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

Science.gov (United States)

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.

Synthesis, Crystal Structure, and Chemical-Bonding Analysis of BaZn(NCN2

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Alex J. Corkett

2017-12-01

Full Text Available The ternary carbodiimide BaZn(NCN2 was prepared by a solid-state metathesis reaction between BaF2, ZnF2, and Li2NCN in a 1:1:2 molar ratio, and its crystal structure was determined from Rietveld refinement of X-ray data. BaZn(NCN2 represents the aristotype of the LiBa2Al(NCN4 structure which is unique to carbodiimide/cyanamide chemistry and is well regarded as being constructed from ZnN4 tetrahedra, sharing edges and vertices through NCN2− units to form corrugated layers with Ba2+ in the interlayer voids. Structural anomalies in the shape of the cyanamide units are addressed via IR spectrometry and DFT calculations, which suggest the presence of slightly bent N=C=N2− carbodiimide units with C2v symmetry. Moreover, chemical-bonding analysis within the framework of crystal orbital Hamilton population (COHP reveals striking similarities between the bonding interactions in BaZn(NCN2 and SrZn(NCN2 despite their contrasting crystal structures. BaZn(NCN2 is only the second example of a ternary post-transition metal carbodiimide, and its realization paves the way for the preparation of analogues featuring divalent transition metals at the tetrahedral Zn2+ site.

Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

Science.gov (United States)

Kumari, Amrita; Dorai, Kavita

2013-06-01

NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

International Nuclear Information System (INIS)

Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

2001-01-01

An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

Extracting and connecting chemical structures from text sources using chemicalize.org.

Science.gov (United States)

Southan, Christopher; Stracz, Andras

2013-04-23

Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 million from patents) the extent of public inter-document and document-to-database links is still well below any estimated total, especially for journal articles. A major expansion in access to text-entombed chemistry is enabled by chemicalize.org. This on-line resource can process IUPAC names, SMILES, InChI strings, CAS numbers and drug names from pasted text, PDFs or URLs to generate structures, calculate properties and launch searches. Here, we explore its utility for answering questions related to chemical structures in documents and where these overlap with database records. These aspects are illustrated using a common theme of Dipeptidyl Peptidase 4 (DPPIV) inhibitors. Full-text open URL sources facilitated the download of over 1400 structures from a DPPIV patent and the alignment of specific examples with IC50 data. Uploading the SMILES to PubChem revealed extensive linking to patents and papers, including prior submissions from chemicalize.org as submitting source. A DPPIV medicinal chemistry paper was completely extracted and structures were aligned to the activity results table, as well as linked to other documents via PubChem. In both cases, key structures with data were partitioned from common chemistry by dividing them into individual new PDFs for conversion. Over 500 structures were also extracted from a batch of PubMed abstracts related to DPPIV inhibition. The drug structures could be stepped through each text occurrence and included some converted MeSH-only IUPAC names not linked in PubChem. Performing set intersections proved effective for detecting compounds-in-common between documents and merged extractions. This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and

A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL

Directory of Open Access Journals (Sweden)

Andrei A. Gakh

2006-03-01

Full Text Available A compact Modular Chemical Descriptor Language (MCDL chemical structure editor (Java applet is described. The small size (approximately 200 KB of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI.

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

Science.gov (United States)

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.

The PubChem chemical structure sketcher

Directory of Open Access Journals (Sweden)

Ihlenfeldt Wolf D

2009-12-01

Full Text Available Abstract PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.

ACToR Chemical Structure processing using Open Source ...

Science.gov (United States)

ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

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

Science.gov (United States)

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.

Advanced chemical analysis service for elements, radionuclides and phases

International Nuclear Information System (INIS)

Sansoni, B.

1986-01-01

A review is given on the structure, organisation and performance of the chemical analysis service of the Central Department for Chemical Analysis at the Kernforschungsanlage Juelich GmbH. The research and development programs together with the infrastructure of the Centre afford to analyse almost all stable elements of the periodical table in almost any material. The corresponding chemical analysis service has been organized according to a new modular system of analytical steps. According to this, the most complicated and, therefore, most general case of an analytical scheme for element and radionuclide analysis in any type of material can be differentiated into about 14 different steps, the modules. They are more or less independent of the special problem. The laboratory is designed and organized according to these steps. (orig./PW) [de

Structural-chemical characteristics of implanted metals

International Nuclear Information System (INIS)

Kozejkin, B.V.; Pavlov, P.V.; Pitirimova, E.A.; Frolov, A.I.

1988-01-01

Corrosion and structural characteristics of metallic layers implanted by ions of chemically active impurities and noble gases are studied. Dependence of experimental results on parameters of initial materials and technological conditions of implantation is established. In studying corrosion characteristics of implanted metals a strong dependence of chemical passivation effect on technological conditions of ion-implantation and structure of initial material is stated. On the basis of developed mathematical model of chemical passivation effect it is shown that increase of corrosion characteristics of implanted metals is defined by superposition of surface and volumetric mechanisms

Conservation-dissipation structure of chemical reaction systems.

Science.gov (United States)

Yong, Wen-An

2012-12-01

In this Brief Report, we show that balanced chemical reaction systems governed by the law of mass action have an elegant conservation-dissipation structure. From this structure a number of important conclusions can be easily deduced. In particular, with the help of this structure we can rigorously justify the classical partial equilibrium approximation in chemical kinetics.

Chemical structure investigation on SFEF fractions of Dagang vacuum residue

Energy Technology Data Exchange (ETDEWEB)

Zhang, Z.; Yan, G.; Zhao, S.; Guo, S. [China Univ. of Petroleum, Beijing (China). State Key Laboratory of Heavy Oil Processing; Zhang, Z. [Beijing Aeronautical Technology Research Center, Beijing (China)

2006-07-01

One of the most important problems in petroleum chemistry is the molecular structure and composition of heavy oil fractions and its importance in applications pertaining to the recovery, refining, and upgrading of petroleum. This paper presented an investigation into the chemical structure on supercritical fluid extraction and fraction (SFEF) factions of Dagang vacuum residue. Dagang vacuum residue was cut into sixteen fractions and a tailing with SFEF instrument. Then, using a chromatography, all SFEF fractions were further separated into four group compositions, notably saturated hydrocarbons, aromatic hydrocarbons, resins and asphaltenes (SARA). Last, the chemical structure was explored through a thorough analysis of the products from the ruthenium ions-catalyzed oxidation (RICO) reaction of those aromatics, resins and asphaltenes. The paper discussed the experiment in terms of samples and chemicals; supercritical fluid extraction and fraction; SARA separation; and RICO. The results and discussions focused on alkyl side chains attached to aromatic carbon; polymethylene bridges connecting two aromatic units; benzenecarboxylic acids an aromatic units; and others. The study has brought to light useful characterization on covalent molecular structure of two typical SFEF fractions, notably the tenth and fifteen fraction. 17 refs., 6 tabs., 16 figs., 1 appendix.

Chemical and structural analysis of the bone-implant interface by TOF-SIMS, SEM, FIB and TEM: Experimental study in animal

International Nuclear Information System (INIS)

Palmquist, Anders; Emanuelsson, Lena; Sjövall, Peter

2012-01-01

Although bone-anchored implants are widely used in reconstructive medicine, the mechanism of osseointegration is still not fully understood. Novel analytical tools are needed to further understand this process, where both the chemical and structural aspects of the bone-implant interface are important. The aim of this study was to evaluate the advantages of combining time-of-flight secondary ion mass spectroscopy (TOF-SIMS) with optical (LM), scanning (SEM) and transmission electron microscopy (TEM) techniques for studying the bone-implant interface of bone-anchored implants. Laser-modified titanium implants with surrounded bone retrieved after 8 weeks healing in rabbit were dehydrated and resin embedded. Three types of sample preparation were studied to evaluate the information gained by combining TOF-SIMS, SEM, FIB and TEM. The results show that imaging TOF-SIMS can provide detailed chemical information, which in combination with structural information from microscopy methods provide a more complete characterization of anatomical structures at the bone-implant interface. By investigating various sample preparation techniques, it is shown that grinded cross section samples can be used for chemical imaging using TOF-SIMS, if careful consideration of potential preparation artifacts is taken into account. TOF-SIMS analysis of FIB-prepared bone/implant cross section samples show distinct areas corresponding to bone tissue and implant with a sharp interface, although without chemical information about the organic components.

Structural and electrochemical analysis of chemically synthesized microcubic architectured lead selenide thin films

Science.gov (United States)

Bhat, T. S.; Shinde, A. V.; Devan, R. S.; Teli, A. M.; Ma, Y. R.; Kim, J. H.; Patil, P. S.

2018-01-01

The present work deals with the synthesis of lead selenide (PbSe) thin films by simple and cost-effective chemical bath deposition method with variation in deposition time. The structural, morphological, and electrochemical properties of as-deposited thin films were examined using characterization techniques such as X-ray diffraction spectroscopy (XRD), field-emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), galvanostatic charge-discharge and electrochemical impedance spectroscopy. XRD reveals formation of rock salt phase cubic structured PbSe. FE-SEM images show the formation of microcubic structured morphology. The existence of the PbSe is confirmed from the XPS analysis. On the other hand, CV curves show four reaction peaks corresponding to oxidation [PbSe and Pb(OH)2] and reduction (PbO2 and Pb(OH)2) at the surface of PbSe thin films. The PbSe:2 sample deposited for 80 min. shows maximum specific capacitance of 454 ± 5 F g- 1 obtained at 0.25 mA cm- 2 current density. The maximum energy density of 69 Wh kg- 1 was showed by PbSe:2 electrode with a power density of 1077 W kg- 1. Furthermore, electrochemical impedance studies of PbSe:2 thin film show 80 ± 3% cycling stability even after 500 CV cycles. Such results show the importance of microcubic structured PbSe thin film as an anode in supercapacitor devices.

Ultrastructural Analysis of Urinary Stones by Microfocus Computed Tomography and Comparison with Chemical Analysis

Directory of Open Access Journals (Sweden)

Tolga Karakan

2016-06-01

Full Text Available Objective: To investigate the ultra-structure of urinary system stones using micro-focus computed tomography (MCT, which makes non-destructive analysis and to compare with wet chemical analysis. Methods: This study was carried out at the Ankara Train­ing and Research hospital. Renal stones, removed from 30 patients during percutaneous nephrolithotomy (PNL surgery, were included in the study. The stones were blindly evaluated by the specialists with MCT and chemi­cal analysis. Results: The comparison of the stone components be­tween chemical analysis and MCT, showed that the rate of consistence was very low (p0.05. It was also seen that there was no significant relation between its 3D structure being heterogeneous or homogenous. Conclusion: The stone analysis with MCT is a time con­suming and costly method. This method is useful to un­derstand the mechanisms of stone formation and an im­portant guide to develop the future treatment modalities.

Chemical structure and dynamics: Annual report 1993

Energy Technology Data Exchange (ETDEWEB)

Colson, S.D.

1994-07-01

The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

Carotenoids Database: structures, chemical fingerprints and distribution among organisms.

Science.gov (United States)

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.

Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

KAUST Repository

Zenil, Hector; Kiani, Narsis A.; Shang, Ming-mei; Tegner, Jesper

2018-01-01

Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the principles of algorithmic probability to chemical structure networks. We profile the sensitivity of the elements and covalent bonds in a chemical structure network algorithmically, asking whether reprogrammability affords information about thermodynamic and chemical processes involved in the transformation of different compound classes. We arrive at numerical results suggesting a correspondence between some physical, structural and functional properties. Our methods are capable of separating chemical classes that reflect functional and natural differences without considering any information about atomic and molecular properties. We conclude that these methods, with their links to chemoinformatics via algorithmic, probability hold promise for future research.

Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

KAUST Repository

Zenil, Hector

2018-02-16

Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the principles of algorithmic probability to chemical structure networks. We profile the sensitivity of the elements and covalent bonds in a chemical structure network algorithmically, asking whether reprogrammability affords information about thermodynamic and chemical processes involved in the transformation of different compound classes. We arrive at numerical results suggesting a correspondence between some physical, structural and functional properties. Our methods are capable of separating chemical classes that reflect functional and natural differences without considering any information about atomic and molecular properties. We conclude that these methods, with their links to chemoinformatics via algorithmic, probability hold promise for future research.

Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

KAUST Repository

Zenil, Hector

2018-04-02

Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the principles of algorithmic probability to chemical structure networks. We profile the sensitivity of the elements and covalent bonds in a chemical structure network algorithmically, asking whether reprogrammability affords information about thermodynamic and chemical processes involved in the transformation of different compound classes. We arrive at numerical results suggesting a correspondence between some physical, structural and functional properties. Our methods are capable of separating chemical classes that reflect functional and natural differences without considering any information about atomic and molecular properties. We conclude that these methods, with their links to chemoinformatics via algorithmic, probability hold promise for future research.

Rapid and reliable protein structure determination via chemical shift threading.

Science.gov (United States)

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

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

Directory of Open Access Journals (Sweden)

Mihai V. Putz

2016-07-01

Full Text Available 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-(phenylthiothymine 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.

An extended chemical analysis of gallstone

OpenAIRE

Chandran, P.; Kuchhal, N. K.; Garg, P.; Pundir, C. S.

2007-01-01

Chemical composition of gall stones is essential for aetiopathogensis of gallstone disease. We have reported quantitative chemical analysis of total cholesterol bilirubin, calcium, iron and inorganic phosphate in 120 gallstones from haryana. To extend this chemical analysis of gall stones by studying more cases and by analyzing more chemical constituents. A quantitative chemical analysis of total cholesterol, total bilirubin, fatty acids, triglycerides, phospholipids, bile acids, soluble prot...

Understanding the chemical and structural transformations of lignin macromolecule during torrefaction

International Nuclear Information System (INIS)

Wen, Jia-Long; Sun, Shao-Long; Yuan, Tong-Qi; Xu, Feng; Sun, Run-Cang

2014-01-01

Highlights: • The terrified bamboo has a high energy yield of 85.7% and a HHV of 20.13 MJ/kg. • The structural changes of hemicelluloses, cellulose, and lignin were investigated. • First study on the structural transformations of lignin during torrefaction. • The mechanism of structural changes of lignin has been proposed. - Abstract: Torrefaction is an efficient method to recover energy from biomass. Herein, the characteristics (mass yield, energy yield, physical, and chemical characteristics) of torrefied bamboo at diverse temperatures (200–300 °C) were firstly evaluated by elemental analysis, XRD, and CP–MAS 13 C NMR methodologies. Under an optimal condition the terrified bamboo has a relative high energy yield of 85.7% and a HHV of 20.13 MJ/kg. The chemical and structural transformations of lignin induced by thermal treatment were thoroughly investigated by FT-IR and solution-state NMR techniques (quantitative 13 C NMR, 2D-HSQC, and 31 P-NMR methodologies). The results highlighted the chemical reactions of the native bamboo lignins towards severe torrefaction treatments occurred, such as depolymerization, demethoxylation, bond cleavage, and condensation reactions. NMR results indicated that aryl-ether bonds (β-O-4) and p-coumaric ester in lignin were cleaved during the torrefaction process at mild conditions. The severe treatments of bamboo (275 °C and 300 °C) induced a dramatic enrichment in lignin content together with the almost complete disappearance of β-O-4, β-β, and β-5 linkages. Further analysis of the molecular weight of milled wood lignin (MWL) indicated that the average molecular weights of “torrefied MWL” were lower than those of control MWL. It is believed that understanding of the reactivity and chemical transformations of lignin during torrefaction will contribute to the integrated torrefaction mechanism

De novo protein structure generation from incomplete chemical shift assignments

Energy Technology Data Exchange (ETDEWEB)

Shen Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vernon, Robert; Baker, David [University of Washington, Department of Biochemistry and Howard Hughes Medical Institute (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2009-02-15

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

Annual Report 2000. Chemical Structure and Dynamics

Energy Technology Data Exchange (ETDEWEB)

Colson, Steven D.; McDowell, Robin S.

2001-04-15

This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

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

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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.

Chemical Security Analysis Center

Data.gov (United States)

Federal Laboratory Consortium — In 2006, by Presidential Directive, DHS established the Chemical Security Analysis Center (CSAC) to identify and assess chemical threats and vulnerabilities in the...

Automated extraction of chemical structure information from digital raster images

Directory of Open Access Journals (Sweden)

Shedden Kerby A

2009-02-01

Full Text Available Abstract Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

Science.gov (United States)

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

Chemical synthesis and structure elucidation of bovine κ-casein (1-44)

International Nuclear Information System (INIS)

Bansal, Paramjit S.; Grieve, Paul A.; Marschke, Ronald J.; Daly, Norelle L.; McGhie, Emily; Craik, David J.; Alewood, Paul F.

2006-01-01

The caseins (α s1 , α s2 , β, and κ) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1-44) of bovine κ-casein, the protein which maintains the micellar structure of the caseins. κ-Casein (1-44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro 8 to Arg 34 . This is First report which demonstrates extensive secondary structure within the casein class of proteins

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

International Nuclear Information System (INIS)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei

2013-01-01

We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

Chemical structure and dynamics. Annual report 1995

Energy Technology Data Exchange (ETDEWEB)

Colson, S.D.; McDowell, R.S.

1996-05-01

The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

Temporal Control over Transient Chemical Systems using Structurally Diverse Chemical Fuels.

Science.gov (United States)

Chen, Jack L-Y; Maiti, Subhabrata; Fortunati, Ilaria; Ferrante, Camilla; Prins, Leonard J

2017-08-25

The next generation of adaptive, intelligent chemical systems will rely on a continuous supply of energy to maintain the functional state. Such systems will require chemical methodology that provides precise control over the energy dissipation process, and thus, the lifetime of the transiently activated function. This manuscript reports on the use of structurally diverse chemical fuels to control the lifetime of two different systems under dissipative conditions: transient signal generation and the transient formation of self-assembled aggregates. The energy stored in the fuels is dissipated at different rates by an enzyme, which installs a dependence of the lifetime of the active system on the chemical structure of the fuel. In the case of transient signal generation, it is shown that different chemical fuels can be used to generate a vast range of signal profiles, allowing temporal control over two orders of magnitude. Regarding self-assembly under dissipative conditions, the ability to control the lifetime using different fuels turns out to be particularly important as stable aggregates are formed only at well-defined surfactant/fuel ratios, meaning that temporal control cannot be achieved by simply changing the fuel concentration. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Science.gov (United States)

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.

Protein Structure Determination Using Chemical Shifts

DEFF Research Database (Denmark)

Christensen, Anders Steen

is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

Chemical structure and dynamics: Annual report 1996

International Nuclear Information System (INIS)

Colson, S.D.; McDowell, R.S.

1997-03-01

The Chemical Structure and Dynamics (CS ampersand D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species

Chemical structure and dynamics: Annual report 1996

Energy Technology Data Exchange (ETDEWEB)

Colson, S.D.; McDowell, R.S.

1997-03-01

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

Energy Technology Data Exchange (ETDEWEB)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

2013-06-15

We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

X-ray structure analysis of soil compositions

International Nuclear Information System (INIS)

Tillaev, T.; Kalonov, M.; Kuziev, Sh.; Khatamov, Sh.; Suvanov, M.

1998-01-01

The analytic characteristics of techniques developed to analyse soil structure by means of X-ray diffraction method are presented. Presence of 8 minerals in Fergana valley soils have been established. It is shown that X-ray structure analysis of soils gives rise to new original possibilities to determine not only their structure but also quantative content and type of chemical compound of element in soil. (author)

Nucleic acid helix structure determination from NMR proton chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

2013-06-15

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

Structure Analysis of Effective Chemical Compounds against Dengue Viruses Isolated from Isatis tinctoria.

Science.gov (United States)

Gao, Bo; Zhang, Jianming; Xie, Lianhui

2018-01-01

The history of Chinese herb research can be traced back to thousands of years ago, and the abundant knowledge accumulated for these herbs makes them good candidates for developing new natural drugs. Isatis tinctoria is probably the most well-studied Chinese herb, which has been identified to be effective against dengue fever. However, the underlying biological mechanisms are still unclear. In this study, we adopt combined methods of bioactive trace technology and phytochemical extraction and separation, to guide the isolation and purification of the effective chemical constituents on the water-soluble components of aerial parts of Isatis tinctoria . In addition, we apply polarimetry and 1D or 2D nuclear magnetic resonance (NMR) spectroscopy to identify their structures, which lay a foundation for further study on the biological mechanisms underlying medicinal effects of Isatis tinctoria using in vitro and in vivo experiments. Specifically, we identify and infer the structures of 27 types of chemical compounds named GB-1, GB-2, …, GB-27, respectively, among which GB-7 is a novel compound. Further study of these compounds is critical to reveal the secrets behind the medicinal effects of Isatis tinctoria .

Structure Analysis of Effective Chemical Compounds against Dengue Viruses Isolated from Isatis tinctoria

Directory of Open Access Journals (Sweden)

Bo Gao

2018-01-01

Full Text Available The history of Chinese herb research can be traced back to thousands of years ago, and the abundant knowledge accumulated for these herbs makes them good candidates for developing new natural drugs. Isatis tinctoria is probably the most well-studied Chinese herb, which has been identified to be effective against dengue fever. However, the underlying biological mechanisms are still unclear. In this study, we adopt combined methods of bioactive trace technology and phytochemical extraction and separation, to guide the isolation and purification of the effective chemical constituents on the water-soluble components of aerial parts of Isatis tinctoria. In addition, we apply polarimetry and 1D or 2D nuclear magnetic resonance (NMR spectroscopy to identify their structures, which lay a foundation for further study on the biological mechanisms underlying medicinal effects of Isatis tinctoria using in vitro and in vivo experiments. Specifically, we identify and infer the structures of 27 types of chemical compounds named GB-1, GB-2, …, GB-27, respectively, among which GB-7 is a novel compound. Further study of these compounds is critical to reveal the secrets behind the medicinal effects of Isatis tinctoria.

Identification of Lilial as a fragrance sensitizer in a perfume by bioassay-guided chemical fractionation and structure-activity relationships.

Science.gov (United States)

Arnau, E G; Andersen, K E; Bruze, M; Frosch, P J; Johansen, J D; Menné, T; Rastogi, S C; White, I R; Lepoittevin, J P

2000-12-01

Fragrance materials are among the most common causes of allergic contact dermatitis. The aim of this study was to identify in a perfume fragrance allergens not included in the fragrance mix, by use of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships (SARs). The basis for the investigation was a 45-year-old woman allergic to her own perfume. She had a negative patch test to the fragrance mix and agreed to participate in the study. Chemical fractionation of the perfume concentrate was used for repeated patch testing and/or repeated open application test on the pre-sensitized patient. The chemical composition of the fractions giving a positive patch-test response and repeated open application test reactions was obtained by gas chromatography-mass spectrometry. From the compounds identified, those that contained a "structural alert" in their chemical structure, indicating an ability to modify skin proteins and thus behave as a skin sensitizer, were tested on the patient. The patient reacted positively to the synthetic fragrance p-t-butyl-alpha-methylhydrocinnamic aldehyde (Lilial), a widely used fragrance compound not present in the fragrance mix. The combination of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships seems to be a valuable tool for the investigation of contact allergy to fragrance materials.

Annual Report 2000. Chemical Structure and Dynamics; FINAL

International Nuclear Information System (INIS)

Colson, Steve D; McDowell, Rod S

2001-01-01

This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS and D) program is meeting the need for a fundamental, molecular-level understanding by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and (3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems

Chemical ecotoxicology

International Nuclear Information System (INIS)

Paasivirta, J.

1991-01-01

This book discusses risk assessment, chemical cycles, structure-activity relations, organohalogens, oil residues, mercury, sampling and analysis of trace chemicals, and emissions from the forestry industry. Topics include: Cycles of chemicals in the environment. Rick assessment and management, strucuture and toxicity, sampling and analysis of trace chemicals in environment, interpretation of the environmental analysis results, mercury in the environment, organohalogen compounds in the environment, emissions from forestry industry, oil residues in the environment: oil spills in the marine environment

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Predicting oil and gas compositional yields via chemical structure-chemical yield modeling (CS-CYM): Part 1 - Concepts and implementation

Energy Technology Data Exchange (ETDEWEB)

Freund, H.; Walters, C.C.; Kelemen, S.R.; Siskin, M.; Gorbaty, M.L.; Curry, D.J.; Bence, A.E. [ExxonMobil Research & Engineering Co., Annandale, NJ (United States)

2007-07-01

We have developed a method to calculate the amounts and composition of products resulting from the thermal decomposition of a solid complex carbonaceous material. This procedure provides a means of using laboratory measurements of complex carbonaceous solids to construct a representative model of its chemical structure (CS) that is then coupled with elementary reaction pathways to predict the chemical yield (CY) upon thermal decomposition. Data from elemental analysis, H, N, O, S, solid state {sup 13}C NMR, X-ray photoelectron spectroscopy (XPS), sulfur X-ray absorption structure spectroscopy (XANES), and pyrolysis-gas chromatography (GC) are used to constrain the construction of core molecular structures representative of the complex carbonaceous material. These core structures are expanded stochastically to describe large macromolecules ({gt} 10{sup 6} cores with similar to 10{sup 6} atoms) with bulk properties that match the experimental results. Gas, liquid and solid product yields, resulting from thermal decomposition, are calculated by identifying reactive functional groups within the CS stochastic ensemble and imposing a reaction network constrained by fundamental thermodynamics and kinetics. An expulsion model is added to the decomposition model to calculate the chemical products in open and closed systems. Product yields may then be predicted under a wide range of time-temperature conditions used in rapid laboratory pyrolysis experiments, refinery processes, or geologic maturation.

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

Science.gov (United States)

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.

Activation analysis. A basis for chemical similarity and classification

Energy Technology Data Exchange (ETDEWEB)

Beeck, J OP de [Ghent Rijksuniversiteit (Belgium). Instituut voor Kernwetenschappen

1977-01-01

It is shown that activation analysis is especially suited to serve as a basis for determining the chemical similarity between samples defined by their trace-element concentration patterns. The general problem of classification and identification is discussed. The nature of possible classification structures and their appropriate clustering strategies is considered. A practical computer method is suggested and its application as well as the graphical representation of classification results are given. The possibility for classification using information theory is mentioned. Classification of chemical elements is discussed and practically realized after Hadamard transformation of the concentration variation patterns in a series of samples.

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

Science.gov (United States)

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.

Chemical and physical analysis of core materials for advanced high temperature reactors with process heat applications

International Nuclear Information System (INIS)

Nickel, H.

1985-08-01

Various chemical and physical methods for the analysis of structural materials have been developed in the research programmes for advanced high temperature reactors. These methods are discussed using as examples the structural materials of the reactor core - the fuel elements consisting of coated particles in a graphite matrix and the structural graphite. Emphasis is given to the methods of chemical analysis. The composition of fuel kernels is investigated using chemical analysis methods to determine the heavy metals content (uranium, plutonium, thorium and metallic impurity elements) and the amount of non-metallic constituents. The properties of the pyrocarbon and silicon carbide coatings of fuel elements are investigated using specially developed physiochemical methods. Regarding the irradiation behaviour of coated particles and fuel elements, methods have been developed for examining specimens in hot cells following exposures under reactor operating conditions, to supplement the measurements of in-reactor performance. For the structural graphite, the determination of impurities is important because certain impurities may cause pitting corrosion during irradiation. The localized analysis of very low impurity concentrations is carried out using spectrochemical d.c. arc excitation, local laser and inductively coupled plasma methods. (orig.)

Molecular structure, vibrational analysis (IR and Raman) and quantum chemical investigations of 1-aminoisoquinoline

Science.gov (United States)

Sivaprakash, S.; Prakash, S.; Mohan, S.; Jose, Sujin P.

2017-12-01

Quantum chemical calculations of energy and geometrical parameters of 1-aminoisoquinoline [1-AIQ] were carried out by using DFT/B3LYP method using 6-311G (d,p), 6-311G++(d,p) and cc-pVTZ basis sets. The vibrational wavenumbers were computed for the energetically most stable, optimized geometry. The vibrational assignments were performed on the basis of potential energy distribution (PED) using VEDA program. The NBO analysis was done to investigate the intra molecular charge transfer of the molecule. The frontier molecular orbital (FMO) analysis was carried out and the chemical reactivity descriptors of the molecule were studied. The Mulliken charge analysis, molecular electrostatic potential (MEP), HOMO-LUMO energy gap and the related properties were also investigated at B3LYP level. The absorption spectrum of the molecule was studied from UV-Visible analysis by using time-dependent density functional theory (TD-DFT). Fourier Transform Infrared spectrum (FT-IR) and Raman spectrum of 1-AIQ compound were analyzed and recorded in the range 4000-400 cm-1 and 3500-100 cm-1 respectively. The experimentally determined wavenumbers were compared with those calculated theoretically and they complement each other.

Development of activated carbon pore structure via physical and chemical activation of biomass fibre waste

International Nuclear Information System (INIS)

Williams, Paul T.; Reed, Anton R.

2006-01-01

Biomass waste in the form of biomass flax fibre, produced as a by-product of the textile industry was processed via both physical and chemical activation to produce activated carbons. The surface area of the physically activated carbons were up to 840 m 2 g -1 and the carbons were of mesoporous structure. Chemical activation using zinc chloride produced high surface area activated carbons up to 2400 m 2 g -1 and the pore size distribution was mainly microporous. However, the process conditions of temperature and zinc chloride concentration could be used to manipulate the surface area and porosity of the carbons to produce microporous, mesoporous and mixed microporous/mesoporous activated carbons. The physically activated carbons were found to be a mixture of Type I and Type IV carbons and the chemically activated carbons were found to be mainly Type I carbons. The development of surface morphology of physically and chemically activated carbons observed via scanning electron microscopy showed that physical activation produced activated carbons with a nodular and pitted surface morphology whereas activated carbons produced through chemical activation had a smooth surface morphology. Transmission electron microscopy analysis could identify mesopore structures in the physically activated carbon and microporous structures in the chemically activated carbons

A robust algorithm for optimizing protein structures with NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

2015-11-15

Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca.

