microbial community structure was dynamic at the genus level due to different environmental factors. The dominant bacteria in high-concentration PM were widely distributed in soils, indicating that the soil contributed more to the increase in the PM. The individual microbes that were detected did not increase significantly as the PM concentration increased. The bacterial community structure was strongly correlated with K + , Ca 2+ , Na + , Mg 2+ , SO 4 2- and TOC in high-concentration PM and had a good correlation with NO 3 - , Cl - , NH 4 + and TIC in low-concentration PM. Soil and dust contributed to the increase in the concentration of the particles, and the relevant chemical components also produced differences in the bacterial community structure in different concentrations of PM. Copyright © 2018. Published by Elsevier B.V.

Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling.

PubMed

Filip, Xenia; Borodi, Gheorghe; Filip, Claudiu

2011-10-28

A solid state structural investigation of ethoxzolamide is performed on microcrystalline powder by using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct space methods with information from (13)C((15)N) solid-state Nuclear Magnetic Resonance (SS-NMR) and molecular modeling. Quantum chemical computations of the crystal were employed for geometry optimization and chemical shift calculations based on the Gauge Including Projector Augmented-Wave (GIPAW) method, whereas a systematic search in the conformational space was performed on the isolated molecule using a molecular mechanics (MM) approach. The applied methodology proved useful for: (i) removing ambiguities in the XRPD crystal structure determination process and further refining the derived structure solutions, and (ii) getting important insights into the relationship between the complex network of non-covalent interactions and the induced supra-molecular architectures/crystal packing patterns. It was found that ethoxzolamide provides an ideal case study for testing the accuracy with which this methodology allows to distinguish between various structural features emerging from the analysis of the powder diffraction data. This journal is © the Owner Societies 2011

Baccharis dracunculifolia-based mouthrinse alters the exopolysaccharide structure in cariogenic biofilms.

PubMed

Aires, Carolina P; Sassaki, Guilherme L; Santana-Filho, Arquimedes P; Spadaro, Augusto C C; Cury, Jaime A

2016-03-01

Baccharis dracunculifolia is a native plant from Brazil with antimicrobial activity. The purpose of this study was to investigate whether a B. dracunculifolia-based mouthrinse (Bd) changes the structure of insoluble exopolysaccharides (IEPS) in Streptococcus mutans UA159 cariogenic biofilm. Biofilms were grown on glass slides and treated with Bd, its vehicle (VC), chlorhexidine digluconate (CHX), or saline solution (NaCl). Among the treatments, only CHX significantly reduced the biofilm biomass and bacterial viability (p<0.05). Gas chromatography-mass spectrometry and nuclear magnetic resonance analyses revealed that IEPS from the four biofilm samples were α- glucans containing different proportions of (1→6) and (1→3) glycosidic linkages. The structural differences among the four IEPS were compared by principal component analysis (PCA). PCA analysis indicated that IEPS from VC- and NaCl-treated biofilms were structurally similar to each other. Compared with the control, IEPS from Bd- and CHX-treated biofilms were structurally different and had distinct chemical profiles. In summary, the fact that Bd changed the IEPS chemical composition indicates that this mouthrinse may affect the cariogenic properties of the S. mutans biofilm formed. Copyright © 2015. Published by Elsevier B.V.

PubChem applications in drug discovery: a bibliometric analysis

PubMed Central

Cheng, Tiejun; Pan, Yongmei; Hao, Ming; Wang, Yanli; Bryant, Stephen H.

2014-01-01

A bibliometric analysis of PubChem applications is presented by reviewing 1132 research articles. The massive volume of chemical structure and bioactivity data in PubChem and its online services has been used globally in various fields including chemical biology, medicinal chemistry and informatics research. PubChem supports drug discovery in many aspects such as lead identification and optimization, compound–target profiling, polypharmacology studies and unknown chemical identity elucidation. PubChem has also become a valuable resource for developing secondary databases, informatics tools and web services. The growing PubChem resource with its public availability offers support and great opportunities for the interrogation of pharmacological mechanisms and the genetic basis of diseases, which are vital for drug innovation and repurposing. PMID:25168772

Attenuated Total Reflection Mid-Infrared (ATR-MIR) Spectroscopy and Chemometrics for the Identification and Classification of Commercial Tannins.

PubMed

Ricci, Arianna; Parpinello, Giuseppina P; Olejar, Kenneth J; Kilmartin, Paul A; Versari, Andrea

2015-11-01

Attenuated total reflection Fourier transform infrared (FT-IR) spectroscopy was used to characterize 40 commercial tannins, including condensed and hydrolyzable chemical classes, provided as powder extracts from suppliers. Spectral data were processed to detect typical molecular vibrations of tannins bearing different chemical groups and of varying botanical origin (univariate qualitative analysis). The mid-infrared region between 4000 and 520 cm(-1) was analyzed, with a particular emphasis on the vibrational modes in the fingerprint region (1800-520 cm(-1)), which provide detailed information about skeletal structures and specific substituents. The region 1800-1500 cm(-1) contained signals due to hydrolyzable structures, while bands due to condensed tannins appeared at 1300-900 cm(-1) and exhibited specific hydroxylation patterns useful to elucidate the structure of the flavonoid monomeric units. The spectra were investigated further using principal component analysis for discriminative purposes, to enhance the ability of infrared spectroscopy in the classification and quality control of commercial dried extracts and to enhance their industrial exploitation.

A comprehensive physiologically based pharmacokinetic ...

EPA Pesticide Factsheets

Published physiologically based pharmacokinetic (PBPK) models from peer-reviewed articles are often well-parameterized, thoroughly-vetted, and can be utilized as excellent resources for the construction of models pertaining to related chemicals. Specifically, chemical-specific parameters and in vivo pharmacokinetic data used to calibrate these published models can act as valuable starting points for model development of new chemicals with similar molecular structures. A knowledgebase for published PBPK-related articles was compiled to support PBPK model construction for new chemicals based on their close analogues within the knowledgebase, and a web-based interface was developed to allow users to query those close analogues. A list of 689 unique chemicals and their corresponding 1751 articles was created after analysis of 2,245 PBPK-related articles. For each model, the PMID, chemical name, major metabolites, species, gender, life stages and tissue compartments were extracted from the published articles. PaDEL-Descriptor, a Chemistry Development Kit based software, was used to calculate molecular fingerprints. Tanimoto index was implemented in the user interface as measurement of structural similarity. The utility of the PBPK knowledgebase and web-based user interface was demonstrated using two case studies with ethylbenzene and gefitinib. Our PBPK knowledgebase is a novel tool for ranking chemicals based on similarities to other chemicals associated with existi

Application of Hydrophilic Silanol-Based Chemical Grout for Strengthening Damaged Reinforced Concrete Flexural Members

PubMed Central

Ju, Hyunjin; Lee, Deuck Hang; Cho, Hae-Chang; Kim, Kang Su; Yoon, Seyoon; Seo, Soo-Yeon

2014-01-01

In this study, hydrophilic chemical grout using silanol (HCGS) was adopted to overcome the performance limitations of epoxy materials used for strengthening existing buildings and civil engineering structures. The enhanced material performances of HCGS were introduced, and applied to the section enlargement method, which is one of the typical structural strengthening methods used in practice. To evaluate the excellent structural strengthening performance of the HCGS, structural tests were conducted on reinforced concrete beams, and analyses on the flexural behaviors of test specimens were performed by modified partial interaction theory (PIT). In particular, to improve the constructability of the section enlargement method, an advanced strengthening method was proposed, in which the precast panel was directly attached to the bottom of the damaged structural member by HCGS, and the degree of connection of the test specimens, strengthened by the section enlargement method, were quantitatively evaluated by PIT-based analysis. PMID:28788708

The study on molecular structure and microbiological activity of alkali metal 3-hydroxyphenylycetates

NASA Astrophysics Data System (ADS)

Samsonowicz, M.; Regulska, E.; Kowczyk-Sadowy, M.; Butarewicz, A.; Lewandowski, W.

2017-10-01

The biological activity of chemical compounds depends on their molecular structure. In this paper molecular structure of 3-hydroxyphenylacetates in comparison to 3-hydroxyphenylacetic acid was studied. FT-IR, FT-Raman and NMR spectroscopy and density functional theory (DFT) calculations was used. The B3LYP/6-311++G(d,p) hybrid functional method was used to calculate optimized geometrical structures of studied compounds. The Mulliken, APT, MK, ChelpG and NBO atomic charges as well as dipole moment and energy values were calculated. Theoretical chemical shifts in NMR spectra and the wavenumbers and intensities of the bands in vibrational spectra were analyzed. Calculated parameters were compared to experimental characteristic of studied compounds. Microbiological analysis of studied compounds was performed relative to: Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli and Klebsiella oxytoca. The relationship between spectroscopic and structure parameters of studied compounds in regard to their activity was analyzed.

Application of Hydrophilic Silanol-Based Chemical Grout for Strengthening Damaged Reinforced Concrete Flexural Members.

PubMed

Ju, Hyunjin; Lee, Deuck Hang; Cho, Hae-Chang; Kim, Kang Su; Yoon, Seyoon; Seo, Soo-Yeon

2014-06-23

In this study, hydrophilic chemical grout using silanol (HCGS) was adopted to overcome the performance limitations of epoxy materials used for strengthening existing buildings and civil engineering structures. The enhanced material performances of HCGS were introduced, and applied to the section enlargement method, which is one of the typical structural strengthening methods used in practice. To evaluate the excellent structural strengthening performance of the HCGS, structural tests were conducted on reinforced concrete beams, and analyses on the flexural behaviors of test specimens were performed by modified partial interaction theory (PIT). In particular, to improve the constructability of the section enlargement method, an advanced strengthening method was proposed, in which the precast panel was directly attached to the bottom of the damaged structural member by HCGS, and the degree of connection of the test specimens, strengthened by the section enlargement method, were quantitatively evaluated by PIT-based analysis.

Analysis of morphological and molecular composition changes in allergenic Artemisia vulgaris L. pollen under traffic pollution using SEM and FTIR spectroscopy.

PubMed

Depciuch, J; Kasprzyk, I; Roga, E; Parlinska-Wojtan, M

2016-11-01

Nowadays, pollen allergy becomes an increasing problem for human population. Common mugwort (Artemisia vulgaris L.) is one of the major allergenic plants in Europe. In this study, the influence of air pollution caused by traffic on the structure and chemical composition of common mugwort pollen was investigated. Scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and curve-fitting analysis of amide I profile was applied to assess the morphological and structural changes of mugwort pollen grains collected from sites with different vehicle pollution levels. Microscopic observations support the conclusion, that the higher the car traffic, the smaller the pollen grains. The obtained results clearly show that air pollution had an impact on different maximum absorbance values of individual functional groups composing the chemical structure of pollen. Moreover, air pollution induced structural changes in macromolecules of mugwort pollen. In pollen collected from the unpolluted site, the content of sporopollenin (850 cm -1 ) was the highest, whereas polysaccharide concentration (1032 cm -1 ) was the lowest. Significant differences were observed in lipids. Pollen collected from the site with heavy traffic had the lowest content of lipids at 1709, 2071, and 2930 cm -1 . The largest differences were observed in the spectra regions corresponding to proteins. In pollen collected from unpolluted site, the highest level of β-sheet (1600 cm -1 ) and α-helix (1650 cm -1 ) was detected. The structural changes in proteins, observed in the second derivative of the FTIR spectrum and in the curve-fitting analysis of amide I profile, could be caused inter alia by air pollutants. Alterations in protein structure and in their content in the pollen may increase the sensitization and subsequent risk of allergy in predisposed people. The obtained results suggest that the changes in chemical composition of pollen may be a good indicator of air quality and that FTIR may be successfully applied in biomonitoring.

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

PubMed Central

Huang, Ruili; Xia, Menghang; Sakamuru, Srilatha; Zhao, Jinghua; Shahane, Sampada A.; Attene-Ramos, Matias; Zhao, Tongan; Austin, Christopher P.; Simeonov, Anton

2016-01-01

Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure–activity relationships that are useful for the generation of mechanistic hypotheses. We apply structural information and activity data to build predictive models for 72 in vivo toxicity end points using a cluster-based approach. Models based on in vitro assay data perform better in predicting human toxicity end points than animal toxicity, while a combination of structural and activity data results in better models than using structure or activity data alone. Our results suggest that in vitro activity profiles can be applied as signatures of compound mechanism of toxicity and used in prioritization for more in-depth toxicological testing. PMID:26811972

Engineering science and mechanics; Proceedings of the International Symposium, Tainan, Republic of China, December 29-31, 1981. Parts 1 & 2

NASA Astrophysics Data System (ADS)

Hsia, H.-M.; Chou, Y.-L.; Longman, R. W.

1983-07-01

The topics considered are related to measurements and controls in physical systems, the control of large scale and distributed parameter systems, chemical engineering systems, aerospace science and technology, thermodynamics and fluid mechanics, and computer applications. Subjects in structural dynamics are discussed, taking into account finite element approximations in transient analysis, buckling finite element analysis of flat plates, dynamic analysis of viscoelastic structures, the transient analysis of large frame structures by simple models, large amplitude vibration of an initially stressed thick plate, nonlinear aeroelasticity, a sensitivity analysis of a combined beam-spring-mass structure, and the optimal design and aeroelastic investigation of segmented windmill rotor blades. Attention is also given to dynamics and control of mechanical and civil engineering systems, composites, and topics in materials. For individual items see A83-44002 to A83-44061

The research on delayed fracture behavior of high-strength bolts in steel structure

NASA Astrophysics Data System (ADS)

Li, Guo dong; Li, Nan

2017-07-01

High-strength bolts have been widely used in power plants. However, the high-strength bolts which being employed in pumping station, steel structure and pipeline anti-whip structure have been found delayed fracture for many times in a power plant, this will affect the reliability of steel fracture and bring blow risk caused by falling objects. The high-strength bolt with delayed fracture was carried out fracture analysis, metallurgical analysis, chemical analysis, mechanical analysis, as well as bolts installation analysis, it can be comprehensively confirmed that the direct cause of high-strength bolts delayed fracture is the stress corrosion, and the root cause of high-strength bolts delayed fracture should be the improper installation at the initial and the imperfect routine anti-corrosion maintenance.

The precursors effects on biomimetic hydroxyapatite ceramic powders.

PubMed

Yoruç, Afife Binnaz Hazar; Aydınoğlu, Aysu

2017-06-01

In this study, effects of the starting material on chemical, physical, and biological properties of biomimetic hydroxyapatite ceramic powders (BHA) were investigated. Characterization and chemical analysis of BHA powders were performed by using XRD, FT-IR, and ICP-AES. Microstructural features such as size and morphology of the resulting BHA powders were characterized by using BET, nano particle sizer, pycnometer, and SEM. Additionally, biological properties of the BHA ceramic powders were also investigated by using water-soluble tetrazolium salts test (WST-1). According to the chemical analysis of BHA ceramic powders, chemical structures of ceramics which are prepared under different conditions and by using different starting materials show differences. Ceramic powders which are produced at 80°C are mainly composed of hydroxyapatite, dental hydroxyapatite (contain Na and Mg elements in addition to Ca), and calcium phosphate sulfide. However, these structures are altered at high temperatures such as 900°C depending on the features of starting materials and form various calcium phosphate ceramics and/or their mixtures such as Na-Mg-hydroxyapatite, hydroxyapatite, Mg-Whitlockit, and chloroapatite. In vitro cytotoxicity studies showed that amorphous ceramics produced at 80°C and ceramics containing chloroapatite structure as main or secondary phases were found to be extremely cytotoxic. Furthermore, cell culture studies showed that highly crystalline pure hydroxyapatite structures were extremely cytotoxic due to their high crystallinity values. Consequently, the current study indicates that the selection of starting materials which can be used in the production of calcium phosphate ceramics is very important. It is possible to produce calcium phosphate ceramics which have sufficient biocompatibility at physiological pH values and by using appropriate starting materials. Copyright © 2017 Elsevier B.V. All rights reserved.

Surface characteristic of chemically converted graphene coated low carbon steel by electro spray coating method for polymer electrolyte membrane fuel cell bipolar plate.

PubMed

Kim, Jungsoo; Kim, Yang Do; Nam, Dae Geun

2013-05-01

Graphene was coated on low carbon steel (SS400) by electro spray coating method to improve its properties of corrosion resistance and contact resistance. Exfoliated graphite was made of the graphite by chemical treatment (Chemically Converted Graphene, CCG). CCG is distributed using dispersing agent, and low carbon steel was coated with diffuse graphene solution by electro spray coating method. The structure of the CCG was analyzed using XRD and the coating layer of surface was analyzed using SEM. Analysis showed that multi-layered graphite structure was destroyed and it was transformed in to fine layers graphene structure. And the result of SEM analysis on the surface and the cross section, graphene layer was uniformly formed with 3-5 microm thickness on the surface of substrate. Corrosion resistance test was applied in the corrosive solution which is similar to the polymer electrolyte membrane fuel cell (PEMFC) stack inside. And interfacial contact resistance (ICR) test was measured to simulate the internal operating conditions of PEMFC stack. As a result of measuring corrosion resistance and contact resistance, it could be confirmed that low carbon steel coated with CCG was revealed to be more effective in terms of its applicability as PEMFC bipolar plate.

Fungicidal activities of soil humic/fulvic acids as related to their chemical structures in greenhouse vegetable fields with cultivation chronosequence

NASA Astrophysics Data System (ADS)

Wu, Meng; Song, Mengya; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2016-09-01

In the background of rapid expansion of plastic greenhouse vegetable production in China, many environmental risks have emerged in recent years. In this study, the soils with a chronosequence in greenhouse vegetable fields were collected and the soil humic acids (HAs) and fluvic acids (FAs) were extracted and purified. The soil HAs and FAs were found to show inhibition activities against phytopathogenic fungi for the first time. Fourier transform infrared spectroscopy was performed to investigate the chemical structures of HAs and FAs. The variation of relative peak areas indicated the chemical structure of HAs become more complex and stable under continuous cultivation. The PCA analysis showed HAs and FAs could be distinctly separated from each other and cultivation years mainly determined the variation. Mantel test and RDA analysis indicated the active components (aliphatic peaks for HAs and COOH, OH peaks for FAs) had positive correlation with the inhibition rates of HAs and FAs against phytopathogenic fungi. According to our research, the active fungicidal components in soil HAs and FAs decreased along with the extension of cultivation years, which made the soil suffer more risk to phytopathogenic fugi. So we believe continuous cultivation too many years in PGVP systems is inadvisable.

Fungicidal activities of soil humic/fulvic acids as related to their chemical structures in greenhouse vegetable fields with cultivation chronosequence

PubMed Central

Wu, Meng; Song, Mengya; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2016-01-01

In the background of rapid expansion of plastic greenhouse vegetable production in China, many environmental risks have emerged in recent years. In this study, the soils with a chronosequence in greenhouse vegetable fields were collected and the soil humic acids (HAs) and fluvic acids (FAs) were extracted and purified. The soil HAs and FAs were found to show inhibition activities against phytopathogenic fungi for the first time. Fourier transform infrared spectroscopy was performed to investigate the chemical structures of HAs and FAs. The variation of relative peak areas indicated the chemical structure of HAs become more complex and stable under continuous cultivation. The PCA analysis showed HAs and FAs could be distinctly separated from each other and cultivation years mainly determined the variation. Mantel test and RDA analysis indicated the active components (aliphatic peaks for HAs and COOH, OH peaks for FAs) had positive correlation with the inhibition rates of HAs and FAs against phytopathogenic fungi. According to our research, the active fungicidal components in soil HAs and FAs decreased along with the extension of cultivation years, which made the soil suffer more risk to phytopathogenic fugi. So we believe continuous cultivation too many years in PGVP systems is inadvisable. PMID:27597259

The structure of premixed particle-cloud flames

NASA Technical Reports Server (NTRS)

Seshadri, K.; Berlad, A. L.; Tangirala, V.

1992-01-01

The structure of premixed flames propagating in combustible systems, containing uniformly distributed volatile fuel particles, in an oxidizing gas mixture, is analyzed. It is presumed that the fuel particles vaporize first to yield a gaseous fuel of known chemical structure, which is subsequently oxidized in the gas phase. The analysis is performed in the asymptotic limit, where the value of the characteristic Zeldovich number, based on the gas-phase oxidation of the gaseous fuel is large, and for values of phi(u) greater than or equal to 1.0, where phi(u) is the equivalence ratio based on the fuel available in the fuel particles. The structure of the flame is presumed to consist of a preheat vaporization zone where the rate of the gas-phase chemical reaction is small, a reaction zone where convection and the rate of vaporization of the fuel particles are small and a convection zone where diffusive terms in the conservation equations are small. For given values phi(u) the analysis yields results for the burning velocity and phi(g) where phi(g) is the effective equivalence ratio in the reaction zone. The analysis shows that even though phi(u) greater than or equal to 1.0, for certain cases the calculated value of phi(g) is less than unity. This prediction is in agreement with experimental observations.

[Study on the chemical constituents of the fruit handles from Schizandra chinensis].

PubMed

Shi, Lin; He, Xiao-Xia; Pan, Ying; Han, Ling; Yang, Xiao-Ou; Zhao, Yu-Qing

2009-07-01

To study the chemical constituents of the fruit handles from Schizandra chinensis. Compounds from the 85% ethanol extracts were isolated by silica gel, Sephadex LH-20, recrystal, etc., and their structures were identified by the spectral analysis and chemical evidence. Eight compounds were isolated and identified as wuweizisu C (I), ganwuweizic acid(II), beta-sitosterol(III), gomisin A(IV), schizandrin(V), daucosterol(VI), wuweizisu A(VII), gamma-schizandrin (VIII). Compounds I - VIII are isolated from the fruit handles of Schizandra chinensis for the first time.

Titanium nitride plasma-chemical synthesis with titanium tetrachloride raw material in the DC plasma-arc reactor

NASA Astrophysics Data System (ADS)

Kirpichev, D. E.; Sinaiskiy, M. A.; Samokhin, A. V.; Alexeev, N. V.

2017-04-01

The possibility of plasmochemical synthesis of titanium nitride is demonstrated in the paper. Results of the thermodynamic analysis of TiCl4 - H2 - N2 system are presented; key parameters of TiN synthesis process are calculated. The influence of parameters of plasma-chemical titanium nitride synthesis process in the reactor with an arc plasmatron on characteristics on the produced powders is experimentally investigated. Structure, chemical composition and morphology dependencies on plasma jet enthalpy, stoichiometric excess of hydrogen and nitrogen in a plasma jet are determined.

LEO-to-GEO low thrust chemical propulsion

NASA Technical Reports Server (NTRS)

Shoji, J. M.

1980-01-01

One approach being considered for transporting large space structures from low Earth orbit (LEO) to geosynchronous equatorial orbit (GEO) is the use of low thrust chemical propulsion systems. A variety of chemical rocket engine cycles evaluated for this application for oxygen/hydrogen and oxygen/hydrocarbon propellants (oxygen/methane and oxygen/RF-1) are discussed. These cycles include conventional propellant turbine drives, turboalternator/electric motor pump drive, and fuel cell/electric motor pump drive as well as pressure fed engines. Thrust chamber cooling analysis results are presented for regenerative/radiation and film/radiation cooling.

Automated Inference of Chemical Discriminants of Biological Activity.

PubMed

Raschka, Sebastian; Scott, Anne M; Huertas, Mar; Li, Weiming; Kuhn, Leslie A

2018-01-01

Ligand-based virtual screening has become a standard technique for the efficient discovery of bioactive small molecules. Following assays to determine the activity of compounds selected by virtual screening, or other approaches in which dozens to thousands of molecules have been tested, machine learning techniques make it straightforward to discover the patterns of chemical groups that correlate with the desired biological activity. Defining the chemical features that generate activity can be used to guide the selection of molecules for subsequent rounds of screening and assaying, as well as help design new, more active molecules for organic synthesis.The quantitative structure-activity relationship machine learning protocols we describe here, using decision trees, random forests, and sequential feature selection, take as input the chemical structure of a single, known active small molecule (e.g., an inhibitor, agonist, or substrate) for comparison with the structure of each tested molecule. Knowledge of the atomic structure of the protein target and its interactions with the active compound are not required. These protocols can be modified and applied to any data set that consists of a series of measured structural, chemical, or other features for each tested molecule, along with the experimentally measured value of the response variable you would like to predict or optimize for your project, for instance, inhibitory activity in a biological assay or ΔG binding . To illustrate the use of different machine learning algorithms, we step through the analysis of a dataset of inhibitor candidates from virtual screening that were tested recently for their ability to inhibit GPCR-mediated signaling in a vertebrate.

A Multidisciplinary Course in Bioengineering.

ERIC Educational Resources Information Center

Bienkowski, Paul R.; And Others

1989-01-01

Outlines a graduate course, "Microbial Systems Analysis," for students in chemical and environmental engineering or engineering mechanics, as well as microbiology, ecology and biotechnology. Describes the objectives, structure and laboratory experiments for the course. (YP)

[Studies on chemical constituents of cultivated Cistanche salsa].

PubMed

Yang, Jian-Hu; Hu, Jun-Ping; Rena, Kasimu; Du, Nian-Sheng

2008-11-01

To study the chemical constituents of cultivated Cistanche salsa. Compounds were isolated and purified on several chromatography, and then were identified by physico-chemical properties and structurally elucidated by spectral analysis. Seven compounds were isolated and identified as beta-sitosterol (I), daucosterol (II), beta-sitosteryl glucoside 3'-O-heptadecoicate (III), 8-hydroxygeraniol 1-beta-D-glucopyranoside (IV), 2-methanol-5-hydroxy-pyridine (V), betaine (VI), galactitol (VII). The chemical constituents of artificial cultivated Cistanche salsa are studied for the first time. Among them, compound III and IV are isolated from the plant for the first time, compound V is isolated from this genus for the first time.