A chemometric analysis of ligand-induced changes in intrinsic fluorescence of folate binding protein indicates a link between altered conformational structure and physico-chemical characteristics

DEFF Research Database (Denmark)

Bruun, Susanne W; Holm, Jan; Hansen, Steen Ingemann

2009-01-01

Ligand binding alters the conformational structure and physico-chemical characteristics of bovine folate binding protein (FBP). For the purpose of achieving further information we analyzed ligand (folate and methotrexate)-induced changes in the fluorescence landscape of FBP. Fluorescence excitation...... of folate accords fairly well with the disappearance of strongly hydrophobic tryptophan residues from the solvent-exposed surface of FBP. The PARAFAC has thus proven useful to establish a hitherto unexplained link between parallel changes in conformational structure and physico-chemical characteristics...... of FBP induced by folate binding. Parameters for ligand binding derived from PARAFAC analysis of the fluorescence data were qualitatively and quantitatively similar to those obtained from binding of radiofolate to FBP. Herein, methotrexate exhibited a higher affinity for FBP than in competition...

Structural and chemical transformations in SnS thin films used in chemically deposited photovoltaic cells

International Nuclear Information System (INIS)

Avellaneda, David; Delgado, Guadalupe; Nair, M.T.S.; Nair, P.K.

2007-01-01

Chemically deposited SnS thin films possess p-type electrical conductivity. We report a photovoltaic structure: SnO 2 :F-CdS-SnS-(CuS)-silver print, with V oc > 300 mV and J sc up to 5 mA/cm 2 under 850 W/m 2 tungsten halogen illumination. Here, SnO 2 :F is a commercial spray-CVD (Pilkington TEC-8) coating, and the rest deposited from different chemical baths: CdS (80 nm) at 333 K, SnS (450 nm) and CuS (80 nm) at 293-303 K. The structure may be heated in nitrogen at 573 K, before applying the silver print. The photovoltaic behavior of the structure varies with heating: V oc ∼ 400 mV and J sc 2 , when heated at 423 K in air, but V oc decreases and J sc increases when heated at higher temperatures. These photovoltaic structures have been found to be stable over a period extending over one year by now. The overall cost of materials, simplicity of the deposition process, and possibility of easily varying the parameters to improve the cell characteristics inspire further work. Here we report two different baths for the deposition of SnS thin films of about 500 nm by chemical deposition. There is a considerable difference in the nature of growth, crystalline structure and chemical stability of these films under air-heating at 623-823 K or while heating SnS-CuS layers, evidenced in XRF and grazing incidence angle XRD studies. Heating of SnS-CuS films results in the formation of SnS-Cu x SnS y . 'All-chemically deposited photovoltaic structures' involving these materials are presented

Chemical Structure and Dynamics annual report 1997

International Nuclear Information System (INIS)

Colson, S.D.; McDowell, R.S.

1998-03-01

The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE's environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous

Chemical Structure and Dynamics annual report 1997

Energy Technology Data Exchange (ETDEWEB)

Colson, S.D.; McDowell, R.S.

1998-03-01

The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

Structural and morphological properties of electroceramics for chemical sensors

International Nuclear Information System (INIS)

Tor Vergata, Via della Ricerca Scientifica, Roma (Italy). Dipartimento di Scienze e Tecnologie Chimiche)" data-affiliation=" (Universita' di Roma Tor Vergata, Via della Ricerca Scientifica, Roma (Italy). Dipartimento di Scienze e Tecnologie Chimiche)" >Enrico Traversa

1996-01-01

Ceramic materials possess a unique structure consisting of grains, grain boundaries, surfaces and pores, which makes them suitable for chemical sensors. The control of the chemical composition and microstructure of electrochemicals is fundamental for controlling their properties. Ceramics with a given composition and microstructure can be produced by controlling the different steps of their processing. The chemical processing of ceramics offer many advantages in terms of control and reproducibility, with respect to the conventional ceramics processing. Results are reported about the chemical processing of perovskite-type oxides for gas sensors and about the novel humidity-sensitive electrical properties of sol-gel processed alkali-doped titania films. The structural and morphological characterization of these materials permits the understanding of the sensitive electrical properties of the ceramics (71 refs.)

Annual Report 1998: Chemical Structure and Dynamics

Energy Technology Data Exchange (ETDEWEB)

SD Colson; RS McDowell

1999-05-10

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

Structural and optical characterization of self-assembled Ge nanocrystal layers grown by plasma-enhanced chemical vapor deposition

NARCIS (Netherlands)

Saeed, S.; Buters, F.; Dohnalova, K.; Wosinski, L.; Gregorkiewicz, T.

2014-01-01

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 SiO2. Optical characterization

Temperature effects on chemical structure and motion in coal. Final report

Energy Technology Data Exchange (ETDEWEB)

Maciel, G.E.

1996-09-30

The objective of this project was to apply recently developed, state-of-the-art nuclear magnetic resonance (NMR) techniques to examine in situ changes in the chemical structure and molecular/macromolecular motion in coal as the temperature is increased above room temperature. Although alterations in the chemical structure of coal have been studied previously by {sup 13}C NMR, using quenched samples, the goal of this project was to examine these chemical structural changes, and changes in molecular/macromolecular mobility that may precede or accompany the chemical changes, at elevated temperatures, using modern {sup 13}C and {sup 1}H NMR techniques, especially {sup 1}H dipolar-dephasing techniques and related experiments pioneered in the laboratory for examining pyridine-saturated coals. This project consisted of the following four primary segments and related efforts on matters relevant to the first four tasks. (1) {sup 1}H NMR characterization of coal structure and mobility as a function of temperature variation over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (2) {sup 1}H NMR characterization of coal structure, mobility and conversion as a function of temperature variation over a temperature range (240--500 C) for which chemical transformations of coal are known to occur. (3) {sup 13}C NMR investigation of coal structure/mobility as a function of temperature over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (4) {sup 13}C NMR investigation of coal structure, dynamics and conversion as a function of temperature variation over a range (240--500 C) for which chemical transformations of coal are known to occur. (5) Related matters relevant to the first four tasks: (a) {sup 1}H CRAMPS NMR characterization of oil shales and their kerogen concentrates; and (b) improved quantitation in {sup 13}C MAS characterization of coals.

Spectroscopic Chemical Analysis Methods and Apparatus

Science.gov (United States)

Hug, William F. (Inventor); Reid, Ray D. (Inventor); Bhartia, Rohit (Inventor); Lane, Arthur L. (Inventor)

2018-01-01

Spectroscopic chemical analysis methods and apparatus are disclosed which employ deep ultraviolet (e.g. in the 200 nm to 300 nm spectral range) electron beam pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor light emitting devices, and hollow cathode metal ion lasers to perform non-contact, non-invasive detection of unknown chemical analytes. These deep ultraviolet sources enable dramatic size, weight and power consumption reductions of chemical analysis instruments. In some embodiments, Raman spectroscopic detection methods and apparatus use ultra-narrow-band angle tuning filters, acousto-optic tuning filters, and temperature tuned filters to enable ultra-miniature analyzers for chemical identification. In some embodiments Raman analysis is conducted along with photoluminescence spectroscopy (i.e. fluorescence and/or phosphorescence spectroscopy) to provide high levels of sensitivity and specificity in the same instrument.

Chemical and structural analysis of Eucalyptus globulus and E. camaldulensis leaf cuticles: a lipidized cell wall region

Directory of Open Access Journals (Sweden)

Paula eGuzmán

2014-09-01

Full Text Available The plant cuticle has traditionally been conceived as an independent hydrophobic layer that covers the external epidermal cell wall. Due to its complexity, the existing relationship between cuticle chemical composition and ultra-structure remains unclear to date. This study aimed to examine the link between chemical composition and structure of isolated, adaxial leaf cuticles of Eucalyptus camaldulensis and E. globulus by the gradual extraction and identification of lipid constituents (cutin and soluble lipids, coupled to spectroscopic and microscopic analyses. The soluble compounds and cutin monomers identified could not be assigned to a concrete internal cuticle ultra-structure. After cutin depolymerization, a cellulose network resembling the cell wall was observed, with different structural patterns in the regions ascribed to the cuticle proper and cuticular layer, respectively. Our results suggest that the current cuticle model should be revised, stressing the presence and major role of cell wall polysaccharides. It is concluded that the cuticle may be interpreted as a modified cell wall region which contains additional lipids. The major heterogeneity of the plant cuticle makes it difficult to establish a direct link between cuticle chemistry and structure with the existing methodologies.

Chemical process hazards analysis

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-02-01

The Office of Worker Health and Safety (EH-5) under the Assistant Secretary for the Environment, Safety and Health of the US Department (DOE) has published two handbooks for use by DOE contractors managing facilities and processes covered by the Occupational Safety and Health Administration (OSHA) Rule for Process Safety Management of Highly Hazardous Chemicals (29 CFR 1910.119), herein referred to as the PSM Rule. The PSM Rule contains an integrated set of chemical process safety management elements designed to prevent chemical releases that can lead to catastrophic fires, explosions, or toxic exposures. The purpose of the two handbooks, ``Process Safety Management for Highly Hazardous Chemicals`` and ``Chemical Process Hazards Analysis,`` is to facilitate implementation of the provisions of the PSM Rule within the DOE. The purpose of this handbook ``Chemical Process Hazards Analysis,`` is to facilitate, within the DOE, the performance of chemical process hazards analyses (PrHAs) as required under the PSM Rule. It provides basic information for the performance of PrHAs, and should not be considered a complete resource on PrHA methods. Likewise, to determine if a facility is covered by the PSM rule, the reader should refer to the handbook, ``Process Safety Management for Highly Hazardous Chemicals`` (DOE- HDBK-1101-96). Promulgation of the PSM Rule has heightened the awareness of chemical safety management issues within the DOE. This handbook is intended for use by DOE facilities and processes covered by the PSM rule to facilitate contractor implementation of the PrHA element of the PSM Rule. However, contractors whose facilities and processes not covered by the PSM Rule may also use this handbook as a basis for conducting process hazards analyses as part of their good management practices. This handbook explains the minimum requirements for PrHAs outlined in the PSM Rule. Nowhere have requirements been added beyond what is specifically required by the rule.

The chemical structure of the insoluble organic matter from carbonaceous meteorites

Science.gov (United States)

Derenne, S.; Robert, F.

2008-09-01

Carbonaceous chondrites are the most primitive objects of the solar system. They contain substantial amounts of carbon (up to 3%), mostly occurring in macromolecular insoluble organic matter (IOM). This IOM is generally considered as a record of interstellar synthesis and may contain precursors of prebiotic molecules possibly deposited on earth by meteoritic bombardments. For these reasons, chondritic IOM has been raising interest for long and it is therefore of special interest to decipher its chemical structure. It is now well established that the chemical structure of this macromolecular material is based on aromatic moieties linked by short aliphatic chains and comprising substantial amounts of heteroatoms. However, its precise chemical structure could only be recently specified. The aim of this presentation is to propose a molecular model for the chemical structure of IOM isolated from non-metamorphosed carbonaceous chondrites. This model is derived from a large set of data obtained through a combination of techniques including various spectrocopies, high resolution transmission electron microscopy (HRTEM) and chemical and thermal degradations. Cosmochemical implications of such a structure will also be discussed.

Physical-chemical structure of VIPRO

International Nuclear Information System (INIS)

Lauri, L.

1986-01-01

PELF is a manufacturer of rigid expanded PVC in the form of panels of different density. There are only three manufacturers of this product in the world. This material is used in self-supporting structures of forms of transport, refrigerator trucks, busses, in the naval industry, for the construction of boats up to 40-50 meters in length, in the aeronautical and military industries. The research was developed in the two following phases: 1st phase: construction of a PVC panel with the density of approximately 1.000 Kg/cm. doped with extremely pure Boron using the base formula of rigid expanded PVC 2nd phase: construction of a completely new panel using for the first time in the world in the sector of plastic matters, the formula 'in alloy' where the absorbing material Boron or Lead become part of the chemical link. Only a simple and at the same time extremely resistant physical-chemical structure, a determined increase of resistance to temperatures, a considerable increase also of the number of Hydrogen atoms/c.m. could give the hoped for results. This is how VIPRO was born

Improving 3D structure prediction from chemical shift data

Energy Technology Data Exchange (ETDEWEB)

Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

2013-09-15

We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

Neutron activation analysis of high-purity iron in comparison with chemical analysis

International Nuclear Information System (INIS)

Kinomura, Atsushi; Horino, Yuji; Takaki, Seiichi; Abiko, Kenji

2000-01-01

Neutron activation analysis of iron samples of three different purity levels has been performed and compared with chemical analysis for 30 metallic and metalloid impurity elements. The concentration of As, Cl, Cu, Sb and V detected by neutron activation analysis was mostly in agreement with that obtained by chemical analysis. The sensitivity limits of neutron activation analysis of three kinds of iron samples were calculated and found to be reasonable compared with measured values or detection limits of chemical analysis; however, most of them were above the detection limits of chemical analysis. Graphite-shielded irradiation to suppress fast neutron reactions was effective for Mn analysis without decreasing sensitivity to the other impurity elements. (author)

Chemical structure and dynamics. Annual report 1994

Energy Technology Data Exchange (ETDEWEB)

Colson, S.D.

1995-07-01

The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

QSAR modeling and chemical space analysis of antimalarial compounds

Science.gov (United States)

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.

Chemical compositions, methods of making the chemical compositions, and structures made from the chemical compositions

Science.gov (United States)

Yang, Lei; Cheng, Zhe; Liu, Ze; Liu, Meilin

2015-01-13

Embodiments of the present disclosure include chemical compositions, structures, anodes, cathodes, electrolytes for solid oxide fuel cells, solid oxide fuel cells, fuel cells, fuel cell membranes, separation membranes, catalytic membranes, sensors, coatings for electrolytes, electrodes, membranes, and catalysts, and the like, are disclosed.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor

DEFF Research Database (Denmark)

Bratholm, Lars Andersen; Jensen, Jan Halborg

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...

Spectral fitting for signal assignment and structural analysis of uniformly {sup 13}C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

Energy Technology Data Exchange (ETDEWEB)

Matsuki, Yoh; Akutsu, Hideo; Fujiwara, Toshimichi [Osaka University, Institute for Protein Research (Japan)], E-mail: tfjwr@protein.osaka-u.ac.jp

2007-08-15

We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional {sup 13}C-{sup 13}C magic-angle-spinning solid-state NMR spectra of uniformly {sup 13}C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C{sup {alpha}} and C{sup {beta}} chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 deg. from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.

13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

DEFF Research Database (Denmark)

Nyrop Albers, Christian; Hansen, Poul Erik

2010-01-01

Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical...... side missing structural elements in the models can be suggested. A number of proposed structures for humic and fulvic acids are discussed based on the above analysis....

Chemical analysis of water in hydrogeology

International Nuclear Information System (INIS)

Flakova, R.; Zenisova, Z.; Seman, M.

2010-01-01

The aim of the monograph is to give complete information on the chemical analysis of water hydrogeology not only for the students program of Geology study (Bachelor degree study), Engineering Geology and Hydrogeology (Master's degree study) and Engineering Geology (doctoral level study), but also for students from other colleges and universities schools in Slovakia, as well as in the Czech Republic, dealing with the chemical composition of water and its quality, from different perspectives. The benefit would be for professionals with hydrogeological, water and environmental practices, who can find there all the necessary information about proper water sampling, the units used in the chemical analysis of water, expressing the proper chemical composition of water in its various parameters through classification of chemical composition of the water up to the basic features of physical chemistry at thermodynamic calculations and hydrogeochemical modelling.

[Construction of chemical information database based on optical structure recognition technique].

Science.gov (United States)

Lv, C Y; Li, M N; Zhang, L R; Liu, Z M

2018-04-18

To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically. Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database. A reasonable construction protocol of chemical information database was created successfully. A total of 174 research

Regioisomers of octanoic acid-containing structured triacylglycerols analyzed by tandem mass spectrometry using ammonia negative ion chemical ionization

DEFF Research Database (Denmark)

Kurvinen, J.P.; Mu, Huiling; Kallio, H.

2001-01-01

Tandem mass spectrometry based on ammonia negative ion chemical ionization and sample introduction via direct exposure probe was applied to analysis of regioisomeric structures of octanoic acid containing structured triacylglycerols (TAG) of type MML, MLM, MLL, and LML (M, medium-chain fatty acid...

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

Science.gov (United States)

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

Molecular activation analysis for chemical speciation studies

International Nuclear Information System (INIS)

Chai-Chifang

1998-01-01

The term of Molecular Activation Analysis (MAA) refers to an activation analysis method that is able to provide information about the chemical species of elements in system of interests, though its definition has remained to be assigned. Its development is strongly stimulated by the urgent need to know the chemical species of elements, because the total concentrations are often without any meaning when assessing health or environmental risks of trace elements.In practice, the MAA is a combination of conventional instrumental or radiochemical activation analysis and physical, chemical or biochemical separation techniques. The MAA is able to play a particular role in speciation studies. However, the critical point in the MAA is that it is not permitted to change the primitive chemical species of elements in systems, or the change has to be under control; in the meantime it is not allowed to form the 'new artifact' originally not present in systems. Some practical examples of MAA for chemical species research performed recently in our laboratory will be presented as follows: Chemical species of platinum group elements in sediment; Chemical species of iodine in marine algae; Chemical species of mercury in human tissues; Chemical species of selenium in corn; Chemical species of rare earth elements in natural plant, etc. The merits and limitations of MAA will be described as well. (author)

Gas analysis during the chemical vapor deposition of carbon

International Nuclear Information System (INIS)

Lieberman, M.L.; Noles, G.T.

1973-01-01

Gas chromatographic analyses were performed during the chemical vapor deposition of carbon in both isothermal and thermal gradient systems. Such data offer insight into the gas phase processes which occur during deposition and the interrelations which exist between gas composition, deposition rate, and resultant structure of the deposit. The results support a carbon CVD model presented previously. The application of chromatographic analysis to research, development, and full-scale facilities is shown. (U.S.)

Chemical analysis of high purity graphite

International Nuclear Information System (INIS)

1993-03-01

The Sub-Committee on Chemical Analysis of Graphite was organized in April 1989, under the Committee on Chemical Analysis of Nuclear Fuels and Reactor Materials, JAERI. The Sub-Committee carried out collaborative analyses among eleven participating laboratories for the certification of the Certified Reference Materials (CRMs), JAERI-G5 and G6, after developing and evaluating analytical methods during the period of September 1989 to March 1992. The certified values were given for ash, boron and silicon in the CRM based on the collaborative analysis. The values for ten elements (Al, Ca, Cr, Fe, Mg, Mo, Ni, Sr, Ti, V) were not certified, but given for information. Preparation, homogeneity testing and chemical analyses for certification of reference materials were described in this paper. (author) 52 refs

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

Science.gov (United States)

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

Science.gov (United States)

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

Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

Science.gov (United States)

Galdeano, Carles; Ciulli, Alessio

2016-09-01

Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

Structure and behavior as determinants: United States nuclear test ban and chemical and biological arms control policy

International Nuclear Information System (INIS)

Reich, J.C.

1991-01-01

US efforts to control chemical and biological warfare and nuclear testing are examined with the aim of explaining the paucity of US backed agreements in these areas. Two theoretical perspectives, the behavioral and structural approaches, are used to explore US arms control outcomes. In the behavioral approach, the effects of governmental organization and the bargaining dynamics of policy-making elites with different cognitive styles are posited as important influences on US nuclear test ban and chemical and biological arms control policy outcomes. The behavioral perspective accounts for the timing of all US failed and successful entries (with one exception) into nuclear test bans and chemical and biological warfare restraints. A shortcoming of the behavior approach, however, is that it tends to overemphasize the chances for successful US entry into nuclear test and chemical and biological warfare limitations. Analysis of the same events from the structural perspective helps to correct for expectations generated by behavioral variables for a higher success rate than ultimately resulted. In the structural approach, the focus is on the effect of the organization of international politics on US nuclear test ban and chemical and biological arms control policy outcomes

Current Challenges in Development of a Database of Three-Dimensional Chemical Structures

Science.gov (United States)

Maeda, Miki H.

2015-01-01

We are developing a database named 3DMET, a three-dimensional structure database of natural metabolites. There are two major impediments to the creation of 3D chemical structures from a set of planar structure drawings: the limited accuracy of computer programs and insufficient human resources for manual curation. We have tested some 2D–3D converters to convert 2D structure files from external databases. These automatic conversion processes yielded an excessive number of improper conversions. To ascertain the quality of the conversions, we compared IUPAC Chemical Identifier and canonical SMILES notations before and after conversion. Structures whose notations correspond to each other were regarded as a correct conversion in our present work. We found that chiral inversion is the most serious factor during the improper conversion. In the current stage of our database construction, published books or articles have been resources for additions to our database. Chemicals are usually drawn as pictures on the paper. To save human resources, an optical structure reader was introduced. The program was quite useful but some particular errors were observed during our operation. We hope our trials for producing correct 3D structures will help other developers of chemical programs and curators of chemical databases. PMID:26075200

Variability of chemical analysis of reinforcing bar produced in Saudi Arabia

Science.gov (United States)

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.

Chemical structure and properties of low-molecular furin inhibitors

Directory of Open Access Journals (Sweden)

T. V. Osadchuk

2016-12-01

Full Text Available The review is devoted to the analysis of the relationship between a chemical structure and properties of low-molecular weight inhibitors of furin, the most studied proprotein convertase, which is involved in the development of some pathologies, such as oncologic diseases, viral and bacterial infections, etc. The latest data concerning the influence of peptides, pseudo-peptides, aromatic and heterocyclic compounds, some natural ones such as flavonoids, coumarins, and others on enzyme inactivation are considered. The power of furin inhibition is shown to rise with the increasing number of positively charged groups in the structure of these compounds. Peptidomimetics (Ki = 5-8 pM are shown to be the most effective furin inhibitors. The synthesized substances, however, have not been used in practical application yet. Nowadays it is very important to find more selective inhibitors, improve their stability, bioavailability and safety for the human organism.

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

Science.gov (United States)

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.

Utilization of chemical derivatives in activation analysis

International Nuclear Information System (INIS)

Ehmann, W.D.

1990-01-01

Derivative activation analysis (DAA) is a method to enhance the sensitivity of nuclear activation analysis for the more elusive elements. It may also allow a degree of chemical speciation for the element of interest. DAA uses a preirradiation chemical reaction on the sample to initiate the formation of, or an exchange with, a chemical complex which contains a surrogate element, M. As a result, the amount of the element or the chemical species to be determined, X, is now represented by measurement of the amount of the surrogate element, M, that is made part of, or released by the complex species. The surrogate element is selected for its superior properties for nuclear activation analysis and the absence of interference reaction in its final determination by instrumental neutron activation analysis (INAA) after some preconcentration or separation chemistry. Published DAA studies have been limited to neutron activation analysis. DAA can offer the analyst some important advantages. It can determine elements, functional groups, or chemical species which cannot be determined directly by INAA, fast neutron activation analysis (FNAA), prompt gamma neutron activation analysis (PGNAA), or charged particle activation analysis (CPAA) procedures. When compared with conventional RNAA, there are fewer precautions with respect to handling of intensely radioactive samples, since the chemistry is done before the irradiation. The preirradiation chemistry may also eliminate many interferences that might occur in INAA and, through use of an appropriate surrogate element, can place the analytical gamma-ray line in an interference-free region of the gamma-ray spectrum

Quantum chemical and spectroscopic analysis of calcium hydroxyapatite and related materials

International Nuclear Information System (INIS)

Khavryuchenko, V.D.; Khavryuchenko, O.V.; Lisnyak, V.V.

2007-01-01

Amorphous calcium hydroxyapatite was examined by vibrational spectroscopy (Raman and infra-red (IR)) and quantum chemical simulation techniques. The structures and vibrational (IR, Raman and inelastic neutron scattering) spectra of PO 4 3- ion, Ca 3 (PO 4 ) 2 , [Ca 3 (PO 4 ) 2 ] 3 , Ca 5 (PO 4 ) 3 OH, CaHPO 4 , [CaHPO 4 ] 2 , Ca 3 (PO 4 ) 2 .H 2 O, Ca 3 (PO 4 ) 2 .2H 2 O and Ca 3 (PO 4 ) 2 .3H 2 O clusters were quantum chemically simulated at ab initio and semiempirical levels of approximation. A complete coordinate analysis of the vibrational spectra was performed. The comparison of the theoretically simulated spectra with the experimental ones allows to identify correctly the phase composition of the amorphous calcium hydroxyapatite and related materials. The shape of the bands in the IR spectra of the hydroxoapatite can be used in order to characterize the structural properties of the material, e.g., the PO 4 3- ion status, the degree of hydrolysis of the material and the presence of hydrolysis products. - Graphical abstract: The structure of the quantum chemically optimized Ca 5 (PO 4 ) 3 (OH) cluster, which was used for vibrations spectra simulation

Development of chemical equilibrium analysis code 'CHEEQ'

International Nuclear Information System (INIS)

Nagai, Shuichiro

2006-08-01

'CHEEQ' code which calculates the partial pressure and the mass of the system consisting of ideal gas and pure condensed phase compounds, was developed. Characteristics of 'CHEEQ' code are as follows. All the chemical equilibrium equations were described by the formation reactions from the mono-atomic gases in order to simplify the code structure and input preparation. Chemical equilibrium conditions, Σν i μ i =0 for the gaseous compounds and precipitated condensed phase compounds and Σν i μ i > 0 for the non-precipitated condensed phase compounds, were applied. Where, ν i and μ i are stoichiometric coefficient and chemical potential of component i. Virtual solid model was introduced to perform the calculation of constant partial pressure condition. 'CHEEQ' was consisted of following 3 parts, (1) analysis code, zc132. f. (2) thermodynamic data base, zmdb01 and (3) input data file, zindb. 'CHEEQ' code can calculate the system which consisted of elements (max.20), condensed phase compounds (max.100) and gaseous compounds. (max.200). Thermodynamic data base, zmdb01 contains about 1000 elements and compounds, and 200 of them were Actinide elements and their compounds. This report describes the basic equations, the outline of the solution procedure and instructions to prepare the input data and to evaluate the calculation results. (author)

Crystal chemical analysis of formation of solid solutions on the basis of compounds with garnet structure

International Nuclear Information System (INIS)

Kuz'micheva, G.M.; Kozlikin, S.N.

1989-01-01

Crystal chemical formulas permitting to evaluate the character of changes in interatomic distances during isomorphous substitution and, hence, the probability of formation of internal solid solutions and successive isomorphous substitution, are presented. The possibility of formation of introduction solid solutions is considered, using as an example Sc, Y oxides, rare earths with garnet structure

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

Science.gov (United States)

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.

Applications of the Cambridge Structural Database in chemical education1

Science.gov (United States)

Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

2010-01-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

Chemical effects in the mine structure

International Nuclear Information System (INIS)

1992-02-01

The main objective of the workshop was to bring together, and get talking to each other, long-term safety modellers, geochemical modellers and experimenters working in the field of chemical effects, and to give an insight into their respective activity areas and problem constellations. Lectures on the following subjects were given: modelling of chemical effects in long-term safety analysis; influence of brines; corrosion experiments; sorption experiments; actinide chemistry experiments; geochemical modelling; requirements of safety analyses and geochemical modelling. The workshop concluded with a detailed discussion of the subjects raised and of interdisciplinary aspects. (orig./DG) [de

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

Science.gov (United States)

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.

Chemical probes of metal cluster structure--Fe, Co, Ni, and Cu

International Nuclear Information System (INIS)

Parks, E.K.; Zhu, L.; Ho, J.; Riley, S.J.

1992-01-01

Chemical reactivity is one of the few methods currently available for investigating the geometrical structure of isolated transition metal clusters. In this paper we summarize what is currently known about the structures of clusters of four transition metals, Fe, Co, Ni, and Cu, in the size range from 13 to 180 atoms. Chemical probes used to determine structural information include reactions with H 2 (D 2 ), H 2 0, NH 3 and N 2 . Measurements at both low coverage and at saturation are discussed

An extended chemical analysis of gallstone.

Science.gov (United States)

Chandran, P; Kuchhal, N K; Garg, P; Pundir, C S

2007-09-01

Chemical composition of gall stones is essential for aetiopathogensis of gallstone disease. We have reported quantitative chemical analysis of total cholesterol bilirubin, calcium, iron and inorganic phosphate in 120 gallstones from haryana. To extend this chemical analysis of gall stones by studying more cases and by analyzing more chemical constituents. A quantitative chemical analysis of total cholesterol, total bilirubin, fatty acids, triglycerides, phospholipids, bile acids, soluble proteins, sodium potassium, magnesium, copper, oxalate and chlorides of biliary calculi (52 cholesterol, 76 mixed and 72 pigment) retrieved from surgical operation of 200 patients from Haryana state was carried out. Total cholesterol as the major component and total bilirubin, phospholipids, triglycerides, bile acids, fatty acids (esterified), soluble protein, calcium, magnesium, iron, copper, sodium, potassium, inorganic phosphate, oxalate and chloride as minor components were found in all types of calculi. The cholesterol stones had higher content of total cholesterol, phospholipids, fatty acids (esterified), inorganic phosphate and copper compared to mixed and pigment stones. The mixed stones had higher content of iron and triglycerides than to cholesterol and pigment stones. The pigment stones were richer in total bilirubin, bile acids, calcium, oxalate, magnesium, sodium, potassium, chloride and soluble protein compared to cholesterol and mixed stones. Although total cholesterol was a major component of cholesterol, mixed and pigment gall stone in Haryana, the content of most of the other lipids, cations and anions was different in different gall stones indicating their different mechanism of formation.

Structure and chemical characteristics of natural mineral deposit Terbunskaya (Lipetsk region, Russia)

Energy Technology Data Exchange (ETDEWEB)

Motyleva, S., E-mail: motyleva-svetlana@mail.ru; Mertvishcheva, M. [All-Russian Horticular Institute for Breeding, Agrotechnology and Nursery Russian Academy of Agricultural Sciences, Moskow (Russian Federation); Shchuchka, R.; Gulidova, V. [Yelets state university named after I. A. Bunin, Yelets (Russian Federation)

2015-07-22

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 and an average chemical composition (wt%): Na (0,64), Mg (0,54), Al (13.48), Si (27 57), K (2.39) Ca (0.75)

Methods of chemical and phase composition analysis of gallstones

Science.gov (United States)

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.

Chemical engineering and structural and pharmacological characterization of the α-scorpion toxin OD1.

Science.gov (United States)

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.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

International Nuclear Information System (INIS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.; Sales, Brian C.; Sefat, Athena S.

2014-01-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe 0.55 Se 0.45 (T c = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe 1−x Se x structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces

Advanced photonic structures for biological and chemical detection

CERN Document Server

Fan, Xudong

2009-01-01

One of a series of books on Integrated Microanalytical Systems, this text discusses the latest applications of photonic technologies in bio/chemical sensing. The book is divided into four sections, each one being based on photonic structures.

Influence of chemical structure on carbon isotope composition of lignite

Science.gov (United States)

Erdenetsogt, Bat-Orshikh; Lee, Insung; Ko, Yoon-Joo; Mungunchimeg, Batsaikhan

2017-04-01

During the last two decades, a number of studies on carbon isotopes in terrestrial organic matter (OM) have been carried out and used to determine changes in paleoatmospheric δ13C value as well as assisting in paleoclimate analysis. Coal is abundant terrestrial OM. However, application of its δ13C value is very limited, because the understanding of changes in isotopic composition during coalification is relatively insufficient. The purpose of this study was to examine the influence of the chemical structure on the carbon isotope composition of lignite. Generally, lignite has more complex chemical structures than other higher rank coal because of the existence of various types of oxygen-containing functional groups that are eliminated at higher rank level. A total of sixteen Lower Cretaceous lignite samples from Baganuur mine (Mongolia) were studied by ultimate, stable carbon isotope and solid-state 13C CP/MAS NMR analyses. The carbon contents of the samples increase with increase in depth, whereas oxygen content decreases continuously. This is undoubtedly due to normal coalification process and also consistent with solid state NMR results. The δ13C values of the samples range from -23.54‰ to -21.34‰ and are enriched in 13C towards the lowermost samples. Based on the deconvolution of the NMR spectra, the ratios between carbons bonded to oxygen (60-90 ppm and 135-220 ppm) over carbons bonded to carbon and hydrogen (0-50 ppm and 90-135 ppm) were calculated for the samples. These correlate well with δ13C values (R2 0.88). The results indicate that the δ13C values of lignite are controlled by two mechanisms: (i) depletion in 13C as a result of loss of isotopically heavy oxygen-bounded carbons and (ii) enrichment in 13C caused by a loss of isotopically light methane from aliphatic and aromatic carbons. At the rank of lignite, coal is enriched in 13C because the amount of isotopically heavy CO2 and CO, released from coal as a result of changes in the chemical

Latest Developments in Data Analysis and Structure Determination and Refinement: Software for Chemical Crystallography

International Nuclear Information System (INIS)

Dix, I.; Adam, M.; Jacob, H. F.; Roter, A.

2003-01-01

The introduction of a two-dimensional CCD X-ray detector nearly 10 years ago by Bruker started a revolution in chemical crystallography. Since then, crystallographers can accomplish a complete data collection even of small and poorly scattering crystals in a few hours instead of days. The launch of the kappa geometry by Nonius a few years ago beforehand equally revolutionized the field of single crystal diffractometry. Currently Bruker Nonius has far more than 500 CCD systems installed. The latest development of Bruker Nonius, the X8 APEX, is the powerful combination of both: the APEX CCD detector and the unique Kappa four-circle goniometer. The APEX 4K CCD detector provides the utmost sensitivity, while the Kappa four-circle goniometer offers a very open geometry, granting all the flexibility to align any crystallographic axis. This provides a more efficient data collection for axial photographs to investigate e.g. diffuse scattering or incommensurate structures. Even the crystal-detector distance is computer-controlled for precise and superior data collection. The X8 APEX software suite gives a whole new look to the CCD users interface. It not only has improved data collection abilities, but also guides the chemist or mineralogist through gathering the raw crystal data to producing the final crystal structure. It provides context-dependent menus, which are well-known from business software packages such as Outlook. The tools for unit cell determination, views into reciprocal space, optimisation of the data collection strategy, data integration, scaling and correcting (SADABS) as well as tools for structure solving and refining (SHELXTL package) will be presented. Low temperature work has become an essential tool for challenging samples. The Bruker Nonius Kryo-Flex cryogenic device makes chemical crystallography at low temperatures a routine method in your laboratory. Of course, the Kryo-Flex is fully controlled by the new graphical user interface of the X8 APEX

Service activities of chemical analysis division

International Nuclear Information System (INIS)

Eom, Tae Yoon; Suh, Moo Yul; Park, Kyoung Kyun; Jung, Ki Suk; Joe, Kih Soo; Jee, Kwang Yong; Jung, Woo Sik; Sohn, Se Chul; Yeo, In Heong; Han, Sun Ho

1988-12-01

Progress of the Division during the year of 1988 was described on the service activities for various R and D projects carrying out in the Institute, for the fuel fabrication and conversion plant, and for the post-irradiation examination facility. Relevant analytical methodologies developed for the chemical analysis of an irradiated fuel, safeguards chemical analysis, and pool water monitoring were included such as chromatographic separation of lanthanides, polarographic determination of dissolved oxygen in water, and automation on potentiometric titration of uranium. Some of the laboratory manuals revised were also included in this progress report. (Author)

Identification of Lilial as a fragrance sensitizer in a perfume by bioassay-guided chemical fractionation and structure-activity relationships

DEFF Research Database (Denmark)

Arnau, E G; Andersen, Klaus Ejner; Bruze, M

2000-01-01

Fragrance materials are among the most common causes of allergic contact dermatitis. The aim of this study was to identify in a perfume fragrance allergens not included in the fragrance mix, by use of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships...... (SARs). The basis for the investigation was a 45-year-old woman allergic to her own perfume. She had a negative patch test to the fragrance mix and agreed to participate in the study. Chemical fractionation of the perfume concentrate was used for repeated patch testing and/or repeated open application......" in their chemical structure, indicating an ability to modify skin proteins and thus behave as a skin sensitizer, were tested on the patient. The patient reacted positively to the synthetic fragrance p-t-butyl-alpha-methylhydrocinnamic aldehyde (Lilial), a widely used fragrance compound not present in the fragrance...

Cluster analysis to evaluate stable chemical elements and physical-chemical parameters behavior on uranium mining waste

International Nuclear Information System (INIS)

Pereira, Wagner de Souza; Py Junior, Delcy de Azevedo; Goncalves, Simone; Kelecom, Alphonse; Morais, Gustavo Ferrari de; Campelo, Emanuele Lazzaretti Cordova; Dores, Luis Augusto de Carvalho Bresser

2011-01-01

The Ore Treating Unit (UTM, in portuguese) is a deactivated uranium mine. A cluster analysis was used to evaluate the behavior of stable chemical elements and physical-chemical parameters in their effluents. The utilization of the cluster analysis proved itself effective in the assessment, allowing the identification of groups of chemical elements, physical-chemical parameters and their joint analysis (elements and parameters). As a result we may assert, based on data analysis, that there is a strong link between calcium and magnesium and between aluminum and rare-earth oxides on UTM's effluents. Sulphate was also identified as strongly linked to total and dissolved solids, and those to electrical conductivity. There were other associations, but not so strongly linked. Further gathering, to seasonal evaluation, are required in order to confirm those analysis. Additional statistical analysis (factor analysis) must be used to try to identify the origin of the identified groups on this analysis. (author)

Cluster analysis to evaluate stable chemical elements and physical-chemical parameters behavior on uranium mining waste

Energy Technology Data Exchange (ETDEWEB)

Pereira, Wagner de Souza; Py Junior, Delcy de Azevedo; Goncalves, Simone, E-mail: wspereira@inb.gov.br [Unidade de Tratamento de Minerio (UTM/INB), Pocos de Caldas, MG (Brazil). Coordenacao de Protecao Radiologica. Grupo Multidisciplinar de Radioprotecao; Kelecom, Alphonse [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Inst. de Biologia. Lab. de Radiobiologia e Radiometria Pedro Lopes dos Santos; Morais, Gustavo Ferrari de; Campelo, Emanuele Lazzaretti Cordova [Unidade de Tratamento de Minerio (UTM/INB), Pocos de Caldas, MG (Brazil). Coordenacao de Desenvolvimento de Processos; Dores, Luis Augusto de Carvalho Bresser [Unidade de Tratamento de Minerio (UTM/INB), Pocos de Caldas, MG (Brazil). Gerencia de Descomissionamento

2011-07-01

The Ore Treating Unit (UTM, in portuguese) is a deactivated uranium mine. A cluster analysis was used to evaluate the behavior of stable chemical elements and physical-chemical parameters in their effluents. The utilization of the cluster analysis proved itself effective in the assessment, allowing the identification of groups of chemical elements, physical-chemical parameters and their joint analysis (elements and parameters). As a result we may assert, based on data analysis, that there is a strong link between calcium and magnesium and between aluminum and rare-earth oxides on UTM's effluents. Sulphate was also identified as strongly linked to total and dissolved solids, and those to electrical conductivity. There were other associations, but not so strongly linked. Further gathering, to seasonal evaluation, are required in order to confirm those analysis. Additional statistical analysis (factor analysis) must be used to try to identify the origin of the identified groups on this analysis. (author)

Structural, optical and electrical properties of chemically deposited ...

Indian Academy of Sciences (India)

Structural, optical and electrical properties of chemically deposited nonstoichiometric copper ... One of these compounds, CuInSe2, with its optical absorption .... is clear from SEM images that the number of grains goes on increasing with the ...

From glass structure to its chemical durability

International Nuclear Information System (INIS)

Angeli, F.

2009-01-01

The author gives an overview of his research activities. He more precisely reports studies related to glass structure based on nuclei observed by NMR and present in glasses of interest for nuclear activities. He discusses the influence of chemical composition on structure, and discusses information which can be extracted from network formers (Al, B) and modifiers (Na, Ca), and from oxygen present in the network linkages of oxide glasses. He discusses the different experimental and modelling approaches which enable structural and morphological information to be obtained at a mesoscopic scale. The last part deals with the investigation of the long term behaviour of confinement matrices (glassy matrix for medium-activity wastes, ceramic matrix)

Analysis of self-organized In(Ga)As quantum structures with the scanning transmission electron microscope

International Nuclear Information System (INIS)

Sauerwald, Andres

2008-01-01

Aim of this thesis was to apply the analytical methods of the scanning transmission electron microscopy to the study of self-organized In(Ga)As quantum structures. With the imaging methods Z contrast and bright field (position resolutions in the subnanometer range) and especially with the possibilities of the quantitative chemical EELS analysis of the scanning transmission electron microscope (STEM) fundamental questions concerning morphology and chemical properties of self-organized quantum structures should be answered. By the high position resolution of the STEM among others essentail morphological and structural parameters in the growth behaviour of ''dot in a well'' (DWell) structures and of vertically correlated quantum dots (QDs) could be analyzed. For the optimization of DWell structures samples were studied, the nominal InAs-QD growth position was directedly varied within the embedding InGaAs quantum wells. The STEM offers in connection with the EELS method a large potential for the chemical analysis of quantum structures. Studied was a sample series of self-organized InGaAs/GaAs structures on GaAs substrate, the stress of which was changed by varying the Ga content of the INGaAs material between 2.4 % and 4.3 % [de

Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

DEFF Research Database (Denmark)

Bratholm, Lars Andersen

to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

Strain-induced structural changes and chemical reactions. 1: Thermomechanical and kinetic models

International Nuclear Information System (INIS)

Levitas, V.I.; Nesterenko, V.F.; Meyers, M.A.

1998-01-01

Strain-induced chemical reactions were observed recently (Nesterenko et al) in experiments in the shear band in both Ti-Si and Nb-Si mixtures. Reactions can start in the solid state or after melting of at least one component. One of the aims is to find theoretically whether there are possible macroscopic mechanisms of mechanical intensification of the above and other chemical reactions due to plastic shear in the solid state. Continuum thermodynamical theory of structural changes with an athermal kinetics, which includes martensitic phase transformations, plastic strain-induced chemical reactions and polymorphic transformations, is developed at finite strains. The theory includes kinematics, criterion of structural change and extremum principle for determination of all unknown variable parameters for the case with neglected elastic strains. Thermodynamically consistent kinetic theory of thermally activated structural changes is suggested. The concept of the effective temperature is introduced which takes into account that temperature can vary significantly (on 1,000 K) during the chemical reactions under consideration. The theory will be applied in Part 2 of the paper for the description of chemical reactions in the shear band

Systems analysis of past, present, and future chemical terrorism scenarios.

Energy Technology Data Exchange (ETDEWEB)

Hoette, Trisha Marie

2012-03-01

Throughout history, as new chemical threats arose, strategies for the defense against chemical attacks have also evolved. As a part of an Early Career Laboratory Directed Research and Development project, a systems analysis of past, present, and future chemical terrorism scenarios was performed to understand how the chemical threats and attack strategies change over time. For the analysis, the difficulty in executing chemical attack was evaluated within a framework of three major scenario elements. First, historical examples of chemical terrorism were examined to determine how the use of chemical threats, versus other weapons, contributed to the successful execution of the attack. Using the same framework, the future of chemical terrorism was assessed with respect to the impact of globalization and new technologies. Finally, the efficacy of the current defenses against contemporary chemical terrorism was considered briefly. The results of this analysis justify the need for continued diligence in chemical defense.

EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

Science.gov (United States)

Montes-Grajales, Diana; Olivero-Verbel, Jesus

2015-01-02

Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co. Copyright © 2014. Published by Elsevier Ireland Ltd.

Chemical, physical, structural and morphological characterization of the electric arc furnace dust

International Nuclear Information System (INIS)

Machado, Janaina G.M.S.; Brehm, Feliciane Andrade; Moraes, Carlos Alberto Mendes; Santos, Carlos Alberto dos; Vilela, Antonio Cezar Faria; Cunha, Joao Batista Marimon da

2006-01-01

Electric arc furnace dust (EAFD) is a hazardous industrial waste generated in the collection of particulate material during steelmaking process via electric arc furnace. Important elements to the industry such as, Fe and Zn are the main ones in EAFD. Due to their presence, it becomes very important to know how these elements are combined before studying new technologies for its processing. The aim of this work was to carry out a chemical, physical, structural and morphological characterization of the EAFD. The investigation was carried out by using granulometry analysis, chemical analysis, scanning electron microscopy (SEM), energy dispersive spectroscopy via SEM (EDS), X-ray mapping analysis via SEM, X-ray diffraction (XRD) and Moessbauer spectroscopy. By XRD the following phases were detected: ZnFe 2 O 4 , Fe 3 O 4 , MgFe 2 O 4 , FeCr 2 O 4 , Ca 0.15 Fe 2.85 O 4 , MgO, Mn 3 O 4 , SiO 2 and ZnO. On the other hand, the phases detected by Moessbauer spectroscopy were: ZnFe 2 O 4 , Fe 3 O 4 , Ca 0.15 Fe 2.85 O 4 and FeCr 2 O 4 . Magnesium ferrite (MgFe 2 O 4 ), observed in the XRD pattern as overlapped peaks, was not identified in the Moessbauer spectroscopy analysis

Heating induced structural and chemical behavior of KD2PO4 in the 25 °C–215 °C temperature range

International Nuclear Information System (INIS)

Botez, Cristian E.; Morris, Joshua L.; Encerrado Manriquez, Andres J.; Anchondo, Adan

2013-01-01

We have used powder x-ray diffraction (XRD) to investigate the structural and chemical modifications undergone by KD 2 PO 4 (DKDP) upon heating from room temperature to 215 °C. Full-profile (Le Bail) analysis of our temperature-resolved data shows no evidence of polymorphic structural transitions or deuterium–hydrogen isotope exchange occurring below T s = 185 °C. The lattice parameters of DKDP vary smoothly upon heating to T s and are 0.2% to 0.6% greater than those of its isostructural hydrogenated counterpart KH 2 PO 4 (KDP). In addition, XRD isotherms collected at T s demonstrate the structural and chemical stability of the title compound at this temperature over a 10.5 h time period. Upon further heating, however, the tetragonal DKDP phase becomes unstable, as evidenced by its transition to a monoclinic DKDP modification and eventual chemical decomposition via dehydration. - Highlights: • Structural and chemical behavior of KD 2 PO 4 is investigated upon heating to 215 °C • No polymorphic transitions or deuterium-hydrogen isotope exchange below T s = 185 °C • KD 2 PO 4 is structurally and chemically stable at T s over a 10.5 h time period • KD 2 PO 4 chemically decomposes via dehydration upon heating above T d = 195 °C

Chemical modulation of electronic structure at the excited state

Science.gov (United States)

Li, F.; Song, C.; Gu, Y. D.; Saleem, M. S.; Pan, F.

2017-12-01

Spin-polarized electronic structures are the cornerstone of spintronics, and have thus attracted a significant amount of interest; in particular, researchers are looking into how to modulate the electronic structure to enable multifunctional spintronics applications, especially in half-metallic systems. However, the control of the spin polarization has only been predicted in limited two-dimensional systems with spin-polarized Dirac structures and is difficult to achieve experimentally. Here, we report the modulation of the electronic structure in the light-induced excited state in a typical half-metal, L a1 /2S r1 /2Mn O3 -δ . According to the spin-transport measurements, there appears a light-induced increase in magnetoresistance due to the enhanced spin scattering, which is closely associated with the excited spin polarization. Strikingly, the light-induced variation can be enhanced via alcohol processing and reduced by oxygen annealing. X-ray photoelectron spectroscopy measurements show that in the chemical process, a redox reaction occurs with a change in the valence of Mn. Furthermore, first-principles calculations reveal that the change in the valence of Mn alters the electronic structure and consequently modulates the spin polarization in the excited state. Our findings thus report a chemically tunable electronic structure, demonstrating interesting physics and the potential for multifunctional applications and ultrafast spintronics.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Weighted voting-based consensus clustering for chemical structure databases

Science.gov (United States)

Saeed, Faisal; Ahmed, Ali; Shamsir, Mohd Shahir; Salim, Naomie

2014-06-01

The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures.

Microprocessors in automatic chemical analysis

International Nuclear Information System (INIS)

Goujon de Beauvivier, M.; Perez, J.-J.

1979-01-01

Application of microprocessors to programming and computing of solutions chemical analysis by a sequential technique is examined. Safety, performances reliability are compared to other methods. An example is given on uranium titration by spectrophotometry [fr

Identification of Lilial as a fragrance sensitizer in a perfume by bioassay-guided chemical fractionation and structure-activity relationships

DEFF Research Database (Denmark)

Gimenéz-Arnau, Elena; Andersen, K E; Bruze, M

2000-01-01

Fragrance materials are among the most common causes of allergic contact dermatitis. The aim of this study was to identify in a perfume fragrance allergens not included in the fragrance mix, by use of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships...... (SARs). The basis for the investigation was a 45-year-old woman allergic to her own perfume. She had a negative patch test to the fragrance mix and agreed to participate in the study. Chemical fractionation of the perfume concentrate was used for repeated patch testing and/or repeated open application...

Molecule database framework: a framework for creating database applications with chemical structure search capability.

Science.gov (United States)

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework

Chemical analysis and base-promoted hydrolysis of locally ...

African Journals Online (AJOL)

Abstract. The study was on the chemical analysis and base- promoted hydrolysis of extracted shea nut fat. The local method of extraction of the shea nut oil was employed in comparison with literature report. A simple cold-process alkali hydrolysis of the shea nut oil was used in producing the soap. The chemical analysis of ...

Calibrating Detailed Chemical Analysis of M dwarfs

Science.gov (United States)

Veyette, Mark; Muirhead, Philip Steven; Mann, Andrew; Brewer, John; Allard, France; Homeier, Derek

2018-01-01

The ability to perform detailed chemical analysis of Sun-like F-, G-, and K-type stars is a powerful tool with many applications including studying the chemical evolution of the Galaxy, assessing membership in stellar kinematic groups, and constraining planet formation theories. Unfortunately, complications in modeling cooler stellar atmospheres has hindered similar analysis of M-dwarf stars. Large surveys of FGK abundances play an important role in developing methods to measure the compositions of M dwarfs by providing benchmark FGK stars that have widely-separated M dwarf companions. These systems allow us to empirically calibrate metallicity-sensitive features in M dwarf spectra. However, current methods to measure metallicity in M dwarfs from moderate-resolution spectra are limited to measuring overall metallicity and largely rely on astrophysical abundance correlations in stellar populations. In this talk, I will discuss how large, homogeneous catalogs of precise FGK abundances are crucial to advancing chemical analysis of M dwarfs beyond overall metallicity to direct measurements of individual elemental abundances. I will present a new method to analyze high-resolution, NIR spectra of M dwarfs that employs an empirical calibration of synthetic M dwarf spectra to infer effective temperature, Fe abundance, and Ti abundance. This work is a step toward detailed chemical analysis of M dwarfs at a similar precision achieved for FGK stars.

Constitutive model and electroplastic analysis of structures under cyclic loading

International Nuclear Information System (INIS)

Wang, X.; Lei, Y; Du, Q.

1989-01-01

Many engineering structures in nuclear reactors, thermal power stations, chemical plants and aerospace vehicles are subjected to cyclic mechanic-thermal loading, which is the main cause of structural fatigue failure. Over the past twenty years, designers and researchers have paid great attention to the research on life prediction and elastoplastic analysis of structures under cyclic loading. One of the key problems in elastoplastic analysis is to construct a reasonable constitutive model for cyclic plasticity. In the paper, the constitutive equations are briefly outlined. Then, the model is implemented in a finite element code to predict the response of cyclic loaded structural components such as a double-edge-notched plate, a grooved bar and a nozzle in spherical shell. Numerical results are compared with those from other theories and experiments

Investigation of hydrogen content in chemically delithiated lithium-ion battery cathodes using prompt gamma activation analysis

International Nuclear Information System (INIS)

Aghara, S.K.; Alvarez II, E.; Venkatraman, S.; Manthiram, A.

2005-01-01

Lithium-ion batteries are widely used as a power source for portable electronic devices. Currently, only 50-70% of the theoretical capacity of the layered oxide cathode (positive electrode) materials could be reversibly used. The reason for this limitation is not fully understood in the literature. Recent structural and chemical characterizations of chemically delithiated (charged) cathodes suggest that loss of oxygen from the lattice may play a role in this regard. However, during the chemical delithiation process any proton inserted from the solvent could adversely affect the oxygen content analysis data. The challenge in addressing this issue is to detect and determine precisely the proton content in the chemically delithiated samples. The prompt gamma-ray activation analysis (PGAA) facility at the Nuclear Engineering Teaching Laboratory (NETL) is used to determine the proton content in the layered oxide cathode LiNi 0.5 Mn 0.5 O 2 before and after chemical delithiation. The data are compared with those obtained with Fourier transform infrared (FTIR) spectroscopy, which can provide mainly qualitative analysis. The technique has proved to be promising for these compounds and will be applied to characterize several other chemically delithiated Li 1-x Co 1-y M y O 2 (M = Cr, Mn, Fe, Ni, Cu, Mg, and Al) cathodes. (author)

Chemical analysis by nuclear methods. v. 2

International Nuclear Information System (INIS)

Alfassi, Z.B.

1998-01-01

'Chemical analysis by Nuclear Methods' is an effort of some renowned authors in field of nuclear chemistry and radiochemistry which is compiled by Alfassi, Z.B. and translated into Farsi version collected in two volumes. The second volume consists of the following chapters: Detecting ion recoil scattering and elastic scattering are dealt in the eleventh chapter, the twelfth chapter is devoted to nuclear reaction analysis using charged particles, X-ray emission is discussed at thirteenth chapter, the fourteenth chapter is about using ion microprobes, X-ray fluorescence analysis is discussed in the fifteenth chapter, alpha, beta and gamma ray scattering in chemical analysis are dealt in chapter sixteen, Moessbauer spectroscopy and positron annihilation are discussed in chapter seventeen and eighteen; The last two chapters are about isotope dilution analysis and radioimmunoassay

Chemical structures and theoretical models of lean premixed ...

African Journals Online (AJOL)

To better understand the chemistry involved in the lean-fuel combustion, the chemical structure of lean premixed propene-oxygen-nitrogen flames stabilized on a flat-flame burner at atmospheric pressure was determined experimentally. The species mole fraction profiles were also computed by the Premix code and three ...

Chemical, physical, structural and morphological characterization of the electric arc furnace dust

Energy Technology Data Exchange (ETDEWEB)

Machado, Janaina G.M.S. [Laboratorio de Siderurgia/LASID, Universidade Federal do Rio Grande do Sul, UFRGS/PPGEM Centro de Tecnologia, AV. Bento Goncalves 9500 CEP, 91501-970 Caixa postal 15021, Porto Alegre, RS (Brazil)]. E-mail: jana@ct.ufrgs.br; Brehm, Feliciane Andrade [Nucleo de Caracterizacao de Materiais/NucMat, Universidade do Vale do Rio dos Sinos, UNISINOS, Sao Leopoldo, RS (Brazil); Moraes, Carlos Alberto Mendes [Nucleo de Caracterizacao de Materiais/NucMat, Universidade do Vale do Rio dos Sinos, UNISINOS, Sao Leopoldo, RS (Brazil); Santos, Carlos Alberto dos [Nucleo de Educacao a Distancia, Universidade Estadual do Rio Grande do Sul, UERGS, Porto Alegre, RS (Brazil); Vilela, Antonio Cezar Faria [Laboratorio de Siderurgia/LASID, Universidade Federal do Rio Grande do Sul, UFRGS/PPGEM Centro de Tecnologia, AV. Bento Goncalves 9500 CEP, 91501-970 Caixa postal 15021, Porto Alegre, RS (Brazil); Cunha, Joao Batista Marimon da [Instituto de Fisica, Universidade Federal do Rio Grande do Sul, UFRGS, Campus do Vale, Porto Alegre, RS (Brazil)

2006-08-25

Electric arc furnace dust (EAFD) is a hazardous industrial waste generated in the collection of particulate material during steelmaking process via electric arc furnace. Important elements to the industry such as, Fe and Zn are the main ones in EAFD. Due to their presence, it becomes very important to know how these elements are combined before studying new technologies for its processing. The aim of this work was to carry out a chemical, physical, structural and morphological characterization of the EAFD. The investigation was carried out by using granulometry analysis, chemical analysis, scanning electron microscopy (SEM), energy dispersive spectroscopy via SEM (EDS), X-ray mapping analysis via SEM, X-ray diffraction (XRD) and Moessbauer spectroscopy. By XRD the following phases were detected: ZnFe{sub 2}O{sub 4}, Fe{sub 3}O{sub 4}, MgFe{sub 2}O{sub 4}, FeCr{sub 2}O {sub 4}, Ca{sub 0.15}Fe{sub 2.85}O{sub 4}, MgO, Mn{sub 3}O{sub 4}, SiO{sub 2} and ZnO. On the other hand, the phases detected by Moessbauer spectroscopy were: ZnFe{sub 2}O{sub 4}, Fe{sub 3}O{sub 4}, Ca{sub 0.15}Fe{sub 2.85}O{sub 4} and FeCr{sub 2}O{sub 4}. Magnesium ferrite (MgFe{sub 2}O{sub 4}), observed in the XRD pattern as overlapped peaks, was not identified in the Moessbauer spectroscopy analysis.

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

Science.gov (United States)

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

Structural analysis of flavonoids in solution through DFT 1H NMR chemical shift calculations: Epigallocatechin, Kaempferol and Quercetin

Science.gov (United States)

De Souza, Leonardo A.; Tavares, Wagner M. G.; Lopes, Ana Paula M.; Soeiro, Malucia M.; De Almeida, Wagner B.

2017-05-01

In this work, we showed that comparison between experimental and theoretical 1H NMR chemical shift patterns, calculated using Density Functional Theory (DFT), can be used for the prediction of molecular structure of flavonoids in solution, what is experimentally accessible for gas phase (electron diffraction methods) and solid samples (X-ray diffraction). The best match between B3LYP/6-31G(d,p)-PCM 1H NMR calculations for B ring rotated structures and experimental spectra can provide information on the conformation adopted by polyphenols in solution (usually DMSO-d6, acetone-d6 as solvents), which may differ from solid state and gas phase observed structures, and also DFT optimized geometry in the vacuum.