From Structural Complexity to Structure-Property Relationships in Intermetallics: Development of Density Functional Theory-Chemical Pressure Analysis

NASA Astrophysics Data System (ADS)

Engelkemier, Joshua

The unparalleled structural diversity of intermetallic compounds provides nearly unlimited potential for the discovery and optimization of materials with useful properties, such as thermoelectricity, superconductivity, magnetism, hydrogen storage, superelasticity, and catalysis. This same diversity, however, creates challenges for understanding and controlling the unpredictable structure of intermetallic phases. Moreover, the fundamental design principles that have proven so powerful in molecular chemistry do not have simple analogues for metallic, solid state materials. One of these basic principles is the concept of atomic size effects. Especially in densely packed crystal structures where the need to fill space is in competition with the atoms' preferences for ideal interatomic distances, substitution of one element in a compound for another with similar chemical properties yet different atomic size can have dramatic effects on the ordering of the atoms (which in turn affects the electronic structure, vibrational properties, and materials properties). But because the forces that hold metallic phases together are less easily understood from a local perspective than covalent or ionic interactions in other kinds of materials, it is usually unclear whether the atoms are organized to optimize stabilizing, bonding interactions or rather forced to be close together despite repulsive, steric interactions. This dissertation details the development of a theoretical method, called Density Functional Theory-Chemical Pressure (DFT-CP) analysis, to address this issue. It works by converting the distribution of total energy density from a DFT calculation into a map of chemical pressure through a numerical approximation of the first derivative of energy with respect to voxel volume. The CP distribution is then carefully divided into contact volumes between neighboring atoms, from which it is possible to determine whether atoms are too close together (positive CP) or too far away from each other (negative CP). This technique is used in combination with the concept of structural plasticity (Berns, 2014) to demonstrate how complex intermetallic phases can be understood as a response of simpler structure types to the destabilizing buildup of CP. From this point of view, interfaces created in complex structures relieve the CP manifest in the more basic, parent structures. This is shown specifically for Ca36Sn23 relative to a hypothetical W5Si3-type Ca5Sn3 phase, LnMn xGa3 (Ln = Ho-Tm, x < 0.15) compared to unstuffed AuCu3-type LnGa3 structures, and structural derivatives of CaCu5- and HoCoGa5-type compounds. As a direct result of the technical developments necessitated by these analyses on structural complexity in intermetallics, a further connection is made in this thesis between the calculated CP schemes and the frequencies of vibrational modes in MgCu2-type CaPd2, the Cr 3Si-type superconductor Nb3Ge, and CaCu5-type CaPd5. Local chemical interactions revealed by DFT-CP analysis are used to identify structure-property relationships for the pseudogap in the phonon density of states (DOS) of CaPd2, the higher critical temperature of Nb3Ge vs. Nb3Sn, and the wide diversity of structures based on the CaCu5 type.

Methods of chemical and phase composition analysis of gallstones

NASA Astrophysics Data System (ADS)

Suvorova, E. I.; Pantushev, V. V.; Voloshin, A. E.

2017-11-01

This review presents the instrumental methods used for chemical and phase composition investigation of gallstones. A great body of data has been collected in the literature on the presence of elements and their concentrations, obtained by fluorescence microscopy, X-ray fluorescence spectroscopy, neutron activation analysis, proton (particle) induced X-ray emission, atomic absorption spectroscopy, high-resolution gamma-ray spectrometry, electron paramagnetic resonance. Structural methods—powder X-ray diffraction, infrared spectroscopy, Raman spectroscopy—provide information about organic and inorganic phases in gallstones. Stone morphology was studied at the macrolevel with optical microscopy. Results obtained by analytical scanning and transmission electron microscopy with X-ray energy dispersive spectrometry are discussed. The chemical composition and structure of gallstones determine the strategy of removing stone from the body and treatment of patients: surgery or dissolution in the body. Therefore one chapter of the review describes the potential of dissolution methods. Early diagnosis and appropriate treatment of the disease depend on the development of clinical methods for in vivo investigation, which gave grounds to present the main characteristics and potential of ultrasonography (ultrasound scanning), magnetic resonance imaging, and X-ray computed tomography.

Computational study of sheath structure in oxygen containing plasmas at medium pressures

NASA Astrophysics Data System (ADS)

Hrach, Rudolf; Novak, Stanislav; Ibehej, Tomas; Hrachova, Vera

2016-09-01

Plasma mixtures containing active species are used in many plasma-assisted material treatment technologies. The analysis of such systems is rather difficult, as both physical and chemical processes affect plasma properties. A combination of experimental and computational approaches is the best suited, especially at higher pressures and/or in chemically active plasmas. The first part of our study of argon-oxygen mixtures was based on experimental results obtained in the positive column of DC glow discharge. The plasma was analysed by the macroscopic kinetic approach which is based on the set of chemical reactions in the discharge. The result of this model is a time evolution of the number densities of each species. In the second part of contribution the detailed analysis of processes taking place during the interaction of oxygen containing plasma with immersed substrates was performed, the results of the first model being the input parameters. The used method was the particle simulation technique applied to multicomponent plasma. The sheath structure and fluxes of charged particles to substrates were analysed in the dependence on plasma pressure, plasma composition and surface geometry.

An efficient approach to identify different chemical markers between fibrous root and rhizome of Anemarrhena asphodeloides by ultra high-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry with multivariate statistical analysis.

PubMed

Wang, Fang-Xu; Yuan, Jian-Chao; Kang, Li-Ping; Pang, Xu; Yan, Ren-Yi; Zhao, Yang; Zhang, Jie; Sun, Xin-Guang; Ma, Bai-Ping

2016-09-10

An ultra high-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry approach coupled with multivariate statistical analysis was established and applied to rapidly distinguish the chemical differences between fibrous root and rhizome of Anemarrhena asphodeloides. The datasets of tR-m/z pairs, ion intensity and sample code were processed by principal component analysis and orthogonal partial least squares discriminant analysis. Chemical markers could be identified based on their exact mass data, fragmentation characteristics, and retention times. And the new compounds among chemical markers could be isolated rapidly guided by the ultra high-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry and their definitive structures would be further elucidated by NMR spectra. Using this approach, twenty-four markers were identified on line including nine new saponins and five new steroidal saponins of them were obtained in pure form. The study validated this proposed approach as a suitable method for identification of the chemical differences between various medicinal parts in order to expand medicinal parts and increase the utilization rate of resources. Copyright © 2016 Elsevier B.V. All rights reserved.

Facile synthesis of silicon nanowire-nanopillar superhydrophobic structures

NASA Astrophysics Data System (ADS)

Roy, Abhijit; Satpati, Biswarup

2018-04-01

We have used metal assisted chemical etching (MACE) method to produce silicon (Si) nanowire-nanopillar array. Nanowire-nanopillar combined structures show higher degree of hydrophobicity compared to its nanowire (Si-NW) counterparts. The rate of etching is depended on initial metal deposition. The structural analysis was carried out using scanning electron microscopy (SEM) in combination with transmission electron microscopy (TEM) to determine different parameters like etching direction, crystallinity etc.

[Contributions of ludic care in nursing to chemical detoxification due to the use of crack cocaine].

PubMed

Pavanatto, Paola Aparecida; Gehlen, Maria Helena; Ilha, Silomar; Zamberlan, Claudia; Rangel, Rosiane Filipin; Nietsche, Elisabeta Albertina

2015-06-01

to understand the contributions of ludic care in nursing by stimulating the acceptance of chemical detoxification from crack on the perception of people in the detoxification process. an exploratory, descriptive study with a qualitative approach, performed with five people hospitalized for chemical detoxification from crack, from March to July 2013 in a chemical detox unit of a midsize hospital in the central region of Rio Grande do Sul. Data was collected using a semi-structured interview and was subjected to content analysis. Two categories emerged: Ludic care in nursing as a stimulus to the acceptance of chemical detoxification; Ludic care in nursing in the promotion for healthy living after chemical detoxification. ludic care in nursing proved to enhance the acceptance of chemical detoxification from crack in the reality investigated.

Phases and interfaces from real space atomically resolved data: Physics-based deep data image analysis

DOE PAGES

Vasudevan, Rama K.; Ziatdinov, Maxim; Jesse, Stephen; ...

2016-08-12

Advances in electron and scanning probe microscopies have led to a wealth of atomically resolved structural and electronic data, often with ~1–10 pm precision. However, knowledge generation from such data requires the development of a physics-based robust framework to link the observed structures to macroscopic chemical and physical descriptors, including single phase regions, order parameter fields, interfaces, and structural and topological defects. Here, we develop an approach based on a synergy of sliding window Fourier transform to capture the local analog of traditional structure factors combined with blind linear unmixing of the resultant 4D data set. This deep data analysismore » is ideally matched to the underlying physics of the problem and allows reconstruction of the a priori unknown structure factors of individual components and their spatial localization. We demonstrate the principles of this approach using a synthetic data set and further apply it for extracting chemical and physically relevant information from electron and scanning tunneling microscopy data. Furthermore, this method promises to dramatically speed up crystallographic analysis in atomically resolved data, paving the road toward automatic local structure–property determinations in crystalline and quasi-ordered systems, as well as systems with competing structural and electronic order parameters.« less

Structural, vibrational, electronic investigations and quantum chemical studies of 2-amino-4-methoxybenzothiazole

NASA Astrophysics Data System (ADS)

Arjunan, V.; Raj, Arushma; Santhanam, R.; Marchewka, M. K.; Mohan, S.

2013-02-01

Extensive vibrational investigations of 2-amino-4-methoxybenzothiazole have been carried out with FTIR and FT-Raman spectral techniques. The electronic structure of the molecule has been analysed by UV-Visible and NMR spectroscopies. The DFT studies were carried out with B3LYP and HF methods utilising 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets to determine the structural, thermodynamical, vibrational, electronic characteristics of the compound and also to understand the electronic and steric influence of the methoxy amino groups on the skeletal frequencies. The mixing of the fundamental modes was determined with the help of total energy distribution (TED). The energies of the frontier molecular orbitals have also been determined. The kinetic and thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intramolecular electronic interactions and their stabilisation energy. 1H and 13C NMR chemical shifts and the electronic transitions of the molecule are also discussed.

Expanding the chemical information science gateway.

PubMed

Bajorath, Jürgen

2017-01-01

Broadly defined, chemical information science (CIS) covers chemical structure and data analysis including biological activity data as well as processing, organization, and retrieval of any form of chemical information. The CIS Gateway (CISG) of F1000Research was created to communicate research involving the entire spectrum of chemical information, including chem(o)informatics. CISG provides a forum for high-quality publications and a meaningful alternative to conventional journals. This gateway is supported by leading experts in the field recognizing the need for open science and a flexible publication platform enabling off-the-beaten path contributions. This editorial aims to further rationalize the scope of CISG, position it within its scientific environment, and open it up to a wider audience. Chemical information science is an interdisciplinary field with high potential to interface with experimental work.

Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

PubMed

Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

2012-03-07

Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

Expanding the chemical information science gateway

PubMed Central

Bajorath, Jürgen

2017-01-01

Broadly defined, chemical information science (CIS) covers chemical structure and data analysis including biological activity data as well as processing, organization, and retrieval of any form of chemical information. The CIS Gateway (CISG) of F1000Research was created to communicate research involving the entire spectrum of chemical information, including chem(o)informatics. CISG provides a forum for high-quality publications and a meaningful alternative to conventional journals. This gateway is supported by leading experts in the field recognizing the need for open science and a flexible publication platform enabling off-the-beaten path contributions. This editorial aims to further rationalize the scope of CISG, position it within its scientific environment, and open it up to a wider audience. Chemical information science is an interdisciplinary field with high potential to interface with experimental work. PMID:29043072

[Study on triterpenes of Microtropis tiflora].

PubMed

Wang, Kui-wu; Hu, Xin-ling; Shen, Lian-qing; Pan, Yuan-jiang

2007-08-01

To study the chemical constituents of Microtropis triflora. The compounds were isolated by chromatography on silica gel and Sephadex LH-20. There structures were elucidatedby by chemical methods and spectral analysis. Five triterpenoids were isolated and elucidated as friedelin (1), 3-oxo-28-friedelanoic acid (2), 29-hydroxy-3-friedelanone (3), salaspermic acid (4), orthosphenic acid (5). Compounds 1-5 are all isolated from M. triflora for the first time.

Prediction of tautomer ratios by embedded-cluster integral equation theory

NASA Astrophysics Data System (ADS)

Kast, Stefan M.; Heil, Jochen; Güssregen, Stefan; Schmidt, K. Friedemann

2010-04-01

The "embedded cluster reference interaction site model" (EC-RISM) approach combines statistical-mechanical integral equation theory and quantum-chemical calculations for predicting thermodynamic data for chemical reactions in solution. The electronic structure of the solute is determined self-consistently with the structure of the solvent that is described by 3D RISM integral equation theory. The continuous solvent-site distribution is mapped onto a set of discrete background charges ("embedded cluster") that represent an additional contribution to the molecular Hamiltonian. The EC-RISM analysis of the SAMPL2 challenge set of tautomers proceeds in three stages. Firstly, the group of compounds for which quantitative experimental free energy data was provided was taken to determine appropriate levels of quantum-chemical theory for geometry optimization and free energy prediction. Secondly, the resulting workflow was applied to the full set, allowing for chemical interpretations of the results. Thirdly, disclosure of experimental data for parts of the compounds facilitated a detailed analysis of methodical issues and suggestions for future improvements of the model. Without specifically adjusting parameters, the EC-RISM model yields the smallest value of the root mean square error for the first set (0.6 kcal mol-1) as well as for the full set of quantitative reaction data (2.0 kcal mol-1) among the SAMPL2 participants.

Introduction to session on materials and structures

NASA Technical Reports Server (NTRS)

Vosteen, L. F.

1978-01-01

A review was given of the development of composites for aircraft. Supporting base technology and the Aircraft Energy Efficiency Composites Program are included. Specific topics discussed include: (1) environmental effects on materials; (2) material quality and chemical characterization; (3) design and analysis methods; (4) structural durability; (5) impact sensitivity; (6) carbon fiber electrical effects; and (7) composite components.

Feasibility Analysis of Incorporating In-Vitro Toxicokinetic Data as a Surrogate for In-Vivo Data for Read-across Predictions (ASCCT meeting)

EPA Science Inventory

The underlying principle of read-across is that biological activity is a function of physical and structural properties of chemicals. Analogs are typically identified on the basis of structural similarity and subsequently evaluated for their use in read-across on the basis of the...

Collaborative Center in Polymer Photonics

DTIC Science & Technology

2009-02-28

the inorganic residue in the thermogravimetric analysis TGA of the samples, Figure 6. It can be noticed that only approximately 1/3 of the...photonics, nanoparticles , structure, organic-inorganic hybrids, nanocomposites, photonic band gap, plasma-enhanced chemical vapor deposition, discotic liquid...the surface structure of nanoparticles made us focus our study on the morphological and thermodynamic properties of metallic nanoparticles . We cannot

A model to systematically employ professional judgment in the Bayesian Decision Analysis for a semiconductor industry exposure assessment.

PubMed

Torres, Craig; Jones, Rachael; Boelter, Fred; Poole, James; Dell, Linda; Harper, Paul

2014-01-01

Bayesian Decision Analysis (BDA) uses Bayesian statistics to integrate multiple types of exposure information and classify exposures within the exposure rating categorization scheme promoted in American Industrial Hygiene Association (AIHA) publications. Prior distributions for BDA may be developed from existing monitoring data, mathematical models, or professional judgment. Professional judgments may misclassify exposures. We suggest that a structured qualitative risk assessment (QLRA) method can provide consistency and transparency in professional judgments. In this analysis, we use a structured QLRA method to define prior distributions (priors) for BDA. We applied this approach at three semiconductor facilities in South Korea, and present an evaluation of the performance of structured QLRA for determination of priors, and an evaluation of occupational exposures using BDA. Specifically, the structured QLRA was applied to chemical agents in similar exposure groups to identify provisional risk ratings. Standard priors were developed for each risk rating before review of historical monitoring data. Newly collected monitoring data were used to update priors informed by QLRA or historical monitoring data, and determine the posterior distribution. Exposure ratings were defined by the rating category with the highest probability--i.e., the most likely. We found the most likely exposure rating in the QLRA-informed priors to be consistent with historical and newly collected monitoring data, and the posterior exposure ratings developed with QLRA-informed priors to be equal to or greater than those developed with data-informed priors in 94% of comparisons. Overall, exposures at these facilities are consistent with well-controlled work environments. That is, the 95th percentile of exposure distributions are ≤50% of the occupational exposure limit (OEL) for all chemical-SEG combinations evaluated; and are ≤10% of the limit for 94% of chemical-SEG combinations evaluated.

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties.

PubMed

Chai, Bei-Bei; Huang, Ting-Lin; Zhao, Xiao-Guang; Li, Ya-Jiao

2015-07-01

Microbial communities in three drinking water reservoirs, with different depth in Xi'an city, were quantified by phospholipids fatty acids analysis and multivariate statistical analysis was employed to interpret their response to different hydrostatic pressure and other physico-chemical properties of sediment and overlying water. Principle component analyses of sediment characteristics parameters showed that hydrostatic pressure was the most important effect factor to differentiate the overlying water quality from three drinking water reservoirs from each other. NH4+ content in overlying water was positive by related to hydrostatic pressure, while DO in water-sediment interface and sediment OC in sediment were negative by related with it. Three drinking water reservoir sediments were characterized by microbial communities dominated by common and facultative anaerobic Gram-positive bacteria, as well as, by sulfur oxidizing bacteria. Hydrostatic pressure and physico-chemical properties of sediments (such as sediment OC, sediment TN and sediment TP) were important effect factors to microbial community structure, especially hydrostatic pressure. It is also suggested that high hydrostatic pressure and low dissolved oxygen concentration stimulated Gram-positive and sulfate-reducing bacteria (SRB) bacterial population in drinking water reservoir sediment. This research supplied a successful application of phospholipids fatty acids and multivariate analysis to investigate microbial community composition response to different environmental factors. Thus, few physico-chemical factors can be used to estimate composition microbial of community as reflected by phospholipids fatty acids, which is difficult to detect.

Chemical kinetics of Cs species in an alkali-activated municipal solid waste incineration fly ash and pyrophyllite-based system using Cs K-edge in situ X-ray absorption fine structure analysis

NASA Astrophysics Data System (ADS)

Shiota, Kenji; Nakamura, Takafumi; Takaoka, Masaki; Nitta, Kiyofumi; Oshita, Kazuyuki; Fujimori, Takashi; Ina, Toshiaki

2017-05-01

We conducted in situ X-ray absorption fine structure (in situ XAFS) analysis at the Cs K-edge to investigate the chemical kinetics of Cs species during reaction in an alkali-activated municipal solid waste incineration fly ash (MSWIFA) and pyrophyllite-based system. Understanding the kinetics of Cs is essential to the design of appropriate conditions for Cs stabilization. In situ XAFS analysis of four pastes, prepared from NaOHaq, sodium silicate solution, pyrophyllite, and MSWIFA with the addition of CsCl, was conducted in custom-built reaction cells at four curing temperatures (room temperature, 60 °C, 80 °C, 105 °C) for approximately 34 h. The results indicated that the change in Cs species during reaction at room temperature was small, while changes at higher temperatures were faster and more extreme, with the fastest conversion to pollucite occurring at 105 °C. Further analysis using a leaching test and a simple reaction model for Cs species during reaction showed that the pollucite formation rate was dependent on the curing temperature and had a significant negative correlation with Cs leaching. The activation energy of pollucite formation was estimated to be 31.5 kJ/mol. These results revealed that an important change in the chemical state of Cs occurs during reaction in the system.

Molecular structure, vibrational, electronic and thermal properties of 4-vinylcyclohexene by quantum chemical calculations

NASA Astrophysics Data System (ADS)

Nagabalasubramanian, P. B.; Periandy, S.; Karabacak, Mehmet; Govindarajan, M.

2015-06-01

The solid phase FT-IR and FT-Raman spectra of 4-vinylcyclohexene (abbreviated as 4-VCH) have been recorded in the region 4000-100 cm-1. The optimized molecular geometry and vibrational frequencies of the fundamental modes of 4-VCH have been precisely assigned and analyzed with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method at 6-311++G(d,p) level basis set. The theoretical frequencies were properly scaled and compared with experimentally obtained FT-IR and FT-Raman spectra. Also, the effect due the substitution of vinyl group on the ring vibrational frequencies was analyzed and a detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated total energy distribution (TED). The time dependent DFT (TD-DFT) method was employed to predict its electronic properties, such as electronic transitions by UV-Visible analysis, HOMO and LUMO energies, molecular electrostatic potential (MEP) and various global reactivity and selectivity descriptors (chemical hardness, chemical potential, softness, electrophilicity index). Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Atomic charges obtained by Mulliken population analysis and NBO analysis are compared. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are also calculated.

Chemically stabilized reduced graphene oxide/zirconia nanocomposite: synthesis and characterization

NASA Astrophysics Data System (ADS)

Sagadevan, Suresh; Zaman Chowdhury, Zaira; Enamul Hoque, Md; Podder, Jiban

2017-11-01

In this research, chemical method was used to fabricate reduced graphene oxide/zirconia (rGO/ZrO2) nanocomposite. X-ray Diffraction analysis (XRD) was carried out to examine the crystalline structure of the nanocomposites. The nanocomposite prepared here has average crystallite size of 14 nm. The surface morphology was observed using scanning electron microscopic analysis (SEM) coupled with electron dispersion spectroscopy (EDS) to detect the chemical element over the surface of the nanocomposites. High-resolution Transmission electron microscopic analysis (HR-TEM) was carried out to determine the particle size and shape of the nanocomposites. The optical property of the prepared samples was determined using UV-visible absorption spectrum. The functional groups were identified using FTIR and Raman spectroscopic analysis. Efficient, cost effective and properly optimized synthesis process of rGO/ZrO2 nanocomposite can ensure the presence of infiltrating graphene network inside the ZrO2 matrix to enhance the electrical properties of the hybrid composites up to a greater scale. Thus the dielectric constant, dielectric loss and AC conductivity of the prepared sample was measured at various frequencies and temperatures. The analytical results obtained here confirmed the homogeneous dispersion of ZrO2 nanostructures over the surface of reduced graphene oxide nanosheets. Overall, the research demonstrated that the rGO/ZrO2 nano-hybrid structure fabricated here can be considered as a promising candidate for applications in nanoelectronics and optoelectronics.

Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

NASA Astrophysics Data System (ADS)

Madanagopal, A.; Periandy, S.; Gayathri, P.; Ramalingam, S.; Xavier, S.

2017-01-01

The pharmaceutical compound; Phenacetin was investigated by analyzing FT-IR, FT-Raman and 1H &13C NMR spectra. The hybrid efficient computational calculations performed for computing physical and chemical parameters. The cause of pharmaceutical activity due to the substitutions; carboxylic, methyl and amine groups in appropriate positions on the pedestal compound was deeply investigated. Moreover, 13C NMR and 1H NMR chemical shifts correlated with TMS standard to explain the truth of compositional ratio of base and ligand groups. The bathochromic shift due to chromophores over the energy levels in UV-Visible region was strongly emphasized the Anti-inflammatory chemical properties. The chemical stability was pronounced by the strong kubo gap which showed the occurring of charge transformation within the molecule. The occurrence of the chemical reaction was feasibly interpreted by Gibbs free energy profile. The standard vibrational analysis stressed the active participation of composed ligand groups for the existence of the analgesic as well as antipyretic properties of the Phenacetin compound. The strong dipole interaction energy utilization for the transition among non-vanishing donor and acceptor for composition of the molecular structure was interpreted.

Theoretical study on the molecular structure and vibrational properties, NBO and HOMO-LUMO analysis of the POX3 (X = F, Cl, Br, I) series of molecules

NASA Astrophysics Data System (ADS)

Galván, Jorge E.; Gil, Diego M.; Lanús, Hernán E.; Altabef, Aida Ben

2015-02-01

The fourth member of the series of compounds of the type POX3 with X = I was synthesized and characterized by infrared spectroscopy. The geometrical parameters and vibrational properties of POX3 (X = F, Cl, Br, I) molecules were investigated theoretically by means DFT and ab initio methods. Available geometrical and vibrational data were used together with theoretical calculations in order to obtain a set of scaled force constants. The observed trends in geometrical parameters are analyzed and compared with those obtained in a previous work for the VOX3 (X = F, Cl, Br, I) series of compounds. NBO analysis was performed in order to know the hyper-conjugative interactions that favor one structure over another. The molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, chemical hardness, softness and global electrophilicity index have been deduced from HOMO-LUMO analysis.

Comparison of the effect of wet and dry torrefaction on chemical structure and pyrolysis behavior of corncobs.

PubMed

Zheng, Anqing; Zhao, Zengli; Chang, Sheng; Huang, Zhen; Zhao, Kun; Wei, Guoqiang; He, Fang; Li, Haibin

2015-01-01

Wet and dry torrefaction of corncobs was conducted in high-pressure reactor and tube-type reactor, respectively. Effect of wet and dry torrefaction on chemical structure and pyrolysis behavior of corncobs was compared. The results showed that hemicellulose could be effectively removed from corncobs by torrefaction. However, dry torrefaction caused severe degradation of cellulose and the cross-linking and charring of corncobs. X-ray diffraction analysis revealed that crystallinity degree of corncobs was evidently enhanced during wet torrefaction, but reduced during dry torrefaction as raising treatment temperature. In thermogravimetric analysis, wet torrefied corncobs produced less carbonaceous residues than raw corncobs, while dry torrefied corncobs gave much more residues owing to increased content of acid insoluble lignin. Pyrolysis-gas chromatography/mass spectroscopy analysis indicated that wet torrefaction significantly promoted levoglucosan yield owing to the removal of alkali metals. Therefore, wet torrefaction can be considered as a more effective pretreatment method for fast pyrolysis of biomass. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural and quantum chemical analysis of exciton coupling in homo- and heteroaggregate stacks of merocyanines

NASA Astrophysics Data System (ADS)

Bialas, David; Zitzler-Kunkel, André; Kirchner, Eva; Schmidt, David; Würthner, Frank

2016-09-01

Exciton coupling is of fundamental importance and determines functional properties of organic dyes in (opto-)electronic and photovoltaic devices. Here we show that strong exciton coupling is not limited to the situation of equal chromophores as often assumed. Quadruple dye stacks were obtained from two bis(merocyanine) dyes with same or different chromophores, respectively, which dimerize in less-polar solvents resulting in the respective homo- and heteroaggregates. The structures of the quadruple dye stacks were assigned by NMR techniques and unambiguously confirmed by single-crystal X-ray analysis. The heteroaggregate stack formed from the bis(merocyanine) bearing two different chromophores exhibits remarkably different ultraviolet/vis absorption bands compared with those of the homoaggregate of the bis(merocyanine) comprising two identical chromophores. Quantum chemical analysis based on an extension of Kasha's exciton theory appropriately describes the absorption properties of both types of stacks revealing strong exciton coupling also between different chromophores within the heteroaggregate.

Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments.

PubMed

Sato, Tomohiro; Hashimoto, Noriaki; Honma, Teruki

2017-12-26

To assist in the structural optimization of hit/lead compounds during drug discovery, various computational approaches to identify potentially useful bioisosteric conversions have been reported. Here, the preference of chemical fragments to hydrogen bonds with specific amino acid residues was used to identify potential bioisosteric conversions. We first compiled a data set of chemical fragments frequently occurring in complex structures contained in the Protein Data Bank. We then used a computational approach to determine the amino acids to which these chemical fragments most frequently hydrogen bonded. The results of the frequency analysis were used to hierarchically cluster chemical fragments according to their amino acid preferences. The Euclid distance between amino acid preferences of chemical fragments for hydrogen bonding was then compared to MMP information in the ChEMBL database. To demonstrate the applicability of the approach for compound optimization, the similarity of amino acid preferences was used to identify known bioisosteric conversions of the epidermal growth factor receptor inhibitor gefitinib. The amino acid preference distance successfully detected bioisosteric fragments corresponding to the morpholine ring in gefitinib with a higher ROC score compared to those based on topological similarity of substituents and frequency of MMP in the ChEMBL database.