At the brink of supercoloniality: genetic, behavioral and chemical assessments of population structure of the desert ant Cataglyphis niger

Directory of Open Access Journals (Sweden)

Maya eSaar

2014-05-01

Full Text Available The nesting habits of ants play an important role in structuring ant populations. They vary from monodomy, a colony occupies a single nest, via polydomy, a colony occupies multiple adjacent nests, to supercoloniality, a colony spans over large territories comprising dozen to thousands nests without having any boundaries. The population structure of the desert ant Cataglyphis niger, previously considered to form supercolonies, was studied using genetic, chemical and behavioral tools in plots of 50x50 meters at two distinct populations. At the Palmahim site, the plot comprised 15 nests that according to the genetic analysis constituted three colonies. Likewise at the Rishon Leziyyon site 14 nests constituted 5 genetic colonies. In both sites, both chemical analysis and the behavioral (aggression tests confirmed the colony genetic architecture. The behavioral tests also revealed that aggression between colonies within a population was higher than that exhibited between colonies of different populations, suggesting the occurrence of the nasty neighbor phenomenon. In contrast to supercolony structure previously reported in another population of this species, the presently studied populations were composed of polydomous colonies. However, both the genetic and chemical data revealed that the inter-colonial differences between sites were larger than those within site, suggesting some within-site population viscosity. Thus, C. niger exhibits flexible nesting characteristics, from polydomy to supercoloniality, and can be considered at the brink of supercoloniality. We attribute the differences in population structure among sites to the intensity of intraspecific competition.

Comparison of descriptive sensory analysis and chemical analysis for oxidative changes in milk

DEFF Research Database (Denmark)

Hedegaard, R V; Kristensen, D; Nielsen, Jacob Holm

2006-01-01

and lipolytic changes occurring in the milk during chill storage for 4 d. Sensory analysis and chemical analysis showed high correlation between the typical descriptors for oxidation such as cardboard, metallic taste, and boiled milk and specific chemical markers for oxidation such as hexanal. Notably, primary......Oxidation in 3 types of bovine milk with different fatty acid profiles obtained through manipulation of feed was evaluated by analytical methods quantifying the content of potential antioxidants, the tendency of formation of free radicals, and the accumulation of primary and secondary oxidation...... products. The milk samples were evaluated in parallel by descriptive sensory analysis by a trained panel, and the correlation between the chemical analysis and the descriptive sensory analysis was evaluated. The fatty acid composition of the 3 types of milk was found to influence the oxidative...

Comparison of descriptive sensory analysis and chemical analysis for oxidative changes in milk

DEFF Research Database (Denmark)

Hedegaard, Rikke Susanne Vingborg; Kristensen, D.; Nielsen, J. H.

2006-01-01

products. The milk samples were evaluated in parallel by descriptive sensory analysis by a trained panel, and the correlation between the chemical analysis and the descriptive sensory analysis was evaluated. The fatty acid composition of the 3 types of milk was found to influence the oxidative...... and lipolytic changes occurring in the milk during chill storage for 4 d. Sensory analysis and chemical analysis showed high correlation between the typical descriptors for oxidation such as cardboard, metallic taste, and boiled milk and specific chemical markers for oxidation such as hexanal. Notably, primary...... oxidation products (i.e., lipid hydroperoxides) and even the tendency of formation of radicals as measured by electron spin resonance spectroscopy were also highly correlated to the sensory descriptors for oxidation. Electron spin resonance spectroscopy should accordingly be further explored as a routine...

An analysis of chemical ingredients network of Chinese herbal formulae for the treatment of coronary heart disease.

Directory of Open Access Journals (Sweden)

Fan Ding

Full Text Available 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.

Structure of adsorbed monolayers. The surface chemical bond

International Nuclear Information System (INIS)

Somorjai, G.A.; Bent, B.E.

1984-06-01

This paper attempts to provide a summary of what has been learned about the structure of adsorbed monolayers and about the surface chemical bond from molecular surface science. While the surface chemical bond is less well understood than bonding of molecules in the gas phase or in the solid state, our knowledge of its properties is rapidly accumulating. The information obtained also has great impact on many surface science based technologies, including heterogeneous catalysis and electronic devices. It is hoped that much of the information obtained from studies at solid-gas interfaces can be correlated with molecular behavior at solid-liquid interfaces. 31 references, 42 figures, 1 table

Chemical and thermal analysis for characterisation of building materials

International Nuclear Information System (INIS)

Kumar, S.C.; Sudersanan, M.; Ravindran, P.V.; Kalekar, B.B.; Mathur, P.K.

2000-01-01

Cement and other construction materials are extensively used for the construction of shielding materials for nuclear and high energy radiations. The design and optimum utilisation of such materials need an accurate analysis of their chemical composition. The moisture content and presence of bound water and other volatile materials are also important. The use of thermal analysis supplements the data obtained by chemical analysis and enables a distinction of moisture and chemically bound water. It also enables an identification of the process leading to the loss on ignition. The work carried out on the analysis of sand, cement and other aggregate materials used for the preparation of concrete is described in the paper. (author)

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape

OpenAIRE

Ferreon, Allan Chris M.; Moosa, Mahdi Muhammad; Gambin, Yann; Deniz, Ashok A.

2012-01-01

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster reson...

Electronic structure, chemical bonding, phase stability, and ground-state properties of YNi2-x(Co/Cu)xB2C

International Nuclear Information System (INIS)

Ravindran, P.; Johansson, B.; Eriksson, O.

1998-01-01

In order to understand the role of Ni site substitution on the electronic structure and chemical bonding in YNi 2 B 2 C, we have made systematic electronic-structure studies on YNi 2 B 2 C as a function of Co and Cu substitution using the supercell approach within the local density approximation. The equilibrium volume, bulk modulus (B 0 ) and its pressure derivative (B 0 ' ), Grueneisen constant (γ G ), Debye temperature (Θ D ), cohesive energy (E c ), and heat of formation (ΔH) are calculated for YNi 2-x (Co/Cu) x B 2 C (x=0,0.5,1.0,1.5,2). From the total energy, electron-energy band structure, site decomposed density of states, and charge-density contour we have analyzed the structural stability and chemical bonding behavior of YNi 2 B 2 C as a function of Co/Cu substitution. We find that the simple rigid band model successfully explains the electronic structure and structural stability of Co/Cu substitution for Ni. In addition to studying the chemical bonding and electronic structure we present a somewhat speculative analysis of the general trends in the behavior of critical temperature for superconductivity as a function of alloying. copyright 1998 The American Physical Society

Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties

Directory of Open Access Journals (Sweden)

Monika Batke

2016-09-01

Full Text Available 1.AbstractInterest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g. the European Union´s Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine structural similarity with shared mechanisms of action. Substances with similar chemical structure and toxicological profile form candidate categories suitable for read-across. We combined two databases on repeated dose toxicity, RepDose database and ELINCS database to form a common database for the identification of categories. The resulting database contained physicochemical, structural and toxicological data, which were refined and curated for cluster analyses. We applied the Predictive Clustering Tree (PCT approach for clustering chemicals based on structural and on toxicological information to detect groups of chemicals with similar toxic profiles and pathways/mechanisms of toxicity. As many of the experimental toxicity values were not available, this data was imputed by predicting them with a multi-label classification method, prior to clustering. The clustering results were evaluated by assessing chemical and toxicological similarities with the aim of identifying clusters with a concordance between structural information and toxicity profiles/mechanisms. From these chosen clusters, seven were selected for a quantitative read-across, based on a small ratio of NOAEL of the members with the highest and the lowest NOAEL in the cluster (<5. We discuss

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

Science.gov (United States)

Hanwell, Marcus D; Curtis, Donald E; Lonie, David C; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R

2012-08-13

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Directory of Open Access Journals (Sweden)

Hanwell Marcus D

2012-08-01

Full Text Available Abstract Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format

Structural analysis of a homogeneous polysaccharide from Achatina fulica.

Science.gov (United States)

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.

PPM-One: a static protein structure based chemical shift predictor

International Nuclear Information System (INIS)

Li, Dawei; Brüschweiler, Rafael

2015-01-01

We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs

Comparative Analysis on Chemical Composition of Bentonite Clays ...

African Journals Online (AJOL)

2017-09-12

Sep 12, 2017 ... Comparative Analysis on Chemical Composition of Bentonite Clays. Obtained from Ashaka and ... versatile material for geotechnical engineering and as well as their demand for ..... A PhD thesis submitted to the Chemical ...

Chemical analysis of the Fornax Dwarf galaxy

NARCIS (Netherlands)

Letarte, Bruno

2007-01-01

This thesis is entitled “Chemical Analysis of the Fornax Dwarf Galaxy”, and it’s main goal is to determine what are the chemical elements present in the stars of this galaxy in order to try and understand it’s evolution. Galaxies are not “static” objects, they move, form stars and can interact with

Application of chemical structure and bonding of actinide oxide materials for forensic science

International Nuclear Information System (INIS)

Wilkerson, Marianne Perry

2010-01-01

We are interested in applying our understanding of actinide chemical structure and bonding to broaden the suite of analytical tools available for nuclear forensic analyses. Uranium- and plutonium-oxide systems form under a variety of conditions, and these chemical species exhibit some of the most complex behavior of metal oxide systems known. No less intriguing is the ability of AnO 2 (An: U, Pu) to form non-stoichiometric species described as AnO 2+x . Environmental studies have shown the value of utilizing the chemical signatures of these actinide oxide materials to understand transport following release into the environment. Chemical speciation of actinide-oxide samples may also provide clues as to the age, source, or process history of the material. The scientific challenge is to identify, measure and understand those aspects of speciation of actinide analytes that carry information about material origin and history most relevant to forensics. Here, we will describe our efforts in material synthesis and analytical methods development that we will use to provide the fundamental science to characterize actinide oxide molecular structures for forensic science. Structural properties and initial results to measure structural variability of uranium oxide samples using synchrotron-based X-ray Absorption Fine Structure will be discussed.

Application of chemical structure and bonding of actinide oxide materials for forensic science

Energy Technology Data Exchange (ETDEWEB)

Wilkerson, Marianne Perry [Los Alamos National Laboratory

2010-01-01

We are interested in applying our understanding of actinide chemical structure and bonding to broaden the suite of analytical tools available for nuclear forensic analyses. Uranium- and plutonium-oxide systems form under a variety of conditions, and these chemical species exhibit some of the most complex behavior of metal oxide systems known. No less intriguing is the ability of AnO{sub 2} (An: U, Pu) to form non-stoichiometric species described as AnO{sub 2+x}. Environmental studies have shown the value of utilizing the chemical signatures of these actinide oxide materials to understand transport following release into the environment. Chemical speciation of actinide-oxide samples may also provide clues as to the age, source, or process history of the material. The scientific challenge is to identify, measure and understand those aspects of speciation of actinide analytes that carry information about material origin and history most relevant to forensics. Here, we will describe our efforts in material synthesis and analytical methods development that we will use to provide the fundamental science to characterize actinide oxide molecular structures for forensic science. Structural properties and initial results to measure structural variability of uranium oxide samples using synchrotron-based X-ray Absorption Fine Structure will be discussed.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape.

Science.gov (United States)

Ferreon, Allan Chris M; Moosa, Mahdi Muhammad; Gambin, Yann; Deniz, Ashok A

2012-10-30

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson's disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 21 [urea][TMAO] ratio has a net neutral effect on the protein's dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape

Science.gov (United States)

Ferreon, Allan Chris M.; Moosa, Mahdi Muhammad; Deniz, Ashok A.

2012-01-01

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson’s disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 2∶1 [urea]∶[TMAO] ratio has a net neutral effect on the protein’s dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments. PMID:22826265

Structural and Optical Properties of Chemical Bath Deposited Silver Oxide Thin Films: Role of Deposition Time

Directory of Open Access Journals (Sweden)

A. C. Nwanya

2013-01-01

Full Text Available Silver oxide thin films were deposited on glass substrates at a temperature of 50°C by chemical bath deposition technique under different deposition times using pure AgNO3 precursor and triethanolamine as the complexing agent. The chemical analysis based on EDX technique shows the presence of Ag and O at the appropriate energy levels. The morphological features obtained from SEM showed that the AgxO structures varied as the deposition time changes. The X-ray diffraction showed the peaks of Ag2O and AgO in the structure. The direct band gap and the refractive index increased as the deposition time increased and was in the range of 1.64–1.95 eV and 1.02–2.07, respectively. The values of the band gap and refractive index obtained indicate possible applications in photovoltaic and photothermal systems.

Handbook of Basic Tables for Chemical Analysis. Final report

International Nuclear Information System (INIS)

Bruno, T.J.; Svoronos, P.D.N.

1988-04-01

This work began as a slim booklet prepared by one of the authors (TJB) to accompany a course on chemical instrumentation presented at the National Bureau of Standards, Boulder Laboratories. The booklet contained tables on chromatography, spectroscopy, and chemical (wet) methods, and was intended to provide the students with enough basic data to design their own analytical methods and procedures. Shortly thereafter, with the co-authorship of Prof. Paris D. N. Svoronos, it was expanded into a more-extensive compilation entitled Basic Tables for Chemical Analysis, published as National Bureau of Standards Technical Note 1096. That work has now been expanded and updated into the present body of tables. Although there have been considerable changes since the first version of these tables, the aim has remained essentially the same. The authors have tried to provide a single source of information for those practicing scientists and research students who must use various aspects of chemical analysis in their work. In this respect, it is geared less toward the researcher in analytical chemistry than to those practitioners in other chemical disciplines who must have routine use of chemical analysis

Structural and XPS studies of PSi/TiO2 nanocomposites prepared by ALD and Ag-assisted chemical etching

International Nuclear Information System (INIS)

Iatsunskyi, Igor; Kempiński, Mateusz; Nowaczyk, Grzegorz; Jancelewicz, Mariusz; Pavlenko, Mykola; Załęski, Karol; Jurga, Stefan

2015-01-01

Highlights: • Porous silicon/TiO 2 nanocomposites have been investigated. • Morphology and chemical composition of PSi/TiO 2 nanocomposites were established. • Valence-band XPS maximums for PSi/TiO 2 nanocomposites were found and analyzed. - Abstract: PSi/TiO 2 nanocomposites fabricated by atomic layer deposition (ALD) and metal-assisted chemical etching (MACE) were investigated. The morphology and phase structure of PSi/TiO 2 nanocomposites were studied by means of scanning electron microscopy (SEM), transmission electron microscopy (TEM) with an energy dispersive X-ray spectroscopy (EDX) and Raman spectroscopy. The mean size of TiO 2 nanocrystals was determined by TEM and Raman spectroscopy. X-ray photoelectron spectroscopy (XPS) was used to analyze the chemical elemental composition by observing the behavior of the Ti 2p, O 1s and Si 2p lines. TEM, Raman spectroscopy and XPS binding energy analysis confirmed the formation of TiO 2 anatase phase inside the PSi matrix. The XPS valence band analysis was performed in order to investigate the modification of PSi/TiO 2 nanocomposites electronic structure. Surface defects states of Ti 3+ at PSi/TiO 2 nanocomposites were identified by analyzing of XPS valence band spectra

Shallow nitrogen ion implantation: Evolution of chemical state and defect structure in titanium

Energy Technology Data Exchange (ETDEWEB)

Manojkumar, P.A., E-mail: manoj@igcar.gov.in [Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Chirayath, V.A.; Balamurugan, A.K.; Krishna, Nanda Gopala; Ilango, S.; Kamruddin, M.; Amarendra, G.; Tyagi, A.K. [Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Raj, Baldev [National Institute of Advanced Studies, Bangalore 560 012 (India)

2016-09-15

Highlights: • Low energy nitrogen ion implantation in titanium was studied. • Chemical and defect states were analyzed using SIMS, XPS and PAS. • SIMS and depth resolved XPS data showed good agreement. • Depth resolved defect and chemical states information were revealed. • Formation of 3 layers of defect states proposed to fit PAS results. - Abstract: Evolution of chemical states and defect structure in titanium during low energy nitrogen ion implantation by Plasma Immersion Ion Implantation (PIII) process is studied. The underlying process of chemical state evolution is investigated using secondary ion mass spectrometry and X-ray photoelectron spectroscopy. The implantation induced defect structure evolution as a function of dose is elucidated using variable energy positron annihilation Doppler broadening spectroscopy (PAS) and the results were corroborated with chemical state. Formation of 3 layers of defect state was modeled to fit PAS results.

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

Science.gov (United States)

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 analysis of reactor and commercial columbium

International Nuclear Information System (INIS)

Anon.

1981-01-01

The methods cover the chemical analysis of reactor and commercial columbium having chemical compositions within specified limits. The following analytical procedures are discussed along with apparatus, reagents, photometric practice, safety precautions, sampling, and rounding calculated values: nitrogen, by distillation (photometric) method; molybdenum and tungsten by the dithiol (photometric) method; iron by the 1,10-phenanthroline (photometric) method

Computational Chemical Synthesis Analysis and Pathway Design

Directory of Open Access Journals (Sweden)

Fan Feng

2018-06-01

Full Text Available With the idea of retrosynthetic analysis, which was raised in the 1960s, chemical synthesis analysis and pathway design have been transformed from a complex problem to a regular process of structural simplification. This review aims to summarize the developments of computer-assisted synthetic analysis and design in recent years, and how machine-learning algorithms contributed to them. LHASA system started the pioneering work of designing semi-empirical reaction modes in computers, with its following rule-based and network-searching work not only expanding the databases, but also building new approaches to indicating reaction rules. Programs like ARChem Route Designer replaced hand-coded reaction modes with automatically-extracted rules, and programs like Chematica changed traditional designing into network searching. Afterward, with the help of machine learning, two-step models which combine reaction rules and statistical methods became the main stream. Recently, fully data-driven learning methods using deep neural networks which even do not require any prior knowledge, were applied into this field. Up to now, however, these methods still cannot replace experienced human organic chemists due to their relatively low accuracies. Future new algorithms with the aid of powerful computational hardware will make this topic promising and with good prospects.

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

Energy Technology Data Exchange (ETDEWEB)

Klein, Adam [Iowa State Univ., Ames, IA (United States)

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.

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

Science.gov (United States)

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.

Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra

Science.gov (United States)

Shimada, Toru; Hasegawa, Takeshi

2017-10-01

The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pKa‧. The determination of pKa‧ is performed for various ionic strengths, which reveals the thermodynamic acid constant (pKa = 7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of - 1 and the blue form that of - 2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed.

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.

Directory of Open Access Journals (Sweden)

Pablo Cordero

2015-11-01

Full Text Available Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral infection [corrected]. We report herein that high-throughput chemical experiments can isolate an RNA's multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2 and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states' structures and populations. In an in silico benchmark on non-coding RNAs with complex landscapes, M2-REEFFIT recovers 95% of RNA helices present with at least 25% population while maintaining a low false discovery rate (10% and conservative error estimates. In experimental benchmarks, M2-REEFFIT recovers the structure landscapes of a 35-nt MedLoop hairpin, a 110-nt 16S rRNA four-way junction with an excited state, a 25-nt bistable hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose characterization previously required expert mutational analysis and specialized NMR or chemical mapping experiments. With this validation, M2-REEFFIT enabled tests of whether artificial RNA sequences might exhibit complex landscapes in the absence of explicit design. An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are found to interconvert between three or more states, including structures for which there was no design, but that could be stabilized through mutations. These results highlight the likely pervasiveness of rich landscapes with multiple secondary structures in both natural and artificial RNAs and demonstrate an automated chemical/computational route for their empirical characterization.

Thermally emissive sensing materials for chemical spectroscopy analysis

Science.gov (United States)

Poole, Zsolt; Ohodnicki, Paul R.

2018-05-08

A sensor using thermally emissive materials for chemical spectroscopy analysis includes an emissive material, wherein the emissive material includes the thermally emissive materials which emit electromagnetic radiation, wherein the electromagnetic radiation is modified due to chemical composition in an environment; and a detector adapted to detect the electromagnetic radiation, wherein the electromagnetic radiation is indicative of the chemical interaction changes and hence chemical composition and/or chemical composition changes of the environment. The emissive material can be utilized with an optical fiber sensor, with the optical fiber sensor operating without the emissive material probed with a light source external to the material.

Structure activity relationships to assess new chemicals under TSCA

Energy Technology Data Exchange (ETDEWEB)

Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

1990-12-31

Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

Molecular activation analysis for chemical species studies

International Nuclear Information System (INIS)

Chai Zhifang; Mao Xueying; Wang Yuqi; Sun Jingxin; Qian Qingfang; Hou Xiaolin; Zhang Peiqun; Chen Chunying; Feng Weiyu; Ding Wenjun; Li Xiaolin; Li Chunsheng; Dai Xiongxin

2001-01-01

The Molecular Activation Analysis (MAA) mainly refers to an activation analysis method that is able to provide information about the chemical species of elements in systems of interest, though its exact definition has remained to be assigned. Its development is strongly stimulated by the urgent need to know the chemical species of elements, because the bulk contents or concentrations are often insignificant for judging biological, environmental or geochemical effects of elements. In this paper, the features, methodology and limitation of MAA were outlined. Further, the up-to-date MAA progress made in our laboratory was introduced as well. (author)

Integrated polymer waveguides for absorbance detection in chemical analysis systems

DEFF Research Database (Denmark)

Mogensen, Klaus Bo; El-Ali, Jamil; Wolff, Anders

2003-01-01

A chemical analysis system for absorbance detection with integrated polymer waveguides is reported for the first time. The fabrication procedure relies on structuring of a single layer of the photoresist SU-8, so both the microfluidic channel network and the optical components, which include planar....... The emphasis of this paper is on the signal-to-noise ratio of the detection and its relation to the sensitivity. Two absorbance cells with an optical path length of 100 μm and 1000 μm were characterized and compared in terms of sensitivity, limit of detection and effective path length for measurements...

KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies

International Nuclear Information System (INIS)

Kobayashi, Naohiro; Iwahara, Junji; Koshiba, Seizo; Tomizawa, Tadashi; Tochio, Naoya; Guentert, Peter; Kigawa, Takanori; Yokoyama, Shigeyuki

2007-01-01

The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput application to a large number of proteins, with each data set including many NMR spectra, chemical shifts, NOE assignments, and calculated structures. We have developed the new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, which is designed to reduce the tediousness of organizing and manipulating a large number of NMR data sets. In combination with CYANA, the program for automated NOE assignment and structure determination, we have established a robust and highly optimized strategy for comprehensive protein structure analysis. An application of KUJIRA in accordance with our new strategy was carried out by a non-expert in NMR structure analysis, demonstrating that the accurate assignment of the chemical shifts and a high-quality structure of a small protein can be completed in a few weeks. The high completeness of the chemical shift assignment and the NOE assignment achieved by the systematic analysis using KUJIRA and CYANA led, in practice, to increased reliability of the determined structure

Structure and chemical composition of layers adsorbed at interfaces with champagne.

Science.gov (United States)

Aguié-Béghin, V; Adriaensen, Y; Péron, N; Valade, M; Rouxhet, P; Douillard, R

2009-11-11

The structure and the chemical composition of the layer adsorbed at interfaces involving champagne have been investigated using native champagne, as well as ultrafiltrate (UFch) and ultraconcentrate (UCch) obtained by ultrafiltration with a 10(4) nominal molar mass cutoff. The layer adsorbed at the air/liquid interface was examined by surface tension and ellipsometry kinetic measurements. Brewster angle microscopy demonstrated that the layer formed on polystyrene by adsorption or drop evaporation was heterogeneous, with a domain structure presenting similarities with the layer adsorbed at the air/liquid interface. The surface chemical composition of polystyrene with the adlayer was determined by X-ray photoelectron spectroscopy (XPS). The contribution of champagne constituents varied according to the liquid (native, UFch, and UCch) and to the procedure of adlayer formation (evaporation, adsorption, and adsorption + rinsing). However, their chemical composition was not significantly influenced either by ultrafiltration or by the procedure of deposition on polystyrene. Modeling this composition in terms of classes of model compounds gave approximately 35% (w/w) of proteins and 65% (w/w) of polysaccharides. In the adlayer, the carboxyl groups or esters represent about 18% of carbon due to nonpolypeptidic compounds, indicating the presence of either uronic acids in the complex structure of pectic polysaccharides or of polyphenolic esters. This structural and chemical information and its relationship with the experimental procedures indicate that proteins alone cannot be used as a realistic model for the macromolecules forming the adsorption layer of champagne. Polysaccharides, the other major macromolecular components of champagne wine, are assembled with proteins at the interfaces, in agreement with the heterogeneous character of the adsorbed layer at interfaces.

VALIDATION GUIDELINES FOR LABORATORIES PERFORMING FORENSIC ANALYSIS OF CHEMICAL TERRORISM

Science.gov (United States)

The Scientific Working Group on Forensic Analysis of Chemical Terrorism (SWGFACT) has developed the following guidelines for laboratories engaged in the forensic analysis of chemical evidence associated with terrorism. This document provides a baseline framework and guidance for...

Theoretical study of relativistic effects in the electronic structure and chemical bonding of UF6

International Nuclear Information System (INIS)

Onoe, Jun; Takeuchi, Kazuo; Sekine, Rika; Nakamatsu, Hirohide; Mukoyama, Takeshi; Adachi, Hirohiko.

1992-01-01

We have performed the relativistic molecular orbital calculation for the ground state of UF 6 , using the discrete-variational Dirac-Slater method (DV-DS), in order to elucidate the relativistic effects in the electronic structure and chemical bonding. Compared with the electronic structure calculated by the non-relativistic Hartree-Fock-Slater (DV-X α )MO method, not only the direct relativistic effects (spin-orbit splitting etc), but also the indirect effect due to the change in screening core potential charge are shown to be important in the MO level structure. From the U-F bond overlap population analysis, we found that the U-F bond formation can be explained only by the DV-DS, not by the DV-X α . The calculated electronic structure in valence energy region (-20-OeV) and excitation energies in UV region are in agreement with experiments. (author)

Evaluation of quantum-chemical methods of radiolysis stability for macromolecular structures

International Nuclear Information System (INIS)

Postolache, Cristian; Matei, Lidia

2005-01-01

The behavior of macromolecular structures in ionising fields was analyzed by quantum-chemical methods. In this study the primary radiolytic effect was analyzed using a two-step radiolytic mechanism: a) ionisation of molecule and spatial redistribution of atoms in order to reach a minimum value of energy, characteristic to the quantum state; b) neutralisation of the molecule by electron capture and its rapid dissociation into free radicals. Chemical bonds suspected to break are located in the distribution region of LUMO orbital and have minimal homolytic dissociation energies. Representative polymer structures (polyethylene, polypropylene, polystyrene, poly α and β polystyrene, polyisobutylene, polytetrafluoroethylene, poly methylsiloxanes) were analyzed. (authors)

Structure activity studies of an analgesic drug tapentadol hydrochloride by spectroscopic and quantum chemical methods

Science.gov (United States)

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.

Local atomic structure and chemical order in amorphous SiGe:H and SiC:H alloys

International Nuclear Information System (INIS)

Pisarkiewicz, T.; Stapinski, T.

1994-01-01

The local structure and chemical ordering in amorphous hydrogenated silicon-germanium and silicon-carbon alloys were analyzed mainly with the help of extended x-ray absorption fine structure (EXAFS) spectroscopy, Raman scattering and electron diffraction. Ge-Ge and Ge-Si distances were found to be independent of concentration and the composition of the first coordination shell around Ge is consistent with a random mixing of the two species in a-Si 1-x Ge:H alloy. The first-coordination-shell average bond lengths for Si-Si and SiC in a-Si 1-x C x :H are also constant with concentration x and the comparison of the first coordination shell composition around Si with average concentration indicates that the alloys tends to be chemically ordered. The degree of crystallinity in microcrystalline Si films determined by EXAFS is in agreement with that obtained in Raman scattering analysis. (author). 16 refs, 5 figs

Coal structure and reactivity changes induced by chemical demineralisation

Energy Technology Data Exchange (ETDEWEB)

Rubiera, F.; Arenillas, A.; Pevida, C.; Garcia, R.; Pis, J.J. [Department of Energy and Environment, Instituto Nacional del Carbon, CSIC, Apartado 73, 33080 Oviedo (Spain); Steel, K.M.; Patrick, J.W. [Fuel Technology Group, School of Chemical, Environmental and Mining Engineering, Nottingham University, University Park, NG7 2RD Nottingham (United Kingdom)

2002-12-01

The aim of this work was to determine the influence that an advanced demineralisation procedure has on the combustion characteristics of coal. A high-volatile bituminous coal with 6.2% ash content was treated in a mixture of hydrofluoric and fluorosilicic acids (HF/H{sub 2}SiF{sub 6}). Nitric acid was used either as a pretreatment, or as a washing stage after HF/H{sub 2}SiF{sub 6} demineralisation, with an ash content as low as 0.3% being attained in the latter case. The structural changes produced by the chemical treatment were evaluated by comparison of the FTIR spectra of the raw and treated coal samples. The devolatilisation and combustibility behaviour of the samples was studied by using a thermobalance coupled to a mass spectrometer (TGA-MS) for evolved gas analysis. The combustibility characteristics of the cleaned samples were clearly improved, there being a decrease in SO{sub 2} emissions.