Iron meteorite fragment studied by atomic and nuclear analytical methods

NASA Astrophysics Data System (ADS)

Cesnek, Martin; Štefánik, Milan; Kmječ, Tomáš; Miglierini, Marcel

2016-10-01

Chemical and structural compositions of a fragment of Sikhote-Alin iron meteorite were investigated by X-ray fluorescence analysis (XRF), neutron activation analysis (NAA) and Mössbauer spectroscopy (MS). XRF and NAA revealed the presence of chemical elements which are characteristic for iron meteorites. XRF also showed a significant amount of Si and Al on the surface of the fragment. MS spectra revealed possible presence of α-Fe(Ni, Co) phase with different local Ni concentration. Furthermore, paramagnetic singlet was detected in Mössbauer spectra recorded at room temperature and at 4.2 K.

Growth and characterization of ammonium nickel-cobalt sulfate Tutton's salt for UV light applications

NASA Astrophysics Data System (ADS)

Ghosh, Santunu; Oliveira, Michelle; Pacheco, Tiago S.; Perpétuo, Genivaldo J.; Franco, Carlos J.

2018-04-01

We have obtained a set of sample crystals of the family of Tutton's salt comprise in the isomorphic series with general chemical formula (NH4)2NixCo(1-x) (SO4)2·6H2O, by employing growth from solutions by slow evaporation technique. The samples crystals were characterized by ICP-AES, X-ray powder diffraction analysis, thermogravimetric analysis, UV-Vis-NIR, Raman and FTIR spectroscopy. This type of material has been studied because of its physical and chemical properties not yet understood and they have potential technological applications. Chemical analysis of the samples by ICP-AES method allowed us to investigate the efficiency of the method of growth used. Thermogravimetric analysis provides the information about the thermal stability of the obtained crystals for high temperature applications, and powder X-ray diffraction analysis at ambient and high temperature reveals the structural quality and structural change of the samples respectively. We have used Raman spectroscopy in the range 100-4000 cm-1 and FTIR spectroscopy in the range 400-4000 cm-1 to understand the internal vibrational mode of the octahedral complexes [Ni(H2O)6]2+ and [Co(H2O)6]2+, SO42- and NH4+ tetrahedra. The transmittance of our mixed ammonium nickel cobalt sulfate hexahydrate (ACNSH) crystals is 75% in the UV region, which indicates that they are ideal to use in UV light filters and UV sensors.

[Study on the chemical constituent from the dichloromethane extract. of the pine needles of Cedrus deodara].

PubMed

Shi, Xiao-Feng; Bai, Zhao-Hui; Liu, Dong-Yan; Li, Shuang

2012-03-01

To study the chemical constituents of the dichloromethane extracted from pine needles of Cedrus deodara. Compounds were isolated and purified from the dichloromethane extract of pine needles by chromatography on silica gel and Sephadex LH-20. Their structures were identified on the basis of spectroscopic analysis and physicochemical property. Nine compounds were isolated and purified. Their structures were identified as stigmasterol (1), oleanolic acid (2), parahydroxybenzaldehyde (3), beta-sitosterol (4), syringaresinol (5), daucosterol (6), p-hydroxybenzoic acid (7), gallicin (8) and gallic acid (9). Compounds 1-3, 5 -9 are isolated from pine needles of this genus for the first time.

Quantum chemical and experimental studies on the structure and vibrational spectra of an alkaloid-Corlumine

NASA Astrophysics Data System (ADS)

Mishra, Rashmi; Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

2014-01-01

The study concentrates on an important natural product, phthalide isoquinoline alkaloid Corlumine (COR) [(6R)-6-[(1S)-1,2,3,4-Tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-yl] furo [3,4-e]-1,3-benzodioxol-8(6H)-one] well known to exhibit spasmolytic and GABA antagonist activity. It was fully characterized by a variety of experimental methods including vibrational spectroscopy (IR and Raman), thermal analysis (DSC), UV and SEM. For a better interpretation and analysis of the results quantum chemical calculations employing DFT were also performed. TD-DFT was employed to elucidate electronic properties for both gaseous and solvent environment using IEF-PCM model. Graphical representation of HOMO and LUMO would provide a valuable insight into the nature of reactivity and some of the structural and physical properties of the title molecule. The structure-activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug-receptor interactions. Stability of the molecule arising from hyper conjugative interactions, charge delocalisation has been analyzed using natural bond orbital (NBO) analysis. Computation of thermodynamical properties would help to have a deep insight into the molecule for further applications.

Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller polycyclic aromatic hydrocarbons.

PubMed

Wan, B; Yarbrough, J W; Schultz, T W

2008-01-01

This study was undertaken to test the hypothesis that structurally similar PAHs induce similar gene expression profiles. THP-1 cells were exposed to a series of 12 selected PAHs at 50 microM for 24 hours and gene expressions profiles were analyzed using both unsupervised and supervised methods. Clustering analysis of gene expression profiles revealed that the 12 tested chemicals were grouped into five clusters. Within each cluster, the gene expression profiles are more similar to each other than to the ones outside the cluster. One-methylanthracene and 1-methylfluorene were found to have the most similar profiles; dibenzothiophene and dibenzofuran were found to share common profiles with fluorine. As expression pattern comparisons were expanded, similarity in genomic fingerprint dropped off dramatically. Prediction analysis of microarrays (PAM) based on the clustering pattern generated 49 predictor genes that can be used for sample discrimination. Moreover, a significant analysis of Microarrays (SAM) identified 598 genes being modulated by tested chemicals with a variety of biological processes, such as cell cycle, metabolism, and protein binding and KEGG pathways being significantly (p < 0.05) affected. It is feasible to distinguish structurally different PAHs based on their genomic fingerprints, which are mechanism based.

The Role of Ultrahigh Resolution Fourier Transform Mass Spectrometry (FT-MS) in Astrobiology-Related Research: Analysis of Meteorites and Tholins.

PubMed

Somogyi, Árpád; Thissen, Roland; Orthous-Daunay, Francois-Régis; Vuitton, Véronique

2016-03-24

It is an important but also a challenging analytical problem to understand the chemical composition and structure of prebiotic organic matter that is present in extraterrestrial materials. Its formation, evolution and content in the building blocks ("seeds") for more complex molecules, such as proteins and DNA, are key questions in the field of exobiology. Ultrahigh resolution mass spectrometry is one of the best analytical techniques that can be applied because it provides reliable information on the chemical composition and structure of individual components of complex organic mixtures. Prebiotic organic material is delivered to Earth by meteorites or generated in laboratories in simulation (model) experiments that mimic space or atmospheric conditions. Recent representative examples for ultrahigh resolution mass spectrometry studies using Fourier-transform (FT) mass spectrometers such as Orbitrap and ion cyclotron resonance (ICR) mass spectrometers are shown and discussed in the present article, including: (i) the analysis of organic matter of meteorites; (ii) modeling atmospheric processes in ICR cells; and (iii) the structural analysis of laboratory made tholins that might be present in the atmosphere and surface of Saturn's largest moon, Titan.

The Role of Ultrahigh Resolution Fourier Transform Mass Spectrometry (FT-MS) in Astrobiology-Related Research: Analysis of Meteorites and Tholins

PubMed Central

Somogyi, Árpád; Thissen, Roland; Orthous-Daunay, Francois-Régis; Vuitton, Véronique

2016-01-01

It is an important but also a challenging analytical problem to understand the chemical composition and structure of prebiotic organic matter that is present in extraterrestrial materials. Its formation, evolution and content in the building blocks (“seeds”) for more complex molecules, such as proteins and DNA, are key questions in the field of exobiology. Ultrahigh resolution mass spectrometry is one of the best analytical techniques that can be applied because it provides reliable information on the chemical composition and structure of individual components of complex organic mixtures. Prebiotic organic material is delivered to Earth by meteorites or generated in laboratories in simulation (model) experiments that mimic space or atmospheric conditions. Recent representative examples for ultrahigh resolution mass spectrometry studies using Fourier-transform (FT) mass spectrometers such as Orbitrap and ion cyclotron resonance (ICR) mass spectrometers are shown and discussed in the present article, including: (i) the analysis of organic matter of meteorites; (ii) modeling atmospheric processes in ICR cells; and (iii) the structural analysis of laboratory made tholins that might be present in the atmosphere and surface of Saturn’s largest moon, Titan. PMID:27023520

Isolation and characterization of a bactericidal withanolide from Physalis virginiana.

PubMed

Gibson, Kathleen A; Reese, R Neil; Halaweish, Fathi T; Ren, Yulin

2012-01-01

Physalis virginiana (Virginia Groundcherry) is a member of the family Solenaceae. Several species of the Physalis genus have been used traditionally by American Indians as medicinal treatments. This study investigated the antibacterial activity of chemicals extracted from P. virginiana through antibacterial disc and cytotoxicity assays. Isolation and purification of an antimicrobial compound was achieved through flash chromatography and preparative HPLC. Finally, identification of chemical structure was determined from (1)H and (13)C NMR and MS. Disc assays showed that crude ethanol extracts were effective antibacterial agents against one gram-negative and seven gram-positive bacterial strains. Cytotoxicity assays indicated that it is less toxic than gentamicin controls. Isolation of the active component showed it to be a relatively polar compound. (1)H and (13)C NMR chemical shifts together with HRMS indicated a similar structure to withanolides previously identified from Physalis angulata. HRMS analysis showed a molecular mass of 472.2857 which corresponds to a molecular formula C(28)H(40)O(6). An antibacterial withanolide was isolated from P. virginiana using flash chromatography and HPLC separations. The chemical structure was determined by NMR and MS to be the withanolide physagulin V.

Isolation and characterization of a bactericidal withanolide from Physalis virginiana

PubMed Central

Gibson, Kathleen A.; Reese, R. Neil; Halaweish, Fathi T.; Ren, Yulin

2012-01-01

Background: Physalis virginiana (Virginia Groundcherry) is a member of the family Solenaceae. Several species of the Physalis genus have been used traditionally by American Indians as medicinal treatments. Materials and Methods: This study investigated the antibacterial activity of chemicals extracted from P. virginiana through antibacterial disc and cytotoxicity assays. Isolation and purification of an antimicrobial compound was achieved through flash chromatography and preparative HPLC. Finally, identification of chemical structure was determined from 1H and 13C NMR and MS. Results: Disc assays showed that crude ethanol extracts were effective antibacterial agents against one gram-negative and seven gram-positive bacterial strains. Cytotoxicity assays indicated that it is less toxic than gentamicin controls. Isolation of the active component showed it to be a relatively polar compound. 1H and 13C NMR chemical shifts together with HRMS indicated a similar structure to withanolides previously identified from Physalis angulata. HRMS analysis showed a molecular mass of 472.2857 which corresponds to a molecular formula C28H40O6. Conclusion: An antibacterial withanolide was isolated from P. virginiana using flash chromatography and HPLC separations. The chemical structure was determined by NMR and MS to be the withanolide physagulin V. PMID:22438659

Quantitative Survey and Structural Classification of Hydraulic Fracturing Chemicals Reported in Unconventional Gas Production.

PubMed

Elsner, Martin; Hoelzer, Kathrin

2016-04-05

Much interest is directed at the chemical structure of hydraulic fracturing (HF) additives in unconventional gas exploitation. To bridge the gap between existing alphabetical disclosures by function/CAS number and emerging scientific contributions on fate and toxicity, we review the structural properties which motivate HF applications, and which determine environmental fate and toxicity. Our quantitative overview relied on voluntary U.S. disclosures evaluated from the FracFocus registry by different sources and on a House of Representatives ("Waxman") list. Out of over 1000 reported substances, classification by chemistry yielded succinct subsets able to illustrate the rationale of their use, and physicochemical properties relevant for environmental fate, toxicity and chemical analysis. While many substances were nontoxic, frequent disclosures also included notorious groundwater contaminants like petroleum hydrocarbons (solvents), precursors of endocrine disruptors like nonylphenols (nonemulsifiers), toxic propargyl alcohol (corrosion inhibitor), tetramethylammonium (clay stabilizer), biocides or strong oxidants. Application of highly oxidizing chemicals, together with occasional disclosures of putative delayed acids and complexing agents (i.e., compounds designed to react in the subsurface) suggests that relevant transformation products may be formed. To adequately investigate such reactions, available information is not sufficient, but instead a full disclosure of HF additives is necessary.

Structure and chemical characteristics of natural mineral deposit Terbunskaya (Lipetsk region, Russia)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Motyleva, S., E-mail: motyleva-svetlana@mail.ru; Mertvishcheva, M.; Shchuchka, R.

New knowledge about the mineralogical features Terbunsky mineral. Investigated 5 fractions isolated from the incision (2-2,5 m). Terbunskaya deposit belongs to minerals Santonian age. Scanning electron microscopy and energy dispersive analysis of fractions isolated studied in detail. In the coarse fractions found ancient organic remains of algae and micro-organisms that have been sedimented together with the mineral component during geological periods. The share of organic inclusions does not exceed 1.5%. Chemical composition confirms the presence of silicon and carbonate organisms. Advantageously proportion of minerals having a layered structure with a plurality of micro and nano pore size 600 - 80-nm andmore » an average chemical composition (wt%): Na (0,64), Mg (0,54), Al (13.48), Si (27 57), K (2.39) Ca (0.75)« less

Porous Organic Nanolayers for Coating of Solid-state Devices

PubMed Central

2011-01-01

Background Highly hydrophobic surfaces can have very low surface energy and such low surface energy biological interfaces can be obtained using fluorinated coatings on surfaces. Deposition of biocompatible organic films on solid-state surfaces is attained with techniques like plasma polymerization, biomineralization and chemical vapor deposition. All these require special equipment or harsh chemicals. This paper presents a simple vapor-phase approach to directly coat solid-state surfaces with biocompatible films without any harsh chemical or plasma treatment. Hydrophilic and hydrophobic monomers were used for reaction and deposition of nanolayer films. The monomers were characterized and showed a very consistent coating of 3D micropore structures. Results The coating showed nano-textured surface morphology which can aid cell growth and provide rich molecular functionalization. The surface properties of the obtained film were regulated by varying monomer concentrations, reaction time and the vacuum pressure in a simple reaction chamber. Films were characterized by contact angle analysis for surface energy and with profilometer to measure the thickness. Fourier Transform Infrared Spectroscopy (FTIR) analysis revealed the chemical composition of the coated films. Variations in the FTIR results with respect to different concentrations of monomers showed the chemical composition of the resulting films. Conclusion The presented approach of vapor-phase coating of solid-state structures is important and applicable in many areas of bio-nano interface development. The exposure of coatings to the solutions of different pH showed the stability of the coatings in chemical surroundings. The organic nanocoating of films can be used in bio-implants and many medical devices. PMID:21569579

Fracture Analysis of Cast Steel Sling

NASA Astrophysics Data System (ADS)

Li, Xinghui

2018-02-01

The fracture reasons of ZG270-500 cast steel sling are analyzed through such means as macroscopic morphology analysis, chemical composition analysis, and microscopic metallography analysis. Results: coarse Widmanstatten structure and casting defects occurring in casting and subsequent heat treatment process reduce the strength, plasticity and toughness of the steel, which is the main reason of brittle fracture of the sling during work, and corresponding improvement suggestions are proposed herein.

In silico designing of power conversion efficient organic lead dyes for solar cells using todays innovative approaches to assure renewable energy for future

NASA Astrophysics Data System (ADS)

Kar, Supratik; Roy, Juganta K.; Leszczynski, Jerzy

2017-06-01

Advances in solar cell technology require designing of new organic dye sensitizers for dye-sensitized solar cells with high power conversion efficiency to circumvent the disadvantages of silicon-based solar cells. In silico studies including quantitative structure-property relationship analysis combined with quantum chemical analysis were employed to understand the primary electron transfer mechanism and photo-physical properties of 273 arylamine organic dyes from 11 diverse chemical families explicit to iodine electrolyte. The direct quantitative structure-property relationship models enable identification of the essential electronic and structural attributes necessary for quantifying the molecular prerequisites of 11 classes of arylamine organic dyes, responsible for high power conversion efficiency of dye-sensitized solar cells. Tetrahydroquinoline, N,N'-dialkylaniline and indoline have been least explored classes under arylamine organic dyes for dye-sensitized solar cells. Therefore, the identified properties from the corresponding quantitative structure-property relationship models of the mentioned classes were employed in designing of "lead dyes". Followed by, a series of electrochemical and photo-physical parameters were computed for designed dyes to check the required variables for electron flow of dye-sensitized solar cells. The combined computational techniques yielded seven promising lead dyes each for all three chemical classes considered. Significant (130, 183, and 46%) increment in predicted %power conversion efficiency was observed comparing with the existing dye with highest experimental %power conversion efficiency value for tetrahydroquinoline, N,N'-dialkylaniline and indoline, respectively maintaining required electrochemical parameters.

Tuning chemical and physical cross-links in silk electrogels for morphological analysis and mechanical reinforcement.

PubMed

Lin, Yinan; Xia, Xiaoxia; Shang, Ke; Elia, Roberto; Huang, Wenwen; Cebe, Peggy; Leisk, Gary; Omenetto, Fiorenzo; Kaplan, David L

2013-08-12

Electrochemically controlled, reversible assembly of biopolymers into hydrogel structures is a promising technique for on-demand cell or drug encapsulation and release systems. An electrochemically sol-gel transition has been demonstrated in regenerated Bombyx mori silk fibroin, offering a controllable way to generate biocompatible and reversible adhesives and other biomedical materials. Despite the involvement of an electrochemically triggered electrophoretic migration of the silk molecules, the mechanism of the reversible electrogelation remains unclear. It is, however, known that the freshly prepared silk electrogels (e-gels) adopt a predominantly random coil conformation, indicating a lack of cross-linking as well as thermal, mechanical, and morphological stabilities. In the present work, the tuning of covalent and physical β-sheet cross-links in silk hydrogels was studied for programming the structural properties. Scanning electron microscopy (SEM) revealed delicate morphology, including locally aligned fibrillar structures, in silk e-gels, preserved by combining glutaraldehyde-cross-linking and ethanol dehydration. Fourier transform infrared (FTIR) spectroscopic analysis of either electrogelled, vortex-induced or spontaneously formed silk hydrogels showed that the secondary structure of silk e-gels was tunable between non-β-sheet-dominated and β-sheet-dominated states. Dynamic oscillatory rheology confirmed the mechanical reinforcement of silk e-gels provided by controlled chemical and physical cross-links. The selective incorporation of either chemical or physical or both cross-links into the electrochemically responsive, originally unstructured silk e-gel should help in the design for electrochemically responsive protein polymers.

Self-assembling iron oxyhydroxide/oxide tubular structures: laboratory-grown and field examples from Rio Tinto.

PubMed

Barge, Laura M; Cardoso, Silvana S S; Cartwright, Julyan H E; Doloboff, Ivria J; Flores, Erika; Macías-Sánchez, Elena; Sainz-Díaz, C Ignacio; Sobrón, Pablo

2016-11-01

Rio Tinto in southern Spain has become of increasing astrobiological significance, in particular for its similarity to environments on early Mars. We present evidence of tubular structures from sampled terraces in the stream bed at the source of the river, as well as ancient, now dry, terraces. This is the first reported finding of tubular structures in this particular environment. We propose that some of these structures could be formed through self-assembly via an abiotic mechanism involving templated precipitation around a fluid jet, a similar mechanism to that commonly found in so-called chemical gardens. Laboratory experiments simulating the formation of self-assembling iron oxyhydroxide tubes via chemical garden/chemobrionic processes form similar structures. Fluid-mechanical scaling analysis demonstrates that the proposed mechanism is plausible. Although the formation of tube structures is not itself a biosignature, the iron mineral oxidation gradients across the tube walls in laboratory and field examples may yield information about energy gradients and potentially habitable environments.

Self-assembling iron oxyhydroxide/oxide tubular structures: laboratory-grown and field examples from Rio Tinto

PubMed Central

Barge, Laura M.; Doloboff, Ivria J.; Flores, Erika; Sobrón, Pablo

2016-01-01

Rio Tinto in southern Spain has become of increasing astrobiological significance, in particular for its similarity to environments on early Mars. We present evidence of tubular structures from sampled terraces in the stream bed at the source of the river, as well as ancient, now dry, terraces. This is the first reported finding of tubular structures in this particular environment. We propose that some of these structures could be formed through self-assembly via an abiotic mechanism involving templated precipitation around a fluid jet, a similar mechanism to that commonly found in so-called chemical gardens. Laboratory experiments simulating the formation of self-assembling iron oxyhydroxide tubes via chemical garden/chemobrionic processes form similar structures. Fluid-mechanical scaling analysis demonstrates that the proposed mechanism is plausible. Although the formation of tube structures is not itself a biosignature, the iron mineral oxidation gradients across the tube walls in laboratory and field examples may yield information about energy gradients and potentially habitable environments. PMID:27956875

Structure activity studies of an analgesic drug tapentadol hydrochloride by spectroscopic and quantum chemical methods

NASA Astrophysics Data System (ADS)

Arjunan, V.; Santhanam, R.; Marchewka, M. K.; Mohan, S.; Yang, Haifeng

2015-11-01

Tapentadol is a novel opioid pain reliever drug with a dual mechanism of action, having potency between morphine and tramadol. Quantum chemical calculations have been carried out for tapentadol hydrochloride (TAP.Cl) to determine the properties. The geometry is optimised and the structural properties of the compound were determined from the optimised geometry by B3LYP method using 6-311++G(d,p), 6-31G(d,p) and cc-pVDZ basis sets. FT-IR and FT-Raman spectra are recorded in the solid phase in the region of 4000-400 and 4000-100 cm-1, respectively. Frontier molecular orbital energies, LUMO-HOMO energy gap, ionisation potential, electron affinity, electronegativity, hardness and chemical potential are also calculated. The stability of the molecule arising from hyperconjugative interactions and charge delocalisation has been analysed using NBO analysis. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule are analysed.

In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

PubMed

Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

2016-10-24

The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ari-Gur, Pnina; Garlea, Vasile O.; Cao, Huibo

In this study, Heusler alloys of Ni-Mn-Ga compositions demonstrate ferromagnetic shape memory effect in the martensitic state. The transformation temperature and the chemical order depend strongly on the composition. In the current work, the structure and chemical order of the martensitic phase of Ni 1.91Mn 1.29Ga 0.8 were studied using neutron diffraction; the diffraction pattern was refined using the FullProf software. It was determined that the structural transition occurs around 330 K. At room temperature, 300 K, which is below the martensite transformation temperature, all the Bragg reflections can be described by a monoclinic lattice with a symmetry of spacemore » group P 1 2/m 1 and lattice constants of a = 4.23047(7) [Å], b = 5.58333(6) [Å], c = 21.0179(2) [Å], beta = 90.328(1). The chemical order is of critical importance in these alloys, and it was previously studied at 363 K. Analysis of the neutron diffraction in the monoclinic phase shows that the chemical order is maintained during the martensitic transformation.« less

Biodegradation of the chitin-protein complex in crustacean cuticle

USGS Publications Warehouse

Artur, Stankiewicz B.; Mastalerz, Maria; Hof, C.H.J.; Bierstedt, A.; Flannery, M.B.; Briggs, D.E.G.; Evershed, R.P.

1998-01-01

Arthropod cuticles consist predominantly of chitin cross-linked with proteins. While there is some experimental evidence that this chitin-protein complex may resist decay, the chemical changes that occur during degradation have not been investigated in detail. The stomatopod crustacean Neogonodactylus oerstedii was decayed in the laboratory under anoxic conditions. A combination of pyrolysis-gas chromatography/mass spectrometry and FTIR revealed extensive chemical changes after just 2 weeks that resulted in a cuticle composition dominated by chitin. Quantitative analysis of amino acids (by HPLC) and chitin showed that the major loss of proteins and chitin occurred between weeks 1 and 2. After 8 weeks tyrosine, tryptophan and valine are the most prominent amino acid moieties, showing their resistance to degradation. The presence of cyclic ketones in the pyrolysates indicates that mucopolysaccharides or other bound non-chitinous carbohydrates are also resistant to decay. There is no evidence of structural degradation of chitin prior to 8 weeks when FTIR revealed a reduction in chitin-specific bands. The chemical changes are paralleled by structural changes in the cuticle, which becomes an increasingly open structure consisting of loose chitinous fibres. The rapid rate of decay in the experiments suggests that where chitin and protein are preserved in fossil cuticles degradation must have been inhibited.Arthropod cuticles consist predominantly of chitin cross-linked with proteins. While there is some experimental evidence that this chitin-protein complex may resist decay, the chemical changes that occur during degradation have not been investigated in detail. The stomatopod crustacean Neogonodactylus oerstedii was decayed in the laboratory under anoxic conditions. A combination of pyrolysis-gas chromatography/mass spectrometry and FTIR revealed extensive chemical changes after just 2 weeks that resulted in a cuticle composition dominated by chitin. Quantitative analysis of amino acids (by HPLC) and chitin showed that the major loss of proteins and chitin occurred between weeks 1 and 2. After 8 weeks tyrosine, tryptophan and valine are the most prominent amino acid moieties, showing their resistance to degradation. The presence of cyclic ketones in the pyrolysates indicates that mucopolysaccharides or other bound non-chitinous carbohydrates are also resistant to decay. There is no evidence of structural degradation of chitin prior to 8 weeks when FTIR revealed a reduction in chitin-specific bands. The chemical changes are paralleled by structural changes in the cuticle, which becomes an increasingly open structure consisting of loose chitinous fibres. The rapid rate of decay in the experiments suggests, that where chitin and protein are preserved in fossil cuticles degradation must have been inhibited.

Calculating the dermal flux of chemicals with OELs based on their molecular structure: An attempt to assign the skin notation.

PubMed

Kupczewska-Dobecka, Małgorzata; Jakubowski, Marek; Czerczak, Sławomir

2010-09-01

Our objectives included calculating the permeability coefficient and dermal penetration rates (flux value) for 112 chemicals with occupational exposure limits (OELs) according to the LFER (linear free-energy relationship) model developed using published methods. We also attempted to assign skin notations based on each chemical's molecular structure. There are many studies available where formulae for coefficients of permeability from saturated aqueous solutions (K(p)) have been related to physicochemical characteristics of chemicals. The LFER model is based on the solvation equation, which contains five main descriptors predicted from chemical structure: solute excess molar refractivity, dipolarity/polarisability, summation hydrogen bond acidity and basicity, and the McGowan characteristic volume. Descriptor values, available for about 5000 compounds in the Pharma Algorithms Database were used to calculate permeability coefficients. Dermal penetration rate was estimated as a ratio of permeability coefficient and concentration of chemical in saturated aqueous solution. Finally, estimated dermal penetration rates were used to assign the skin notation to chemicals. Defined critical fluxes defined from the literature were recommended as reference values for skin notation. The application of Abraham descriptors predicted from chemical structure and LFER analysis in calculation of permeability coefficients and flux values for chemicals with OELs was successful. Comparison of calculated K(p) values with data obtained earlier from other models showed that LFER predictions were comparable to those obtained by some previously published models, but the differences were much more significant for others. It seems reasonable to conclude that skin should not be characterised as a simple lipophilic barrier alone. Both lipophilic and polar pathways of permeation exist across the stratum corneum. It is feasible to predict skin notation on the basis of the LFER and other published models; from among 112 chemicals 94 (84%) should have the skin notation in the OEL list based on the LFER calculations. The skin notation had been estimated by other published models for almost 94% of the chemicals. Twenty-nine (25.8%) chemicals were identified to have significant absorption and 65 (58%) the potential for dermal toxicity. We found major differences between alternative published analytical models and their ability to determine whether particular chemicals were potentially dermotoxic. Copyright © 2010 Elsevier B.V. All rights reserved.