Structural analysis of bioceramic materials for denture application

Energy Technology Data Exchange (ETDEWEB)

Rauf, Nurlaela, E-mail: n-rauf@fmipa.unhas.ac.id; Tahir, Dahlang; Arbiansyah, Muhammad [Dept of Physics, FMIPA-Univ. Hasanuddin Makassar Indonesia (Indonesia)

2016-03-11

Structural analysis has been performed on bioceramic materials for denture application by using X-ray diffraction (XRD), X-ray fluorescence (XRF), and Scanning Electron Microscopy (SEM). XRF is using for analysis chemical composition of raw materials. XRF shows the ratio 1 : 1 : 1 : 1 between feldspar, quartz, kaolin and eggshell, respectively, resulting composition CaO content of 56.78 %, which is similar with natural tooth. Sample preparation was carried out on temperature of 800 °C, 900 °C and 1000 °C. X-ray diffraction result showed that the structure is crystalline with trigonal crystal system for SiO{sub 2} (a=b=4.9134 Å and c=5.4051 Å) and CaH{sub 2}O{sub 2} (a=b=3.5925 Å and c=4.9082 Å). Based on the Scherrer’s equation showed the crystallite size of the highest peak (SiO{sub 2}) increase with increasing the temperature preparation. The highest hardness value (87 kg/mm{sup 2}) and match with the standards of dentin hardness. The surface structure was observed by using SEM also discussed.

Automated detection of structural alerts (chemical fragments in (ecotoxicology

Directory of Open Access Journals (Sweden)

Ronan Bureau

2013-02-01

Full Text Available This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (ecotoxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.

AUTOMATED DETECTION OF STRUCTURAL ALERTS (CHEMICAL FRAGMENTS IN (ECOTOXICOLOGY

Directory of Open Access Journals (Sweden)

Alban Lepailleur

2013-02-01

Full Text Available This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (ecotoxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.

Probabilistic risk analysis in chemical engineering

International Nuclear Information System (INIS)

Schmalz, F.

1991-01-01

In risk analysis in the chemical industry, recognising potential risks is considered more important than assessing their quantitative extent. Even in assessing risks, emphasis is not on the probability involved but on the possible extent. Qualitative assessment has proved valuable here. Probabilistic methods are used in individual cases where the wide implications make it essential to be able to assess the reliability of safety precautions. In this case, assessment therefore centres on the reliability of technical systems and not on the extent of a chemical risk. 7 figs

Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra.

Science.gov (United States)

Shimada, Toru; Hasegawa, Takeshi

2017-10-05

The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pK a '. The determination of pK a ' is performed for various ionic strengths, which reveals the thermodynamic acid constant (pK a =7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of -1 and the blue form that of -2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed. Copyright © 2017 Elsevier B.V. All rights reserved.

Model abstraction addressing long-term simulations of chemical degradation of large-scale concrete structures

International Nuclear Information System (INIS)

Jacques, D.; Perko, J.; Seetharam, S.; Mallants, D.

2012-01-01

This paper presents a methodology to assess the spatial-temporal evolution of chemical degradation fronts in real-size concrete structures typical of a near-surface radioactive waste disposal facility. The methodology consists of the abstraction of a so-called full (complicated) model accounting for the multicomponent - multi-scale nature of concrete to an abstracted (simplified) model which simulates chemical concrete degradation based on a single component in the aqueous and solid phase. The abstracted model is verified against chemical degradation fronts simulated with the full model under both diffusive and advective transport conditions. Implementation in the multi-physics simulation tool COMSOL allows simulation of the spatial-temporal evolution of chemical degradation fronts in large-scale concrete structures. (authors)

All-Russia conference on chemical analysis of substances and materials. Abstracts of reports

International Nuclear Information System (INIS)

2000-01-01

Collection contains abstracts of reports on chemical analysis of foods, drugs, environmental materials. Methods of chemical analysis used in such regions as chemical control in agriculture, criminology, art and archaeology, biotechnology, geology, chemistry and petrochemistry, metallurgy, metrology are presented. Theoretical, methodological and applied aspects of chemical analysis are considered [ru

Chemical compatibility of structural materials in alkali metals

International Nuclear Information System (INIS)

Natesan, K.; Rink, D.L.; Haglund, R.

1995-01-01

The objectives of this task are to (a) evaluate the chemical compatibility of structural alloys such as V-5 wt.%Cr-5 wt.%Ti alloy and Type 316 stainless steel for application in liquid alkali metals such as lithium and sodium-78 wt.% potassium (NaK) at temperatures in the range that are of interest for International Thermonuclear Experimental Reactor (ITER); (b) evaluate the transfer of nonmetallic elements such as oxygen, nitrogen, carbon, and hydrogen between structural materials and liquid metals; and (c) evaluate the effects of such transfers on the mechanical and microstructural characteristics of the materials for long-term service in liquid-metal-environments

Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)

Science.gov (United States)

Amberg, Alexander; Barrett, Dave; Beale, Michael H.; Beger, Richard; Daykin, Clare A.; Fan, Teresa W.-M.; Fiehn, Oliver; Goodacre, Royston; Griffin, Julian L.; Hankemeier, Thomas; Hardy, Nigel; Harnly, James; Higashi, Richard; Kopka, Joachim; Lane, Andrew N.; Lindon, John C.; Marriott, Philip; Nicholls, Andrew W.; Reily, Michael D.; Thaden, John J.; Viant, Mark R.

2013-01-01

There is a general consensus that supports the need for standardized reporting of metadata or information describing large-scale metabolomics and other functional genomics data sets. Reporting of standard metadata provides a biological and empirical context for the data, facilitates experimental replication, and enables the re-interrogation and comparison of data by others. Accordingly, the Metabolomics Standards Initiative is building a general consensus concerning the minimum reporting standards for metabolomics experiments of which the Chemical Analysis Working Group (CAWG) is a member of this community effort. This article proposes the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation, experimental analysis, quality control, metabolite identification, and data pre-processing. These minimum standards currently focus mostly upon mass spectrometry and nuclear magnetic resonance spectroscopy due to the popularity of these techniques in metabolomics. However, additional input concerning other techniques is welcomed and can be provided via the CAWG on-line discussion forum at http://msi-workgroups.sourceforge.net/ or http://Msi-workgroups-feedback@lists.sourceforge.net. Further, community input related to this document can also be provided via this electronic forum. PMID:24039616

Chemical bonding analysis for solid-state systems using intrinsic oriented quasiatomic minimal-basis-set orbitals

International Nuclear Information System (INIS)

Yao, Y.X.; Wang, C.Z.; Ho, K.M.

2010-01-01

A chemical bonding scheme is presented for the analysis of solid-state systems. The scheme is based on the intrinsic oriented quasiatomic minimal-basis-set orbitals (IO-QUAMBOs) previously developed by Ivanic and Ruedenberg for molecular systems. In the solid-state scheme, IO-QUAMBOs are generated by a unitary transformation of the quasiatomic orbitals located at each site of the system with the criteria of maximizing the sum of the fourth power of interatomic orbital bond order. Possible bonding and antibonding characters are indicated by the single particle matrix elements, and can be further examined by the projected density of states. We demonstrate the method by applications to graphene and (6,0) zigzag carbon nanotube. The oriented-orbital scheme automatically describes the system in terms of sp 2 hybridization. The effect of curvature on the electronic structure of the zigzag carbon nanotube is also manifested in the deformation of the intrinsic oriented orbitals as well as a breaking of symmetry leading to nonzero single particle density matrix elements. In an additional study, the analysis is performed on the Al 3 V compound. The main covalent bonding characters are identified in a straightforward way without resorting to the symmetry analysis. Our method provides a general way for chemical bonding analysis of ab initio electronic structure calculations with any type of basis sets.

Chemical analysis of carbonates and carbonate rocks by atomic absorption analysis

Energy Technology Data Exchange (ETDEWEB)

Tardon, S

1981-01-01

Evaluates methods of determining chemical composition of rocks surrounding black coal seams. Carbonate rock samples were collected in the Ostrava-Karvina coal mines. Sampling methods are described. Determination of the following elements and compounds in carbonate rocks is discussed: calcium, magnesium, iron, manganese, barium, silicon, aluminium, titanium, sodium, potassium, sulfur trioxide, phosphorus pentoxide, water and carbon dioxide. Proportion of compounds insoluble in water in the investigated rocks is also determined. Most of the elements are determined by means of atomic absorption analysis. Phosphorus is also determined by atomic absorption analysis. Other compounds are determined gravimetrically. The described procedure permits weight of a rock sample to be reduced to 0.5 g without reducing analysis accuracy. The results of determining carbonate rock components by X-ray analysis and by chemical analysis are compared. Equipment used for atomic absorption analysis is characterized (the 503 Perkin-Elmer and the CF-4 Optica-Milano spectrophotometers). The analyzed method for determining carbonate rock permits more accurate classification of rocks surrounding coal seams and rock impurities in run-of-mine coal. (22 refs.) (In Czech)

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Chemical detection, identification, and analysis system

International Nuclear Information System (INIS)

Morel, R.S.; Gonzales, D.; Mniszewski, S.

1990-01-01

The chemical detection, identification, and analysis system (CDIAS) has three major goals. The first is to display safety information regarding chemical environment before personnel entry. The second is to archive personnel exposure to the environment. Third, the system assists users in identifying the stage of a chemical process in progress and suggests safety precautions associated with that process. In addition to these major goals, the system must be sufficiently compact to provide transportability, and it must be extremely simple to use in order to keep user interaction at a minimum. The system created to meet these goals includes several pieces of hardware and the integration of four software packages. The hardware consists of a low-oxygen, carbon monoxide, explosives, and hydrogen sulfide detector; an ion mobility spectrometer for airborne vapor detection; and a COMPAQ 386/20 portable computer. The software modules are a graphics kernel, an expert system shell, a data-base management system, and an interface management system. A supervisory module developed using the interface management system coordinates the interaction of the other software components. The system determines the safety of the environment using conventional data acquisition and analysis techniques. The low-oxygen, carbon monoxide, hydrogen sulfide, explosives, and vapor detectors are monitored for hazardous levels, and warnings are issued accordingly

Silicon Oxysulfide, OSiS: Rotational Spectrum, Quantum-Chemical Calculations, and Equilibrium Structure.

Science.gov (United States)

Thorwirth, Sven; Mück, Leonie Anna; Gauss, Jürgen; Tamassia, Filippo; Lattanzi, Valerio; McCarthy, Michael C

2011-06-02

Silicon oxysulfide, OSiS, and seven of its minor isotopic species have been characterized for the first time in the gas phase at high spectral resolution by means of Fourier transform microwave spectroscopy. The equilibrium structure of OSiS has been determined from the experimental data using calculated vibration-rotation interaction constants. The structural parameters (rO-Si = 1.5064 Å and rSi-S = 1.9133 Å) are in very good agreement with values from high-level quantum chemical calculations using coupled-cluster techniques together with sophisticated additivity and extrapolation schemes. The bond distances in OSiS are very short in comparison with those in SiO and SiS. This unexpected finding is explained by the partial charges calculated for OSiS via a natural population analysis. The results suggest that electrostatic effects rather than multiple bonding are the key factors in determining bonding in this triatomic molecule. The data presented provide the spectroscopic information needed for radio astronomical searches for OSiS.

Microarray technology for major chemical contaminants analysis in food: current status and prospects.

Science.gov (United States)

Zhang, Zhaowei; Li, Peiwu; Hu, Xiaofeng; Zhang, Qi; Ding, Xiaoxia; Zhang, Wen

2012-01-01

Chemical contaminants in food have caused serious health issues in both humans and animals. Microarray technology is an advanced technique suitable for the analysis of chemical contaminates. In particular, immuno-microarray approach is one of the most promising methods for chemical contaminants analysis. The use of microarrays for the analysis of chemical contaminants is the subject of this review. Fabrication strategies and detection methods for chemical contaminants are discussed in detail. Application to the analysis of mycotoxins, biotoxins, pesticide residues, and pharmaceutical residues is also described. Finally, future challenges and opportunities are discussed.

Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

Science.gov (United States)

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.

Microfabricated Gas Phase Chemical Analysis Systems

International Nuclear Information System (INIS)

FRYE-MASON, GREGORY CHARLES; HELLER, EDWIN J.; HIETALA, VINCENT M.; KOTTENSTETTE, RICHARD; LEWIS, PATRICK R.; MANGINELL, RONALD P.; MATZKE, CAROLYN M.; WONG, CHUNGNIN C.

1999-01-01

A portable, autonomous, hand-held chemical laboratory ((micro)ChemLab(trademark)) is being developed for trace detection (ppb) of chemical warfare (CW) agents and explosives in real-world environments containing high concentrations of interfering compounds. Microfabrication is utilized to provide miniature, low-power components that are characterized by rapid, sensitive and selective response. Sensitivity and selectivity are enhanced using two parallel analysis channels, each containing the sequential connection of a front-end sample collector/concentrator, a gas chromatographic (GC) separator, and a surface acoustic wave (SAW) detector. Component design and fabrication and system performance are described

Lincosamides: Chemical structure, biosynthesis, mechanism of action, resistance, and applications

Czech Academy of Sciences Publication Activity Database

Spížek, Jaroslav; Řezanka, Tomáš

2017-01-01

Roč. 133, June 1 SI (2017), s. 20-28 ISSN 0006-2952 Institutional support: RVO:61388971 Keywords : Lincosamides * Chemical structure * Biosynthesis and mechanism of action Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 4.581, year: 2016

Surface Nano Structures Manufacture Using Batch Chemical Processing Methods for Tooling Applications

DEFF Research Database (Denmark)

Tosello, Guido; Calaon, Matteo; Gavillet, J.

2011-01-01

The patterning of large surface areas with nano structures by using chemical batch processes to avoid using highenergy intensive nano machining processes was investigated. The capability of different surface treatment methods of creating micro and nano structured adaptable mould inserts for subse...

Quantitative chemical state XPS analysis of first row transition metals, oxides and hydroxides

International Nuclear Information System (INIS)

Biesinger, M C; Payne, B P; McIntryre, N S; Hart, B R; Lau, L Wm; Grosvenor, A P; Smart, R StC

2008-01-01

Practical quantitative chemical state X-ray photoelectron spectroscopy (XPS) analysis of first row transition metals, oxides and hydroxides is challenging due to the complexity of their M 2p spectra. Complex multiplet splitting, shake-up and plasmon loss structure can play a role in the interpretation of the chemical states present. This paper will show practical curve fitting procedures for the quantitative measurement of different chemical states for metal oxides and hydroxides from a survey of transition metals. It will also discuss some of the limitations and pitfalls present as well as give practical examples of their successful use. These curve-fitting procedures are based on 1) standard spectra from quality reference samples, 2) a survey of appropriate literature databases and/or a compilation of literature references, 3) fitting of multiplet split spectra based on spectra of numerous reference materials and theoretical modelling, 4) spectral subtractions routines, again using reference spectra, and 5) specific literature references where fitting procedures are available

Quantitative chemical state XPS analysis of first row transition metals, oxides and hydroxides

Energy Technology Data Exchange (ETDEWEB)

Biesinger, M C; Payne, B P; McIntryre, N S [Department of Chemistry, University of Western Ontario, London, Ontario, N6A 5B7 (Canada); Hart, B R; Lau, L Wm [Surface Science Western, Room G1, Western Science Centre, University of Western Ontario, London, Ontario, N6A 5B7 (Canada); Grosvenor, A P [Department of Chemistry, Gunning/Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada); Smart, R StC [ACeSSS, Applied Centre for Structural and Synchrotron Studies, University of South Australia, Mawson Lakes, SA 5095 (Australia)], E-mail: biesingr@uwo.ca

2008-03-15

Practical quantitative chemical state X-ray photoelectron spectroscopy (XPS) analysis of first row transition metals, oxides and hydroxides is challenging due to the complexity of their M 2p spectra. Complex multiplet splitting, shake-up and plasmon loss structure can play a role in the interpretation of the chemical states present. This paper will show practical curve fitting procedures for the quantitative measurement of different chemical states for metal oxides and hydroxides from a survey of transition metals. It will also discuss some of the limitations and pitfalls present as well as give practical examples of their successful use. These curve-fitting procedures are based on 1) standard spectra from quality reference samples, 2) a survey of appropriate literature databases and/or a compilation of literature references, 3) fitting of multiplet split spectra based on spectra of numerous reference materials and theoretical modelling, 4) spectral subtractions routines, again using reference spectra, and 5) specific literature references where fitting procedures are available.

Morphological, chemical and structural characterisation of deciduous enamel: SEM, EDS, XRD, FTIR and XPS analysis.

Science.gov (United States)

Zamudio-Ortega, C M; Contreras-Bulnes, R; Scougall-Vilchis, R J; Morales-Luckie, R A; Olea-Mejía, O F; Rodríguez-Vilchis, L E

2014-09-01

The purpose of this study was to characterise the enamel surface of sound deciduous teeth in terms of morphology, chemical composition, structure and crystalline phases. The enamel of 30 human deciduous teeth was examined by: Scanning Electron Microscopy (SEM), Energy Dispersive X-Ray Spectroscopy (EDS), X-ray Powder Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Photoelectron Spectroscopy (XPS). Chemical differences between incisors and canines were statistically evaluated using the Mann-Whitney U test (p ≤ 0.05). Three enamel patterns were observed by SEM: 'mostly smooth with some groves', 'abundant microporosities' and 'exposed prisms'. The average Ca/P molar ratios were 1.37 and 1.03 by EDS and XPS, respectively. The crystallite size determined by XRD was 210.82 ± 16.78 Å. The mean ratio between Ca bonded to phosphate and Ca bonded to hydroxyl was approximately 10:1. The enamel of sound deciduous teeth showed two main patterns: 'mostly smooth with some groves' and 'abundant microporosities'. 'Exposed prisms' was a secondary pattern. There were slight variations among the Ca/P molar ratios found by EDS and XPS, suggesting differences in the mineral content from the enamel surface to the interior. The crystalline phases found in enamel were hydroxyapatite and carbonate apatite, with major type B than type A carbonate incorporation.

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

Science.gov (United States)

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.

Physico-Chemical Analysis and Sensory Evaluation of Bread

African Journals Online (AJOL)

Shuaibu et al.

Physico-Chemical Analysis and Sensory Evaluation of Bread Produced Using ... analysis of the bread samples revealed that the moisture content ..... 72. Jarup, L. ,2003. Hazards of heavy metal contamination. Br Med. Bull; 68, pp.167-82.

Algorithm for advanced canonical coding of planar chemical structures that considers stereochemical and symmetric information.

Science.gov (United States)

Koichi, Shungo; Iwata, Satoru; Uno, Takeaki; Koshino, Hiroyuki; Satoh, Hiroko

2007-01-01

We describe a rigorous and fast algorithm for advanced canonical coding of planar chemical structures based on the algorithm of Faulon et al. (J. Chem. Inf. Comput. Sci. 2004, 44, 427-436). Our algorithm works well even for highly symmetric structures; moreover, an advantage of our algorithm includes providing a rigorous canonical numbering of atoms with a consideration of stereochemistry and recognizing symmetric moieties. The planar structural line notation with the canonical numbering is also fit for use with stereochemical line notation. These capabilities are usable for general purposes in chemical structural coding and are particularly essential for detecting equivalent atoms in NMR studies. This algorithm was implemented on a 13C NMR chemical shift prediction system CAST/CNMR. Applications of the algorithm to several organic compounds demonstrate the practical efficiency of the rigorous coding.

Rapid chemical analysis of allanite

International Nuclear Information System (INIS)

Nishiyama, Goro; Hayashi, Hiroshi

1981-01-01

Rapid chemical analysis of allanite was studied by atomic absorption spectrophotometry. Powdered sample was fused with mixture of sodium carbonate anhydrous and borax (4 : 1 weight) in platinum crucible and sample solution was prepared. SiO 2 , Fe 2 O 3 , Al 2 O 3 , MnO and rare earth metals were determined by atomic absorption spectrophotometry, CaO, MgO and Ce 2 O 3 by titration, ThO 2 by colorimetry, and La 2 O 3 by flame photometry respectively. For sample solution treated with hydrofluoric acid and sulfuric acid. Na 2 O and K 2 O were determined by atomic absorption spectrophotometry, TiO 2 and P 2 O 5 by colorimetry. Chemical analyses for four samples were carried out and gave consistent results. (author)

Structural studies of chemical constituents of Thithonia Tagetiflora Desv (Asteraceae)

DEFF Research Database (Denmark)

Ngoc Huynh, Vinh; Nguyen Thi Hoai, Thu; Phi Phung Nguyen, Kim

2013-01-01

Tithonia tagetiflora Desv. (Asteraceae) is a widespread plant in Vietnam, and the species of Tithonia are known as plants containing many biologically active compounds. However, T. tagetiflora's chemical composition remains mostly unknown. Therefore, we now report the structural elucidation of tw...

Energy saving analysis and management modeling based on index decomposition analysis integrated energy saving potential method: Application to complex chemical processes

International Nuclear Information System (INIS)

Geng, Zhiqiang; Gao, Huachao; Wang, Yanqing; Han, Yongming; Zhu, Qunxiong

2017-01-01

Highlights: • The integrated framework that combines IDA with energy-saving potential method is proposed. • Energy saving analysis and management framework of complex chemical processes is obtained. • This proposed method is efficient in energy optimization and carbon emissions of complex chemical processes. - Abstract: Energy saving and management of complex chemical processes play a crucial role in the sustainable development procedure. In order to analyze the effect of the technology, management level, and production structure having on energy efficiency and energy saving potential, this paper proposed a novel integrated framework that combines index decomposition analysis (IDA) with energy saving potential method. The IDA method can obtain the level of energy activity, energy hierarchy and energy intensity effectively based on data-drive to reflect the impact of energy usage. The energy saving potential method can verify the correctness of the improvement direction proposed by the IDA method. Meanwhile, energy efficiency improvement, energy consumption reduction and energy savings can be visually discovered by the proposed framework. The demonstration analysis of ethylene production has verified the practicality of the proposed method. Moreover, we can obtain the corresponding improvement for the ethylene production based on the demonstration analysis. The energy efficiency index and the energy saving potential of these worst months can be increased by 6.7% and 7.4%, respectively. And the carbon emissions can be reduced by 7.4–8.2%.

Chemical analysis of geological samples

International Nuclear Information System (INIS)

Malhotra, R.K.

1997-01-01

Most of the analytical methodology used in geochemical exploration has been based on molecular absorption, atomic absorption, and ICP-AES, ICPMAS etc. Detection limit and precision are factors in the choice of methodology in search of metallic ores and are related to the accuracy of data. A brief outline of the various chemical analysis techniques explaining essentially the basics of measurement principles and instrumentation is discussed

Theoretical study of the electronic structure of f-element complexes by quantum chemical methods

International Nuclear Information System (INIS)

Vetere, V.

2002-09-01

This thesis is related to comparative studies of the chemical properties of molecular complexes containing lanthanide or actinide trivalent cations, in the context of the nuclear waste disposal. More precisely, our aim was a quantum chemical analysis of the metal-ligand bonding in such species. Various theoretical approaches were compared, for the inclusion of correlation (density functional theory, multiconfigurational methods) and of relativistic effects (relativistic scalar and 2-component Hamiltonians, relativistic pseudopotentials). The performance of these methods were checked by comparing computed structural properties to published experimental data, on small model systems: lanthanide and actinide tri-halides and on X 3 M-L species (X=F, Cl; M=La, Nd, U; L = NH 3 , acetonitrile, CO). We have thus shown the good performance of density functionals combined with a quasi-relativistic method, as well as of gradient-corrected functionals associated with relativistic pseudopotentials. In contrast, functionals including some part of exact exchange are less reliable to reproduce experimental trends, and we have given a possible explanation for this result . Then, a detailed analysis of the bonding has allowed us to interpret the discrepancies observed in the structural properties of uranium and lanthanides complexes, based on a covalent contribution to the bonding, in the case of uranium(III), which does not exist in the lanthanide(III) homologues. Finally, we have examined more sizeable systems, closer to experimental species, to analyse the influence of the coordination number, of the counter-ions and of the oxidation state of uranium, on the metal-ligand bonding. (author)

QUALITY ASSURANCE GUIDELINES FOR LABORATORIES PERFORMING FORENSIC ANALYSIS OF CHEMICAL TERRORISM

Science.gov (United States)

The Scientific Working Group on Forensic Analysis of Chemical Terrorism (SWGFACT) has developed the following quality assurance guidelines to provide laboratories engaged in forensic analysis of chemical evidence associated with terrorism a framework to implement a quality assura...

Quantitative Survey and Structural Classification of Fracking Chemicals Reported in Unconventional Gas Exploitation

Science.gov (United States)

Elsner, Martin; Schreglmann, Kathrin

2015-04-01

Few technologies are being discussed in such controversial terms as hydraulic fracturing ("fracking") in the recovery of unconventional gas. Particular concern regards the chemicals that may return to the surface as a result of hydraulic fracturing. These are either "fracking chemicals" - chemicals that are injected together with the fracking fluid to optimize the fracturing performance or geogenic substances which may turn up during gas production, in the so-called produced water originating from the target formation. Knowledge about them is warranted for several reasons. (1) Monitoring. Air emissions are reported to arise from well drilling, the gas itself or condensate tanks. In addition, potential spills and accidents bear the danger of surface and shallow groundwater contaminations. Monitoring strategies are therefore warranted to screen for "indicator" substances of potential impacts. (2) Chemical Analysis. To meet these analytical demands, target substances must be defined so that adequate sampling approaches and analytical methods can be developed. (3) Transformation in the Subsurface. Identification and classification of fracking chemicals (aromatics vs. alcohols vs. acids, esters, etc.) is further important to assess the possibility of subsurface reactions which may potentially generate new, as yet unidentified transformation products. (4) Wastewater Treatment. For the same reason chemical knowledge is important for optimized wastewater treatment strategies. (5) Human and Ecosystem Health. Knowledge of the most frequent fracking chemicals is further essential for risk assessment (environmental behavior, toxicity) (6) Public Discussions. Finally, an overview of reported fracking chemicals can provide unbiased scientific into current public debates and enable critical reviews of Green Chemistry approaches. Presently, however, such information is not readily available. We aim to close this knowledge gap by providing a quantitative overview of chemical

Scanning photoelectron microscope for nanoscale three-dimensional spatial-resolved electron spectroscopy for chemical analysis.

Science.gov (United States)

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

Structural and Chemical Analysis of the Zirconia-Veneering Ceramic Interface.

Science.gov (United States)

Inokoshi, M; Yoshihara, K; Nagaoka, N; Nakanishi, M; De Munck, J; Minakuchi, S; Vanmeensel, K; Zhang, F; Yoshida, Y; Vleugels, J; Naert, I; Van Meerbeek, B

2016-01-01

The interfacial interaction of veneering ceramic with zirconia is still not fully understood. This study aimed to characterize morphologically and chemically the zirconia-veneering ceramic interface. Three zirconia-veneering conditions were investigated: 1) zirconia-veneering ceramic fired on sandblasted zirconia, 2) zirconia-veneering ceramic on as-sintered zirconia, and 3) alumina-veneering ceramic (lower coefficient of thermal expansion [CTE]) on as-sintered zirconia. Polished cross-sectioned ceramic-veneered zirconia specimens were examined using field emission gun scanning electron microscopy (Feg-SEM). In addition, argon-ion thinned zirconia-veneering ceramic interface cross sections were examined using scanning transmission electron microscopy (STEM)-energy dispersive X-ray spectrometry (EDS) at high resolution. Finally, the zirconia-veneering ceramic interface was quantitatively analyzed for tetragonal-to-monoclinic phase transformation and residual stress using micro-Raman spectroscopy (µRaman). Feg-SEM revealed tight interfaces for all 3 veneering conditions. High-resolution transmission electron microscopy (HRTEM) disclosed an approximately 1.0-µm transformed zone at sandblasted zirconia, in which distinct zirconia grains were no longer observable. Straight grain boundaries and angular grain corners were detected up to the interface of zirconia- and alumina-veneering ceramic with as-sintered zirconia. EDS mapping disclosed within the zirconia-veneering ceramic a few nanometers thick calcium/aluminum-rich layer, touching the as-sintered zirconia base, with an equally thick silicon-rich/aluminum-poor layer on top. µRaman revealed t-ZrO2-to-m-ZrO2 phase transformation and residual compressive stress at the sandblasted zirconia surface. The difference in CTE between zirconia- and the alumina-veneering ceramic resulted in residual tensile stress within the zirconia immediately adjacent to its interface with the veneering ceramic. The rather minor chemical

Growth control, structure, chemical state, and photoresponse of CuO-CdS core-shell heterostructure nanowires.

Science.gov (United States)

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.

Calculating the dermal flux of chemicals with OELs based on their molecular structure: An attempt to assign the skin notation.

Science.gov (United States)

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

Optical MEMS for chemical analysis and biomedicine

CERN Document Server

Jiang, Hongrui

2016-01-01

This book describes the current state of optical MEMS in chemical and biomedical analysis and brings together current trends and highlights topics representing the most exciting progress in recent years in the field.

Denaturation of collagen structures and their transformation under the physical and chemical effects

Science.gov (United States)

Ivankin, A.; Boldirev, V.; Fadeev, G.; Baburina, M.; Kulikovskii, A.; Vostrikova, N.

2017-11-01

The process of denaturation of collagen structures under the influence of physical and chemical factors play an important role in the manufacture of food technology and the production of drugs for medicine and cosmetology. The paper discussed the problem of the combined effects of heat treatment, mechanical dispersion and ultrasonic action on the structural changes of the animal collagen in the presence of weak protonated organic acids. Algorithm combined effects of physical and chemical factors as a result of the formation of the technological properties of products containing collagen has been shown.