Quantitative Chemical Imaging and Unsupervised Analysis Using Hyperspectral Coherent Anti-Stokes Raman Scattering Microscopy

PubMed Central

2013-01-01

In this work, we report a method to acquire and analyze hyperspectral coherent anti-Stokes Raman scattering (CARS) microscopy images of organic materials and biological samples resulting in an unbiased quantitative chemical analysis. The method employs singular value decomposition on the square root of the CARS intensity, providing an automatic determination of the components above noise, which are retained. Complex CARS susceptibility spectra, which are linear in the chemical composition, are retrieved from the CARS intensity spectra using the causality of the susceptibility by two methods, and their performance is evaluated by comparison with Raman spectra. We use non-negative matrix factorization applied to the imaginary part and the nonresonant real part of the susceptibility with an additional concentration constraint to obtain absolute susceptibility spectra of independently varying chemical components and their absolute concentration. We demonstrate the ability of the method to provide quantitative chemical analysis on known lipid mixtures. We then show the relevance of the method by imaging lipid-rich stem-cell-derived mouse adipocytes as well as differentiated embryonic stem cells with a low density of lipids. We retrieve and visualize the most significant chemical components with spectra given by water, lipid, and proteins segmenting the image into the cell surrounding, lipid droplets, cytosol, and the nucleus, and we reveal the chemical structure of the cells, with details visualized by the projection of the chemical contrast into a few relevant channels. PMID:24099603

Toxicokinetic Triage for Environmental Chemicals | Science ...

EPA Pesticide Factsheets

Toxicokinetic (TK) models are essential for linking administered doses to blood and tissue concentrations. In vitro-to-in vivo extrapolation (IVIVE) methods have been developed to determine TK from limited in vitro measurements and chemical structure-based property predictions, providing a less resource–intensive alternative to traditional in vivo TK approaches. High throughput TK (HTTK) methods use IVIVE to estimate doses that produce steady-state plasma concentrations equivalent to those producing biological activity in in vitro screening studies (e.g., ToxCast). In this study, the domain of applicability and assumptions of HTTK approaches were evaluated using both in vivo data and simulation analysis. Based on in vivo data for 87 chemicals, specific properties (e.g., in vitro HTTK data, physico-chemical descriptors, chemical structure, and predicted transporter affinities) were identified that correlate with poor HTTK predictive ability. For 350 xenobiotics with literature HTTK data, we then differentiated those xenobiotics for which HTTK approaches are likely to be sufficient, from those that may require additional data. For 272 chemicals we also developed a HT physiologically-based TK (HTPBTK) model that requires somewhat greater information than a steady-state model, but allows non-steady state dynamics and can predict chemical concentration time-courses for a variety of exposure scenarios, tissues, and species. We used this HTPBTK model to show that the

Identification of the chemical constituents of Chinese medicine Yi-Xin-Shu capsule by molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation.

PubMed

Wang, Hong-ping; Chen, Chang; Liu, Yan; Yang, Hong-Jun; Wu, Hong-Wei; Xiao, Hong-Bin

2015-11-01

The incomplete identification of the chemical components of traditional Chinese medicinal formula has been one of the bottlenecks in the modernization of traditional Chinese medicine. Tandem mass spectrometry has been widely used for the identification of chemical substances. Current automatic tandem mass spectrometry acquisition, where precursor ions were selected according to their signal intensity, encounters a drawback in chemical substances identification when samples contain many overlapping signals. Compounds in minor or trace amounts could not be identified because most tandem mass spectrometry information was lost. Herein, a molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation method for complex Chinese medicine chemical constituent analysis was developed. The precursor ions were selected according to their two-dimensional characteristics of retention times and mass-to-charge ratio ranges from herbal compounds, so that all precursor ions from herbal compounds were included and more minor chemical constituents in Chinese medicine were identified. Compared to the conventional automatic tandem mass spectrometry setups, the approach is novel and can overcome the drawback for chemical substances identification. As an example, 276 compounds from the Chinese Medicine of Yi-Xin-Shu capsule were identified. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Primary and secondary structural analyses of glutathione S-transferase pi from human placenta.

PubMed

Ahmad, H; Wilson, D E; Fritz, R R; Singh, S V; Medh, R D; Nagle, G T; Awasthi, Y C; Kurosky, A

1990-05-01

The primary structure of glutathione S-transferase (GST) pi from a single human placenta was determined. The structure was established by chemical characterization of tryptic and cyanogen bromide peptides as well as automated sequence analysis of the intact enzyme. The structural analysis indicated that the protein is comprised of 209 amino acid residues and gave no evidence of post-translational modifications. The amino acid sequence differed from that of the deduced amino acid sequence determined by nucleotide sequence analysis of a cDNA clone (Kano, T., Sakai, M., and Muramatsu, M., 1987, Cancer Res. 47, 5626-5630) at position 104 which contained both valine and isoleucine whereas the deduced sequence from nucleotide sequence analysis identified only isoleucine at this position. These results demonstrated that in the one individual placenta studied at least two GST pi genes are coexpressed, probably as a result of allelomorphism. Computer assisted consensus sequence evaluation identified a hydrophobic region in GST pi (residues 155-181) that was predicted to be either a buried transmembrane helical region or a signal sequence region. The significance of this hydrophobic region was interpreted in relation to the mode of action of the enzyme especially in regard to the potential involvement of a histidine in the active site mechanism. A comparison of the chemical similarity of five known human GST complete enzyme structures, one of pi, one of mu, two of alpha, and one microsomal, gave evidence that all five enzymes have evolved by a divergent evolutionary process after gene duplication, with the microsomal enzyme representing the most divergent form.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis.

PubMed

Stauch, Tim; Dreuw, Andreas

2016-11-23

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Structural changes in gluten protein structure after addition of emulsifier. A Raman spectroscopy study

NASA Astrophysics Data System (ADS)

Ferrer, Evelina G.; Gómez, Analía V.; Añón, María C.; Puppo, María C.

2011-06-01

Food protein product, gluten protein, was chemically modified by varying levels of sodium stearoyl lactylate (SSL); and the extent of modifications (secondary and tertiary structures) of this protein was analyzed by using Raman spectroscopy. Analysis of the Amide I band showed an increase in its intensity mainly after the addition of the 0.25% of SSL to wheat flour to produced modified gluten protein, pointing the formation of a more ordered structure. Side chain vibrations also confirmed the observed changes.

Crystal Structure Prediction via Deep Learning.

PubMed

Ryan, Kevin; Lengyel, Jeff; Shatruk, Michael

2018-06-06

We demonstrate the application of deep neural networks as a machine-learning tool for the analysis of a large collection of crystallographic data contained in the crystal structure repositories. Using input data in the form of multi-perspective atomic fingerprints, which describe coordination topology around unique crystallographic sites, we show that the neural-network model can be trained to effectively distinguish chemical elements based on the topology of their crystallographic environment. The model also identifies structurally similar atomic sites in the entire dataset of ~50000 crystal structures, essentially uncovering trends that reflect the periodic table of elements. The trained model was used to analyze templates derived from the known binary and ternary crystal structures in order to predict the likelihood to form new compounds that could be generated by placing elements into these structural templates in combinatorial fashion. Statistical analysis of predictive performance of the neural-network model, which was applied to a test set of structures never seen by the model during training, indicates its ability to predict known elemental compositions with a high likelihood of success. In ~30% of cases, the known compositions were found among top-10 most likely candidates proposed by the model. These results suggest that the approach developed in this work can be used to effectively guide the synthetic efforts in the discovery of new materials, especially in the case of systems composed of 3 or more chemical elements.

Sensitive sub-Doppler nonlinear spectroscopy for hyperfine-structure analysis using simple atomizers

NASA Astrophysics Data System (ADS)

Mickadeit, Fritz K.; Kemp, Helen; Schafer, Julia; Tong, William M.

1998-05-01

Laser wave-mixing spectroscopy is presented as a sub-Doppler method that offers not only high spectral resolution, but also excellent detection sensitivity. It offers spectral resolution suitable for hyperfine structure analysis and isotope ratio measurements. In a non-planar backward- scattering four-wave mixing optical configuration, two of the three input beams counter propagate and the Doppler broadening is minimized, and hence, spectral resolution is enhanced. Since the signal is a coherent beam, optical collection is efficient and signal detection is convenient. This simple multi-photon nonlinear laser method offers un usually sensitive detection limits that are suitable for trace-concentration isotope analysis using a few different types of simple analytical atomizers. Reliable measurement of hyperfine structures allows effective determination of isotope ratios for chemical analysis.

Tantalum protective coatings for fusion reactor applications

NASA Astrophysics Data System (ADS)

Brossa, Francesco; Piatti, Giovanni; Bardy, Michel

Tantalum has a very low sputtering yield, high melting point, low vapour pressure and good mechanical properties at low and high temperatures, so it is a very interesting candidate for the first wall and blanket structural components. Tantalum coatings overcome the problems of fabrication and joining bulk Ta, thus reducing also dead weight and cost. Ta coatings were produced by chemical vapour deposition and plasma spraying on four conventional structural materials: Al, Cu, AISI 316 L and Inconel 600. The conditions which improve adherence have been studied. The composition of the films was determined by chemical means and by X-ray analysis. Metallographie examination was employed to define the morphological structure of the deposits. The adherence of the coatings was determined by subjecting the samples to bend tests and to thermal shocks.

Structural and optical characterization of self-assembled Ge nanocrystal layers grown by plasma-enhanced chemical vapor deposition.

PubMed

Saeed, Saba; Buters, Frank; Dohnalova, Katerina; Wosinski, Lech; Gregorkiewicz, Tom

2014-10-10

We present a structural and optical study of solid-state dispersions of Ge nanocrystals prepared by plasma-enhanced chemical vapor deposition. Structural analysis shows the presence of nanocrystalline germanium inclusions embedded in an amorphous matrix of Si-rich SiO(2).Optical characterization reveals two prominent emission bands centered around 2.6 eV and 3.4 eV, and tunable by excitation energy. In addition, the lower energy band shows an excitation power-dependent blue shift of up to 0.3 eV. Decay dynamics of the observed emission contains fast (nanosecond) and slow (microseconds) components, indicating contributions of several relaxation channels. Based on these material characteristics, a possible microscopic origin of the individual emission bands is discussed.

Mapping of Drug-like Chemical Universe with Reduced Complexity Molecular Frameworks.

PubMed

Kontijevskis, Aleksejs

2017-04-24

The emergence of the DNA-encoded chemical libraries (DEL) field in the past decade has attracted the attention of the pharmaceutical industry as a powerful mechanism for the discovery of novel drug-like hits for various biological targets. Nuevolution Chemetics technology enables DNA-encoded synthesis of billions of chemically diverse drug-like small molecule compounds, and the efficient screening and optimization of these, facilitating effective identification of drug candidates at an unprecedented speed and scale. Although many approaches have been developed by the cheminformatics community for the analysis and visualization of drug-like chemical space, most of them are restricted to the analysis of a maximum of a few millions of compounds and cannot handle collections of 10 8 -10 12 compounds typical for DELs. To address this big chemical data challenge, we developed the Reduced Complexity Molecular Frameworks (RCMF) methodology as an abstract and very general way of representing chemical structures. By further introducing RCMF descriptors, we constructed a global framework map of drug-like chemical space and demonstrated how chemical space occupied by multi-million-member drug-like Chemetics DNA-encoded libraries and virtual combinatorial libraries with >10 12 members could be analyzed and mapped without a need for library enumeration. We further validate the approach by performing RCMF-based searches in a drug-like chemical universe and mapping Chemetics library selection outputs for LSD1 targets on a global framework chemical space map.

Observations of Pre-Stellar Cores

NASA Astrophysics Data System (ADS)

Tafalla, M.

2005-08-01

Our understanding of the physical and chemical structure of pre-stellar cores, the simplest star-forming sites, has significantly improved since the last IAU Symposium on Astrochemistry (South Korea, 1999). Research done over these years has revealed that major molecular species like CO and CS systematically deplete onto dust grains in the interior of pre-stellar cores, while species like N2H+ and NH3 survive in the gas phase and can usually be detected toward the core centers. Such a selective behavior of molecular species gives rise to a differentiated (onion-like) chemical composition, and manifests itself in molecular maps as a dichotomy between centrally peaked and ring-shaped distributions. From the point of view of star-formation studies, the identification of molecular inhomogeneities in cores helps to resolve past discrepancies between observations made using different tracers, and brings the possibility of self-consistent modelling of the core internal structure. Here I present recent work on determining the physical and chemical structure of two pre-stellar cores, L1498 and L1517B, using observations in a large number of molecules and Monte Carlo radiative transfer analysis. These two cores are typical examples of the pre-stellar core population, and their chemical composition is characterized by the presence of large `freeze out holes' in most molecular species. In contrast with these chemically processed objects, a new population of chemically young cores has begun to emerge. The characteristics of its most extreme representative, L1521E, are briefly reviewed.

Development of TLSER model and QSAR model for predicting partition coefficients of hydrophobic organic chemicals between low density polyethylene film and water.

PubMed

Liu, Huihui; Wei, Mengbi; Yang, Xianhai; Yin, Cen; He, Xiao

2017-01-01

Partition coefficients are vital parameters for measuring accurately the chemicals concentrations by passive sampling devices. Given the wide use of low density polyethylene (LDPE) film in passive sampling, we developed a theoretical linear solvation energy relationship (TLSER) model and a quantitative structure-activity relationship (QSAR) model for the prediction of the partition coefficient of chemicals between LDPE and water (K pew ). For chemicals with the octanol-water partition coefficient (log K ow ) <8, a TLSER model with V x (McGowan volume) and qA - (the most negative charge on O, N, S, X atoms) as descriptors was developed, but the model had relatively low determination coefficient (R 2 ) and cross-validated coefficient (Q 2 ). In order to further explore the theoretical mechanisms involved in the partition process, a QSAR model with four descriptors (MLOGP (Moriguchi octanol-water partition coeff.), P_VSA_s_3 (P_VSA-like on I-state, bin 3), Hy (hydrophilic factor) and NssO (number of atoms of type ssO)) was established, and statistical analysis indicated that the model had satisfactory goodness-of-fit, robustness and predictive ability. For chemicals with log K OW >8, a TLSER model with V x and a QSAR model with MLOGP as descriptor were developed. This is the first paper to explore the models for highly hydrophobic chemicals. The applicability domain of the models, characterized by the Euclidean distance-based method and Williams plot, covered a large number of structurally diverse chemicals, which included nearly all the common hydrophobic organic compounds. Additionally, through mechanism interpretation, we explored the structural features those governing the partition behavior of chemicals between LDPE and water. Copyright © 2016 Elsevier B.V. All rights reserved.

Carotenoids Database: structures, chemical fingerprints and distribution among organisms.

PubMed

Yabuzaki, Junko

2017-01-01

To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system 'Search similar carotenoids' using our original chemical fingerprint 'Carotenoid DB Chemical Fingerprints'. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool 'Search similar profiled organisms'. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. : http://carotenoiddb.jp. © The Author(s) 2017. Published by Oxford University Press.

Carotenoids Database: structures, chemical fingerprints and distribution among organisms

PubMed Central

2017-01-01

Abstract To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system ‘Search similar carotenoids’ using our original chemical fingerprint ‘Carotenoid DB Chemical Fingerprints’. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool ‘Search similar profiled organisms’. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. Database URL: http://carotenoiddb.jp PMID:28365725

The effect of radiation on the thermal properties of chitosan/mimosa tenuiflora and chitosan/mimosa tenuiflora/multiwalled carbon nanotubes (MWCNT) composites for bone tissue engineering

NASA Astrophysics Data System (ADS)

Martel-Estrada, S. A.; Santos-Rodríguez, E.; Olivas-Armendáriz, I.; Cruz-Zaragoza, E.; Martínez-Pérez, C. A.

2014-07-01

The purpose of this study is to examine the effect of gamma radiation and UV radiation on the microstructure, chemical structure and thermal stability of Chitosan/Mimosa Tenuiflora and Chitosan/Mimosa Tenuiflora/MWCNT composites scaffolds produced by thermally induced phase separation. The composites were irradiated and observed to undergo radiation-induced degradation through chain scission. Morphology, thermal properties and effects on chemical and semi-crystalline structures were obtained by scanning electronic microscopy (SEM), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), FT-IR analysis and X-ray Diffraction. A relationship between radiation type and the thermal stability of the composites, were also established. This relationship allows a more accurate and precise control of the life span of Chitosan/Mimosa Tenuiflora and Chitosan/Mimosa Tenuiflora/MWCNT composites through the use of radiation in materials for use in tissue engineering.

Aging effects on vertical graphene nanosheets and their thermal stability

NASA Astrophysics Data System (ADS)

Ghosh, S.; Polaki, S. R.; Ajikumar, P. K.; Krishna, N. G.; Kamruddin, M.

2018-03-01

The present study investigates environmental aging effects and thermal stability of vertical graphene nanosheets (VGN). Self-organized VGN is synthesized by plasma enhanced chemical vapor deposition and exposed to ambient conditions over 6-month period to examine its aging behavior. A systematic inspection is carried out on morphology, chemical structure, wettability and electrical property by scanning electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, water contact angle and four-probe resistivity measurements at regular intervals, respectively. Detailed microscopic and spectroscopic analysis substantiated the retention of graphitic quality and surface chemistry of VGN over the test period. An unchanged sheet resistance and hydrophobicity reveals its electrical and wetting stability over the time, respectively. Thermogravimetric analysis ensures an excellent thermal stability of VGN up to 575 °C in ambient atmosphere. These findings of long-term morphological, structural, wetting, electrical and thermal stability of VGN validate their potential utilization for the next-generation device applications.

Comprehensive DFT study on molecular structures of Lewisites in support of the Chemical Weapons Convention

NASA Astrophysics Data System (ADS)

Saeidian, Hamid; Sahandi, Morteza

2015-11-01

The structure of all of Lewisite's stereoisomers has been examined by B3LYP/6-311++G(3df,3pd) calculations. The geometry analysis for trans Lewisite L1-1 shows that the calculated bond angles, bond distances and dipole moment have a satisfactory relation compared with experimental values. HOMO-LUMO analysis of Lewisites reveals that L1-2 and L3-7 have the maximum and minimum electrophilicity index, respectively. The calculated chemical shifts were compared with experimental data, showing a very good agreement both for 1H and 13C. The vibrational and Raman frequencies of Lewisites have been precisely assigned and theoretical data were compared with the experimental vibrations. The bonding trends and Mulliken and atomic polar tensor charge distribution in Lewisites can be explained by the Bent's rule and the donor-acceptor interaction, respectively.

A spectroscopic and computational study of Al(III) complexes in sodium cryolite melts: ionic composition in a wide range of cryolite ratios.

PubMed

Nazmutdinov, Renat R; Zinkicheva, Tamara T; Vassiliev, Sergey Yu; Glukhov, Dmitri V; Tsirlina, Galina A; Probst, Michael

2010-04-01

The structure of sodium cryolite melts was studied using Raman spectroscopy and quantum chemical calculations performed at the density functional theory level. The existence of bridged forms in the melts was argued first from the analysis of experimental Raman spectra. In the quantum chemical modelling emphasis was put on the construction of potential energy surfaces describing the formation/dissociation of certain complex species. Effects of the ionic environment were found to play a crucial role in the energetics of model processes. The structure of the simplest possible polymeric forms involving two Al centres linked through F atoms ("dimers") was thoroughly investigated. The calculated equilibrium constants and model Raman spectra yield additional evidence in favour of the dimers. This agrees with a self-consistent analysis of a series of Raman spectra for a wide range of the melt composition. Copyright 2010. Published by Elsevier B.V.

Structure elucidation and chemical synthesis of stigmolone, a novel type of prokaryotic pheromone.

PubMed

Hull, W E; Berkessel, A; Plaga, W

1998-09-15

Approximately 2 micromol of a novel prokaryotic pheromone, involved in starvation-induced aggregation and formation of fruiting bodies by the myxobacterium Stigmatella aurantiaca, were isolated by a large-scale elution procedure. The pheromone was purified by HPLC, and high-resolution MS, IR, 1H-NMR, and 13C-NMR were used to identify the active substance as the hydroxy ketone 2,5, 8-trimethyl-8-hydroxy-nonan-4-one, which has been named stigmolone. The analysis was complicated by a solvent-dependent equilibrium between stigmolone and the cyclic enol-ether 3,4-dihydro-2,2, 5-trimethyl-6-(2-methylpropyl)-2H-pyran formed by intramolecular nucleophilic attack of the 8-OH group at the ketone C4 followed by loss of H2O. Both compounds were synthesized chemically, and their structures were confirmed by NMR analysis. Natural and synthetic stigmolone have the same biological activity at ca. 1 nM concentration.

Definitive Mineralogical Analysis of Mars Analog Rocks Using the CheMin XRD/XRF Instrument

NASA Technical Reports Server (NTRS)

Blake, D. F.; Sarrazin, P.; Bish, D. L.; Feldman, S.; Chipera, S. J.; Vaniman, D. T.; Collins, S.

2004-01-01

Mineral identification is a critical component of Mars Astrobiological missions. Chemical or elemental data alone are not definitive because a single elemental or chemical composition or even a single bonding type can represent a range of substances or mineral assemblages. Minerals are defined as unique structural and compositional phases that occur naturally. There are about 15,000 minerals that have been described on Earth, all uniquely identifiable via diffraction methods. There are likely many minerals yet undiscovered on Earth, and likewise on Mars. If an unknown phase is identified on Mars, it can be fully characterized by structural (X-ray Diffraction, XRD) and elemental analysis (X-ray Fluorescence, XRF) without recourse to other data because XRD relies on the principles of atomic arrangement for its determinations. XRD is the principal means of identification and characterization of minerals on Earth.

3rd annual symposium of chemical and pharmaceutical structure analysis.

PubMed

Weng, Naidong; Zheng, Jenny; Lee, Mike

2012-08-01

The 3rd Annual Symposium on Chemical and Pharmaceutical Structure Analysis was once again held in Shanghai, where a rich history of 'East meets West' continued. This meeting is dedicated to bringing together scientists from pharmaceutical companies, academic institutes, CROs and instrument vendors to discuss current challenges and opportunities on the forefront of pharmaceutical research and development. The diversified symposia and roundtables are highly interactive events where scientists share their experiences and visions in a collegial setting. The symposium highlighted speakers and sessions that provided first-hand experiences as well as the latest guidance and industrial/regulatory thinking, which was reflected by the theme of this year's meeting 'From Bench to Decision Making - from Basics to Application.' In addition to the highly successful Young Scientist Excellence Award, new events were featured at this year's meeting, such as the Executive Roundtable and the inaugural Innovator Award.

Molecular structure, chemical reactivity, nonlinear optical activity and vibrational spectroscopic studies on 6-(4-n-heptyloxybenzyoloxy)-2-hydroxybenzylidene)amino)-2H-chromen-2-one: A combined density functional theory and experimental approach

NASA Astrophysics Data System (ADS)

Pegu, David; Deb, Jyotirmoy; Saha, Sandip Kumar; Paul, Manoj Kumar; Sarkar, Utpal

2018-05-01

In this work, we have synthesized new coumarin Schiff base molecule, viz., 6-(4-n-heptyloxybenzyoloxy)-2-hydroxybenzylidene)amino)-2H-chromen-2-one and characterized its structural, electronic and spectroscopic properties experimentally and theoretically. The theoretical analysis of UV-visible absorption spectra reflects a red shift in the absorption maximum in comparison to the experimental results. Most of the vibrational assignments of infrared and Raman spectra predicted using density functional theory approach match well with the experimental findings. Further, the chemical reactivity analysis confirms that solvent highly affects the reactivity of the studied compound. The large hyperpolarizability value of the compound concludes that the system exhibits significant nonlinear optical features and thus, points out their possibility in designing material with high nonlinear activity.

Preparation, crystal structure, vibrational spectral and density functional studies of bis (4-nitrophenol)-2,4,6-triamino-1,3,5-triazine monohydrate

NASA Astrophysics Data System (ADS)

Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Renganathan, N. G.; Gunasekaran, S.; Anbalagan, G.

2013-10-01

An organic-organic salt, bis (4-nitrophenol) 2,4,6-triamino 1,3,5-triazine monohydrate (BNPM) has been prepared by slow evaporation technique at room temperature. Single crystal X-ray diffraction analysis reveals that the compound crystallizes in triclinic system with centrosymmetric space group P-1. IR and Raman spectra of BNPM have been recorded and analyzed. The study has been extended to confocal Raman spectral analysis. Band assignments have been made for the melamine and p-nitrophenol molecules. Vibrational spectra have also been discussed on the basis of quantum chemical density functional theory calculations using Firefly (PC GAMESS) Version 7.1 G. Vibrational frequencies are calculated and scaled values are compared with the experimental one. The Mulliken charges, HOMO-LUMO orbital energies are calculated and analyzed. The chemical structure of the compound was established by 1H NMR and 13C NMR spectra.

DFT, FT-IR, FT-Raman and NMR studies of 4-(substituted phenylazo)-3,5-diacetamido-1H-pyrazoles

NASA Astrophysics Data System (ADS)

Kınalı, Selin; Demirci, Serkan; Çalışır, Zühre; Kurt, Mustafa; Ataç, Ahmet

2011-05-01

We present a detailed analysis of the structural and vibrational spectra of some novel azo dyes. 2-(Substituted phenylazo)malononitriles were synthesized by the coupling reaction of the diazonium salts, which were prepared with the use of various aniline derivatives with malononitrile, and then 4-(substituted phenylazo)-3,5-diamino-1H-pyrazole azo dyes were obtained via the ring closure of the azo compounds with hydrazine monohydrate. The experimental and theoretical vibrational spectra of azo dyes were studied. The structural and spectroscopic analysis of the molecules were carried out by using Becke's three-parameters hybrid functional (B3LYP) and density functional harmonic calculations. The 1H nuclear magnetic resonance (NMR) chemical shifts of the azo dye molecules were calculated using the gauge-invariant-atomic orbital (GIAO) method. The calculated vibrational wavenumbers and chemical shifts were compared with the experimental data of the molecules.