X-ray photoelectron spectra structure and chemical bonding in AmO2

Directory of Open Access Journals (Sweden)

Teterin Yury A.

2015-01-01

Full Text Available Quantitative analysis was done of the X-ray photoelectron spectra structure in the binding energy range of 0 eV to ~35 eV for americium dioxide (AmO2 valence electrons. The binding energies and structure of the core electronic shells (~35 eV-1250 eV, as well as the relativistic discrete variation calculation results for the Am63O216 and AmO8 (D4h cluster reflecting Am close environment in AmO2 were taken into account. The experimental data show that the many-body effects and the multiplet splitting contribute to the spectral structure much less than the effects of formation of the outer (0-~15 eV binding energy and the inner (~15 eV-~35 eV binding energy valence molecular orbitals. The filled Am 5f electronic states were shown to form in the AmO2 valence band. The Am 6p electrons participate in formation of both the inner and the outer valence molecular orbitals (bands. The filled Am 6p3/2 and the O 2s electronic shells were found to make the largest contributions to the formation of the inner valence molecular orbitals. Contributions of electrons from different molecular orbitals to the chemical bond in the AmO8 cluster were evaluated. Composition and sequence order of molecular orbitals in the binding energy range 0-~35 eV in AmO2 were established. The experimental and theoretical data allowed a quantitative scheme of molecular orbitals for AmO2, which is fundamental for both understanding the chemical bond nature in americium dioxide and the interpretation of other X-ray spectra of AmO2.

A framework for analysing relationships between chemical composition and crystal structure in metal oxides

International Nuclear Information System (INIS)

Thomas, N.W.

1991-01-01

A computer program has been written to characterize the coordination polyhedra of metal cations in terms of their volumes and polyhedral elements, i.e. corners, edges and faces. The sharing of these corners, edges and faces between polyhedra is also quantitatively monitored. In order to develop the methodology, attention is focused on ternary oxides containing the Al 3+ ion, whose structures were retrieved from the Inorganic Crystal Structure Database (ICSD). This also permits an objective assessment of the applicability of Pauling's rules. The influence of ionic valence on the structures of these compounds is examined, by calculating electrostatic bond strengths. Although Pauling's second rule is not supported in detail, the calculation of oxygen-ion valence reveals a basic structural requirement, that the average calculated oxygen-ion valence in any ionic oxide structure is equal to 2. The analysis is further developed to define a general method for the prediction of novel chemical compositions likely to adopt a given desired structure. The polyhedral volumes of this structure are calculated, and use is made of standard ionic radii for cations in sixfold coordination. The electroneutrality principle is invoked to take valence considerations into account. This method can be used to guide the development of new compositions of ceramic materials with certain desirable physical properties. (orig.)

Assessment of a subtropical riparian forest focusing on botanical, meteorological, ecological characterization and chemical analysis of rainwater

Directory of Open Access Journals (Sweden)

Vanessa Graeff

2018-05-01

Full Text Available Riparian forests are heterogeneous environments, in which epiphytes find ideal conditions to develop. These plants absorb the necessary nutrients for survival from the atmosphere, and their occurrence and distribution can be influenced by the quality and quantity of precipitation. The objective of this research was to perform an integrated analysis of botanical, meteorological and chemical precipitation parameters so as to compare them in fragments of the riparian forest in the lower (São Leopoldo-SL and upper (Caraá-CA stretches of the Rio dos Sinos Hydrographic Basin (RSHB, RS, Brazil. Rainwater was chemically analyzed, the community structure of epiphytic ferns was surveyed and the ecological characterization was evaluated through the Rapid Habitat Assessment Protocol (RHAP. The results showed that the chemical composition of rainwater is influenced by the environment of each area. In the upper stretch (CA, for instance, the main contribution is that of marine ions, while in the lower stretch (SL, the most impacting aspects are urbanization and industrialization. Similarly, the results depict a reduction of richness and a simplification of the community structure of epiphytic ferns and their environmental quality according to the RHAP categories, towards the base level of the RSHB. The integrated analysis, in which different methods were applied, proved to be an efficient tool to evaluate environmental quality. This analysis considers that a greater number of biotic and abiotic variables may be applied in different scenarios.

Relationships between chemical structure, mechanical properties and materials processing in nanopatterned organosilicate fins

Directory of Open Access Journals (Sweden)

Gheorghe Stan

2017-04-01

Full Text Available The exploitation of nanoscale size effects to create new nanostructured materials necessitates the development of an understanding of relationships between molecular structure, physical properties and material processing at the nanoscale. Numerous metrologies capable of thermal, mechanical, and electrical characterization at the nanoscale have been demonstrated over the past two decades. However, the ability to perform nanoscale molecular/chemical structure characterization has only been recently demonstrated with the advent of atomic-force-microscopy-based infrared spectroscopy (AFM-IR and related techniques. Therefore, we have combined measurements of chemical structures with AFM-IR and of mechanical properties with contact resonance AFM (CR-AFM to investigate the fabrication of 20–500 nm wide fin structures in a nanoporous organosilicate material. We show that by combining these two techniques, one can clearly observe variations of chemical structure and mechanical properties that correlate with the fabrication process and the feature size of the organosilicate fins. Specifically, we have observed an inverse correlation between the concentration of terminal organic groups and the stiffness of nanopatterned organosilicate fins. The selective removal of the organic component during etching results in a stiffness increase and reinsertion via chemical silylation results in a stiffness decrease. Examination of this effect as a function of fin width indicates that the loss of terminal organic groups and stiffness increase occur primarily at the exposed surfaces of the fins over a length scale of 10–20 nm. While the observed structure–property relationships are specific to organosilicates, we believe the combined demonstration of AFM-IR with CR-AFM should pave the way for a similar nanoscale characterization of other materials where the understanding of such relationships is essential.

Nonradiological chemical pathway analysis and identification of chemicals of concern for environmental monitoring at the Hanford Site

International Nuclear Information System (INIS)

Blanton, M.L.; Cooper, A.T.; Castleton, K.J.

1995-11-01

Pacific Northwest's Surface Environmental Surveillance Project (SESP) is an ongoing effort tot design, review, and conducted monitoring on and off the Hanford site. Chemicals of concern that were selected are listed. Using modeled exposure pathways, the offsite cancer incidence and hazard quotient were calculated and a retrospective pathway analysis performed to estimate what onsite concentrations would be required in the soil for each chemical of concern and other detected chemicals that would be required to obtain an estimated offsite human-health risk of 1.0E-06 cancer incidence or 1.0 hazard quotient. This analysis indicates that current nonradiological chemical contamination occurring on the site does not pose a significant offsite human-health risk; the highest cancer incidence to the offsite maximally exposed individual was from arsenic (1.76E-10); the highest hazard quotient was chromium(VI) (1.48E-04). The most sensitive pathways of exposure were surfacewater and aquatic food consumption. Combined total offsite excess cancer incidence was 2.09E-10 and estimated hazard quotient was 2.40E-04. Of the 17 identified chemicals of concern, the SESP does not currently (routinely) monitor arsenic, benzo(a)pyrene, bis(2- ethylhexyl)phthalate (BEHP), and chrysene. Only 3 of the chemicals of concern (arsenic, BEHP, chloroform) could actually occur in onsite soil at concern high enough to cause a 1.0E-06 excess cancer incidence or a 1.0 hazard index for a given offsite exposure pathway. During the retrospective analysis, 20 other chemicals were also evaluated; only vinyl chloride and thallium could reach targeted offsite risk values

Chemical analysis of bleach and hydroxide-based solutions after decontamination of the chemical warfare agent O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate (VX).

Science.gov (United States)

Hopkins, F B; Gravett, M R; Self, A J; Wang, M; Chua, Hoe-Chee; Hoe-Chee, C; Lee, H S Nancy; Sim, N Lee Hoi; Jones, J T A; Timperley, C M; Riches, J R

2014-08-01

Detailed chemical analysis of solutions used to decontaminate chemical warfare agents can be used to support verification and forensic attribution. Decontamination solutions are amongst the most difficult matrices for chemical analysis because of their corrosive and potentially emulsion-based nature. Consequently, there are relatively few publications that report their detailed chemical analysis. This paper describes the application of modern analytical techniques to the analysis of decontamination solutions following decontamination of the chemical warfare agent O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate (VX). We confirm the formation of N,N-diisopropylformamide and N,N-diisopropylamine following decontamination of VX with hypochlorite-based solution, whereas they were not detected in extracts of hydroxide-based decontamination solutions by nuclear magnetic resonance (NMR) spectroscopy or gas chromatography-mass spectrometry. We report the electron ionisation and chemical ionisation mass spectroscopic details, retention indices, and NMR spectra of N,N-diisopropylformamide and N,N-diisopropylamine, as well as analytical methods suitable for their analysis and identification in solvent extracts and decontamination residues.

Influence of chemical structures on biodegradation of azo dyes by ...

African Journals Online (AJOL)

Influence of chemical structures on biodegradation of azo dyes by Pseudomonas sp. NA Oranusi, CJ Ogugbue. Abstract. No Abstract. Global Journal of Environmental Sciences Vol. 5(1) 2006: 19-25. Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT.

Dependence of the extraction capacity of neutral bidentate organophosphorus compounds on their structure: a quantum chemical study

International Nuclear Information System (INIS)

Sudarushkin, S.K.; Morgalyuk, V.P.; Tananaev, I.G.; Gribov, L.A.; Myasoedov, B.F.

2006-01-01

Correlations between the extraction capacities and molecular structures of organic phosphorus compounds (reagents for extraction of transplutonium elements from spent nuclear fuel) were studied using a quantum chemical approach. The results of calculations are in qualitative agreement with experimental data. The approach proposed can be used for analysis of the extraction properties of all classes of organic phosphorus compounds and also for prediction of the most efficient organic phosphorus extractants with preset properties [ru

Experimental and numerical reaction analysis on sodium-water chemical reaction field

International Nuclear Information System (INIS)

Deguchi, Yoshihiro; Takata, Takashi; Yamaguchi, Akira; Kikuchi, Shin; Ohshima, Hiroyuki

2015-01-01

In a sodium-cooled fast reactor (SFR), liquid sodium is used as a heat transfer fluid because of its excellent heat transport capability. On the other hand, it has strong chemical reactivity with water vapor. One of the design basis accidents of the SFR is the water leakage into the liquid sodium flow by a breach of heat transfer tubes. This process ends up damages on the heat transport equipment in the SFR. Therefore, the study on sodium-water chemical reactions is of paramount importance for security reasons. This study aims to clarify the sodium-water reaction mechanisms using an elementary reaction analysis. A quasi one-dimensional flame model is applied to a sodium-water counter-flow reaction field. The analysis contains 25 elementary reactions, which consist of 17 H_2-O_2 and 8 Na-H_2O reactions. Temperature and species concentrations in the counter-flow reaction field were measured using laser diagnostics such as LIF and CARS. The main reaction in the experimental conditions is Na+H_2O → NaOH+H and OH is produced by H_2O+H → H_2+OH. It is demonstrated that the reaction model in this study well explains the structure of the sodium-water counter-flow diffusion flame. (author)

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

Science.gov (United States)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

YNi and its hydrides: Phase stabilities, electronic structures and chemical bonding properties from first principles

International Nuclear Information System (INIS)

Matar, S.F.; Nakhl, M.; Al Alam, A.F.; Ouaini, N.; Chevalier, B.

2010-01-01

Graphical abstract: Base centered orthorhombic YNiH X structure. For x = 3, only H1 and H2 are present. Highest hydrogen content YNiH 4 is obtained when H3 are added. - Abstract: Within density functional theory, establishing the equations of states of YNi in two different controversial structures in the literature, leads to determine the orthorhombic FeB-type as the ground state one with small energy difference. For YNiH 3 and YNiH 4 hydrides crystallizing in the orthorhombic CrB-type structure the geometry optimization and the ab initio determination of the H atomic positions show that the stability of hydrogen decreases from the tri- to the tetra- hydride. New states brought by hydrogen within the valence band lead to its broadening and to enhanced localization of metal density of states. The chemical bonding analysis shows a preferential Ni-H bonding versus Y-H.

Structural plasticity: how intermetallics deform themselves in response to chemical pressure, and the complex structures that result.

Science.gov (United States)

Berns, Veronica M; Fredrickson, Daniel C

2014-10-06

Interfaces between periodic domains play a crucial role in the properties of metallic materials, as is vividly illustrated by the way in which the familiar malleability of many metals arises from the formation and migration of dislocations. In complex intermetallics, such interfaces can occur as an integral part of the ground-state crystal structure, rather than as defects, resulting in such marvels as the NaCd2 structure (whose giant cubic unit cell contains more than 1000 atoms). However, the sources of the periodic interfaces in intermetallics remain mysterious, unlike the dislocations in simple metals, which can be associated with the exertion of physical stresses. In this Article, we propose and explore the concept of structural plasticity, the hypothesis that interfaces in complex intermetallic structures similarly result from stresses, but ones that are inherent in a defect-free parent structure, rather than being externally applied. Using DFT-chemical pressure analysis, we show how the complex structures of Ca2Ag7 (Yb2Ag7 type), Ca14Cd51 (Gd14Ag51 type), and the 1/1 Tsai-type quasicrystal approximant CaCd6 (YCd6 type) can all be traced to large negative pressures around the Ca atoms of a common progenitor structure, the CaCu5 type with its simple hexagonal 6-atom unit cell. Two structural paths are found by which the compounds provide relief to the Ca atoms' negative pressures: a Ca-rich pathway, where lower coordination numbers are achieved through defects eliminating transition metal (TM) atoms from the structure; and a TM-rich path, along which the addition of spacer Cd atoms provides the Ca coordination environments greater independence from each other as they contract. The common origins of these structures in the presence of stresses within a single parent structure highlights the diverse paths by which intermetallics can cope with competing interactions, and the role that structural plasticity may play in navigating this diversity.

The relationship between chemical structure and dielectric properties of plasma-enhanced chemical vapor deposited polymer thin films

Energy Technology Data Exchange (ETDEWEB)

Jiang Hao [Materials Sci and Tech Applications, LLC, 409 Maple Springs Drive, Dayton OH 45458 (United States)]. E-mail: hao.jiang@wpafb.af.mil; Hong Lianggou [Materials Sci and Tech Applications, LLC, 409 Maple Springs Drive, Dayton OH 45458 (United States); Venkatasubramanian, N. [Research Institute, University of Dayton, 300 College Park, Dayton, OH 45469-0168 (United States); Grant, John T. [Research Institute, University of Dayton, 300 College Park, Dayton, OH 45469-0168 (United States); Eyink, Kurt [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States); Wiacek, Kevin [Air Force Research Laboratory, Propulsion Directorate, 1950 Fifth Street, Wright-Patterson Air Force Base, OH 45433-7251 (United States); Fries-Carr, Sandra [Air Force Research Laboratory, Propulsion Directorate, 1950 Fifth Street, Wright-Patterson Air Force Base, OH 45433-7251 (United States); Enlow, Jesse [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States); Bunning, Timothy J. [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States)

2007-02-26

Polymer dielectric films fabricated by plasma enhanced chemical vapor deposition (PECVD) have unique properties due to their dense crosslinked bulk structure. These spatially uniform films exhibit good adhesion to a variety of substrates, excellent chemical inertness, high thermal resistance, and are formed from an inexpensive, solvent-free, room temperature process. In this work, we studied the dielectric properties of plasma polymerized (PP) carbon-based polymer thin films prepared from two precursors, benzene and octafluorocyclobutane. Two different monomer feed locations, directly in the plasma zone or in the downstream region (DS) and two different pressures, 80 Pa (high pressure) or 6.7 Pa (low pressure), were used. The chemical structure of the PECVD films was examined by X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy. The dielectric constant ({epsilon} {sub r}) and dielectric loss (tan {delta}) of the films were investigated over a range of frequencies up to 1 MHz and the dielectric strength (breakdown voltage) (F {sub b}) was characterized by the current-voltage method. Spectroscopic ellipsometry was performed to determine the film thickness and refractive index. Good dielectric properties were exhibited, as PP-benzene films formed in the high pressure, DS region showed a F{sub b} of 610 V/{mu}m, an {epsilon} {sub r} of 3.07, and a tan {delta} of 7.0 x 10{sup -3} at 1 kHz. The PECVD processing pressure has a significant effect on final film structure and the film's physical density has a strong impact on dielectric breakdown strength. Also noted was that the residual oxygen content in the PP-benzene films significantly affected the frequency dependences of the dielectric constant and loss.

The relationship between chemical structure and dielectric properties of plasma-enhanced chemical vapor deposited polymer thin films

International Nuclear Information System (INIS)

Jiang Hao; Hong Lianggou; Venkatasubramanian, N.; Grant, John T.; Eyink, Kurt; Wiacek, Kevin; Fries-Carr, Sandra; Enlow, Jesse; Bunning, Timothy J.

2007-01-01

Polymer dielectric films fabricated by plasma enhanced chemical vapor deposition (PECVD) have unique properties due to their dense crosslinked bulk structure. These spatially uniform films exhibit good adhesion to a variety of substrates, excellent chemical inertness, high thermal resistance, and are formed from an inexpensive, solvent-free, room temperature process. In this work, we studied the dielectric properties of plasma polymerized (PP) carbon-based polymer thin films prepared from two precursors, benzene and octafluorocyclobutane. Two different monomer feed locations, directly in the plasma zone or in the downstream region (DS) and two different pressures, 80 Pa (high pressure) or 6.7 Pa (low pressure), were used. The chemical structure of the PECVD films was examined by X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy. The dielectric constant (ε r ) and dielectric loss (tan δ) of the films were investigated over a range of frequencies up to 1 MHz and the dielectric strength (breakdown voltage) (F b ) was characterized by the current-voltage method. Spectroscopic ellipsometry was performed to determine the film thickness and refractive index. Good dielectric properties were exhibited, as PP-benzene films formed in the high pressure, DS region showed a F b of 610 V/μm, an ε r of 3.07, and a tan δ of 7.0 x 10 -3 at 1 kHz. The PECVD processing pressure has a significant effect on final film structure and the film's physical density has a strong impact on dielectric breakdown strength. Also noted was that the residual oxygen content in the PP-benzene films significantly affected the frequency dependences of the dielectric constant and loss

Study of post annealing influence on structural, chemical and electrical properties of ZTO thin films

International Nuclear Information System (INIS)

Jain, Vipin Kumar; Kumar, Praveen; Kumar, Mahesh; Jain, Praveen; Bhandari, Deepika; Vijay, Y.K.

2011-01-01

Research highlights: → Structural, chemical and electrical properties of cost effective ZTO thin films with varying concentrations. → Effect of annealing of ZTO films. - Abstract: Zinc-Tin-Oxide (ZTO) thin films were deposited on glass substrate with varying concentrations (ZnO:SnO 2 ; 100:0, 90:10, 70:30 and 50:50 wt.%) at room temperature by flash evaporation technique. These deposited ZTO films were annealed at 450 deg. C in vacuum. These films were characterized to study the effect of annealing and addition of SnO 2 concentration on the structural, chemical and electrical properties. The XRD analysis indicates that crystallization of the ZTO films strongly depends on the concentration of SnO 2 and post annealing where annealed films showed polycrystalline nature. Atomic force microscopy (AFM) images manifest the surface morphology of these ZTO thin films. The XPS core level spectra of Zn(2p), O(1s) and Sn(3d) have been deconvoluted into their Gaussian component to evaluate the chemical changes, while valence band spectra reveal the electronic structures of these films. A small shift in Zn(2p) and Sn(3d) core level towards higher binding energy and O(1s) core level towards lower binding energy have been observed. The minimum electrical resistivity (ρ ∼ 3.69 x 10 -2 Ω-cm), maximum carrier concentration (n ∼ 3.26 x 10 19 cm -3 ) and Hall mobility (μ ∼ 5.2 cm 2 v -1 s -1 ) were obtained for as-prepared ZTO (50:50) film thereafter move towards lowest resistivity (ρ ∼ 1.12 x 10 -3 Ω-cm), highest carrier concentration (n ∼ 2.96 x 10 20 cm -3 ) and mobility (μ ∼ 18.8 cm 2 v -1 s -1 ) for annealed ZTO (50:50) thin film.

Chemical analysis of cyanide in cyanidation process: review of methods

International Nuclear Information System (INIS)

Nova-Alonso, F.; Elorza-Rodriguez, E.; Uribe-Salas, A.; Perez-Garibay, R.

2007-01-01

Cyanidation, the world wide method for precious metals recovery, the chemical analysis of cyanide, is a very important, but complex operation. Cyanide can be present forming different species, each of them with different stability, toxicity, analysis method and elimination technique. For cyanide analysis, there exists a wide selection of analytical methods but most of them present difficulties because of the interference of species present in the solution. This paper presents the different available methods for chemical analysis of cyanide: titration, specific electrode and distillation, giving special emphasis on the interferences problem, with the aim of helping in the interpretation of the results. (Author)

Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease.

Science.gov (United States)

Beck, Michael W; Derrick, Jeffrey S; Kerr, Richard A; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D; Kim, Kwang S; Lee, Joo-Yong; Ruotolo, Brandon T; Lim, Mi Hee

2016-10-13

The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

Hierarchically structured photonic crystals for integrated chemical separation and colorimetric detection.

Science.gov (United States)

Fu, Qianqian; Zhu, Biting; Ge, Jianping

2017-02-16

A SiO 2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO 2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

Quantum chemical analysis of binary and ternary ferromagnetic alloys; Quantenchemische Untersuchungen binaerer und ternaerer ferromagnetischer Legierungen

Energy Technology Data Exchange (ETDEWEB)

Jacobs, Yasemin Erika Charlotte

2007-02-23

In this work the electronic structures, densities of states, chemical bonding, magnetic exchange Parameters and Curie temperatures of binary and ternary ferromagnetic alloys are analyzed. The electronic structure of ferromagnetic MnAl has been calculated using density-functional techniques (TB-LMTO-ASA, FPLAPW) and quantum chemically analyzed by means of the crystal orbital Hamilton population analysis. The crystal structure of the ferromagnetic tetragonal MnAl may be understood to originate from the structure of nonmagnetic cubic MnAl with a CsCl motif through a two-step process. While the nonmagnetic cubic structure is stable against a structural deformation, antibonding Mn-Mn interactions at the Fermi level lead to spin polarization and the onset of magnetism, i.e., a symmetry reduction taking place solely in the electronic degrees of freedom, by that emptying antibonding Mn-Mn states. Residual antibonding Al--Al states can only be removed by a subsequent, energetically smaller structural deformation towards the tetragonal system. As a final result, homonuclear bonding is strengthened and heteronuclear bonding is weakened. Corresponding DFT calculations of the electronic structure as well as the calculation of the chemical bonding and the magnetic exchange interactions have been performed on the basis of LDA and GGA for a series of ferromagnetic full Heusler alloys of general formula Co2MnZ (Z=Ga,Si,Ge,Sn), Rh2MnZ (Z=Ge,Sn,Pb), Ni2MnZ (Z=Ga,In,Sn), Pd2MnZ (Z=Sn,Sb) and Cu2MnZ (Z=Al,In,Sn). The connection between the electronic spectra and the magnetic interactions have been studied. Correlations between the chemical bondings in Heusler alloys derived from COHP analysis and magnetic phenomena are obvious, and different mechanisms leading to spin polarization and ferromagnetism are derived. The band dependence of the exchange parameters, their dependence on volume and valence electron concentration have been thoroughly analyzed within the Green function technique

Quantum chemical analysis of the electronic structure and Moessbauer spectra parameters for low spin cyanide- and pyridine-hemichromes

International Nuclear Information System (INIS)

Khleskov, V.I.; Kolpakov, E.V.; Smirnov, A.B.

1992-01-01

The work contains results of quantum-chemical calculations of electronic structure and Moessbauer spectra parameters for low spin S=1/2 hexa-coordinated ferri-porphyrin complexes with cyanide (CN) and pyridine (Py) as axial ligands. Theoretical results made it possible to explain experimentally observed regularity of anomalous quadrupole splitting decrease after substitution of Py-ligands by CN. Comparison of theoretical and experimental data indicated that 2 E g must be the ground state of investigated hemichromes. In this state unpaired electron symmetrically occupies d π -orbitals of Fe-ion. (orig.)

Continuous-flow centrifugation to collect suspended sediment for chemical analysis

Science.gov (United States)

Conn, Kathleen E.; Dinicola, Richard S.; Black, Robert W.; Cox, Stephen E.; Sheibley, Richard W.; Foreman, James R.; Senter, Craig A.; Peterson, Norman T.

2016-12-22

Recent advances in suspended-sediment monitoring tools and surrogate technologies have greatly improved the ability to quantify suspended-sediment concentrations and to estimate daily, seasonal, and annual suspended-sediment fluxes from rivers to coastal waters. However, little is known about the chemical composition of suspended sediment, and how it may vary spatially between water bodies and temporally within a single system owing to climate, seasonality, land use, and other natural and anthropogenic drivers. Many water-quality contaminants, such as organic and inorganic chemicals, nutrients, and pathogens, preferentially partition in sediment rather than water. Suspended sediment-bound chemical concentrations may be undetected during analysis of unfiltered water samples, owing to small water sample volumes and analytical limitations. Quantification of suspended sediment‑bound chemical concentrations is needed to improve estimates of total chemical concentrations, chemical fluxes, and exposure levels of aquatic organisms and humans in receiving environments. Despite these needs, few studies or monitoring programs measure the chemical composition of suspended sediment, largely owing to the difficulty in consistently obtaining samples of sufficient quality and quantity for laboratory analysis.A field protocol is described here utilizing continuous‑flow centrifugation for the collection of suspended sediment for chemical analysis. The centrifuge used for development of this method is small, lightweight, and portable for the field applications described in this protocol. Project scoping considerations, deployment of equipment and system layout options, and results from various field and laboratory quality control experiments are described. The testing confirmed the applicability of the protocol for the determination of many inorganic and organic chemicals sorbed on suspended sediment, including metals, pesticides, polycyclic aromatic hydrocarbons, and

Chemical analysis by nuclear techniques

Energy Technology Data Exchange (ETDEWEB)

Sohn, S. C.; Kim, W. H.; Park, Y. J.; Song, B. C.; Jeon, Y. S.; Jee, K. Y.; Pyo, H. Y

2002-01-01

This state art report consists of four parts, production of micro-particles, analysis of boron, alpha tracking method and development of neutron induced prompt gamma ray spectroscopy (NIPS) system. The various methods for the production of micro-paticles such as mechanical method, electrolysis method, chemical method, spray method were described in the first part. The second part contains sample treatment, separation and concentration, analytical method, and application of boron analysis. The third part contains characteristics of alpha track, track dectectors, pretreatment of sample, neutron irradiation, etching conditions for various detectors, observation of track on the detector, etc. The last part contains basic theory, neutron source, collimator, neutron shields, calibration of NIPS, and application of NIPS system.

Chemical analysis by nuclear techniques

International Nuclear Information System (INIS)

Sohn, S. C.; Kim, W. H.; Park, Y. J.; Park, Y. J.; Song, B. C.; Jeon, Y. S.; Jee, K. Y.; Pyo, H. Y.

2002-01-01

This state art report consists of four parts, production of micro-particles, analysis of boron, alpha tracking method and development of neutron induced prompt gamma ray spectroscopy (NIPS) system. The various methods for the production of micro-paticles such as mechanical method, electrolysis method, chemical method, spray method were described in the first part. The second part contains sample treatment, separation and concentration, analytical method, and application of boron analysis. The third part contains characteristics of alpha track, track dectectors, pretreatment of sample, neutron irradiation, etching conditions for various detectors, observation of track on the detector, etc. The last part contains basic theory, neutron source, collimator, neutron shields, calibration of NIPS, and application of NIPS system

Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

Energy Technology Data Exchange (ETDEWEB)

Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

2005-03-01

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

20180318 - Sharing chemical structures with peer-reviewed publications. Are we there yet? (ACS Spring)

Science.gov (United States)

In the domain of chemistry one of the greatest benefits to publishing research is that data are shared. Unfortunately, the vast majority of chemical structure data remain locked up in document form, primarily as PDF files. Despite the explosive growth of online chemical databases...

Chemical and physical structures of proteinoids and related polyamino acids

Science.gov (United States)

Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

Studies of polyamino acid formation pathways in the prebiotic condition are important for the study of the origins of life. Several pathways of prebiotic polyamino acid formation have been reported. Heating of monoammonium malate [1] and heating of amino acids in molten urea [2] are important pathways of the prebiotic peptide formation. The former case, globular structure called proteinoid microsphere is formed in aqueous conditions. The later case, polyamino acids are formed from unrestricted amino acid species. Heating of aqueous aspargine is also interesting pathway for the prebiotic polyamino acid formation, because polyamino acid formation proceeds in aqueous condition [3]. In this study, we analyzed the chemical structure of the proteinoids and related polyamino acids formed in the above three pathways using with mass spectrometer. In addition, their physical structures are analyzed by the electron and optical microscopes, in order to determine the self-organization abilities. We discuss the relation between the chemical and the physical structures for the origins of life. References [1] Harada, K., J. Org. Chem., 24, 1662 (1959), Fox, S. W., Harada, K., and Kendrick, J., Science, 129, 1221 (1959). [2] Terasaki, M., Nomoto, S., Mita, H., and Shimoyama, A., Chem. Lett., 480 (2002), Mita, H., Nomoto, S., Terasaki, M., Shimoyama, A., and Yamamoto, Y., Int. J. Astrobiol., 4, 145 (2005). [3] Kovacs, K and Nagy, H., Nature, 190, 531 (1961), Munegumi, T., Tanikawa, N., Mita, H. and Harada, K., Viva Origino, 22, 109 (1994).

Structural analysis of CdS thin films obtained by multiple dips of oscillating chemical bath

Energy Technology Data Exchange (ETDEWEB)

Gutierrez Lazos, C.D. [Seccion de Electronica del Estado Solido, Centro de Investigacion y de Estudios Avanzados, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, 07360 Mexico, D.F. (Mexico); Rosendo, E., E-mail: erosendo@siu.buap.m [Centro de Investigacion en Dispositivos Semiconductores, Universidad Autonoma de Puebla, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico); Ortega, M. [Seccion de Electronica del Estado Solido, Centro de Investigacion y de Estudios Avanzados, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, 07360 Mexico, D.F. (Mexico); Oliva, A.I. [Departamento de Fisica Aplicada, Centro de Investigacion y de Estudios Avanzados, Unidad Merida, A.P. 73 Cordemex, 97310 Merida, Yucatan (Mexico); Tapia, O.; Diaz, T.; Juarez, H.; Garcia, G. [Centro de Investigacion en Dispositivos Semiconductores, Universidad Autonoma de Puebla, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico); Rubin, M. [Facultad de Ciencias de la Computacion, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico)

2009-11-25

Highly oriented CdS thin films with thicknesses greater than 1 mum were deposited by multiple dips, using oscillating chemical bath deposition (OCBD) at the bath temperature of 75 deg. C, and deposition time ranging from 15 to 75 min for a single dip. Samples with different thickness were prepared by repeating the deposition process for two and three times. The films deposited by a single dip have the alpha-greenockite structure showing the (0 0 2) as preferred orientation, as indicated by the X-ray diffraction measurements. This notable characteristic is preserved in the samples obtained from two or three dips. The crystallite size for the samples deposited by a single dip depends on the deposition time, because it varied from 23 to 37 nm as the deposition time increased. Nevertheless for samples deposited by two and three dips, the grain size shows no noticeable change, being about 22 nm.

Structural, chemical and electrical characterisation of conductive graphene-polymer composite films

Energy Technology Data Exchange (ETDEWEB)

Brennan, Barry; Spencer, Steve J.; Belsey, Natalie A. [National Physical Laboratory, Teddington, TW11 0LW (United Kingdom); Faris, Tsegie [DZP Technologies Ltd., Future Business Centre, Cambridge, CB4 2HY (United Kingdom); Cronin, Harry [DZP Technologies Ltd., Future Business Centre, Cambridge, CB4 2HY (United Kingdom); Advanced Technology Institute (ATI), University of Surrey, Guildford, GU2 7XH (United Kingdom); Silva, S. Ravi P. [Advanced Technology Institute (ATI), University of Surrey, Guildford, GU2 7XH (United Kingdom); Sainsbury, Toby; Gilmore, Ian S. [National Physical Laboratory, Teddington, TW11 0LW (United Kingdom); Stoeva, Zlatka [DZP Technologies Ltd., Future Business Centre, Cambridge, CB4 2HY (United Kingdom); Pollard, Andrew J., E-mail: andrew.pollard@npl.co.uk [National Physical Laboratory, Teddington, TW11 0LW (United Kingdom)

2017-05-01

Graphical abstract: Secondary Ion Mass Spectrometry (SIMS) imaging of the dispersion of graphene within graphene-polymer composites using the Na{sup +} signal. - Highlights: • Relation of properties of graphene flakes with electrical properties of composite. • Standardised characterisation method for structural properties of graphene flakes. • Structural and chemical characterisation of commercial graphene flakes. • ToF-SIMS used to determine dispersion of graphene in polymer. - Abstract: Graphene poly-acrylic and PEDOT:PSS nanocomposite films were produced using two alternative commercial graphene powders to explore how the graphene flake dimensions and chemical composition affected the electrical performance of the film. A range of analytical techniques, including scanning electron microscopy (SEM), atomic force microscopy (AFM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), were employed to systematically analyse the initial graphene materials as well as the nanocomposite films. Electrical measurements indicated that the sheet resistance of the films was affected by the properties of the graphene flakes used. To further explore the composition of the films, ToF-SIMS mapping was employed and provided a direct means to elucidate the nature of the graphene dispersion in the films and to correlate this with the electrical analysis. These results reveal important implications for how the dispersion of the graphene material in films produced from printable inks can be affected by the type of graphene powder used and the corresponding effect on electrical performance of the nanocomposites. This work provides direct evidence for how accurate and comparable characterisation of the graphene material is required for real-world graphene materials to develop graphene enabled films and proposes a measurement protocol for comparing graphene materials that can be used for international

Positron annihilation spectroscopy for chemical analysis (PASCA). Chapter 9

International Nuclear Information System (INIS)

Cheng, K.L.; Jean, Y.C.

1988-01-01

This chapter gives an up to date overview of positron annihilation spectroscopy for chemical analysis (PASCA). As an in situ technique PASCA is especially suitable for studying processes occurring at surfaces. The in situ characteristics of PASCA are treated. The principes of positron annihilation life time spectroscopy (PAL) are discussed and some important analytical applications such as, in determining of total surface areas and cavity volumes in chemical reactions, in the study of chemisorption and catalytic reactions on porous surfaces, in the analysis of bulk materials, in determining molecular association constants in biological systems, in proton and neutron activation analysis, in thin layer chromatography and in tracer technology. 28 refs.; 15 figs.; 8 tabs

BioGPS descriptors for rational engineering of enzyme promiscuity and structure based bioinformatic analysis.

Directory of Open Access Journals (Sweden)

Valerio Ferrario

Full Text Available A new bioinformatic methodology was developed founded on the Unsupervised Pattern Cognition Analysis of GRID-based BioGPS descriptors (Global Positioning System in Biological Space. The procedure relies entirely on three-dimensional structure analysis of enzymes and does not stem from sequence or structure alignment. The BioGPS descriptors account for chemical, geometrical and physical-chemical features of enzymes and are able to describe comprehensively the active site of enzymes in terms of "pre-organized environment" able to stabilize the transition state of a given reaction. The efficiency of this new bioinformatic strategy was demonstrated by the consistent clustering of four different Ser hydrolases classes, which are characterized by the same active site organization but able to catalyze different reactions. The method was validated by considering, as a case study, the engineering of amidase activity into the scaffold of a lipase. The BioGPS tool predicted correctly the properties of lipase variants, as demonstrated by the projection of mutants inside the BioGPS "roadmap".

Chemical structure and physical properties of radiation-induced crosslinking of polytetrafluoroethylene

International Nuclear Information System (INIS)

Oshima, Akihiro; Ikeda, Shigetoshi; Katoh, Etsuko; Tabata, Yoneho

2001-01-01

The chemical structure and physical properties of polytetrafluoroethylene (PTFE) that has been crosslinked by radiation have been studied by various methods. It has been found that a Y-type crosslinking structure and a Y-type structure incorporating a double bond (modified Y-type) is formed in PTFE by radiation-crosslinking in the molten state. In addition, various types of double bond structures, excluding the crosslinking site, have been identified. The crosslinked PTFE has a good light transparency due to the loss of crystallites, whilst it retains the excellent properties of electrical insulation and heat resistance. The coefficient of abrasion and the permanent creep are also greatly improved by crosslinking

Photoluminescence study of ZnO structures grown by aqueous chemical growth

International Nuclear Information System (INIS)

Kenanakis, G.; Androulidaki, M.; Vernardou, D.; Katsarakis, N.; Koudoumas, E.

2011-01-01

ZnO micro-structures were deposited by aqueous chemical growth on Si (100) substrates, their morphology and size depending on the growth period. Characterization of the structures was performed using X-ray diffraction, scanning electron microscopy and Raman spectroscopy. Photoluminescence spectra recorded at 18 and 295 K for 325 nm CW excitation indicated that these are strongly affected by the morphology of the structures. Rods and tubes emit stronger UV radiation, in contrast to stronger yellow-green emission observed for flower-like structures. A red shift of the UV emission was found for increasing input power, while, thermal annealing of the samples induced stimulated emission for quite high excitation intensities.

YNi and its hydrides: Phase stabilities, electronic structures and chemical bonding properties from first principles

Energy Technology Data Exchange (ETDEWEB)

Matar, S.F., E-mail: matar@icmcb-bordeaux.cnrs.fr [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Docteur Albert Schweitzer, F-33608 Pessac (France); Nakhl, M. [Universite Libanaise, Laboratoire de Chimie-Physique des Materiaux LCPM, Fanar (Lebanon); Al Alam, A.F.; Ouaini, N. [Universite Saint-Esprit de Kaslik, Faculte des Sciences et de Genie Informatique, Jounieh (Lebanon); Chevalier, B. [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Docteur Albert Schweitzer, F-33608 Pessac (France)

2010-11-25

Graphical abstract: Base centered orthorhombic YNiH{sub X} structure. For x = 3, only H1 and H2 are present. Highest hydrogen content YNiH{sub 4} is obtained when H3 are added. - Abstract: Within density functional theory, establishing the equations of states of YNi in two different controversial structures in the literature, leads to determine the orthorhombic FeB-type as the ground state one with small energy difference. For YNiH{sub 3} and YNiH{sub 4} hydrides crystallizing in the orthorhombic CrB-type structure the geometry optimization and the ab initio determination of the H atomic positions show that the stability of hydrogen decreases from the tri- to the tetra- hydride. New states brought by hydrogen within the valence band lead to its broadening and to enhanced localization of metal density of states. The chemical bonding analysis shows a preferential Ni-H bonding versus Y-H.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

Science.gov (United States)

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

ANALYSIS OF SAMPLES FROM TANK 5F CHEMICAL CLEANING

Energy Technology Data Exchange (ETDEWEB)

Poirier, M.; Fink, S.

2011-03-07

The Savannah River Site (SRS) is preparing Tank 5F for closure. The first step in preparing the tank for closure is mechanical sludge removal. Following mechanical sludge removal, SRS performed chemical cleaning with oxalic acid to remove the sludge heel. Personnel are currently assessing the effectiveness of the chemical cleaning. SRS personnel collected liquid samples during chemical cleaning and submitted them to Savannah River National Laboratory (SRNL) for analysis. Following chemical cleaning, they collected a solid sample (also known as 'process sample') and submitted it to SRNL for analysis. The authors analyzed these samples to assess the effectiveness of the chemical cleaning process. The conclusions from this work are: (1) With the exception of iron, the dissolution of sludge components from Tank 5F agreed with results from the actual waste demonstration performed in 2007. The fraction of iron removed from Tank 5F by chemical cleaning was significantly less than the fraction removed in the SRNL demonstrations. The likely cause of this difference is the high pH following the first oxalic acid strike. (2) Most of the sludge mass remaining in the tank is iron and nickel. (3) The remaining sludge contains approximately 26 kg of barium, 37 kg of chromium, and 37 kg of mercury. (4) Most of the radioactivity remaining in the residual material is beta emitters and {sup 90}Sr. (5) The chemical cleaning removed more than {approx} 90% of the uranium isotopes and {sup 137}Cs. (6) The chemical cleaning removed {approx} 70% of the neptunium, {approx} 83% of the {sup 90}Sr, and {approx} 21% of the {sup 60}Co. (7) The chemical cleaning removed less than 10% of the plutonium, americium, and curium isotopes. (8) The chemical cleaning removed more than 90% of the aluminium, calcium, and sodium from the tank. (9) The cleaning operations removed 61% of lithium, 88% of non-radioactive strontium, and 65% of zirconium. The {sup 90}Sr and non-radioactive strontium were

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata

Energy Technology Data Exchange (ETDEWEB)

Singh, Sunil; Gupta, Rashi; Sharma, Shilpi, E-mail: shilpi@dbeb.iitd.ac.in

2015-06-30

Highlights: • Non-target effects of pesticides employing qualitative and quantitative approaches. • Qualitative shifts in resident and active bacterial community structure. • Abundance of 16S rRNA gene and transcripts were reduced significantly. • Effects of biological pesticide similar to chemical pesticides on rhizospheric bacteria. - Abstract: With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture.

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata

International Nuclear Information System (INIS)

Singh, Sunil; Gupta, Rashi; Sharma, Shilpi

2015-01-01

Highlights: • Non-target effects of pesticides employing qualitative and quantitative approaches. • Qualitative shifts in resident and active bacterial community structure. • Abundance of 16S rRNA gene and transcripts were reduced significantly. • Effects of biological pesticide similar to chemical pesticides on rhizospheric bacteria. - Abstract: With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture

Structure elucidation and chemical synthesis of stigmolone, a novel type of prokaryotic pheromone.

Science.gov (United States)

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.

Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors.

Science.gov (United States)

Nandi, Sisir; Monesi, Alessandro; Drgan, Viktor; Merzel, Franci; Novič, Marjana

2013-10-30

In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.

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

Science.gov (United States)

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.

Quantitative magnetometry analysis and structural characterization of multisegmented cobalt–nickel nanowires

Energy Technology Data Exchange (ETDEWEB)

Cantu-Valle, Jesus [Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 (United States); Díaz Barriga-Castro, Enrique [Centro de Investigación de Ciencias Físico Matemáticas/Facultad de Ciencias Físico Matemáticas, Universidad Autónoma de Nuevo León, Pedro de Alba s/n, San Nicolás de Los Garza, Nuevo León 66450 (Mexico); Vega, Víctor; García, Javier [Departamento de Física, Universidad de Oviedo, Calvo Sotelo s/n, Oviedo 33007 (Spain); Mendoza-Reséndez, Raquel [Facultad de Ingeniería Mecánica y Eléctrica. Universidad Autónoma de Nuevo León, Pedro de Alba s/n, San Nicolás de Los Garza, Nuevo León 66450 (Mexico); Luna, Carlos [Centro de Investigación de Ciencias Físico Matemáticas/Facultad de Ciencias Físico Matemáticas, Universidad Autónoma de Nuevo León, Pedro de Alba s/n, San Nicolás de Los Garza, Nuevo León 66450 (Mexico); Manuel Prida, Víctor [Departamento de Física, Universidad de Oviedo, Calvo Sotelo s/n, Oviedo 33007 (Spain); and others

2015-04-01

Understanding and measuring the magnetic properties of an individual nanowire and their relationship with crystalline structure and geometry are of scientific and technological great interest. In this work, we report the localized study of the magnetic flux distribution and the undisturbed magnetization of a single ferromagnetic nanowire that poses a bar-code like structure using off-axis electron holography (EH) under Lorentz conditions. The nanowires were grown by template-assisted electrodeposition, using AAO templates. Electron holography allows the visualization of the magnetic flux distribution within and surroundings as well as its quantification. The magnetic analysis performed at individual nanowires was correlated with the chemical composition and crystalline orientation of the nanowires. - Highlights: • The structure-magnetic property relationship of CoNi nanowires is determined. • Off axis electron holography for the magnetic nanowires is used for the analysis. • The magnetization is quantitatively obtained from the retrieved phase images. • These results lead to a better comprehension of the magneto-crystalline phenomena.

Quantitative magnetometry analysis and structural characterization of multisegmented cobalt–nickel nanowires

International Nuclear Information System (INIS)

Cantu-Valle, Jesus; Díaz Barriga-Castro, Enrique; Vega, Víctor; García, Javier; Mendoza-Reséndez, Raquel; Luna, Carlos; Manuel Prida, Víctor

2015-01-01

Understanding and measuring the magnetic properties of an individual nanowire and their relationship with crystalline structure and geometry are of scientific and technological great interest. In this work, we report the localized study of the magnetic flux distribution and the undisturbed magnetization of a single ferromagnetic nanowire that poses a bar-code like structure using off-axis electron holography (EH) under Lorentz conditions. The nanowires were grown by template-assisted electrodeposition, using AAO templates. Electron holography allows the visualization of the magnetic flux distribution within and surroundings as well as its quantification. The magnetic analysis performed at individual nanowires was correlated with the chemical composition and crystalline orientation of the nanowires. - Highlights: • The structure-magnetic property relationship of CoNi nanowires is determined. • Off axis electron holography for the magnetic nanowires is used for the analysis. • The magnetization is quantitatively obtained from the retrieved phase images. • These results lead to a better comprehension of the magneto-crystalline phenomena

Electronic structure and chemical bonding in LaIrSi-type intermetallics

Energy Technology Data Exchange (ETDEWEB)

Matar, Samir F. [Bordeaux Univ., Pessac (France). CNRS; Poettgen, Rainer [Muenster Univ. (Germany). Inst. fuer Anorganische und Analytische Chemie; Nakhl, Michel [Univ. Libanaise, Fanar (Lebanon). Ecole Doctorale Sciences et Technologies

2017-05-01

The cubic LaIrSi type has 23 representatives in aluminides, gallides, silicides, germanides, phosphides, and arsenides, all with a valence electron count of 16 or 17. The striking structural motif is a three-dimensional network of the transition metal (T) and p element (X) atoms with TX{sub 3/3} respectively XT{sub 3/3} coordination. Alkaline earth or rare earth atoms fill cavities within the polyanionic [TX]{sup δ-} networks. The present work presents a detailed theoretical study of chemical bonding in LaIrSi-type representatives, exemplarily for CaPtSi, BaIrP, BaAuGa, LaIrSi, CeRhSi, and CeIrSi. DFT-GGA-based electronic structure calculations show weakly metallic compounds with itinerant small magnitude DOSs at E{sub F} except for CeRhSi whose large Ce DOS at E{sub F} leads to a finite magnetization on Ce (0.73 μ{sub B}) and induced small moments of opposite sign on Rh and Si in a ferromagnetic ground state. The chemical bonding analyses show dominant bonding within the [TX]{sup δ-} polyanionic networks. Charge transfer magnitudes were found in accordance with the course of the electronegativites of the chemical constituents.

Structural and optical characterization of self-assembled Ge nanocrystal layers grown by plasma-enhanced chemical vapor deposition.

Science.gov (United States)

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.

Structural investigation of chemically synthesized ferrite magnetic nanomaterials

Science.gov (United States)

Uyanga, E.; Sangaa, D.; Hirazawa, H.; Tsogbadrakh, N.; Jargalan, N.; Bobrikov, I. A.; Balagurov, A. M.

2018-05-01

In recent times, interest in ferrite magnetic nanomaterials has considerably grown, mainly due to their highly promising medical and biological applications. Spinel ferrite powder samples, with high heat generation abilities in AC magnetic fields, were studied for their application to the hyperthermia treatment of cancer tumors. These properties of ferrites strongly depend on their chemical composition, ion distribution between crystallographic positions, magnetic structure and method of preparation. In this study, crystal and magnetic structures of several magnetic spinels were investigated by neutron diffraction. The explanation of the mechanism triggering the heat generation ability in the magnetic materials, and the electronic and magnetic states of ferrite-spinel type structures, were theoretically defined by a first-principles method. Ferrites with the composition of CuxMg1-xFe2O4 have been investigated as a heat generating magnetic nanomaterial. Atomic fraction of copper in ferrite was varied between 0 and 100% (that is, x between 0 and 1.0 with 0.2 steps), with the copper dope limit corresponding to appear a tetragonal phase.

Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

Science.gov (United States)

Senger, Stefan; Bartek, Luca; Papadatos, George; Gaulton, Anna

2015-12-01

First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large corpus of documents is the automated extraction of chemical structures. A number of patent chemistry databases generated by using the latter approach are now available but little is known that can help to manage expectations when using them. This study aims to address this by comparing two such freely available sources, SureChEMBL and IBM SIIP (IBM Strategic Intellectual Property Insight Platform), with manually curated commercial databases. When looking at the percentage of chemical structures successfully extracted from a set of patents, using SciFinder as our reference, 59 and 51 % were also found in our comparison in SureChEMBL and IBM SIIP, respectively. When performing this comparison with compounds as starting point, i.e. establishing if for a list of compounds the databases provide the links between chemical structures and patents they appear in, we obtained similar results. SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys. In our comparison of automatically generated vs. manually curated patent chemistry databases, the former successfully provided approximately 60 % of links between chemical structure and patents. It needs to be stressed that only a very limited number of patents and compound-patent pairs were used for our comparison. Nevertheless, our results will hopefully help to manage expectations of users of patent chemistry databases of this type and provide a useful framework for more studies like ours as well as guide future developments of the workflows used for the automated extraction of chemical structures from patents. The challenges we have encountered

Application of Spectroscopic Methods for Structural Analysis of Chitin and Chitosan

Directory of Open Access Journals (Sweden)

Jolanta Kumirska

2010-04-01

Full Text Available 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.

Structural and chemical aspects of HPMA copolymers as drug carriers.

Science.gov (United States)

Ulbrich, Karel; Subr, Vladimír

2010-02-17

Synthetic strategies and chemical and structural aspects of the synthesis of HPMA copolymer conjugates with various drugs and other biologically active molecules are described and discussed in this chapter. The discussion is held from the viewpoint of design and structure of the polymer backbone and biodegradable spacer between a polymer and drug, structure and methods of attachment of the employed drugs to the carrier and structure and methods of conjugation with targeting moieties. Physicochemical properties of the water-soluble polymer-drug conjugates and polymer micelles including mechanisms of drug release are also discussed. Detailed description of biological behavior of the polymer-drug conjugates as well as application of the copolymers for surface modification and targeting of gene delivery vectors are not included, they are presented and discussed in separate chapters of this issue. Copyright 2009 Elsevier B.V. All rights reserved.

Effect of chemical structure on the radioactive decay rate of 71Ge

International Nuclear Information System (INIS)

Makariunas, K.; Makariuniene, E.; Dragunas, A.

1979-01-01

The influence of the chemical structure on the electron capture radioactive decay rate of 71 Ge was observed. 71 Ge nuclei in bivalent sulphide GeS decay faster than in quadrivalent sulphide GeS 2 . The relative change Δlambda/lambda of the decay constant lambda is + (11.4 +- 1.7) X 10 -4 . A possibility to use the experimental values of Δlambda/lambda to determine the chemical changes in the electron density at germanium nuclei in germanium chemical compounds is discussed. Quantitative determination of the changes in the electron density is complicated because of insufficient reliability of the published values of exchange and overlap corrections to the electron capture probabilities. (Auth.)

Chemical process control using Mat lab

International Nuclear Information System (INIS)

Kang, Sin Chun; Kim, Raeh Yeon; Kim, Yang Su; Oh, Min; Yeo, Yeong Gu; Jung, Yeon Su

2001-07-01

This book is about chemical process control, which includes the basis of process control with conception, function, composition of system and summary, change of laplace and linearization, modeling of chemical process, transfer function and block diagram, the first dynamic property of process, the second dynamic property of process, the dynamic property of combined process, control structure of feedback on component of control system, the dynamic property of feedback control loop, stability of closed loop control structure, expression of process, modification and composition of controller, analysis of vibration response and adjustment controller using vibration response.

Effects of chemical treatments on hemp fibre structure

Energy Technology Data Exchange (ETDEWEB)

Kabir, M.M., E-mail: kabirm@usq.edu.au [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Wang, H. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Lau, K.T. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Department of Mechanical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region (Hong Kong); Cardona, F. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia)

2013-07-01

In this study, hemp fibres were treated with alkali, acetyl and silane chemicals. Fibre constituents such as cellulose, hemicellulose and lignin constituents were separated from treated fibres. The chemical and thermal influences of these constituents on the treated fibres were examined by using scanning electron microscope (SEM), fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). Experimental results revealed that, hemicellulose was degraded faster than that of cellulose and lignin. Cellulose exhibited better thermal stability and lignin was degraded in a wide range of temperatures. The hydrophilic nature of the fibres was predominantly caused by the presence of hemicellulose and then lignin constituents. Hemicellulose and lignin were mostly removed by the alkalisation with higher concentrations of NaOH, followed by acetylation. Silane treatment could not remove the hemicellulose and lignin, rather this treatment facilitated coupling with the fibre constituents.

Effects of chemical treatments on hemp fibre structure

International Nuclear Information System (INIS)

Kabir, M.M.; Wang, H.; Lau, K.T.; Cardona, F.

2013-01-01

In this study, hemp fibres were treated with alkali, acetyl and silane chemicals. Fibre constituents such as cellulose, hemicellulose and lignin constituents were separated from treated fibres. The chemical and thermal influences of these constituents on the treated fibres were examined by using scanning electron microscope (SEM), fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). Experimental results revealed that, hemicellulose was degraded faster than that of cellulose and lignin. Cellulose exhibited better thermal stability and lignin was degraded in a wide range of temperatures. The hydrophilic nature of the fibres was predominantly caused by the presence of hemicellulose and then lignin constituents. Hemicellulose and lignin were mostly removed by the alkalisation with higher concentrations of NaOH, followed by acetylation. Silane treatment could not remove the hemicellulose and lignin, rather this treatment facilitated coupling with the fibre constituents.

Host-guest complex of N-(2-chloroethyl), N-nitroso, N‧, N‧ -dicyclohexylsulfamid with β-cyclodextrin: Fluorescence, QTAIM analysis and structure-chemical reactivity

Science.gov (United States)

Bensouilah, Nadjia; Fisli, Hassina; Bensouilah, Hamza; Zaater, Sihem; Abdaoui, Mohamed; Boutemeur-Kheddis, Baya

2017-10-01

In this work, the inclusion complex of DCY/CENS: N-(2-chloroethyl), N-nitroso, N‧, N‧-dicyclohexylsulfamid and β-cyclodextrin (β-CD) is investigated using the fluorescence spectroscopy, PM3, ONIOM2 and DFT methods. The experimental part reveals that DCY/CENS forms a 1:1 stoichiometric ratio inclusion complex with β-CD. The constant of stability is evaluated using the Benesi-Hildebrand equation. The results of the theoretical optimization showed that the lipophilic fraction of molecule (cyclohexyl group) is inside of β-CD. Accordingly, the Nitroso-Chloroethyl moiety is situated outside the cavity of the macromolecule host. The favorable structure of the optimized complex indicates the existence of weak intermolecular hydrogen bonds and the most important van der Waals (vdW) interactions which are studied on the basis of Natural Bonding Orbital (NBO) analysis. The NBO is employed to compute the electronic donor-acceptor exchanges between drug and β-CD. Furthermore, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM), has been accomplished on the most favorable complex using B3LYP/6-31G(d) method. The presence of stabilizing intermolecular hydrogen bonds and van der Waals interactions in the most favorable complex is predicted. Also, the energies of these interactions are estimated with Espinosa's formula. The findings of this investigation reveal that the correlation between the structural parameters and the electronic density is good. Finally, and based on DFT calculations, the reactivity of the interesting molecule in free state was studied and compared with that in the complexed state using chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors.

Chemical structures and characteristics of animal manures and composts during composting and assessment of maturity indices.

Directory of Open Access Journals (Sweden)

Jieying Huang

Full Text Available Changes in physicochemical characteristics, chemical structures and maturity of swine, cattle and chicken manures and composts during 70-day composting without addition of bulking agents were investigated. Physicochemical characteristics were measured by routine analyses and chemical structures by solid-state 13C NMR and FT-IR. Three manures were of distinct properties. Their changes in physicochemical characteristics, chemical structures, and maturity were different not only from each other but also from those with addition of bulking agents during composting. Aromaticity in chicken manure composts decreased at first, and then increased whereas that in cattle and swine manure composts increased. Enhanced ammonia volatilization occurred without addition of bulking agents. NMR structural information indicated that cattle and chicken composts were relatively stable at day 36 and 56, respectively, but swine manure composts were not mature up to day 70. Finally, the days required for three manures to reach the threshold values of different maturity indices were different.

Coal Liquefaction characteristics and chemical structure of product oil; Sekitan ekika hanno tokusei to seiseibutsu no kagaku kozo

Energy Technology Data Exchange (ETDEWEB)

Endo, H.; Sato, M.; Chiba, T.; Hattori, H. [Hokkaido University, Sapporo (Japan). Center for Advanced Research of Energy Technology; Sasaki, M. [Hokkaido National Industrial Research Institute, Sapporo (Japan)

1996-10-28

Through the hydrogenolysis of Wandoan coal and Tanito Harum coal which are used for the NEDOL process, differences of liquefaction characteristics between them were found. The purpose of this study is to grasp these differences as differences of chemical structures of oil fractions. The compound type analysis was conducted for oil fractions obtained at varied reaction temperature for varied reaction time. Coal liquefaction characteristics of these coals were discussed by relating oil yields and chemical structures. For Tanito Harum coal, yields of gas and oil were considered to be lower than those for Wandoan coal, which reflected that the contents of partially hydrogenated hydroaromatics in oil fraction from the former were lower than those from the latter, and that the remarkable change of composition did not occur with the progress of the reaction. For both the coals, the remarkable changes in the average molecular weight of oil fraction were not observed with the progress of the reaction. While, the content of methane gradually increased with the progress of the reaction, which suggested that oil was gradually dealkylated. 5 figs.

Voting-based consensus clustering for combining multiple clusterings of chemical structures

Directory of Open Access Journals (Sweden)

Saeed Faisal

2012-12-01

Full Text Available Abstract Background Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster. Results The cumulative voting-based aggregation algorithm (CVAA, cluster-based similarity partitioning algorithm (CSPA and hyper-graph partitioning algorithm (HGPA were examined. The F-measure and Quality Partition Index method (QPI were used to evaluate the clusterings and the results were compared to the Ward’s clustering method. The MDL Drug Data Report (MDDR dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward’s method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward’s method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria. Conclusions The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA was the method of choice among consensus clustering methods.