Phase I Metabolic Stability and Electrophilic Reactivity of 2-Phenylaminophenylacetic Acid Derived Compounds.

PubMed

Pang, Yi Yun; Tan, Yee Min; Chan, Eric Chun Yong; Ho, Han Kiat

2016-07-18

Diclofenac and lumiracoxib are two highly analogous 2-phenylaminophenylacetic acid anti-inflammatory drugs exhibiting occasional dose-limiting hepatotoxicities. Prior data indicate that bioactivation and reactive metabolite formation play roles in the observed toxicity, but the exact chemical influence of the substituents remains elusive. In order to elucidate the role of chemical influence on metabolism related toxicity, metabolic stability and electrophilic reactivity were investigated for a series of structurally related analogues and their resulting metabolites. The resulting analogues embody progressive physiochemical changes through varying halogeno- and aliphatic substituents at two positions and were subjected to in vitro human liver microsomal metabolic stability and cell-based GSH depletion assays (to measure electrophilic reactivity). LC-MS/MS analysis of the GSH trapped reactive intermediates derived from the analogues was then used to identify the putative structures of reactive metabolites. We found that chemical modifications of the structural backbone led to noticeable perturbations of metabolic stability, electrophilic reactivity, and structures and composition of reactive metabolites. With the acquired data, the relationships between stability, reactivity, and toxicity were investigated in an attempt to correlate between Phase I metabolism and in vitro toxicity. A positive correlation was identified between reactivity and in vitro toxicity, indicating that electrophilic reactivity can be an indicator for in vitro toxicity. All in all, the effect of substituents on the structures and reactivity of the metabolites, however subtle the changes, should be taken into consideration during future drug design involving similar chemical features.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

Structural characterization/correlation of calorimetric properties of coal fluids: Final report, September 1, 1985--August 31, 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, IR, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined. 8 refs.« less

Structural characterization/correlation of calorimetric properties of coal fluids: Second annual report, September 1, 1986-August 31, 1987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, ir, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined.« less

Structural characterization/correlation of calorimetric properties of coal fluids. First annual report, September 1, 1985-August 31, 1986

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal liquids and their molecular functional group composition. Coal liquid samples which have had their calorimetric properties measured are characterized using proton NMR, ir and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal liquid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for heat capacities will then be examined within anmore » existing equation of state methodology to determine an optimal correlation. Also, the optimal recipe for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model will be examined and determined. 7 refs.« less

Chemical constituents from aerial part of Curcuma wenyujin.

PubMed

Tao, Zheng-Ming; Li, Ying-Yu; Ji, Ping; Wang, Yu-Bo; Qin, Guo-Wei

2007-12-01

To investigate the chemical constituents from aerial part of Curcuma wenyujin. Compounds were isolated by repeated column chromatography on silica gel. Their structures were elucidated on the basis of spectral analysis and comparison with literature data. Six compounds were isolated and identified as codonolactone (1), voleneol (2), octacosanoic acid (3), beta-sitosterol (4), mangdesisterol (5), and daucosterol (6). Compounds 1, 2, and 5 were isolated from the plant for the first time.

New antitumour fungal metabolites from Alternaria porri.

PubMed

Phuwapraisirisan, Preecha; Rangsan, Jakaphan; Siripong, Pongpan; Tip-Pyang, Santi

2009-01-01

Chemical investigation of the onion pathogenic fungus Alternaria porri resulted in the isolation of two new phthalides named zinnimide (2) and deprenylzinnimide (8), along with a new bianthraquinone, alterporriol F (10). The structures of the new metabolites were characterised by spectroscopic analysis and chemical degradation. Of the new compounds isolated, alterporriol F was highly cytotoxic towards HeLa and KB cells, with IC(50) values of 6.5 and 7.0 microg mL(-1).

A strategy to improve the identification reliability of the chemical constituents by high-resolution mass spectrometry-based isomer structure prediction combined with a quantitative structure retention relationship analysis: Phthalide compounds in Chuanxiong as a test case.

PubMed

Zhang, Qingqing; Huo, Mengqi; Zhang, Yanling; Qiao, Yanjiang; Gao, Xiaoyan

2018-06-01

High-resolution mass spectrometry (HRMS) provides a powerful tool for the rapid analysis and identification of compounds in herbs. However, the diversity and large differences in the content of the chemical constituents in herbal medicines, especially isomerisms, are a great challenge for mass spectrometry-based structural identification. In the current study, a new strategy for the structural characterization of potential new phthalide compounds was proposed by isomer structure predictions combined with a quantitative structure-retention relationship (QSRR) analysis using phthalide compounds in Chuanxiong as an example. This strategy consists of three steps. First, the structures of phthalide compounds were reasonably predicted on the basis of the structure features and MS/MS fragmentation patterns: (1) the collected raw HRMS data were preliminarily screened by an in-house database; (2) the MS/MS fragmentation patterns of the analogous compounds were summarized; (3) the reported phthalide compounds were identified, and the structures of the isomers were reasonably predicted. Second, the QSRR model was established and verified using representative phthalide compound standards. Finally, the retention times of the predicted isomers were calculated by the QSRR model, and the structures of these peaks were rationally characterized by matching retention times of the detected chromatographic peaks and the predicted isomers. A multiple linear regression QSRR model in which 6 physicochemical variables were screened was built using 23 phthalide standards. The retention times of the phthalide isomers in Chuanxiong were well predicted by the QSRR model combined with reasonable structure predictions (R 2 =0.955). A total of 81 peaks were detected from Chuanxiong and assigned to reasonable structures, and 26 potential new phthalide compounds were structurally characterized. This strategy can improve the identification efficiency and reliability of homologues in complex materials. Copyright © 2018 Elsevier B.V. All rights reserved.

Discrimination Enhancement with Transient Feature Analysis of a Graphene Chemical Sensor.

PubMed

Nallon, Eric C; Schnee, Vincent P; Bright, Collin J; Polcha, Michael P; Li, Qiliang

2016-01-19

A graphene chemical sensor is subjected to a set of structurally and chemically similar hydrocarbon compounds consisting of toluene, o-xylene, p-xylene, and mesitylene. The fractional change in resistance of the sensor upon exposure to these compounds exhibits a similar response magnitude among compounds, whereas large variation is observed within repetitions for each compound, causing a response overlap. Therefore, traditional features depending on maximum response change will cause confusion during further discrimination and classification analysis. More robust features that are less sensitive to concentration, sampling, and drift variability would provide higher quality information. In this work, we have explored the advantage of using transient-based exponential fitting coefficients to enhance the discrimination of similar compounds. The advantages of such feature analysis to discriminate each compound is evaluated using principle component analysis (PCA). In addition, machine learning-based classification algorithms were used to compare the prediction accuracies when using fitting coefficients as features. The additional features greatly enhanced the discrimination between compounds while performing PCA and also improved the prediction accuracy by 34% when using linear discrimination analysis.

Scanning photoelectron microscope for nanoscale three-dimensional spatial-resolved electron spectroscopy for chemical analysis.

PubMed

Horiba, K; Nakamura, Y; Nagamura, N; Toyoda, S; Kumigashira, H; Oshima, M; Amemiya, K; Senba, Y; Ohashi, H

2011-11-01

In order to achieve nondestructive observation of the three-dimensional spatially resolved electronic structure of solids, we have developed a scanning photoelectron microscope system with the capability of depth profiling in electron spectroscopy for chemical analysis (ESCA). We call this system 3D nano-ESCA. For focusing the x-ray, a Fresnel zone plate with a diameter of 200 μm and an outermost zone width of 35 nm is used. In order to obtain the angular dependence of the photoelectron spectra for the depth-profile analysis without rotating the sample, we adopted a modified VG Scienta R3000 analyzer with an acceptance angle of 60° as a high-resolution angle-resolved electron spectrometer. The system has been installed at the University-of-Tokyo Materials Science Outstation beamline, BL07LSU, at SPring-8. From the results of the line-scan profiles of the poly-Si/high-k gate patterns, we achieved a total spatial resolution better than 70 nm. The capability of our system for pinpoint depth-profile analysis and high-resolution chemical state analysis is demonstrated. © 2011 American Institute of Physics

Detection of anabolic androgenic steroid abuse in doping control using mammalian reporter gene bioassays.

PubMed

Houtman, Corine J; Sterk, Saskia S; van de Heijning, Monique P M; Brouwer, Abraham; Stephany, Rainer W; van der Burg, Bart; Sonneveld, Edwin

2009-04-01

Anabolic androgenic steroids (AAS) are a class of steroid hormones related to the male hormone testosterone. They are frequently detected as drugs in sport doping control. Being similar to or derived from natural male hormones, AAS share the activation of the androgen receptor (AR) as common mechanism of action. The mammalian androgen responsive reporter gene assay (AR CALUX bioassay), measuring compounds interacting with the AR can be used for the analysis of AAS without the necessity of knowing their chemical structure beforehand, whereas current chemical-analytical approaches may have difficulty in detecting compounds with unknown structures, such as designer steroids. This study demonstrated that AAS prohibited in sports and potential designer AAS can be detected with this AR reporter gene assay, but that also additional steroid activities of AAS could be found using additional mammalian bioassays for other types of steroid hormones. Mixtures of AAS were found to behave additively in the AR reporter gene assay showing that it is possible to use this method for complex mixtures as are found in doping control samples, including mixtures that are a result of multi drug use. To test if mammalian reporter gene assays could be used for the detection of AAS in urine samples, background steroidal activities were measured. AAS-spiked urine samples, mimicking doping positive samples, showed significantly higher androgenic activities than unspiked samples. GC-MS analysis of endogenous androgens and AR reporter gene assay analysis of urine samples showed how a combined chemical-analytical and bioassay approach can be used to identify samples containing AAS. The results indicate that the AR reporter gene assay, in addition to chemical-analytical methods, can be a valuable tool for the analysis of AAS for doping control purposes.

Prediction of biodegradability from chemical structure: Modeling or ready biodegradation test data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loonen, H.; Lindgren, F.; Hansen, B.

1999-08-01

Biodegradation data were collected and evaluated for 894 substances with widely varying chemical structures. All data were determined according to the Japanese Ministry of International Trade and Industry (MITI) I test protocol. The MITI I test is a screening test for ready biodegradability and has been described by Organization for Economic Cooperation and Development (OECD) test guideline 301 C and European Union (EU) test guideline C4F. The chemicals were characterized by a set of 127 predefined structural fragments. This data set was used to develop a model for the prediction of the biodegradability of chemicals under standardized OECD and EUmore » ready biodegradation test conditions. Partial least squares (PLS) discriminant analysis was used for the model development. The model was evaluated by means of internal cross-validation and repeated external validation. The importance of various structural fragments and fragment interactions was investigated. The most important fragments include the presence of a long alkyl chain; hydroxy, ester, and acid groups (enhancing biodegradation); and the presence of one or more aromatic rings and halogen substituents (regarding biodegradation). More than 85% of the model predictions were correct for using the complete data set. The not readily biodegradable predictions were slightly better than the readily biodegradable predictions (86 vs 84%). The average percentage of correct predictions from four external validation studies was 83%. Model optimization by including fragment interactions improve the model predicting capabilities to 89%. It can be concluded that the PLS model provides predictions of high reliability for a diverse range of chemical structures. The predictions conform to the concept of readily biodegradable (or not readily biodegradable) as defined by OECD and EU test guidelines.« less

Use of thermal analysis coupled with differential scanning calorimetry, quadrupole mass spectrometry and infrared spectroscopy (TG-DSC-QMS-FTIR) to monitor chemical properties and thermal stability of fulvic and humic acids.

PubMed

Boguta, Patrycja; Sokołowska, Zofia; Skic, Kamil

2017-01-01

Thermogravimetry-coupled with differential scanning calorimetry, quadrupole mass spectrometry, and Fourier-transform infrared spectroscopy (TG-DSC-QMS-FTIR)-was applied to monitor the thermal stability (in an N2 pyrolytic atmosphere) and chemical properties of natural polymers, fulvic (FA) and humic acids (HA), isolated from chemically different soils. Three temperature ranges, R1, 40-220°C; R2, 220-430°C; and R3, 430-650°C, were distinguished from the DSC data, related to the main thermal processes of different structures (including transformations without weight loss). Weight loss (ΔM) estimated from TG curves at the above temperature intervals revealed distinct differences within the samples in the content of physically adsorbed water (at R1), volatile and labile functional groups (at R2) as well as recalcitrant and refractory structures (at R3). QMS and FTIR modules enabled the chemical identification (by masses and by functional groups, respectively) of gaseous species evolved during thermal decomposition at R1, R2 and R3. Variability in shape, area and temperature of TG, DSC, QMS and FTIR peaks revealed differences in thermal stability and chemical structure of the samples between the FAs and HAs fractions of different origin. The statistical analysis showed that the parameters calculated from QMS (areas of m/z = 16, 17, 18, 44), DSC (MaxDSC) and TG (ΔM) at R1, R2 and R3 correlated with selected chemical properties of the samples, such as N, O and COOH content as well as E2/E6 and E2/E4 indexes. This indicated a high potential for the coupled method to monitor the chemical changes of humic substances. A new humification parameter, HTD, based on simple calculations of weight loss at specific temperature intervals proved to be a good alternative to indexes obtained from other methods. The above findings showed that the TG-DSC-QMS-FTIR coupled technique can represent a useful tool for the comprehensive assessment of FAs and HAs properties related to their various origin.

Use of thermal analysis coupled with differential scanning calorimetry, quadrupole mass spectrometry and infrared spectroscopy (TG-DSC-QMS-FTIR) to monitor chemical properties and thermal stability of fulvic and humic acids

PubMed Central

Sokołowska, Zofia; Skic, Kamil

2017-01-01

Thermogravimetry–coupled with differential scanning calorimetry, quadrupole mass spectrometry, and Fourier-transform infrared spectroscopy (TG-DSC-QMS-FTIR)–was applied to monitor the thermal stability (in an N2 pyrolytic atmosphere) and chemical properties of natural polymers, fulvic (FA) and humic acids (HA), isolated from chemically different soils. Three temperature ranges, R1, 40–220°C; R2, 220–430°C; and R3, 430–650°C, were distinguished from the DSC data, related to the main thermal processes of different structures (including transformations without weight loss). Weight loss (ΔM) estimated from TG curves at the above temperature intervals revealed distinct differences within the samples in the content of physically adsorbed water (at R1), volatile and labile functional groups (at R2) as well as recalcitrant and refractory structures (at R3). QMS and FTIR modules enabled the chemical identification (by masses and by functional groups, respectively) of gaseous species evolved during thermal decomposition at R1, R2 and R3. Variability in shape, area and temperature of TG, DSC, QMS and FTIR peaks revealed differences in thermal stability and chemical structure of the samples between the FAs and HAs fractions of different origin. The statistical analysis showed that the parameters calculated from QMS (areas of m/z = 16, 17, 18, 44), DSC (MaxDSC) and TG (ΔM) at R1, R2 and R3 correlated with selected chemical properties of the samples, such as N, O and COOH content as well as E2/E6 and E2/E4 indexes. This indicated a high potential for the coupled method to monitor the chemical changes of humic substances. A new humification parameter, HTD, based on simple calculations of weight loss at specific temperature intervals proved to be a good alternative to indexes obtained from other methods. The above findings showed that the TG-DSC-QMS-FTIR coupled technique can represent a useful tool for the comprehensive assessment of FAs and HAs properties related to their various origin. PMID:29240819

[Study on chemical constituents of Orobanche coerulescens].

PubMed

Zhao, Jun; Yan, Ming; Huang, Yi; He, Wen-yi; Zhao, Yu

2007-10-01

Six compounds were isolated and purified from Orobanche coerulescens by extraction and different kinds of column chromatography. The structures were determined on the basis of spectral analysis. The structures were elucidated as D-mannitol(I), beta-sitosterol(II), succinic acid(III), caffeic acid(IV), protocatechuic aldehyde(V) and daucosterol(VI). All compounds are obtained from this plant for the first time.

Physical Construction of the Chemical Atom: Is It Convenient to Go All the Way Back?

ERIC Educational Resources Information Center

Izquierdo-Aymerich, Merce; Aduriz-Bravo, Agustin

2009-01-01

In this paper we present an analysis of chemistry texts (mainly textbooks) published during the first half of the 20th century. We show the evolution of the explanations therein in terms of atoms and of atomic structure, when scientists were interpreting phenomena as evidence of the discontinuous, corpuscular structure of matter. In this process…

X-Ray Diffraction and the Discovery of the Structure of DNA

ERIC Educational Resources Information Center

Crouse, David T.

2007-01-01

A method is described for teaching the analysis of X-ray diffraction of DNA through a series of steps utilizing the original methods used by James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin. The X-ray diffraction pattern led to the conclusion of the basic helical structure of DNA and its dimensions while basic chemical principles…

Chemometric Analysis of Bacterial Peptidoglycan Reveals Atypical Modifications That Empower the Cell Wall against Predatory Enzymes and Fly Innate Immunity.

PubMed

Espaillat, Akbar; Forsmo, Oskar; El Biari, Khouzaima; Björk, Rafael; Lemaitre, Bruno; Trygg, Johan; Cañada, Francisco Javier; de Pedro, Miguel A; Cava, Felipe

2016-07-27

Peptidoglycan is a fundamental structure for most bacteria. It contributes to the cell morphology and provides cell wall integrity against environmental insults. While several studies have reported a significant degree of variability in the chemical composition and organization of peptidoglycan in the domain Bacteria, the real diversity of this polymer is far from fully explored. This work exploits rapid ultraperformance liquid chromatography and multivariate data analysis to uncover peptidoglycan chemical diversity in the Class Alphaproteobacteria, a group of Gram negative bacteria that are highly heterogeneous in terms of metabolism, morphology and life-styles. Indeed, chemometric analyses revealed novel peptidoglycan structures conserved in Acetobacteria: amidation at the α-(l)-carboxyl of meso-diaminopimelic acid and the presence of muropeptides cross-linked by (1-3) l-Ala-d-(meso)-diaminopimelate cross-links. Both structures are growth-controlled modifications that influence sensitivity to Type VI secretion system peptidoglycan endopeptidases and recognition by the Drosophila innate immune system, suggesting relevant roles in the environmental adaptability of these bacteria. Collectively our findings demonstrate the discriminative power of chemometric tools on large cell wall-chromatographic data sets to discover novel peptidoglycan structural properties in bacteria.

Determination of a refractive index and an extinction coefficient of standard production of CVD-graphene.

PubMed

Ochoa-Martínez, Efraín; Gabás, Mercedes; Barrutia, Laura; Pesquera, Amaia; Centeno, Alba; Palanco, Santiago; Zurutuza, Amaia; Algora, Carlos

2015-01-28

The refractive index and extinction coefficient of chemical vapour deposition grown graphene are determined by ellipsometry analysis. Graphene films were grown on copper substrates and transferred as both monolayers and bilayers onto SiO2/Si substrates by using standard manufacturing procedures. The chemical nature and thickness of residual debris formed after the transfer process were elucidated using photoelectron spectroscopy. The real layered structure so deduced has been used instead of the nominal one as the input in the ellipsometry analysis of monolayer and bilayer graphene, transferred onto both native and thermal silicon oxide. The effect of these contamination layers on the optical properties of the stacked structure is noticeable both in the visible and the ultraviolet spectral regions, thus masking the graphene optical response. Finally, the use of heat treatment under a nitrogen atmosphere of the graphene-based stacked structures, as a method to reduce the water content of the sample, and its effect on the optical response of both graphene and the residual debris layer are presented. The Lorentz-Drude model proposed for the optical response of graphene fits fairly well the experimental ellipsometric data for all the analysed graphene-based stacked structures.

Assessment of pollution impact on biological activity and structure of seabed bacterial communities in the Port of Livorno (Italy).

PubMed

Iannelli, Renato; Bianchi, Veronica; Macci, Cristina; Peruzzi, Eleonora; Chiellini, Carolina; Petroni, Giulio; Masciandaro, Grazia

2012-06-01

The main objective of this study was to assess the impact of pollution on seabed bacterial diversity, structure and activity in the Port of Livorno. Samples of seabed sediments taken from five selected sites within the port were subjected to chemical analyses, enzymatic activity detection, bacterial count and biomolecular analysis. Five different statistics were used to correlate the level of contamination with the detected biological indicators. The results showed that the port is mainly contaminated by variable levels of petroleum hydrocarbons and heavy metals, which affect the structure and activity of the bacterial population. Irrespective of pollution levels, the bacterial diversity did not diverge significantly among the assessed sites and samples, and no dominance was observed. The type of impact of hydrocarbons and heavy metals was controversial, thus enforcing the supposition that the structure of the bacterial community is mainly driven by the levels of nutrients. The combined use of chemical and biological essays resulted in an in-depth observation and analysis of the existing links between pollution macro-indicators and biological response of seabed bacterial communities. Copyright © 2012 Elsevier B.V. All rights reserved.

Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.

PubMed

Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

2010-05-24

We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.

[Chemical constituents from Neo-Taraxacum siphonathum].

PubMed

Shi, Shuyun; Zhou, Honghao; Zhang, Yuping; Huang, Kelong; Liu, Suqin

2009-04-01

To study the chemical constituents from the antioxidant fraction of Neo-Taraxacum siphonathum. Various chromatographic techniques were used to isolate and purify the constituents. The structures were elucidated on the basis of chemical evidence and spectral analysis. Ten compounds were isolated and identified from Neo-T. siphonathum, caffeic acid (1), chlorogenic acid (2), quercetin (3), luteolin (4), quercetin-3-O-beta-D-glucopyranoside (5), quercetin-3-O-alpha-D-arabinofuranoside (6), quercetin-3-O-alpha-D-arabinopyranoside (7), luteolin-7-O-beta-D-glucopyranoside (8), beta-sitosterol (9) and daucosterol (10). Compounds 1-10 were isolated from this plant for the first time.

Emil Fischer and the "art of chemical experimentation".

PubMed

Jackson, Catherine M

2017-03-01

What did nineteenth-century chemists know? This essay uses Emil Fischer's classic study of the sugars in 1880s and 90s Germany to argue that chemists' knowledge was not primarily vested in the theories of valence, structure, and stereochemistry that have been the subject of so much historical and philosophical analysis of chemistry in this period. Nor can chemistry be reduced to a merely manipulative exercise requiring little or no intellectual input. Examining what chemists themselves termed the "art of chemical experimentation" reveals chemical practice as inseparable from its cognitive component, and it explains how chemists integrated theory with experiment through reason.

Forensic analysis of tire rubbers based on their sulfur chemical states.

PubMed

Funatsuki, Atsushi; Shiota, Kenji; Takaoka, Masaki; Tamenori, Yusuke

2015-05-01

The chemical states of sulfur in 11 tires were analyzed using X-ray absorption near-edge structure (XANES) in order to discriminate between various tire rubbers. All tires had peaks around 2471.5 and 2480.5eV, and the shapes and heights of these peaks differed among tires, suggesting that the sulfur chemical state could be used for discrimination between tire rubbers. Based on t-tests on the results of XANES, 43 of 55 combinations were different at a significance level of 5%. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Conditions for extinction events in chemical reaction networks with discrete state spaces.

PubMed

Johnston, Matthew D; Anderson, David F; Craciun, Gheorghe; Brijder, Robert

2018-05-01

We study chemical reaction networks with discrete state spaces and present sufficient conditions on the structure of the network that guarantee the system exhibits an extinction event. The conditions we derive involve creating a modified chemical reaction network called a domination-expanded reaction network and then checking properties of this network. Unlike previous results, our analysis allows algorithmic implementation via systems of equalities and inequalities and suggests sequences of reactions which may lead to extinction events. We apply the results to several networks including an EnvZ-OmpR signaling pathway in Escherichia coli.

Cross-Link Guided Molecular Modeling with ROSETTA

PubMed Central

Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2013-01-01

Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods. PMID:24069194

Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

PubMed

Singh, Sunil; Gupta, Rashi; Kumari, Madhu; Sharma, Shilpi

2015-08-01

Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments.

Intraspecific differences in plant chemotype determine the structure of arthropod food webs.

PubMed

Bálint, János; Zytynska, Sharon E; Salamon, Rozália Veronika; Mehrparvar, Mohsen; Weisser, Wolfgang W; Schmitz, Oswald J; Benedek, Klára; Balog, Adalbert

2016-03-01

It is becoming increasingly appreciated that the structure and functioning of ecological food webs are controlled by the nature and level of plant chemicals. It is hypothesized that intraspecific variation in plant chemical resistance, in which individuals of a host-plant population exhibit genetic differences in their chemical contents (called 'plant chemotypes'), may be an important determinant of variation in food web structure and functioning. We evaluated this hypothesis using field assessments and plant chemical assays in the tansy plant Tanacetum vulgare L. (Asteraceae). We examined food webs in which chemotypes of tansy plants are the resource for two specialized aphids, their predators and mutualistic ants. The density of the ant-tended aphid Metopeurum fuscoviride was significantly higher on particular chemotypes (borneol) than others. Clear chemotype preferences between predators were also detected. Aphid specialist seven-spotted ladybird beetles (Coccinella septempunctata) were more often found on camphor plants, while significantly higher numbers of the polyphagous nursery web spider (Pisaura mirabilis) were observed on borneol plants. The analysis of plant chemotype effects on the arthropod community clearly demonstrates a range of possible outcomes between plant-aphid-predator networks. The findings help to offer a deeper insight into how one important factor--plant chemical content--influences which species coexist within a food web on a particular host plant and the nature of their trophic linkages.

Spectral and structural studies of the anti-cancer drug Flutamide by density functional theoretical method

NASA Astrophysics Data System (ADS)

Mariappan, G.; Sundaraganesan, N.

2014-01-01

A comprehensive screening of the more recent DFT theoretical approach to structural analysis is presented in this section of theoretical structural analysis. The chemical name of 2-methyl-N-[4-nitro-3-(trifluoromethyl)phenyl]-propanamide is usually called as Flutamide (In the present study it is abbreviated as FLT) and is an important and efficacious drug in the treatment of anti-cancer resistant. The molecular geometry, vibrational spectra, electronic and NMR spectral interpretation of Flutamide have been studied with the aid of density functional theory method (DFT). The vibrational assignments of the normal modes were performed on the basis of the PED calculations using the VEDA 4 program. Comparison of computational results with X-ray diffraction results of Flutamide allowed the evaluation of structure predictions and confirmed B3LYP/6-31G(d,p) as accurate for structure determination. Application of scaling factors for IR and Raman frequency predictions showed good agreement with experimental values. This is supported the assignment of the major contributors of the vibration modes of the title compound. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The comparison of measured FTIR, FT-Raman, and UV-Visible data to calculated values allowed assignment of major spectral features of the title molecule. Besides, Frontier molecular orbital analyze was also investigated using theoretical calculations.

THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

Local structural and chemical ordering of nanosized Pt3±δCo probed by multiple-scattering x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Greco, Giorgia; Witkowska, Agnieszka; Principi, Emiliano; Minicucci, Marco; di Cicco, Andrea

2011-04-01

This work reports a detailed investigation of the local structure and chemical disorder of a Pt3±δCo thin film and Pt3±δCo nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). High-quality XAS spectra at the Co K edge and Pt L3 edge have been analyzed using double-edge multiple-scattering data analysis. Structural extended x-ray absorption fine structure (EXAFS) refinements have been performed accounting for the reduction of the coordination numbers and degeneracy of three-atom configurations, resulting from the measured size distribution and stoichiometry. The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations based on a simple model accounting for substitutional disorder, defined by an order parameter s. It has been found that individual EXAFS signals related to the minority species (Co) are extremely sensitive to substitutional disorder so their intensities, especially those of the collinear three-atom configurations, can be used as a measure of the ordering level. The thin film has been found to be chemically disordered (s⩽0.4), in agreement with previous estimates. The Pt3±δCo nanoalloy has been found to be partially ordered (s=0.6±0.1) while the local structure around Co atoms is characterized by a higher level of structural disorder as compared to the bulk-like thin film. The robust approach for nanomaterial characterization used in this work combining different techniques can, in principle, be applied for structural refinements of any binary nanocrystalline functional system.

Normal Science Education and its Dangers: The Case of School Chemistry

NASA Astrophysics Data System (ADS)

Van Berkel, Berry; De Vos, Wobbe; Verdonk, Adri H.; Pilot, Albert

We started the Conceptual Structure of School Chemistry research project, a part of which is reported on here, with an attempt to solve the problem of the hidden structure in school chemistry. In order to solve that problem, and informed by previous research, we performed a content analysis of school chemistry textbooks and syllabi. This led us to the hypothesis that school chemistry curricula are based on an underlying, coherent structure of chemical concepts that students are supposed to learn for the purpose of explaining and predicting chemical phenomena. The elicited comments and criticisms of an International Forum of twenty-eight researchers of chemical education, though, refuted the central claims of this hypothesis. This led to a descriptive theory of the currently dominant school chemistry curriculum in terms of a rigid combination of a specific substantive structure, based on corpuscular theory, a specific philosophical structure, educational positivism, and a specific pedagogical structure, involving initiatory and preparatory training of future chemists. Secondly, it led to an explanatory theory of the structure of school chemistry - based on Kuhn's theory of normal science and scientific training - in which dominant school chemistry is interpreted as a form of normal science education. Since the former has almost all characteristics in common with the latter, dominant school chemistry must be regarded as normal chemistry education. Forum members also formulated a number of normative criticisms on dominant school chemistry, which we interpret as specific dangers of normal chemistry education, complementing Popper's discussion of the general dangers of normal science and its teaching. On the basis of these criticisms, it is argued that normal chemistry education is isolated from common sense, everyday life and society, history and philosophy of science, technology, school physics, and from chemical research.

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

PubMed Central

Schweppe, Devin K.; Zheng, Chunxiang; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Eng, Jimmy K.; Bruce, James E.

2016-01-01

Motivation: Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein–protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis. Availability and Implementation: XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/. Contact: jimbruce@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153666

On-Line Synthesis and Analysis by Mass Spectrometry

ERIC Educational Resources Information Center

Bain, Ryan M.; Pulliam, Christopher J.; Raab, Shannon A.; Cooks, R. Graham

2015-01-01

In this laboratory experiment, students learn how to use ESI to accelerate chemical synthesis and to couple it with on-line mass spectrometry for structural analysis. The Hantzsch synthesis of symmetric 1,4-dihydropyridines is a classic example of a one-pot reaction in which multiple intermediates can serve to indicate the progress of the reaction…

Computer-aided drug design of falcipain inhibitors: virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis.

PubMed

Shah, Falgun; Gut, Jiri; Legac, Jennifer; Shivakumar, Devleena; Sherman, Woody; Rosenthal, Philip J; Avery, Mitchell A

2012-03-26

Falcipains (FPs) are hemoglobinases of Plasmodium falciparum that are validated targets for the development of antimalarial chemotherapy. A combined ligand- and structure-based virtual screening of commercial databases was performed to identify structural analogs of virtual screening hits previously discovered in our laboratory. A total of 28 low micromolar inhibitors of FP-2 and FP-3 were identified and the structure-activity relationship (SAR) in each series was elaborated. The SAR of the compounds was unusually steep in some cases and could not be explained by a traditional analysis of the ligand-protein interactions (van der Waals, electrostatics, and hydrogen bonds). To gain further insights, a statistical thermodynamic analysis of explicit solvent in the ligand binding domains of FP-2 and FP-3 was carried out to understand the roles played by water molecules in binding of these inhibitors. Indeed, the energetics associated with the displacement of water molecules upon ligand binding explained some of the complex trends in the SAR. Furthermore, low potency of a subset of FP-2 inhibitors that could not be understood by the water energetics was explained in the context of poor chemical reactivity of the reactive centers of these compounds. The present study highlights the importance of considering energetic contributors to binding beyond traditional ligand-protein interactions. © 2012 American Chemical Society

Growth control, structure, chemical state, and photoresponse of CuO-CdS core-shell heterostructure nanowires.

PubMed

El Mel, A A; Buffière, M; Bouts, N; Gautron, E; Tessier, P Y; Henzler, K; Guttmann, P; Konstantinidis, S; Bittencourt, C; Snyders, R

2013-07-05

The growth of single-crystal CuO nanowires by thermal annealing of copper thin films in air is studied. We show that the density, length, and diameter of the nanowires can be controlled by tuning the morphology and structure of the copper thin films deposited by DC magnetron sputtering. After identifying the optimal conditions for the growth of CuO nanowires, chemical bath deposition is employed to coat the CuO nanowires with CdS in order to form p-n nanojunction arrays. As revealed by high-resolution TEM analysis, the thickness of the polycrystalline CdS shell increases when decreasing the diameter of the CuO core for a given time of CdS deposition. Near-edge x-ray absorption fine-structure spectroscopy combined with transmission x-ray microscopy allows the chemical analysis of isolated nanowires. The absence of modification in the spectra at the Cu L and O K edges after the deposition of CdS on the CuO nanowires indicates that neither Cd nor S diffuse into the CuO phase. We further demonstrate that the core-shell nanowires exhibit the I-V characteristic of a resistor instead of a diode. The electrical behavior of the device was found to be photosensitive, since increasing the incident light intensity induces an increase in the collected electrical current.

Evaluation of structure-reactivity descriptors and biological activity spectra of 4-(6-methoxy-2-naphthyl)-2-butanone using spectroscopic techniques

NASA Astrophysics Data System (ADS)

Agrawal, Megha; Deval, Vipin; Gupta, Archana; Sangala, Bagvanth Reddy; Prabhu, S. S.

2016-10-01

The structure and several spectroscopic features along with reactivity parameters of the compound 4-(6-methoxy-2-naphthyl)-2-butanone (Nabumetone) have been studied using experimental techniques and tools derived from quantum chemical calculations. Structure optimization is followed by force field calculations based on density functional theory (DFT) at the B3LYP/6-311++G(d,p) level of theory. The vibrational spectra have been interpreted with the aid of normal coordinate analysis. UV-visible spectrum and the effect of solvent have been discussed. The electronic properties such as HOMO and LUMO energies have been determined by TD-DFT approach. In order to understand various aspects of pharmacological sciences several new chemical reactivity descriptors - chemical potential, global hardness and electrophilicity have been evaluated. Local reactivity descriptors - Fukui functions and local softnesses have also been calculated to find out the reactive sites within molecule. Aqueous solubility and lipophilicity have been calculated which are crucial for estimating transport properties of organic molecules in drug development. Estimation of biological effects, toxic/side effects has been made on the basis of prediction of activity spectra for substances (PASS) prediction results and their analysis by Pharma Expert software. Using the THz-TDS technique, the frequency-dependent absorptions of NBM have been measured in the frequency range up to 3 THz.

General Platform for Systematic Quantitative Evaluation of Small-Molecule Permeability in Bacteria

PubMed Central

2015-01-01

The chemical features that impact small-molecule permeability across bacterial membranes are poorly understood, and the resulting lack of tools to predict permeability presents a major obstacle to the discovery and development of novel antibiotics. Antibacterials are known to have vastly different structural and physicochemical properties compared to nonantiinfective drugs, as illustrated herein by principal component analysis (PCA). To understand how these properties influence bacterial permeability, we have developed a systematic approach to evaluate the penetration of diverse compounds into bacteria with distinct cellular envelopes. Intracellular compound accumulation is quantitated using LC-MS/MS, then PCA and Pearson pairwise correlations are used to identify structural and physicochemical parameters that correlate with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations between chemical structure and permeability that differ among the various bacteria. Effects of cotreatment with efflux pump inhibitors were also investigated. This sets the stage for use of this platform in larger prospective analyses of diverse chemotypes to identify global relationships between chemical structure and bacterial permeability that would enable the development of predictive tools to accelerate antibiotic drug discovery. PMID:25198656

[Influence of surface chemical properties and pore structure characteristics of activated carbon on the adsorption of nitrobenzene from aqueous solution].

PubMed

Liu, Shou-Xin; Chen, Xi; Zhang, Xian-Quan

2008-05-01

Commercial activated carbon was treated by HNO3 oxidation and then subsequently heat treated under N2 atmosphere. Effect of surface chemical properties and pore structure on the adsorption performance of nitrobenzene was investigated. N2/77K adsorption isotherm and scanning electron microscopy (SEM) were used to characterize the pore structure and surface morphology of carbon. Boehm titration, Fourier transform infrared spectroscopy (FTIR), the point of zero charge (pH(PZC)) measurement and elemental analysis were used to characterize the surface properties. The results reveal that HNO3 oxidation can modify the surface chemical properties, increase the number of acidic surface oxygen-containing groups and has trivial effect on the pore structure of carbon. Further heat treatment can cause the decomposition of surface oxygen-containing groups, and increase the external surface area and the number of mesopores. Adsorption capacity of nitrobenzene on AC(NO-T), AC(raw) and AC(NO) was 1011.31, 483.09 and 321.54 mg x g(-1), respectively. Larger external surface area and the number of meso-pores, together with the less acid surface oxygen-containing groups were the main reason for the larger adsorption capacity AC(NO-T).

ANALYSIS OF LOTIC MACROINVERTEBRATE ASSEMBLAGES IN CALIFORNIA'S CENTRAL VALLEY

EPA Science Inventory

Using multivariate and cluster analyses, we examined the relaitonships between chemical and physical characteristics and macroinvertebrate assemblages at sites sampled by R-EMAP in California's Central Valley. By contrasting results where community structure was summarized as met...

Structural and chemical orders in N i 64.5 Z r 35.5 metallic glass by molecular dynamics simulation

DOE PAGES

Tang, L.; Wen, T. Q.; Wang, N.; ...

2018-03-06

The atomic structure of Ni 64.5Zr 35.5 metallic glass has been investigated by molecular dynamics (MD) simulations. The calculated structure factors from the MD glassy sample at room temperature agree well with the X-ray diffraction (XRD) and neutron diffraction (ND) experimental data. Using the pairwise cluster alignment and clique analysis methods, we show that there are three types dominant short-range order (SRO) motifs around Ni atoms in the glass sample of Ni 64.5Zr 35.5, i.e., Mixed- Icosahedron(ICO)-Cube, Twined-Cube and icosahedron-like clusters. Furthermore, chemical order and medium-range order (MRO) analysis show that the Mixed-ICOCube and Twined-Cube clusters exhibit the characteristics ofmore » the crystalline B2 phase. In conclusion, our simulation results suggest that the weak glass-forming ability (GFA) of Ni 64.5Zr 35.5 can be attributed to the competition between the glass forming ICO SRO and the crystalline Mixed-ICO-Cube and Twined-Cube motifs.« less

Structural and chemical orders in N i 64.5 Z r 35.5 metallic glass by molecular dynamics simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, L.; Wen, T. Q.; Wang, N.

The atomic structure of Ni 64.5Zr 35.5 metallic glass has been investigated by molecular dynamics (MD) simulations. The calculated structure factors from the MD glassy sample at room temperature agree well with the X-ray diffraction (XRD) and neutron diffraction (ND) experimental data. Using the pairwise cluster alignment and clique analysis methods, we show that there are three types dominant short-range order (SRO) motifs around Ni atoms in the glass sample of Ni 64.5Zr 35.5, i.e., Mixed- Icosahedron(ICO)-Cube, Twined-Cube and icosahedron-like clusters. Furthermore, chemical order and medium-range order (MRO) analysis show that the Mixed-ICOCube and Twined-Cube clusters exhibit the characteristics ofmore » the crystalline B2 phase. In conclusion, our simulation results suggest that the weak glass-forming ability (GFA) of Ni 64.5Zr 35.5 can be attributed to the competition between the glass forming ICO SRO and the crystalline Mixed-ICO-Cube and Twined-Cube motifs.« less

Antifeedant effect of polygodial and drimenol derivatives against Spodoptera frugiperda and Epilachna paenulata and quantitative structure-activity analysis.

PubMed

Montenegro, Iván J; Del Corral, Soledad; Diaz Napal, Georgina N; Carpinella, María C; Mellado, Marco; Madrid, Alejandro M; Villena, Joan; Palacios, Sara M; Cuellar, Mauricio A

2018-07-01

The antifeedant activity of 18 sesquiterpenoids of the drimane family (polygodial, drimenol and derivatives) was investigated. Polygodial, drimanic and nordrimanic derivatives were found to exert antifeedant effects against two insect species, Spodoptera frugiperda and Epilachna paenulata, which are pests of agronomic interest, indicating that they have potential as biopesticide agents. Among the 18 compounds tested, the epoxynordrimane compound (11) and isonordrimenone (4) showed the highest activity [50% effective concentration (EC 50 ) = 23.28 and 25.63 nmol cm - 2 , respectively, against S. frugiperda, and 50.50 and 59.00 nmol/cm 2 , respectively, against E. paenulata]. The results suggest that drimanic compounds have potential as new agents against S. frugiperda and E. paenulata. A quantitative structure-activity relationship (QSAR) analysis of the whole series, supported by electronic studies, suggested that drimanic compounds have structural features necessary for increasing antifeedant activity, namely a C-9 carbonyl group and an epoxide at C-8 and C-9. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Structural and chemical orders in N i64.5Z r35.5 metallic glass by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Tang, L.; Wen, T. Q.; Wang, N.; Sun, Y.; Zhang, F.; Yang, Z. J.; Ho, K. M.; Wang, C. Z.

2018-03-01

The atomic structure of N i64.5Z r35.5 metallic glass has been investigated by molecular dynamics (MD) simulations. The calculated structure factors from the MD glassy sample at room temperature agree well with the x-ray diffraction (XRD) and neutron diffraction (ND) experimental data. Using the pairwise cluster alignment and clique analysis methods, we show that there are three types of dominant short-range order (SRO) motifs around Ni atoms in the glass sample of N i64.5Z r35.5 , i.e., mixed-icosahedron(ICO)-cube, intertwined-cube, and icosahedronlike clusters. Furthermore, chemical order and medium-range order (MRO) analysis show that the mixed-ICO-cube and intertwined-cube clusters exhibit the characteristics of the crystalline B2 phase. Our simulation results suggest that the weak glass-forming ability (GFA) of N i64.5Z r35.5 can be attributed to the competition between the glass forming ICO SRO and the crystalline mixed-ICO-cube and intertwined-cube motifs.

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

PubMed Central

Lo, Yu-Chen; Senese, Silvia; Li, Chien-Ming; Hu, Qiyang; Huang, Yong; Damoiseaux, Robert; Torres, Jorge Z.

2015-01-01

Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico target identification methods, including chemical similarity database searches, are limited to single or sequential ligand analysis that have limited capabilities for accurate deconvolution of a large number of compounds with diverse chemical structures. Here, we present CSNAP (Chemical Similarity Network Analysis Pulldown), a new computational target identification method that utilizes chemical similarity networks for large-scale chemotype (consensus chemical pattern) recognition and drug target profiling. Our benchmark study showed that CSNAP can achieve an overall higher accuracy (>80%) of target prediction with respect to representative chemotypes in large (>200) compound sets, in comparison to the SEA approach (60–70%). Additionally, CSNAP is capable of integrating with biological knowledge-based databases (Uniprot, GO) and high-throughput biology platforms (proteomic, genetic, etc) for system-wise drug target validation. To demonstrate the utility of the CSNAP approach, we combined CSNAP's target prediction with experimental ligand evaluation to identify the major mitotic targets of hit compounds from a cell-based chemical screen and we highlight novel compounds targeting microtubules, an important cancer therapeutic target. The CSNAP method is freely available and can be accessed from the CSNAP web server (http://services.mbi.ucla.edu/CSNAP/). PMID:25826798

Chemical engineering and structural and pharmacological characterization of the α-scorpion toxin OD1.

PubMed

Durek, Thomas; Vetter, Irina; Wang, Ching-I Anderson; Motin, Leonid; Knapp, Oliver; Adams, David J; Lewis, Richard J; Alewood, Paul F

2013-01-01

Scorpion α-toxins are invaluable pharmacological tools for studying voltage-gated sodium channels, but few structure-function studies have been undertaken due to their challenging synthesis. To address this deficiency, we report a chemical engineering strategy based upon native chemical ligation. The chemical synthesis of α-toxin OD1 was achieved by chemical ligation of three unprotected peptide segments. A high resolution X-ray structure (1.8 Å) of synthetic OD1 showed the typical βαββ α-toxin fold and revealed important conformational differences in the pharmacophore region when compared with other α-toxin structures. Pharmacological analysis of synthetic OD1 revealed potent α-toxin activity (inhibition of fast inactivation) at Nav1.7, as well as Nav1.4 and Nav1.6. In addition, OD1 also produced potent β-toxin activity at Nav1.4 and Nav1.6 (shift of channel activation in the hyperpolarizing direction), indicating that OD1 might interact at more than one site with Nav1.4 and Nav1.6. Investigation of nine OD1 mutants revealed that three residues in the reverse turn contributed significantly to selectivity, with the triple OD1 mutant (D9K, D10P, K11H) being 40-fold more selective for Nav1.7 over Nav1.6, while OD1 K11V was 5-fold more selective for Nav1.6 than Nav1.7. This switch in selectivity highlights the importance of the reverse turn for engineering α-toxins with altered selectivity at Nav subtypes.

Efficient first-principles prediction of solid stability: Towards chemical accuracy

NASA Astrophysics Data System (ADS)

Zhang, Yubo; Kitchaev, Daniil A.; Yang, Julia; Chen, Tina; Dacek, Stephen T.; Sarmiento-Pérez, Rafael A.; Marques, Maguel A. L.; Peng, Haowei; Ceder, Gerbrand; Perdew, John P.; Sun, Jianwei

2018-03-01

The question of material stability is of fundamental importance to any analysis of system properties in condensed matter physics and materials science. The ability to evaluate chemical stability, i.e., whether a stoichiometry will persist in some chemical environment, and structure selection, i.e. what crystal structure a stoichiometry will adopt, is critical to the prediction of materials synthesis, reactivity and properties. Here, we demonstrate that density functional theory, with the recently developed strongly constrained and appropriately normed (SCAN) functional, has advanced to a point where both facets of the stability problem can be reliably and efficiently predicted for main group compounds, while transition metal compounds are improved but remain a challenge. SCAN therefore offers a robust model for a significant portion of the periodic table, presenting an opportunity for the development of novel materials and the study of fine phase transformations even in largely unexplored systems with little to no experimental data.

Nuclear magnetic resonance spectral analysis and molecular properties of berberine

NASA Astrophysics Data System (ADS)

Huang, Ming-Ju; Lee, Ken S.; Hurley, Sharon J.

An extensive theoretical study of berberine has been performed at the ab initio HF/6-31G**, HF/6-311G**, and B3LYP/6-311G** levels with and without solvent effects. The optimized structures are compared with X-ray data. We found that the optimized structures with solvent effects are in slightly better agreement with X-ray data than those without solvent effects. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of berberine were calculated by using the gauge-independent atomic orbital (GIAO) (with and without solvent effects), CSGT, and IGAIM methods. The calculated chemical shifts were compared with the two-dimensional NMR experimental data. Overall, the calculated chemical shifts show very good agreement with the experimental results. The harmonic vibrational frequencies for berberine were calculated at the B3LYP/6-311G** level.

Synergistic activation of human pregnane X receptor by binary cocktails of pharmaceutical and environmental compounds.

PubMed

Delfosse, Vanessa; Dendele, Béatrice; Huet, Tiphaine; Grimaldi, Marina; Boulahtouf, Abdelhay; Gerbal-Chaloin, Sabine; Beucher, Bertrand; Roecklin, Dominique; Muller, Christina; Rahmani, Roger; Cavaillès, Vincent; Daujat-Chavanieu, Martine; Vivat, Valérie; Pascussi, Jean-Marc; Balaguer, Patrick; Bourguet, William

2015-09-03

Humans are chronically exposed to multiple exogenous substances, including environmental pollutants, drugs and dietary components. Many of these compounds are suspected to impact human health, and their combination in complex mixtures could exacerbate their harmful effects. Here we demonstrate that a pharmaceutical oestrogen and a persistent organochlorine pesticide, both exhibiting low efficacy when studied separately, cooperatively bind to the pregnane X receptor, leading to synergistic activation. Biophysical analysis shows that each ligand enhances the binding affinity of the other, so the binary mixture induces a substantial biological response at doses at which each chemical individually is inactive. High-resolution crystal structures reveal the structural basis for the observed cooperativity. Our results suggest that the formation of 'supramolecular ligands' within the ligand-binding pocket of nuclear receptors contributes to the synergistic toxic effect of chemical mixtures, which may have broad implications for the fields of endocrine disruption, toxicology and chemical risk assessment.

Bioprospecting for Exopolysaccharides from Deep-Sea Hydrothermal Vent Bacteria: Relationship between Bacterial Diversity and Chemical Diversity

PubMed Central

Delbarre-Ladrat, Christine; Leyva Salas, Marcia; Zykwinska, Agata; Colliec-Jouault, Sylvia

2017-01-01

Many bacteria biosynthesize structurally diverse exopolysaccharides (EPS) and excrete them into their surrounding environment. The EPS functional features have found many applications in industries such as cosmetics and pharmaceutics. In particular, some EPS produced by marine bacteria are composed of uronic acids, neutral sugars, and N-acetylhexosamines, and may also bear some functional sulfate groups. This suggests that they can share common structural features with glycosaminoglycans (GAG) like the two EPS (HE800 and GY785) originating from the deep sea. In an attempt to discover new EPS that may be promising candidates as GAG-mimetics, fifty-one marine bacterial strains originating from deep-sea hydrothermal vents were screened. The analysis of the EPS chemical structure in relation to bacterial species showed that Vibrio, Alteromonas, and Pseudoalteromonas strains were the main producers. Moreover, they produced EPS with distinct structural features, which might be useful for targeting marine bacteria that could possibly produce structurally GAG-mimetic EPS. PMID:28930185

Crystal-chemical characteristics of nontronites from bottom sediments of Pacific ocean

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palchik, N. A., E-mail: nadezhda@igm.nsc.ru; Moroz, T. N.; Grigorieva, T. N.

A crystal-chemical analysis of the nontronite samples formed in deep-water sediments of the underwater Juan-de-Fuca ridge in the Pacific ocean has been performed using powder X-ray diffraction, IR spectroscopy, and Mössbauer spectroscopy. A comparison with the previously investigated nontronites from different regions of the Sea of Okhotsk showed that the structural features of these formations are due to the difference in the physicochemical parameters of their crystallization. The values of the basal interplanar spacing d{sub 001} (within 11–13 Å) in the samples analyzed are determined by the degree of hydration and cation filling of the interlayer space, while the differencesmore » in the IR spectra are due to isomorphic substitutions in the structure. The character of cation distribution and the nature and concentration of stacking faults in nontronite structures are determined. The differences in the composition, structure, and properties of nontronites of different origin are confirmed by theoretical calculations of their structural parameters.« less

Data Sets Representative of the Structures and Experimental Properties of FDA-Approved Drugs.

PubMed

Douguet, Dominique

2018-03-08

Presented here are several data sets that gather information collected from the labels of the FDA approved drugs: their molecular structures and those of the described active metabolites, their associated pharmacokinetics and pharmacodynamics data, and the history of their marketing authorization by the FDA. To date, 1852 chemical structures have been identified with a molecular weight less than 2000 of which 492 are or have active metabolites. To promote the sharing of data, the original web server was upgraded for browsing the database and downloading the data sets (http://chemoinfo.ipmc.cnrs.fr/edrug3d). It is believed that the multidimensional chemistry-oriented collections are an essential resource for a thorough analysis of the current drug chemical space. The data sets are envisioned as being used in a wide range of endeavors that include drug repurposing, drug design, privileged structures analyses, structure-activity relationship studies, and improving of absorption, distribution, metabolism, and elimination predictive models.

Fabrication and characterization of nano-gas sensor arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hassan, H. S., E-mail: hassan.shokry@gmail.com; Kashyout, A. B., E-mail: hady8@yahoo.com; Morsi, I., E-mail: drimanmorsi@yahoo.com

2015-03-30

A novel structures of Nanomaterials gas sensors array constructed using ZnO, and ZnO doped with Al via sol-gel technique. Two structure arrays are developed; the first one is a double sensor array based on doping with percentages of 1% and 5%. The second is a quadrature sensor array based on several doping ratios concentrations (0%, 1%, 5% and 10%). The morphological structures of prepared ZnO were revealed using scanning electron microscope (SEM). X-ray diffraction (XRD) patterns reveal a highly crystallized wurtzite structure and used for identifying phase structure and chemical state of both ZnO and ZnO doped with Al undermore » different preparation conditions and different doping ratios. Chemical composition of Al-doped ZnO nanopowders was performed using energy dispersive x-ray (EDS) analysis. The electrical characteristics of the sensor are determined by measuring the two terminal sensor’s output resistance for O{sub 2}, H{sub 2} and CO{sub 2} gases as a function of temperature.« less

Protein Structural Analysis via Mass Spectrometry-Based Proteomics

PubMed Central

Artigues, Antonio; Nadeau, Owen W.; Rimmer, Mary Ashley; Villar, Maria T.; Du, Xiuxia; Fenton, Aron W.; Carlson, Gerald M.

2017-01-01

Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: 1) hydrogen/deuterium exchange (HDX), 2) limited proteolysis, and 3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography. PMID:27975228

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry.

PubMed

Williams, Antony J; Grulke, Christopher M; Edwards, Jeff; McEachran, Andrew D; Mansouri, Kamel; Baker, Nancy C; Patlewicz, Grace; Shah, Imran; Wambaugh, John F; Judson, Richard S; Richard, Ann M

2017-11-28

Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protection Agency's (EPA) web-based CompTox Chemistry Dashboard is addressing these needs by integrating diverse types of relevant domain data through a cheminformatics layer, built upon a database of curated substances linked to chemical structures. These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats. This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time). Advanced search capabilities are available to support, for example, non-targeted analysis and identification of chemicals using mass spectrometry. The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA's DSSTox project. DSSTox chemical content is subject to strict quality controls to enforce consistency among chemical substance-structure identifiers, as well as list curation review to ensure accurate linkages of DSSTox substances to chemical lists and associated data. The Dashboard, publicly launched in April 2016, has expanded considerably in content and user traffic over the past year. It is continuously evolving with the growth of DSSTox into high-interest or data-rich domains of interest to EPA, such as chemicals on the Toxic Substances Control Act listing, while providing the user community with a flexible and dynamic web-based platform for integration, processing, visualization and delivery of data and resources. The Dashboard provides support for a broad array of research and regulatory programs across the worldwide community of toxicologists and environmental scientists.

Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

PubMed

Jeannerat, Damien

2017-01-01

The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The use of analytical surface tools in the fundamental study of wear. [atomic nature of wear

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1977-01-01

Various techniques and surface tools available for the study of the atomic nature of the wear of materials are reviewed These include chemical etching, x-ray diffraction, electron diffraction, scanning electron microscopy, low-energy electron diffraction, Auger emission spectroscopy analysis, electron spectroscopy for chemical analysis, field ion microscopy, and the atom probe. Properties of the surface and wear surface regions which affect wear, such as surface energy, crystal structure, crystallographic orientation, mode of dislocation behavior, and cohesive binding, are discussed. A number of mechanisms involved in the generation of wear particles are identified with the aid of the aforementioned tools.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

PubMed Central

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1–0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift. PMID:28451325

Electronic-topological study of the structure-activity relationships in a series of steroids with mineralocorticoid binding affinity.

PubMed

Kandemirli, Fatma; Tokay, Nesrin; Shvets, Nataly M; Dimoglo, Anatoly S

2003-01-01

Conformational analysis and quantum chemical calculations were carried out using molecular mechanics (MMP2) and semi-empirical quantum chemistry (CNDO/2) methods for 51 steroid homologues belonging to a series of 17-spirolactones. Matrices called Electronic-Topological Matrices of Conjunction (ETMCs) were formed using data obtained from quantum chemical calculations. A structural fragment of activity was identified in the series of steroids. As seen from the fragment's properties, active compounds are characterized by the presence of two atoms of oxygen, O1 and O3, which are situated at a distance of 13.5 A and possess high negative charges (-0.29 to -0.31 e).

Solid-state NMR sequential assignment of the β-endorphin peptide in its amyloid form.

PubMed

Seuring, Carolin; Gath, Julia; Verasdonck, Joeri; Cadalbert, Riccardo; Rivier, Jean; Böckmann, Anja; Meier, Beat H; Riek, Roland

2016-10-01

Insights into the three-dimensional structure of hormone fibrils are crucial for a detailed understanding of how an amyloid structure allows the storage of hormones in secretory vesicles prior to hormone secretion into the blood stream. As an example for various hormone amyloids, we have studied the endogenous opioid neuropeptide β-endorphin in one of its fibril forms. We have achieved the sequential assignment of the chemical shifts of the backbone and side-chain heavy atoms of the fibril. The secondary chemical shift analysis revealed that the β-endorphin peptide adopts three β-strands in its fibril state. This finding fosters the amyloid nature of a hormone at the atomic level.

Solid-state NMR studies of form I of atorvastatin calcium.

PubMed

Wang, Wei David; Gao, Xudong; Strohmeier, Mark; Wang, Wei; Bai, Shi; Dybowski, Cecil

2012-03-22

Solid-state (13)C, (19)F, and (15)N magic angle spinning NMR studies of Form I of atorvastatin calcium are reported, including chemical shift tensors of all resolvable carbon sites and fluorine sites. The complete (13)C and (19)F chemical shift assignments are given based on an extensive analysis of (13)C-(1)H HETCOR and (13)C-(19)F HETCOR results. The solid-state NMR data indicate that the asymmetric unit of this material contains two atorvastatin molecules. A possible structure of Form I of atorvastatin calcium (ATC-I), derived from solid-state NMR data and density functional theory calculations of various structures, is proposed for this important active pharmaceutical ingredient (API).

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

PubMed

Leontis, N B; Westhof, E

1998-09-01

A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings. Thus, each non-Watson-Crick pair could be characterized by a phylogenetic signature of variations between isosteric-like pairings. In addition to the conservative changes, which form a dictionary of pairings isosterically compatible with those observed in the crystal structure, concerted changes involving several base pairs also occur. The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA.

Isolation and structure elucidation of the nucleoside antibiotic strepturidin from Streptomyces albus DSM 40763.

PubMed

Pesic, Alexander; Steinhaus, Britta; Kemper, Sebastian; Nachtigall, Jonny; Kutzner, Hans Jürgen; Höfle, Gerhard; Süssmuth, Roderich D

2014-06-01

The antibiotic strepturidin (1) was isolated from the microorganism Streptomyces albus DSM 40763, and its structure elucidated by spectroscopic methods and chemical degradation studies. The determination of the relative and absolute stereocenters was partially achieved using chiral GC/EI-MS analysis and microderivatization by acetal ring formation and subsequent 2D-NMR analysis of key (1)H,(1)H-NOESY NMR correlations and extraction of (1)H,(13)C coupling constants from (1)H,(13)C-HMBC NMR spectra. Based on these results, a biosynthesis model was proposed.

Process monitoring and control with CHEMIN, a miniaturized CCD-based instrument for simultaneous XRD/XRF analysis

NASA Astrophysics Data System (ADS)

Vaniman, David T.; Bish, D.; Guthrie, G.; Chipera, S.; Blake, David E.; Collins, S. Andy; Elliott, S. T.; Sarrazin, P.

1999-10-01

There is a large variety of mining and manufacturing operations where process monitoring and control can benefit from on-site analysis of both chemical and mineralogic constituents. CHEMIN is a CCD-based instrument capable of both X-ray fluorescence (XRF; chemical) and X-ray diffraction (XRD; mineralogic) analysis. Monitoring and control with an instrument like CHEMIN can be applied to feedstocks, intermediate materials, and final products to optimize production. Examples include control of cement feedstock, of ore for smelting, and of minerals that pose inhalation hazards in the workplace. The combined XRD/XRF capability of CHEMIN can be used wherever a desired commodity is associated with unwanted constituents that may be similar in chemistry or structure but not both (e.g., Ca in both gypsum and feldspar, where only the gypsum is desired to make wallboard). In the mining industry, CHEMIN can determine mineral abundances on the spot and enable more economical mining by providing the means to assay when is being mined, quickly and frequently, at minimal cost. In manufacturing, CHEMIN could be used to spot-check the chemical composition and crystalline makeup of a product at any stage of production. Analysis by CHEMIN can be used as feedback in manufacturing processes where rates of heating, process temperature, mixture of feedstocks, and other variables must be adjusted in real time to correct structure and/or chemistry of the product (e.g., prevention of periclase and alkali sulfate coproduction in cement manufacture).

Structural determination of intact proteins using mass spectrometry

DOEpatents

Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

2008-05-06

The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

Chemical study of the fungus Psilocybe merdaria.

PubMed

Yang, Ning-Ning; Ma, Qing-Yun; Huang, Sheng-Zhuo; Kong, Fan-Dong; Dai, Hao-Fu; Yu, Zhi-Fang; Zhao, You-Xing

2017-04-01

Chemical investigation on the cultures of the fungus Psilocybe merdaria resulted in the first isolation of 10 compounds including two new ones 11,14-dihydroxylneoechinulin E (1) and (S)-4-(4-methylpent-3-en-1-yl)-butyrolactone (2). Their structures were elucidated from the analysis of 1D and 2D NMR and MS data. Among them, compound 7 showed inhibitory activity against AChE with 20% percentage at a concentration of 50 μg/ml.

Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass.

PubMed

Eichorst, Stephanie A; Joshua, Chijioke; Sathitsuksanoh, Noppadon; Singh, Seema; Simmons, Blake A; Singer, Steven W

2014-12-01

Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of the Firmicutes, the Bacteroidetes, and Deinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Assessing and grouping chemicals applying partial ordering Alkyl anilines as an illustrative example.

PubMed

Carlsen, Lars; Bruggemann, Rainer

2018-06-03

In chemistry there is a long tradition in classification. Usually methods are adopted from the wide field of cluster analysis. Here, based on the example of 21 alkyl anilines we show that also concepts taken out from the mathematical discipline of partially ordered sets may also be applied. The chemical compounds are described by a multi-indicator system. For the present study four indicators, mainly taken from the field of environmental chemistry were applied and a Hasse diagram was constructed. A Hasse diagram is an acyclic, transitively reduced, triangle free graph that may have several components. The crucial question is, whether or not the Hasse diagram can be interpreted from a structural chemical point of view. This is indeed the case, but it must be clearly stated that a guarantee for meaningful results in general cannot be given. For that further theoretical work is needed. Two cluster analysis methods are applied (K-means and a hierarchical cluster method). In both cases the partitioning of the set of 21 compounds by the component structure of the Hasse diagram appears to be better interpretable. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Ellipsoidal analysis of coordination polyhedra

PubMed Central

Cumby, James; Attfield, J. Paul

2017-01-01

The idea of the coordination polyhedron is essential to understanding chemical structure. Simple polyhedra in crystalline compounds are often deformed due to structural complexity or electronic instabilities so distortion analysis methods are useful. Here we demonstrate that analysis of the minimum bounding ellipsoid of a coordination polyhedron provides a general method for studying distortion, yielding parameters that are sensitive to various orders in metal oxide examples. Ellipsoidal analysis leads to discovery of a general switching of polyhedral distortions at symmetry-disallowed transitions in perovskites that may evidence underlying coordination bistability, and reveals a weak off-centre ‘d5 effect' for Fe3+ ions that could be exploited in multiferroics. Separating electronic distortions from intrinsic deformations within the low temperature superstructure of magnetite provides new insights into the charge and trimeron orders. Ellipsoidal analysis can be useful for exploring local structure in many materials such as coordination complexes and frameworks, organometallics and organic molecules. PMID:28146146

Impact of ozone observations on the structure of a tropical cyclone using coupled atmosphere-chemistry data assimilation

NASA Astrophysics Data System (ADS)

Lim, S.; Park, S. K.; Zupanski, M.

2015-04-01

Since the air quality forecast is related to both chemistry and meteorology, the coupled atmosphere-chemistry data assimilation (DA) system is essential to air quality forecasting. Ozone (O3) plays an important role in chemical reactions and is usually assimilated in chemical DA. In tropical cyclones (TCs), O3 usually shows a lower concentration inside the eyewall and an elevated concentration around the eye, impacting atmospheric as well as chemical variables. To identify the impact of O3 observations on TC structure, including atmospheric and chemical information, we employed the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) with an ensemble-based DA algorithm - the maximum likelihood ensemble filter (MLEF). For a TC case that occurred over the East Asia, our results indicate that the ensemble forecast is reasonable, accompanied with larger background state uncertainty over the TC, and also over eastern China. Similarly, the assimilation of O3 observations impacts atmospheric and chemical variables near the TC and over eastern China. The strongest impact on air quality in the lower troposphere was over China, likely due to the pollution advection. In the vicinity of the TC, however, the strongest impact on chemical variables adjustment was at higher levels. The impact on atmospheric variables was similar in both over China and near the TC. The analysis results are validated using several measures that include the cost function, root-mean-squared error with respect to observations, and degrees of freedom for signal (DFS). All measures indicate a positive impact of DA on the analysis - the cost function and root mean square error have decreased by 16.9 and 8.87%, respectively. In particular, the DFS indicates a strong positive impact of observations in the TC area, with a weaker maximum over northeast China.

Ensemble data assimilation of total column ozone using a coupled meteorology-chemistry model and its impact on the structure of Typhoon Nabi (2005)

NASA Astrophysics Data System (ADS)

Lim, S.; Park, S. K.; Zupanski, M.

2015-09-01

Ozone (O3) plays an important role in chemical reactions and is usually incorporated in chemical data assimilation (DA). In tropical cyclones (TCs), O3 usually shows a lower concentration inside the eyewall and an elevated concentration around the eye, impacting meteorological as well as chemical variables. To identify the impact of O3 observations on TC structure, including meteorological and chemical information, we developed a coupled meteorology-chemistry DA system by employing the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) and an ensemble-based DA algorithm - the maximum likelihood ensemble filter (MLEF). For a TC case that occurred over East Asia, Typhoon Nabi (2005), our results indicate that the ensemble forecast is reasonable, accompanied with larger background state uncertainty over the TC, and also over eastern China. Similarly, the assimilation of O3 observations impacts meteorological and chemical variables near the TC and over eastern China. The strongest impact on air quality in the lower troposphere was over China, likely due to the pollution advection. In the vicinity of the TC, however, the strongest impact on chemical variables adjustment was at higher levels. The impact on meteorological variables was similar in both over China and near the TC. The analysis results are verified using several measures that include the cost function, root mean square (RMS) error with respect to observations, and degrees of freedom for signal (DFS). All measures indicate a positive impact of DA on the analysis - the cost function and RMS error have decreased by 16.9 and 8.87 %, respectively. In particular, the DFS indicates a strong positive impact of observations in the TC area, with a weaker maximum over northeastern China.

Isolation and characterization of new lignin streams derived from extractive-ammonia (EA) pretreatment

DOE Office of Scientific and Technical Information (OSTI.GOV)

da Costa Sousa, Leonardo; Foston, Marcus; Bokade, Vijay

One of the key challenges facing lignin conversion to fuels and chemicals is related to the level of carbohydrate and ash impurities found in extracted lignin. Structural modifications of lignin may also occur as a result of biomass pretreatment and harsh lignin extraction protocols. Extractive-Ammonia (EA) is a new pretreatment technology that uses liquid ammonia to cleave lignin–carbohydrate complexes, decrystallize cellulose, solubilize lignin, and selectively extract lignin from lignocellulosic biomass, enabling better utilization of both lignin and carbohydrate components in a biorefinery. The EA-based biorefinery produces two different lignin-rich streams, with different properties, that could potentially be upgraded to fuelsmore » and chemicals using green processes. Here, a water/ethanol-based fractionation method was developed to enrich the ammonia-soluble extractives, resulting in a major product stream containing 92% lignin. Detailed characterization of the various streams resulting from EA treatment, including compositional analysis, structural characterization by nuclear magnetic resonance (NMR) spectrometry, elemental analysis, molecular weight analysis, and thermo-gravimetric analysis provides a broad evaluation of the EA-derived lignin product stream structures and properties, assessing their potential for commercial applications. In conclusion, EA-derived lignins preserve much of lignin's functionality, including the sensitive β-aryl ether units. Furthermore, we observed nitrogen incorporation in the lignin-rich streams, notably due to the presence of hydroxycinnamoyl amides formed during ammonia pretreatment.« less

Quantitative Structure-Cytotoxicity Relationship of Cinnamic Acid Phenetyl Esters.

PubMed

Uesawa, Yoshihiro; Sakagami, Hiroshi; Okudaira, Noriyuki; Toda, Kazuhiro; Takao, Koichi; Kagaya, Hajime; Sugita, Yoshiaki

2018-02-01

Many phenolic acid phenethyl esters possess diverse biological effects including antioxidant, cytoprotective, anti-inflammation and anti-tumor activities. However, most previous antitumor studies have not considered the cytotoxicity against normal cells. Ten cinnamic acid phenetyl esters were subjected to quantitative structure-activity relationship (QSAR) analysis, based on their cytotoxicity and tumor-specificity, in order to find their new biological activities. Cytotoxicity against four human oral squamous cell carcinoma cell lines and three oral normal mesenchymal cells was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Tumor specificity (TS) was evaluated by the ratio of the mean 50% cytotoxic concentration (CC 50 ) against normal oral cells to that against human oral squamous cell carcinoma cell lines. Potency-selectivity expression (PSE) value was calculated by dividing the TS value by CC 50 against tumor cells. Apoptosis markers were detected by western blot analysis. Physicochemical, structural and quantum-chemical parameters were calculated based on the conformations optimized by force-field minimization. Western blot analysis demonstrated that [ 9 ] stimulated the cleavage of caspase-3, suggesting the induction of apoptosis. QSAR analysis demonstrated that TS values were correlated with shape, size and ionization potential. Chemical modification of the lead compound may be a potential choice for designing a new type of anticancer drugs. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

A correlative study on data from pork carcass and processed meat (Bauernspeck) for automatic estimation of chemical parameters by means of near-infrared spectroscopy.

PubMed

Boschetti, Lucio; Ottavian, Matteo; Facco, Pierantonio; Barolo, Massimiliano; Serva, Lorenzo; Balzan, Stefania; Novelli, Enrico

2013-11-01

The use of near-infrared spectroscopy (NIRS) is proposed in this study for the characterization of the quality parameters of a smoked and dry-cured meat product known as Bauernspeck (originally from Northern Italy), as well as of some technological traits of the pork carcass used for its manufacturing. In particular, NIRS is shown to successfully estimate several key quality parameters (including water activity, moisture, dry matter, ash and protein content), suggesting its suitability for real time application in replacement of expensive and time consuming chemical analysis. Furthermore, a correlative approach based on canonical correlation analysis was used to investigate the spectral regions that are mostly correlated to the characteristics of interest. The identification of these regions, which can be linked to the absorbance of the main functional chemical groups, is intended to provide a better understanding of the chemical structure of the substrate under investigation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Hyperspectral infrared nanoimaging of organic samples based on Fourier transform infrared nanospectroscopy

PubMed Central

Amenabar, Iban; Poly, Simon; Goikoetxea, Monika; Nuansing, Wiwat; Lasch, Peter; Hillenbrand, Rainer

2017-01-01

Infrared nanospectroscopy enables novel possibilities for chemical and structural analysis of nanocomposites, biomaterials or optoelectronic devices. Here we introduce hyperspectral infrared nanoimaging based on Fourier transform infrared nanospectroscopy with a tunable bandwidth-limited laser continuum. We describe the technical implementations and present hyperspectral infrared near-field images of about 5,000 pixel, each one covering the spectral range from 1,000 to 1,900 cm−1. To verify the technique and to demonstrate its application potential, we imaged a three-component polymer blend and a melanin granule in a human hair cross-section, and demonstrate that multivariate data analysis can be applied for extracting spatially resolved chemical information. Particularly, we demonstrate that distribution and chemical interaction between the polymer components can be mapped with a spatial resolution of about 30 nm. We foresee wide application potential of hyperspectral infrared nanoimaging for valuable chemical materials characterization and quality control in various fields ranging from materials sciences to biomedicine. PMID:28198384

Chemical composition and biological activity of ripe pumpkin fruits (Cucurbita pepo L.) cultivated in Egyptian habitats.

PubMed

Badr, Sherif E A; Shaaban, Mohamed; Elkholy, Yehya M; Helal, Maher H; Hamza, Akila S; Masoud, Mohamed S; El Safty, Mounir M

2011-09-01

The chemical composition and biological activity of three parts (rind, flesh and seeds) of pumpkin fruits (Cucurbita pepo L.) cultivated in Egypt were studied. Chemical analysis of fibre, protein, β-carotene, carbohydrates, minerals and fatty acids present in the rind, flesh, seeds and defatted seeds meal was conducted. Chemical, GC-MS and biological assays of organic extracts of the main fruit parts, rind and flesh established their unique constituents. Chromatographic purification of the extracts afforded triglyceride fatty acid mixture (1), tetrahydro-thiophene (2), linoleic acid (3), calotropoleanly ester (4), cholesterol (5) and 13(18)-oleanen-3-ol (6). GC-MS analysis of the extract's unpolar fraction revealed the existence of dodecane and tetradecane. Structures of the isolated compounds (1-6) were confirmed by NMR and EI-MS spectrometry. Antimicrobial, antiviral and antitumour activities of the fruit parts were discussed. The promising combined extract of rind and flesh was biologically studied for microbial and cytotoxic activities in comparison with the whole isolated components.

Hyperspectral infrared nanoimaging of organic samples based on Fourier transform infrared nanospectroscopy

NASA Astrophysics Data System (ADS)

Amenabar, Iban; Poly, Simon; Goikoetxea, Monika; Nuansing, Wiwat; Lasch, Peter; Hillenbrand, Rainer

2017-02-01

Infrared nanospectroscopy enables novel possibilities for chemical and structural analysis of nanocomposites, biomaterials or optoelectronic devices. Here we introduce hyperspectral infrared nanoimaging based on Fourier transform infrared nanospectroscopy with a tunable bandwidth-limited laser continuum. We describe the technical implementations and present hyperspectral infrared near-field images of about 5,000 pixel, each one covering the spectral range from 1,000 to 1,900 cm-1. To verify the technique and to demonstrate its application potential, we imaged a three-component polymer blend and a melanin granule in a human hair cross-section, and demonstrate that multivariate data analysis can be applied for extracting spatially resolved chemical information. Particularly, we demonstrate that distribution and chemical interaction between the polymer components can be mapped with a spatial resolution of about 30 nm. We foresee wide application potential of hyperspectral infrared nanoimaging for valuable chemical materials characterization and quality control in various fields ranging from materials sciences to biomedicine.

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

EPA Pesticide Factsheets

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

Interrelationships among carcinogenicity, mutagenicity, acute toxicity, and chemical structure in a genotoxicity data base

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benigni, R.; Andreoli, C.; Giuliani, A.

1989-01-01

The interrelationships among carcinogenicity, mutagenicity, acute toxicity (LD50), and a number of molecular descriptors were studied by computerized data analysis methods on the data base generated by the International Program for the Evaluation of Short-Term Test for Carcinogens (IPESTTC). With the use of statistical regression methods, three main associations were evidenced: (1) the well-known correlation between carcinogenicity and mutagenicity; (2) a correlation between mutagenicity and toxicity (LD50 ip in mice); and (3) a correlation between toxicity and a recently introduced estimator of the free energy of binding of the molecules to biological receptors. As expected on the basis of themore » large variety of chemical classes represented in the IPESTTC data base, no simple relationship between mutagenicity or carcinogenicity and chemical descriptors was found. To overcome this problem, a new pattern recognition method (REPAD), developed by us for structure-activity studies of noncongeneric chemicals, has been used. This allowed us to highlight a significant difference between the whole patterns of relationships among chemicophysical variables in the two groups to active (mutagenicity and/or carcinogenic) and inactive chemicals. This approach generated a classification rule able to correctly assign about 80% of carcinogens or mutagens.« less

(3, 2)D 1H, 13C BIRDr,X-HSQC-TOCSY for NMR structure elucidation of mixtures: application to complex carbohydrates.

PubMed

Brodaczewska, Natalia; Košťálová, Zuzana; Uhrín, Dušan

2018-02-01

Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of 1 H chemical shifts; larger dispersion of 13 C chemical shifts is often used to reduce this overlap, while still providing the proton-proton correlation information e.g. in the form of a 2D 1 H, 13 C HSQC-TOCSY experiment. For this methodology to work, 13 C chemical shift must be resolved. In case of 13 C chemical shifts overlap, 1 H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D 1 H, 13 C BIRD r,X -HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F 1 dimension. The required high-resolution in the 13 C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.

Neutron diffraction study of the martensitic transformation and chemical order in Heusler alloy Ni 1.91Mn 1.29Ga 0.8

DOE PAGES

Ari-Gur, Pnina; Garlea, Vasile O.; Cao, Huibo; ...

2015-11-05

In this study, Heusler alloys of Ni-Mn-Ga compositions demonstrate ferromagnetic shape memory effect in the martensitic state. The transformation temperature and the chemical order depend strongly on the composition. In the current work, the structure and chemical order of the martensitic phase of Ni 1.91Mn 1.29Ga 0.8 were studied using neutron diffraction; the diffraction pattern was refined using the FullProf software. It was determined that the structural transition occurs around 330 K. At room temperature, 300 K, which is below the martensite transformation temperature, all the Bragg reflections can be described by a monoclinic lattice with a symmetry of spacemore » group P 1 2/m 1 and lattice constants of a = 4.23047(7) [Å], b = 5.58333(6) [Å], c = 21.0179(2) [Å], beta = 90.328(1). The chemical order is of critical importance in these alloys, and it was previously studied at 363 K. Analysis of the neutron diffraction in the monoclinic phase shows that the chemical order is maintained during the martensitic transformation.« less

Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.

PubMed

Sahakyan, Aleksandr B; Vendruscolo, Michele

2013-02-21

Ring current and electric field effects can considerably influence NMR chemical shifts in biomolecules. Understanding such effects is particularly important for the development of accurate mappings between chemical shifts and the structures of nucleic acids. In this work, we first analyzed the Pople and the Haigh-Mallion models in terms of their ability to describe nitrogen base conjugated ring effects. We then created a database (DiBaseRNA) of three-dimensional arrangements of RNA base pairs from X-ray structures, calculated the corresponding chemical shifts via a hybrid density functional theory approach and used the results to parametrize the ring current and electric field effects in RNA bases. Next, we studied the coupling of the electric field and ring current effects for different inter-ring arrangements found in RNA bases using linear model fitting, with joint electric field and ring current, as well as only electric field and only ring current approximations. Taken together, our results provide a characterization of the interdependence of ring current and electric field geometric factors, which is shown to be especially important for the chemical shifts of non-hydrogen atoms in RNA bases.

Magic-angle spinning NMR of a class I filamentous bacteriophage virus.

PubMed

Abramov, Gili; Morag, Omry; Goldbourt, Amir

2011-08-11

The fd bacteriophage is a filamentous virus that is widely used for bio- and nanotechnology applications ranging from phage display to battery materials. The possibility of obtaining a detailed description of its structural properties regardless of its state is therefore essential not only for understanding its physical arrangement and its bacterial infection process but also for many other applications. Here we present a study of the fd phage by magic-angle spinning solid-state NMR. While current structures rely on a Y21M mutant, experiments performed on a strain bearing a wild-type capsid report on high symmetry of the phage and lack of explicit subunit polymorphism. Chemical shift analysis confirmed that the coat protein mostly consists of a rigid right-handed curved α-helix (residues 6-47 of 50), preceded by a flexible loop-structured N-terminus. We were able to qualitatively assign the resonances belonging to the DNA, including the deoxyribose sugars and the thymine bases. These chemical shifts are consistent with base stacking and a C2'-endo/C3'-exo sugar pucker. © 2011 American Chemical Society

Structural, vibrational, electronic investigations and quantum chemical studies of 2-amino-4-methoxybenzothiazole.

PubMed

Arjunan, V; Raj, Arushma; Santhanam, R; Marchewka, M K; Mohan, S

2013-02-01

Extensive vibrational investigations of 2-amino-4-methoxybenzothiazole have been carried out with FTIR and FT-Raman spectral techniques. The electronic structure of the molecule has been analysed by UV-Visible and NMR spectroscopies. The DFT studies were carried out with B3LYP and HF methods utilising 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets to determine the structural, thermodynamical, vibrational, electronic characteristics of the compound and also to understand the electronic and steric influence of the methoxy amino groups on the skeletal frequencies. The mixing of the fundamental modes was determined with the help of total energy distribution (TED). The energies of the frontier molecular orbitals have also been determined. The kinetic and thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intramolecular electronic interactions and their stabilisation energy. (1)H and (13)C NMR chemical shifts and the electronic transitions of the molecule are also discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

Combined EXAFS Spectroscopic and Quantum Chemical Study on the Complex Formation of Am(III) with Formate.

PubMed

Fröhlich, Daniel R; Kremleva, Alena; Rossberg, André; Skerencak-Frech, Andrej; Koke, Carsten; Krüger, Sven; Rösch, Notker; Panak, Petra J

2017-06-19

The complexation of Am(III) with formate in aqueous solution is studied as a function of the pH value using a combination of extended X-ray absorption fine structure (EXAFS) spectroscopy, iterative transformation factor analysis (ITFA), and quantum chemical calculations. The Am L III -edge EXAFS spectra are analyzed to determine the molecular structure (coordination numbers; Am-O and Am-C distances) of the formed Am(III)-formate species and to track the shift of the Am(III) speciation with increasing pH. The experimental data are compared to predictions from density functional calculations. The results indicate that formate binds to Am(III) in a monodentate fashion, in agreement with crystal structures of lanthanide formates. Furthermore, the investigations are complemented by thermodynamic speciation calculations to verify further the results obtained.

The extracellular matrix of Volvox carteri: molecular structure of the cellular compartment.

PubMed

Ertl, H; Mengele, R; Wenzl, S; Engel, J; Sumper, M

1989-12-01

The extracellular matrix (ECM) of Volvox contains insoluble fibrous layers that surround individual cells at a distance to form contiguous cellular compartments. Using immunological techniques, we identified a sulfated surface glycoprotein (SSG 185) as the monomeric precursor of this substructure within the ECM. The primary structure of the SSG 185 poly-peptide chain has been derived from cDNA and genomic DNA. A central domain of the protein, 80 amino acid residues long, consists almost exclusively of hydroxyproline residues. The chemical structure of the highly sulfated polysaccharide covalently attached to SSG 185 has been determined by permethylation analysis. As revealed by EM, SSG 185 is a rod-shaped molecule with a 21-nm-long polysaccharide strand protruding from its central region. The chemical nature of the cross-links between SSG 185 monomers is discussed.

Chemical, Physical, and Biological Factors Shape Littoral Invertebrate Community Structure in Coal-Mining End-Pit Lakes

NASA Astrophysics Data System (ADS)

Luek, Andreas; Rasmussen, Joseph B.

2017-04-01

Aquatic invertebrates form the base of the consumer food web in lakes. In coal-mining end-pit lakes, invertebrates are exposed to an environment with potentially challenging physical and chemical features. We hypothesized that the physical and chemical features of end-pit lakes reduce critical littoral habitat and thus reduce invertebrate diversity, thereby limiting the potential for these lakes to be naturalized. We used a multivariate approach using principle component analysis and redundancy analysis to study relationships between invertebrate community structure, habitat features, and water quality in five end-pit lakes and five natural lakes in the Rocky Mountain foothills of west-central Alberta, Canada. Results show a significantly different invertebrate community structure was present in end-pit lakes as compared with reference lakes in the same region, which could be accounted for by water hardness, conductivity, slope of the littoral zone, and phosphorus concentrations. Habitat diversity in end-pit lakes was also limited, cover provided by macrophytes was scarce, and basin slopes were significantly steeper in pit lakes. Although water chemistry is currently the strongest influencing factor on the invertebrate community, physical challenges of habitat homogeneity and steep slopes in the littoral zones were identified as major drivers of invertebrate community structure. The addition of floating wetlands to the littoral zone of existing pit lakes can add habitat complexity without the need for large-scale alterations to basing morphology, while impermeable capping of waste-rock and the inclusion of littoral habitat in the planning process of new pit lakes can improve the success of integrating new pit lakes into the landscape.

Chemical, Physical, and Biological Factors Shape Littoral Invertebrate Community Structure in Coal-Mining End-Pit Lakes.

PubMed

Luek, Andreas; Rasmussen, Joseph B

2017-04-01

Aquatic invertebrates form the base of the consumer food web in lakes. In coal-mining end-pit lakes, invertebrates are exposed to an environment with potentially challenging physical and chemical features. We hypothesized that the physical and chemical features of end-pit lakes reduce critical littoral habitat and thus reduce invertebrate diversity, thereby limiting the potential for these lakes to be naturalized. We used a multivariate approach using principle component analysis and redundancy analysis to study relationships between invertebrate community structure, habitat features, and water quality in five end-pit lakes and five natural lakes in the Rocky Mountain foothills of west-central Alberta, Canada. Results show a significantly different invertebrate community structure was present in end-pit lakes as compared with reference lakes in the same region, which could be accounted for by water hardness, conductivity, slope of the littoral zone, and phosphorus concentrations. Habitat diversity in end-pit lakes was also limited, cover provided by macrophytes was scarce, and basin slopes were significantly steeper in pit lakes. Although water chemistry is currently the strongest influencing factor on the invertebrate community, physical challenges of habitat homogeneity and steep slopes in the littoral zones were identified as major drivers of invertebrate community structure. The addition of floating wetlands to the littoral zone of existing pit lakes can add habitat complexity without the need for large-scale alterations to basing morphology, while impermeable capping of waste-rock and the inclusion of littoral habitat in the planning process of new pit lakes can improve the success of integrating new pit lakes into the landscape.

Production of Printed Indexes of Chemical Reactions. I. Analysis of Functional Group Interconversions

ERIC Educational Resources Information Center

Clinging, R.; Lynch, M. F.

1973-01-01

A program is described which identifies functional group interconversion reactions, hydrogenations, and dehydrogenations in a data base containing structures encoded as Wiswesser Line Notations. Production of the data base is briefly described. (17 references) (Authors)

Antifungal cyclic peptides from the marine sponge Microscleroderma herdmani

USDA-ARS?s Scientific Manuscript database

Screening natural product extracts from National Cancer Institute Open Repository for antifungal discovery afforded hits for bioassay-guided fractionation. Upon LC-MS analysis of column fractions with antifungal activities to generate information on chemical structure, two new cyclic hexapeptides, m...

Electrochemistry at Nanometer-Scaled Electrodes

ERIC Educational Resources Information Center

Watkins, John J.; Bo Zhang; White, Henry S.

2005-01-01

Electrochemical studies using nanometer-scaled electrodes are leading to better insights into electrochemical kinetics, interfacial structure, and chemical analysis. Various methods of preparing electrodes of nanometer dimensions are discussed and a few examples of their behavior and applications in relatively simple electrochemical experiments…

One new benzyldihydrophenanthrene from Arundina graminifolia.

PubMed

Liu, Mei-Feng; Han, Yun; Xing, Dong-Ming; Wang, Wei; Xu, Li-Zhen; Du, Li-Jun; Ding, Yi

2005-10-01

A novel benzyldihydrophenanthrene named arundinaol has been isolated from the rhizoma of Arundina graminifolia. The structure of has been elucidated as 7-hydroxy-1-(p-hydroxybenzyl)-2,4-dimethoxy-9,10-dihydrophenanthrene on the basis of physical and chemical evidence and spectral analysis.

Optimizing use of the structural chemical analyser (variable pressure FESEM-EDX Raman spectroscopy) on micro-size complex historical paintings characterization.

PubMed

Guerra, I; Cardell, C

2015-10-01

The novel Structural Chemical Analyser (hyphenated Raman spectroscopy and scanning electron microscopy equipped with an X-ray detector) is gaining popularity since it allows 3-D morphological studies and elemental, molecular, structural and electronic analyses of a single complex micro-sized sample without transfer between instruments. However, its full potential remains unexploited in painting heritage where simultaneous identification of inorganic and organic materials in paintings is critically yet unresolved. Despite benefits and drawbacks shown in literature, new challenges have to be faced analysing multifaceted paint specimens. SEM-Structural Chemical Analyser systems differ since they are fabricated ad hoc by request. As configuration influences the procedure to optimize analyses, likewise analytical protocols have to be designed ad hoc. This paper deals with the optimization of the analytical procedure of a Variable Pressure Field Emission scanning electron microscopy equipped with an X-ray detector Raman spectroscopy system to analyse historical paint samples. We address essential parameters, technical challenges and limitations raised from analysing paint stratigraphies, archaeological samples and loose pigments. We show that accurate data interpretation requires comprehensive knowledge of factors affecting Raman spectra. We tackled: (i) the in-FESEM-Raman spectroscopy analytical sequence, (ii) correlations between FESEM and Structural Chemical Analyser/laser analytical position, (iii) Raman signal intensity under different VP-FESEM vacuum modes, (iv) carbon deposition on samples under FESEM low-vacuum mode, (v) crystal nature and morphology, (vi) depth of focus and (vii) surface-enhanced Raman scattering effect. We recommend careful planning of analysis strategies prior to research which, although time consuming, guarantees reliable results. The ultimate goal of this paper is to help to guide future users of a FESEM-Structural Chemical Analyser system in order to increase applications. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action.

PubMed

Nelson, Justin; Simpkins, Scott W; Safizadeh, Hamid; Li, Sheena C; Piotrowski, Jeff S; Hirano, Hiroyuki; Yashiroda, Yoko; Osada, Hiroyuki; Yoshida, Minoru; Boone, Charles; Myers, Chad L

2018-04-01

Chemical-genomic approaches that map interactions between small molecules and genetic perturbations offer a promising strategy for functional annotation of uncharacterized bioactive compounds. We recently developed a new high-throughput platform for mapping chemical-genetic (CG) interactions in yeast that can be scaled to screen large compound collections, and we applied this system to generate CG interaction profiles for more than 13 000 compounds. When integrated with the existing global yeast genetic interaction network, CG interaction profiles can enable mode-of-action prediction for previously uncharacterized compounds as well as discover unexpected secondary effects for known drugs. To facilitate future analysis of these valuable data, we developed a public database and web interface named MOSAIC. The website provides a convenient interface for querying compounds, bioprocesses (Gene Ontology terms) and genes for CG information including direct CG interactions, bioprocesses and gene-level target predictions. MOSAIC also provides access to chemical structure information of screened molecules, chemical-genomic profiles and the ability to search for compounds sharing structural and functional similarity. This resource will be of interest to chemical biologists for discovering new small molecule probes with specific modes-of-action as well as computational biologists interested in analysing CG interaction networks. MOSAIC is available at http://mosaic.cs.umn.edu. hisyo@riken.jp, yoshidam@riken.jp, charlie.boone@utoronto.ca or chadm@umn.edu. Supplementary data are available at Bioinformatics online.

Capturing Nature's Diversity

PubMed Central

Pascolutti, Mauro; Campitelli, Marc; Nguyen, Bao; Pham, Ngoc; Gorse, Alain-Dominique; Quinn, Ronald J.

2015-01-01

Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a high proportion of the individual molecular interaction motifs embedded within natural products using a fragment screening library spanning 422 structural clusters and comprised of approximately 2800 natural products. PMID:25902039

Isolation and Characterization of Gramineae and Fabaceae Soda Lignins

PubMed Central

Domínguez-Robles, Juan; Sánchez, Rafael; Espinosa, Eduardo; Savy, Davide; Mazzei, Pierluigi; Piccolo, Alessandro; Rodríguez, Alejandro

2017-01-01

Some agricultural residues such as wheat or barley straw, as well as certain fast-growing plants like Leucaena leucocephala and Chamaecytisus proliferus, could be used as raw materials for the paper industry as an alternative to traditional plants (eucalyptus, pine, etc.). In the present study, four types of lignin obtained from the spent liquors produced by the pulping processes using the abovementioned feedstocks were isolated and characterized. Lignin samples were acquired through an acid precipitation from these spent liquors. The characterization of the precipitated lignin samples were performed using a Fourier transform infrared spectroscopy (FT-IR) and both liquid- and solid-state nuclear magnetic resonance spectroscopy (NMR) to analyse the chemical structure, and thermogravimetric analysis (TGA) for determining the thermal properties. Additionally, chemical composition of lignin fractions was also measured. Even though they were of different botanical origin, all the studied samples except for wheat straw lignin had a similar chemical composition and thermal behaviour, and identical chemical structure. Wheat straw lignin showed a greater amount of Klason lignin and lower carbohydrate content. Furthermore, this lignin sample showed a higher thermal stability and significantly different cross-peak patterns in the 2D-NMR experiments. The molecular structures corresponding to p-coumarate (PCA), ferulate (FA) and cinnamyl aldehyde end-groups (J) were only detected in wheat isolated lignin. PMID:28165411

Isolation and Characterization of Gramineae and Fabaceae Soda Lignins.

PubMed

Domínguez-Robles, Juan; Sánchez, Rafael; Espinosa, Eduardo; Savy, Davide; Mazzei, Pierluigi; Piccolo, Alessandro; Rodríguez, Alejandro

2017-02-04

Some agricultural residues such as wheat or barley straw, as well as certain fast-growing plants like Leucaena leucocephala and Chamaecytisus proliferus , could be used as raw materials for the paper industry as an alternative to traditional plants (eucalyptus, pine, etc.). In the present study, four types of lignin obtained from the spent liquors produced by the pulping processes using the abovementioned feedstocks were isolated and characterized. Lignin samples were acquired through an acid precipitation from these spent liquors. The characterization of the precipitated lignin samples were performed using a Fourier transform infrared spectroscopy (FT-IR) and both liquid- and solid-state nuclear magnetic resonance spectroscopy (NMR) to analyse the chemical structure, and thermogravimetric analysis (TGA) for determining the thermal properties. Additionally, chemical composition of lignin fractions was also measured. Even though they were of different botanical origin, all the studied samples except for wheat straw lignin had a similar chemical composition and thermal behaviour, and identical chemical structure. Wheat straw lignin showed a greater amount of Klason lignin and lower carbohydrate content. Furthermore, this lignin sample showed a higher thermal stability and significantly different cross-peak patterns in the 2D-NMR experiments. The molecular structures corresponding to p -coumarate (PCA), ferulate (FA) and cinnamyl aldehyde end-groups (J) were only detected in wheat isolated lignin.

Exploring the structure-activity relations of N-carbethoxyphthalimide by combining FTIR, FT-Raman and NMR spectroscopy with DFT electronic structure method.

PubMed

Arjunan, V; Govindaraja, S Thillai; Ravindran, P; Mohan, S

2014-01-01

The complete vibrational assignment and analysis of N-carbethoxyphthalimide were carried out using the experimental FTIR and FT-Raman data in the range 4000-450 and 4000-100 cm(-1), respectively along with quantum chemical studies of the compound using DFT-B3LYP gradient calculations employing the 6-31G**, 6-311++G** and cc-pVDZ basis sets. The 1H (400 MHz; CDCl3) and 13C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra were also recorded. Due to the partial ionic nature of the carbonyl group, the carbon atoms C1 and C3 in NCEP show downfield effect and the corresponding observed chemical shift of both are observed at 163.76 ppm and the carbon atom C16 in the carbethoxy group also give signal in the downfield at 148.45 ppm. The active sites are determined by molecular electrostatic potential. The possible electronic transitions are determined by HOMO and LUMO orbital shapes and their energies. The structure-chemical reactivity relations of the compound were determined through chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. Copyright © 2013 Elsevier B.V. All rights reserved.

A chemical proteomics approach for global analysis of lysine monomethylome profiling.

PubMed

Wu, Zhixiang; Cheng, Zhongyi; Sun, Mingwei; Wan, Xuelian; Liu, Ping; He, Tieming; Tan, Minjia; Zhao, Yingming

2015-02-01

Methylation of lysine residues on histone proteins is known to play an important role in chromatin structure and function. However, non-histone protein substrates of this modification remain largely unknown. An effective approach for system-wide analysis of protein lysine methylation, particularly lysine monomethylation, is lacking. Here we describe a chemical proteomics approach for global screening for monomethyllysine substrates, involving chemical propionylation of monomethylated lysine, affinity enrichment of the modified monomethylated peptides, and HPLC/MS/MS analysis. Using this approach, we identified with high confidence 446 lysine monomethylation sites in 398 proteins, including three previously unknown histone monomethylation marks, representing the largest data set of protein lysine monomethylation described to date. Our data not only confirms previously discovered lysine methylation substrates in the nucleus and spliceosome, but also reveals new substrates associated with diverse biological processes. This method hence offers a powerful approach for dynamic study of protein lysine monomethylation under diverse cellular conditions and in human diseases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Use of valence band Auger electron spectroscopy to study thin film growth: oxide and diamond-like carbon films

NASA Astrophysics Data System (ADS)

Steffen, H. J.

1994-12-01

It is demonstrated how Auger line shape analysis with factor analysis (FA), least-squares fitting and even simple peak height measurements may provide detailed information about the composition, different chemical states and also defect concentration or crystal order. Advantage is taken of the capability of Auger electron spectroscopy to give valence band structure information with high surface sensitivity and the special aspect of FA to identify and discriminate quantitatively unknown chemical species. Valence band spectra obtained from Ni, Fe, Cr and NiFe40Cr20 during oxygen exposure at room temperature reveal the oxidation process in the initial stage of the thin layer formation. Furthermore, the carbon chemical states that were formed during low energy C(+) and Ne(+) ion irradiation of graphite are delineated and the evolution of an amorphous network with sp3 bonds is disclosed. The analysis represents a unique method to quantify the fraction of sp3-hybridized carbon in diamond-like materials.

Functional RNA structures throughout the Hepatitis C Virus genome.

PubMed

Adams, Rebecca L; Pirakitikulr, Nathan; Pyle, Anna Marie

2017-06-01

The single-stranded Hepatitis C Virus (HCV) genome adopts a set of elaborate RNA structures that are involved in every stage of the viral lifecycle. Recent advances in chemical probing, sequencing, and structural biology have facilitated analysis of RNA folding on a genome-wide scale, revealing novel structures and networks of interactions. These studies have underscored the active role played by RNA in every function of HCV and they open the door to new types of RNA-targeted therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural analysis of photosystem I polypeptides using chemical crosslinking

NASA Technical Reports Server (NTRS)

Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

1994-01-01

Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

Stochastic flux analysis of chemical reaction networks

PubMed Central

2013-01-01

Background Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. Results We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. Conclusions We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network. PMID:24314153

Stochastic flux analysis of chemical reaction networks.

PubMed

Kahramanoğulları, Ozan; Lynch, James F

2013-12-07

Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network.

[Studies on chemical constituents from leaves of Vaccinium bracteatum].

PubMed

Li, Zeng-Liang; Zhang, Lin; Tian, Jing-Kui; Zhou, Wen-Ming

2008-09-01

To investigate the chemical constituents from the leaves of Vaccinium bracteatum. Many column chromatographic techniques were used for the isolation and separation of chemical constituents. Their structures were elucidated on the basis of spectral analysis and chemical evidences. Twelve compounds were isolated from the plant, and they were identified as chrysoeriol (1), scopoletin (2), trans-p-hydroxycinnamic acid (3), trans-p-hydroxycinnamic acid ethyl ester (4), cafeic acid ethyl ester (5), beta-sitosterol (6), iuteolin (7), quercetin (8), esculetin (9), cafeic acid (10), isolariciresinol-9-O-beta-D-xyloside (11), 10-O-trans-p-coumaroylsandoside (12). Compounds 4, 5, 11, 12 were isolated from the genus Vaccinium for the first time, and compounds 1, 2, 9, 10 were isolated from this plant for the first time.

A volumetric ablation model of EPDM considering complex physicochemical process in porous structure of char layer

NASA Astrophysics Data System (ADS)

Yang, Liu; Xiao-Jing, Yu; Jian-Ming, Ma; Yi-Wen, Guan; Jiang, Li; Qiang, Li; Sa, Yang

2017-06-01

A volumetric ablation model for EPDM (ethylene- propylene-diene monomer) is established in this paper. This model considers the complex physicochemical process in the porous structure of a char layer. An ablation physics model based on a porous structure of a char layer and another model of heterogeneous volumetric ablation char layer physics are then built. In the model, porosity is used to describe the porous structure of a char layer. Gas diffusion and chemical reactions are introduced to the entire porous structure. Through detailed formation analysis, the causes of the compact or loose structure in the char layer and chemical vapor deposition (CVD) reaction between pyrolysis gas and char layer skeleton are introduced. The Arrhenius formula is adopted to determine the methods for calculating carbon deposition rate C which is the consumption rate caused by thermochemical reactions in the char layer, and porosity evolution. The critical porosity value is used as a criterion for char layer porous structure failure under gas flow and particle erosion. This critical porosity value is obtained by fitting experimental parameters and surface porosity of the char layer. Linear ablation and mass ablation rates are confirmed with the critical porosity value. Results of linear ablation and mass ablation rate calculations generally coincide with experimental results, suggesting that the ablation analysis proposed in this paper can accurately reflect practical situations and that the physics and mathematics models built are accurate and reasonable.

Metabolic biotransformation half-lives in fish: QSAR modeling and consensus analysis.

PubMed

Papa, Ester; van der Wal, Leon; Arnot, Jon A; Gramatica, Paola

2014-02-01

Bioaccumulation in fish is a function of competing rates of chemical uptake and elimination. For hydrophobic organic chemicals bioconcentration, bioaccumulation and biomagnification potential are high and the biotransformation rate constant is a key parameter. Few measured biotransformation rate constant data are available compared to the number of chemicals that are being evaluated for bioaccumulation hazard and for exposure and risk assessment. Three new Quantitative Structure-Activity Relationships (QSARs) for predicting whole body biotransformation half-lives (HLN) in fish were developed and validated using theoretical molecular descriptors that seek to capture structural characteristics of the whole molecule and three data set splitting schemes. The new QSARs were developed using a minimal number of theoretical descriptors (n=9) and compared to existing QSARs developed using fragment contribution methods that include up to 59 descriptors. The predictive statistics of the models are similar thus further corroborating the predictive performance of the different QSARs; Q(2)ext ranges from 0.75 to 0.77, CCCext ranges from 0.86 to 0.87, RMSE in prediction ranges from 0.56 to 0.58. The new QSARs provide additional mechanistic insights into the biotransformation capacity of organic chemicals in fish by including whole molecule descriptors and they also include information on the domain of applicability for the chemical of interest. Advantages of consensus modeling for improving overall prediction and minimizing false negative errors in chemical screening assessments, for identifying potential sources of residual error in the empirical HLN database, and for identifying structural features that are not well represented in the HLN dataset to prioritize future testing needs are illustrated. © 2013.

Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations

NASA Astrophysics Data System (ADS)

Suhasini, M.; Sailatha, E.; Gunasekaran, S.; Ramkumaar, G. R.

2015-04-01

A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the 13C and 1H NMR chemical shifts of Carbamazepine.

Structural and magnetic properties of nanocomposite iron-containing SiCxNy films

NASA Astrophysics Data System (ADS)

Pushkarev, R. V.; Fainer, N. I.; Maurya, K. K.

2017-02-01

New ferromagnetic films with composition SiCxNyFez were synthesized using chemical vapor deposition technique. Films were deposited using ferrocene, 1,1,1,3,3,3-hexamethyldisilazane (HMDS) and hydrogen gaseous mixture. Chemical and phase composition of the films were studied by FTIR, Raman spectroscopy and X-ray diffraction with grazing incidence (GI-XRD). FTIR spectra analysis confirmed the existence of Si-C and Si-N bonds. Graphite inclusions and amorphous carbon were determined by Raman spectra analysis. The surface of the SiCxNyFez films studied by SEM is covered by nanocrystallites of iron oxide Fe3O4 phase. The main purpose of GI-XRD analysis is to describe the layered structure of the films in detail. It was shown by GI-XRD study, that phase composition of the SiCxNyFez films varies from iron oxide Fe3O4 to iron silicide Fe3Si and silicon carbide SiC with the deposition temperature growing. It was established, that SiCxNyFez films are perspective for application in the spintronic field.

Chemical Analysis of Cellular and Extracellular Carbohydrates of a Biofilm-Forming Strain Pseudomonas aeruginosa PA14

PubMed Central

Coulon, Charlène; Vinogradov, Evgeny; Filloux, Alain; Sadovskaya, Irina

2010-01-01

Background Pseudomonas aeruginosa is a Gram-negative bacterium and an opportunistic pathogen, which causes persisting life-threatening infections in cystic fibrosis (CF) patients. Biofilm mode of growth facilitates its survival in a variety of environments. Most P. aeruginosa isolates, including the non-mucoid laboratory strain PA14, are able to form a thick pellicle, which results in a surface-associated biofilm at the air-liquid (A–L) interface in standing liquid cultures. Exopolysaccharides (EPS) are considered as key components in the formation of this biofilm pellicle. In the non-mucoid P. aeruginosa strain PA14, the “scaffolding” polysaccharides of the biofilm matrix, and the molecules responsible for the structural integrity of rigid A–L biofilm have not been identified. Moreover, the role of LPS in this process is unclear, and the chemical structure of the LPS O-antigen of PA14 has not yet been elucidated. Principal Findings In the present work we carried out a systematic analysis of cellular and extracellular (EC) carbohydrates of P. aeruginosa PA14. We also elucidated the chemical structure of the LPS O-antigen by chemical methods and 2-D NMR spectroscopy. Our results showed that it is composed of linear trisaccharide repeating units, identical to those described for P. aeruginosa Lanýi type O:2a,c (Lanýi-Bergman O-serogroup 10a, 10c; IATS serotype 19) and having the following structure: -4)-α-L-GalNAcA-(1–3)-α-D-QuiNAc-(1–3)- α-L-Rha-(1-. Furthermore, an EC O-antigen polysaccharide (EC O-PS) and the glycerol-phosphorylated cyclic β-(1,3)-glucans were identified in the culture supernatant of PA14, grown statically in minimal medium. Finally, the extracellular matrix of the thick biofilm formed at the A-L interface contained, in addition to eDNA, important quantities (at least ∼20% of dry weight) of LPS-like material. Conclusions We characterized the chemical structure of the LPS O-antigen and showed that the O-antigen polysaccharide is an abundant extracellular carbohydrate of PA14. We present evidence that LPS-like material is found as a component of a biofilm matrix of P. aeruginosa. PMID:21151973

ANALYSIS OF SECONDARY ORGANIC AEROSOL COMPOUNDS FROM THE PHOTOOXIDATION OF D-LIMONENE IN THE PRESENCE OF NO X AND THEIR DETECTION IN AMBIENT PM 2.5

EPA Science Inventory

Chemical analysis of secondary organic aerosol (SOA) from the photooxidation of a d-limonene/NOx/air mixture was carried out. SOA, generated in a smog chamber, was collected on Zefluor filters. To determine the structural characteristics of the compounds, the filter sample...