From glass structure to its chemical durability; De la structure du verre a sa durabilite chimique

Energy Technology Data Exchange (ETDEWEB)

Angeli, F.

2009-07-01

The author gives an overview of his research activities. He more precisely reports studies related to glass structure based on nuclei observed by NMR and present in glasses of interest for nuclear activities. He discusses the influence of chemical composition on structure, and discusses information which can be extracted from network formers (Al, B) and modifiers (Na, Ca), and from oxygen present in the network linkages of oxide glasses. He discusses the different experimental and modelling approaches which enable structural and morphological information to be obtained at a mesoscopic scale. The last part deals with the investigation of the long term behaviour of confinement matrices (glassy matrix for medium-activity wastes, ceramic matrix)

Structure and properties of braided sleeve preforms for chemical vapor infiltration

Energy Technology Data Exchange (ETDEWEB)

Starr, T.L.; Fiadzo, O.G.; Hablutzel, N. [Georgia Inst. of Tech., Atlanta, GA (United States). School of Materials Science and Technology

1998-04-01

In all composites the properties and structure of the reinforcement strongly influence the performance of the material. For some composites, however, the reinforcement also affects the fabrication process itself exerting an additional, second order influence on performance. This is the case for the chemical vapor infiltration (CVI) process for fabrication of ceramic matrix composites. In this process the matrix forms progressively as a solid deposit, first onto the fiber surfaces, then onto the previous layer of deposit, ultimately growing to fill the inter-fiber porosity. The transport of reactants to the surfaces and the evolved morphology of the matrix depend on the initial reinforcement structure. This structure can vary greatly and is controlled by such factors as fiber size and cross-section, the number of filaments and amount of twist per tow or yarn, and the weave or braid architecture. Often the choice of reinforcement is based on mechanical performance analysis or on the cost and availability of the material or on the temperature stability of the fiber. Given this choice, the composite densification process--CVI--must be optimized to attain a successful material. Ceramic fiber in the form of cylindrical braided sleeve is an attractive choice for fabrication of tube-form ceramic matrix composites. Multiple, concentric layers of sleeve can be placed over a tubular mandrel, compressed and fixed with a binder to form a freestanding tube preform. This fiber architecture is different than that created by layup of plain weave cloth--the material used in most previous CVI development. This report presents the results of the investigation of CVI densification of braided sleeve preforms and the evolution of their structure and transport properties during processing.

Determination of the thickness of chemically removed thin layers on GaAs VPE structures

Energy Technology Data Exchange (ETDEWEB)

Somogyi, K.; Nemeth-Sallay, M.; Nemcsics, A. (Research Inst. for Technical Physics, Hungarian Academy of Sciences, Budapest (Hungary))

1991-01-01

Thinning of epitaxial GaAs layers was studied during the surface etching, with a special attention to submicron epitaxial structures, like MESFET or varactor-type structures. Each chemical treatment influences the crystal surface during the device preparation processes, though the possible thinning of the active layer is small. Therefore a method allowing determination of thicknesses as small as at about 20 nm of the layer removed by chemical etching from GaAs VPE structures was applied. Using special multilayered structures and a continuous electrochemical carrier concentration depth profiling, the influence of the layer thickness inhomogeneity and of some measurement errors can be minimized. Some frequently used etchants and the influence of different - so called - non-etching processes were compared in different combinations. It was shown that besides the direct etching a change of the surface conditions occurs, which influences the etch rate in the succeeding etching procedure. (orig.).

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

Science.gov (United States)

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.

Failure analysis on a chemical waste pipe

International Nuclear Information System (INIS)

Ambler, J.R.

1985-01-01

A failure analysis of a chemical waste pipe illustrates how nuclear technology can spin off metallurgical consultant services. The pipe, made of zirconium alloy (Zr-2.5 wt percent Nb, UNS 60705), had cracked in several places, all at butt welds. A combination of fractography and metallography indicated delayed hydride cracking

Analysis of forward and inverse problems in chemical dynamics and spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Rabitz, H. [Princeton Univ., NJ (United States)

1993-12-01

The overall scope of this research concerns the development and application of forward and inverse analysis tools for problems in chemical dynamics and chemical kinetics. The chemical dynamics work is specifically associated with relating features in potential surfaces and resultant dynamical behavior. The analogous inverse research aims to provide stable algorithms for extracting potential surfaces from laboratory data. In the case of chemical kinetics, the focus is on the development of systematic means to reduce the complexity of chemical kinetic models. Recent progress in these directions is summarized below.

Statistic analysis of grouping in evaluation of the behavior of stable chemical elements and physical-chemical parameters in effluent from uranium mining

International Nuclear Information System (INIS)

Pereira, Wagner de S.

2013-01-01

The Ore Treatment Unit (UTM) is a uranium mine off. The statistical analysis of clustering was used to evaluate the behavior of stable chemical elements and physico-chemical variables in their effluents. The use of cluster analysis proved effective in the evaluation, allowing to identify groups of chemical elements in physico-chemical variables and group analyzes (element and variables ). As a result, we can say, based on the analysis of the data, a strong link between Ca and Mg and between Al and TR 2 O 3 (rare earth oxides) in the UTM effluents. The SO 4 was also identified as strongly linked to total solids and dissolved and these linked to electrical conductivity. Other associations existed, but were not as strongly linked. Additional collections for seasonal evaluation are required so that assessments can be confirmed. Additional statistics analysis (ordination techniques) should be used to help identify the origins of the groups identified in this analysis. (author)

On the structure, morphology, and optical properties of chemical bath deposited Sb2S3 thin films

International Nuclear Information System (INIS)

Krishnan, B.; Arato, A.; Cardenas, E.; Roy, T.K. Das; Castillo, G.A.

2008-01-01

In the present paper, we have reported the room temperature growth of antimony sulphide (Sb 2 S 3 ) thin films by chemical bath deposition and detailed characterization of these films. The films were deposited from a chemical bath containing SbCl 3 and Na 2 S 2 O 3 at 27 deg. C. We have analysed the structure, morphology, composition and optical properties of as deposited Sb 2 S 3 films as well as those subjected to annealing in nitrogen atmosphere or in air. As-deposited films are amorphous to X-ray diffraction (XRD). However, the diffused rings in the electron diffraction pattern revealed the existence of nanocrystalline grains in these films. XRD analysis showed that upon annealing in nitrogen atmosphere these films transformed into polycrystalline with orthorhombic structure. Also, we have observed that during heating in air, Sb 2 S 3 first converts into orthorhombic form and then further heating results in the formation of Sb 2 O 3 crystallites. Optical bandgap energy of as deposited and annealed films was evaluated from UV-vis absorption spectra. The values obtained were 2.57 and 1.73 eV for the as-deposited and the annealed films respectively

Comparative structural analysis of human DEAD-box RNA helicases.

Science.gov (United States)

Schütz, Patrick; Karlberg, Tobias; van den Berg, Susanne; Collins, Ruairi; Lehtiö, Lari; Högbom, Martin; Holmberg-Schiavone, Lovisa; Tempel, Wolfram; Park, Hee-Won; Hammarström, Martin; Moche, Martin; Thorsell, Ann-Gerd; Schüler, Herwig

2010-09-30

DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

Comparative structural analysis of human DEAD-box RNA helicases.

Directory of Open Access Journals (Sweden)

Patrick Schütz

2010-09-01

Full Text Available DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

Native chemical ligation at Asx-Cys, Glx-Cys: chemical synthesis and high-resolution X-ray structure of ShK toxin by racemic protein crystallography.

Science.gov (United States)

Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Kent, Stephen B H

2013-08-14

We have re-examined the utility of native chemical ligation at -Gln/Glu-Cys- [Glx-Cys] and -Asn/Asp-Cys- [Asx-Cys] sites. Using the improved thioaryl catalyst 4-mercaptophenylacetic acid (MPAA), native chemical ligation could be performed at -Gln-Cys- and Asn-Cys- sites without side reactions. After optimization, ligation at a -Glu-Cys- site could also be used as a ligation site, with minimal levels of byproduct formation. However, -Asp-Cys- is not appropriate for use as a site for native chemical ligation because of formation of significant amounts of β-linked byproduct. The feasibility of native chemical ligation at -Gln-Cys- enabled a convergent total chemical synthesis of the enantiomeric forms of the ShK toxin protein molecule. The D-ShK protein molecule was ~50,000-fold less active in blocking the Kv1.3 channel than the L-ShK protein molecule. Racemic protein crystallography was used to obtain high-resolution X-ray diffraction data for ShK toxin. The structure was solved by direct methods and showed significant differences from the previously reported NMR structures in some regions of the ShK protein molecule.

Molecular design chemical structure generation from the properties of pure organic compounds

CERN Document Server

Horvath, AL

1992-01-01

This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

Comprehensive DFT study on molecular structures of Lewisites in support of the Chemical Weapons Convention

Science.gov (United States)

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 physicochemical mechanism of chemical gas sensors using an AC analysis.

Science.gov (United States)

Moon, Jaehyun; Park, Jin-Ah; Lee, Su-Jae; Lee, Jeong-Ik; Zyung, Taehyong; Shin, Eui-Chol; Lee, Jong-Sook

2013-06-21

Electrical modeling of the chemical gas sensors was successfully applied to TiO2 nanofiber gas sensors by developing an equivalent circuit model where the junction capacitance as well as the resistance can be separated from the comparable stray capacitance. The Schottky junction impedance exhibited a characteristic skewed arc described by a Cole-Davidson function, and the variation of the fit and derived parameters with temperature, bias, and NO2 gas concentration indicated definitely a physicochemical sensing mechanism based on the Pt|TiO2 Schottky junctions against the conventional supposition of the enhanced sensitivity in nanostructured gas sensors with high grain boundary/surface area. Analysis on a model Pt|TiO2|Pt structure also confirmed the characteristic impedance response of TiO2 nanofiber sensors.

Methodology for national risk analysis and prioritization of toxic industrial chemicals.

Science.gov (United States)

Taxell, Piia; Engström, Kerstin; Tuovila, Juha; Söderström, Martin; Kiljunen, Harri; Vanninen, Paula; Santonen, Tiina

2013-01-01

The identification of chemicals that pose the greatest threat to human health from incidental releases is a cornerstone in public health preparedness for chemical threats. The present study developed and applied a methodology for the risk analysis and prioritization of industrial chemicals to identify the most significant chemicals that pose a threat to public health in Finland. The prioritization criteria included acute and chronic health hazards, physicochemical and environmental hazards, national production and use quantities, the physicochemical properties of the substances, and the history of substance-related incidents. The presented methodology enabled a systematic review and prioritization of industrial chemicals for the purpose of national public health preparedness for chemical incidents.

I. Forensic data analysis by pattern recognition. Categorization of white bond papers by elemental composition. II. Source identification of oil spills by pattern recognition analysis of natural elemental composition. III. Improving the reliability of factor analysis of chemical measured analytical data by utilizing the measured analytical uncertainity. IV. Elucidating the structure of some clinical data

International Nuclear Information System (INIS)

Duewer, D.L.

1977-01-01

Pattern recognition techniques are applied to the analysis of white bond papers and the problem of determining the source of an oil spill. In each case, an elemental analysis by neutron activation is employed. For the determination of source of oil spills, the field sample was weathered prior to activation analysis. A procedure for including measured analytical uncertainty into data analysis methodology is discussed, with particular reference to factor analysis. The suitability of various dispersion matrices and matrix rank determination criteria for data having analytical uncertainty is investigated. A criterion useful for judging the number of factors insensitive to analytical uncertainty is presented. A model data structure for investigating the behavior of factor analysis techniques in a known, controlled manner is described and analyzed. A chemically interesting test data base having analytical uncertainty is analyzed and compared with the model data. The data structure of 22 blood constituents in three categories of liver disease (viral or toxic hepatitis, alcoholic liver diseases and obstructive processes) is studied using various statistical and pattern recognition techniques. Comparison of classification results on the original data, in combination with principal component analysis, suggests a possible underlying structure for the data. This model structure is tested by the application of two simple data transformations. Analysis of the transformed data appears to confirm that some basic understanding of the studied data has been achieved

Structural analysis of heat-treated birch (Betule papyrifera) surface during artificial weathering

International Nuclear Information System (INIS)

Huang Xianai; Kocaefe, Duygu; Kocaefe, Yasar; Boluk, Yaman; Krause, Cornélia

2013-01-01

Highlights: ► Investigate detailed structural changes of heat-treated wood due to weathering. ► Identify connection between physical structural changes and chemical degradation. ► Study effect of heat treatment conditions on weathering degradation process. - Abstract: Effect of artificial weathering on the surface structural changes of birch (Betule papyrifera) wood, heat-treated to different temperatures, was studied using the fluorescence microscopy and the scanning electron microscopy (SEM). Changes in the chemical structure of wood components were analyzed by FTIR in order to understand the mechanism of degradation taking place due to heat treatment and artificial weathering. The results are compared with those of the untreated (kiln-dried) birch. The SEM analysis results show that the effect of weathering on the cell wall of the untreated birch surface is more than that of heat-treated samples. The FTIR spectroscopy results indicate that lignin is the most sensitive component of heat-treated birch to the weathering degradation process. Elimination of the amorphous and highly crystallised cellulose is observed for both heat-treated and untreated wood during weathering. It is also observed that heat treatment increases the lignin and crystallised cellulose contents, which to some extent protects heat-treated birch against degradation due to weathering.

Structural changes in amorphous organic compounds and their role during chemical transformations

International Nuclear Information System (INIS)

Gusakovskaya, I.G.

1994-01-01

Using butanediol vinylacetate and dimetacrylate as an example, it can be shown that structural changes of amorphous-liquid substance play an important part at chemical transformations of amorphous compounds and chemical reaction rate provides an function of local order. When the amorphous polymer is viewed as an system of multiple transformations, each gives birth to the definite local order, the calculation of recombination reaction of active centers accumulated during irradiation of polymer at 77 K is carried out. Concentration of recombinated centers rises steeply near each transformation T k

Pollen source effects on growth of kernel structures and embryo chemical compounds in maize.

Science.gov (United States)

Tanaka, W; Mantese, A I; Maddonni, G A

2009-08-01

Previous studies have reported effects of pollen source on the oil concentration of maize (Zea mays) kernels through modifications to both the embryo/kernel ratio and embryo oil concentration. The present study expands upon previous analyses by addressing pollen source effects on the growth of kernel structures (i.e. pericarp, endosperm and embryo), allocation of embryo chemical constituents (i.e. oil, protein, starch and soluble sugars), and the anatomy and histology of the embryos. Maize kernels with different oil concentration were obtained from pollinations with two parental genotypes of contrasting oil concentration. The dynamics of the growth of kernel structures and allocation of embryo chemical constituents were analysed during the post-flowering period. Mature kernels were dissected to study the anatomy (embryonic axis and scutellum) and histology [cell number and cell size of the scutellums, presence of sub-cellular structures in scutellum tissue (starch granules, oil and protein bodies)] of the embryos. Plants of all crosses exhibited a similar kernel number and kernel weight. Pollen source modified neither the growth period of kernel structures, nor pericarp growth rate. By contrast, pollen source determined a trade-off between embryo and endosperm growth rates, which impacted on the embryo/kernel ratio of mature kernels. Modifications to the embryo size were mediated by scutellum cell number. Pollen source also affected (P embryo chemical compounds. Negative correlations among embryo oil concentration and those of starch (r = 0.98, P embryos with low oil concentration had an increased (P embryo/kernel ratio and allocation of embryo chemicals seems to be related to the early established sink strength (i.e. sink size and sink activity) of the embryos.

Layered Metal Hydroxides Containing Calcium and Their Structural Analysis

Energy Technology Data Exchange (ETDEWEB)

Kim, Tae Hyun; Heo, Il; Lee, Sung Han; Oh, Jae Min [College of Science and Technology, Yonsei University, Wonju (Korea, Republic of); Paek, Seung Min [Kyungpook National University, Daegu (Korea, Republic of); Park, Chung Berm; Choi, Ae Jin [National Institute of Horticultural and Herbal Science of R and D Eumseong (Korea, Republic of); Choy, Jin Ho [Ewha Womans University, Seoul (Korea, Republic of)

2012-06-15

Layered metal hydroxides (LMHs) containing calcium were synthesized by coprecipitation in solution having two different trivalent metal ions, iron and aluminum. Two mixed metal solutions (Ca{sup 2+}/Al{sup 3+} and Ca{sup 2+}/Fe{sup 3+} = 2/1) were added to sodium hydroxide solution and the final pH was adjusted to {approx}11.5 and {approx}13 for CaAl-and CaFe-LMHs. Powder X-ray diffraction (XRD) for the two LMH samples showed well developed (00l) diffractions indicating 2-dimensional crystal structure of the synthesized LMHs. Rietveld refinement of the X-ray diffraction pattern, the local structure analysis through X-ray absorption spectroscopy, and thermal analysis also confirmed that the synthesized precipitates show typical structure of LMHs. The chemical formulae, Ca{sub 2.04}Al{sub 1}(OH){sub 6}(NO{sub 3}){center_dot}5.25H{sub 2}O and Ca{sub 2.01}Fe{sub 1}(OH){sub 6}(NO{sub 3}){center_dot}4.75H{sub 2}O were determined by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). Particle morphology and thermal behavior for the synthesized LMHs were examined by field emission scanning electron microscopy and thermogravimetric differential scanning calorimetry

Chemical interaction of B4C, B, and C with Mo/Si layered structures

International Nuclear Information System (INIS)

Rooij-Lohmann, V. I. T. A. de; Veldhuizen, L. W.; Zoethout, E.; Yakshin, A. E.; Kruijs, R. W. E. van de; Thijsse, B. J.; Gorgoi, M.; Schaefers, F.; Bijkerk, F.

2010-01-01

To enhance the thermal stability, B 4 C diffusion barrier layers are often added to Mo/Si multilayer structures for extreme ultraviolet optics. Knowledge about the chemical interaction between B 4 C and Mo or Si, however is largely lacking. Therefore, the chemical processes during annealing up to 600 deg. C of a Mo/B 4 C/Si layered structure have been investigated in situ with hard x-ray photoelectron spectroscopy and ex situ with depth profiling x-ray photoelectron spectroscopy. Mo/B/Si and Mo/C/Si structures have also been analyzed as reference systems. The chemical processes in these systems have been identified, with two stages being distinguished. In the first stage, B and C diffuse and react predominantly with Mo. MoSi x forms in the second stage. If the diffusion barrier consists of C or B 4 C, a compound forms that is stable up to the maximum probed temperature and annealing time. We suggest that the diffusion barrier function of B 4 C interlayers as reported in literature can be caused by the stability of the formed compound, rather than by the stability of B 4 C itself.

Microscopic silicon-based lateral high-aspect-ratio structures for thin film conformality analysis

International Nuclear Information System (INIS)

Gao, Feng; Arpiainen, Sanna; Puurunen, Riikka L.

2015-01-01

Film conformality is one of the major drivers for the interest in atomic layer deposition (ALD) processes. This work presents new silicon-based microscopic lateral high-aspect-ratio (LHAR) test structures for the analysis of the conformality of thin films deposited by ALD and by other chemical vapor deposition means. The microscopic LHAR structures consist of a lateral cavity inside silicon with a roof supported by pillars. The cavity length (e.g., 20–5000 μm) and cavity height (e.g., 200–1000 nm) can be varied, giving aspect ratios of, e.g., 20:1 to 25 000:1. Film conformality can be analyzed with the microscopic LHAR by several means, as demonstrated for the ALD Al 2 O 3 and TiO 2 processes from Me 3 Al/H 2 O and TiCl 4 /H 2 O. The microscopic LHAR test structures introduced in this work expose a new parameter space for thin film conformality investigations expected to prove useful in the development, tuning and modeling of ALD and other chemical vapor deposition processes

Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics

NARCIS (Netherlands)

Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert; Dekker, Frans

Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain

Development of a Mechanical Analysis System Considering Chemical Transitions of Barrier Materials

International Nuclear Information System (INIS)

Sahara, F.; Murakami, T.; Ito, H.; Kobayashi, I.; Yokozeki, K.

2006-01-01

An analysis system for the long-term mechanical behavior of barrier materials (MACBECE: Mechanical Analysis system considering Chemical transitions of Bentonite-based and Cement-based materials) was developed in order to improve the reliability of the evaluation of the hydraulic field that is one of the important environmental conditions in the safety assessment of the TRU waste disposal in Japan. The MACBECE is a system that calculates the deformation of barrier materials using their chemical property changes as inputs, and subsequently their hydraulic conductivity taking both their chemical property changes and deformation into consideration. This paper provides a general description of MACBECE and the results of experimental analysis carried out using MACBECE. (authors)

Structural and optical properties of nano-structured CdS thin films prepared by chemical bath deposition

Energy Technology Data Exchange (ETDEWEB)

Bai, Rekha, E-mail: rekha.mittal07@gmail.com; Kumar, Dinesh; Chaudhary, Sujeet; Pandya, Dinesh K. [Thin Film Laboratory, Physics Department, Indian Institute of Technology Delhi, New Delhi-110016 (India)

2016-05-06

Cadmium sulfide (CdS) thin films have been deposited on conducting glass substrates by chemical bath deposition (CBD) technique. The effect of precursor concentration on the structural, morphological, compositional, and optical properties of the CdS films has been studied. Crystal structure of these CdS films is characterized by X-ray diffraction (XRD) and it reveals polycrystalline structure with mixture of cubic and wurtzite phases with grain size decreasing as precursor concentration is increased. Optical studies reveal that the CdS thin films have high transmittance in visible spectral region reaching 90% and the films possess direct optical band gap that decreases from 2.46 to 2.39 eV with decreasing bath concentration. Our study suggests that growth is nucleation controlled.

Structural and optical properties of nano-structured CdS thin films prepared by chemical bath deposition

International Nuclear Information System (INIS)

Bai, Rekha; Kumar, Dinesh; Chaudhary, Sujeet; Pandya, Dinesh K.

2016-01-01

Cadmium sulfide (CdS) thin films have been deposited on conducting glass substrates by chemical bath deposition (CBD) technique. The effect of precursor concentration on the structural, morphological, compositional, and optical properties of the CdS films has been studied. Crystal structure of these CdS films is characterized by X-ray diffraction (XRD) and it reveals polycrystalline structure with mixture of cubic and wurtzite phases with grain size decreasing as precursor concentration is increased. Optical studies reveal that the CdS thin films have high transmittance in visible spectral region reaching 90% and the films possess direct optical band gap that decreases from 2.46 to 2.39 eV with decreasing bath concentration. Our study suggests that growth is nucleation controlled.

Cheminformatics Analysis of EPA ToxCast Chemical Libraries ...

Science.gov (United States)

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 on a set of 320 compounds, mostly pesticide actives, that have well characterized in vivo toxicity. These 320 compounds (EPA-320 set evaluated in Phase I of ToxCast) are a subset of a much larger set of ~10,000 candidates that are of interest to the EPA (called here EPA-10K). Predictive models of in vivo toxicity are being constructed from the in vitro assay data on the EPA-320 chemical set. These models require validation on additional chemicals prior to wide acceptance, and this will be carried out by evaluating compounds from EPA-10K in Phase II of ToxCast. We have used cheminformatics approaches including clustering, data visualization, and QSAR to develop models for EPA-320 that could help prioritizing EPA-10K validation chemicals. Both chemical descriptors, as well as calculated physicochemical properties have been used. Compounds from EPA-10K are prioritized based on their similarity to EPA-320 using different similarity metrics, with similarity thresholds defining the domain of applicability for the predictive models built for EPA-320 set. In addition, prioritized lists of compounds of increasing dissimilarity from the EPA-320 have been produced, to test the ability of the EPA-320

Kinematics analysis on hinges of robot arm gripper for harmful chemical handling

Science.gov (United States)

Razali, Zol Bahri; Kader, Mohamed Mydin M. Abdul; Mustafa, Nurul Fahimah; Daud, Mohd Hisam

2017-09-01

The development of manufacturing industry is booming the application of industrial robot, and proportional to the use of robot arm. Some of the purpose of robot arm gripper is to sort things and place to the proper place. And some of the things are harmful to human, such as harmful chemical. By using robot arm to do picking and placing, it is expected to replace human tasks, as well as to reduce human from the harmful job. The problem of the robot arm gripper, most likely the problem of hinge, thus the analysis on the hinges of robot arm gripper to prevent claw is essential. By using robot arm, instead of human, is labored to do the harmful tasks and unexpected accident happen, costs and expenses in handling injured employee due to the harmful chemicals can be minimized. Thus the objective of this project is to make a kinematics analysis on the hinges of the robot arm gripper. Suitable material such as steel structure has also been selected for the construction of this hinges. This material has properties associated with compressive strength, fire resistance, corrosion and has a shape that is easy to move. Solid Works and ANSYS software is used to create animated movement on the design model and to detect deficiencies in the hinges. Detail methodology is described in this paper.

The Architecture of Chemical Alternatives Assessment.

Science.gov (United States)

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.

Quinones from plants of northeastern Brazil: structural diversity, chemical transformations, NMR data and biological activities.

Science.gov (United States)

Lemos, Telma L G; Monte, Francisco J Q; Santos, Allana Kellen L; Fonseca, Aluisio M; Santos, Hélcio S; Oliveira, Mailcar F; Costa, Sonia M O; Pessoa, Otilia D L; Braz-Filho, Raimundo

2007-05-20

The present review focus in quinones found in species of Brazilian northeastern Capraria biflora, Lippia sidoides, Lippia microphylla and Tabebuia serratifolia. The review cover ethnopharmacological aspects including photography of species, chemical structure feature, NMR datea and biological properties. Chemical transformations of lapachol to form enamine derivatives and biological activities are discussed.

Thai students' mental model of chemical bonding

Science.gov (United States)

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.

Anti-trypanosomal activities and structural chemical properties of selected compound classes.

Science.gov (United States)

Ponte-Sucre, Alicia; Bruhn, Heike; Schirmeister, Tanja; Cecil, Alexander; Albert, Christian R; Buechold, Christian; Tischer, Maximilian; Schlesinger, Susanne; Goebel, Tim; Fuß, Antje; Mathein, Daniela; Merget, Benjamin; Sotriffer, Christoph A; Stich, August; Krohne, Georg; Engstler, Markus; Bringmann, Gerhard; Holzgrabe, Ulrike

2015-02-01

Potent compounds do not necessarily make the best drugs in the market. Consequently, with the aim to describe tools that may be fundamental for refining the screening of candidates for animal and preclinical studies and further development, molecules of different structural classes synthesized within the frame of a broad screening platform were evaluated for their trypanocidal activities, cytotoxicities against murine macrophages J774.1 and selectivity indices, as well as for their ligand efficiencies and structural chemical properties. To advance into their modes of action, we also describe the morphological and ultrastructural changes exerted by selected members of each compound class on the parasite Trypanosoma brucei. Our data suggest that the potential organelles targeted are either the flagellar pocket (compound 77, N-Arylpyridinium salt; 15, amino acid derivative with piperazine moieties), the endoplasmic reticulum membrane systems (37, bisquaternary bisnaphthalimide; 77, N-Arylpyridinium salt; 68, piperidine derivative), or mitochondria and kinetoplasts (88, N-Arylpyridinium salt; 68, piperidine derivative). Amino acid derivatives with fumaric acid and piperazine moieties (4, 15) weakly inhibiting cysteine proteases seem to preferentially target acidic compartments. Our results suggest that ligand efficiency indices may be helpful to learn about the relationship between potency and chemical characteristics of the compounds. Interestingly, the correlations found between the physico-chemical parameters of the selected compounds and those of commercial molecules that target specific organelles indicate that our rationale might be helpful to drive compound design toward high activities and acceptable pharmacokinetic properties for all compound families.

Chemical and structural order in silicon oxynitrides by methods of surface physics

Science.gov (United States)

Finster, J.; Heeg, J.; Klinkenberg, E.-D.

A large number of thin amorphous layers of SiO xN y and several (crystalline) reference compounds (SiO 2, Si 3N 4, Si 2N 2O) are studied. Although XANES and SEXAFS are well sulted to derive structural and chemical order, for these compounds many problems remain to be solved. We show how core level spectra (XPS, AES) can be used to gain such information (e.g. random bonding structure, N coordination, oxidation behaviour).

Biophysical insight into structure-function relation of Allium sativum Protease Inhibitor by thermal, chemical and pH-induced modulation using comprehensive spectroscopic analysis.

Science.gov (United States)

Shamsi, Tooba Naz; Parveen, Romana; Naz, Huma; Haque, Md Anzarul; Fatima, Sadaf

2017-10-01

In this study, we have analyzed the structural and functional changes in the nature of Allium sativum Protease Inhibitor (ASPI) on undergoing various denaturation with variable range of pH, temperature and urea (at pH 8.2). ASPI being anti-tryptic in nature has native molecular mass of ∼15kDa. The conformational stability, functional parameters and their correlation were estimated under different conditions using circular dichroism, fluorescence and activity measurements. ASPI was found to fall in belongs to α+β protein. It demonstrated structural and functional stability in the pH range 5.0-12.0 and up to70°C temperature. Further decrease in pH and increase in temperature induces unfolding followed by aggregation. Chemical induced denaturation was found to be cooperative and transitions were reversible and sigmoid. T m (midpoint of denaturation), ΔC p (constant pressure heat capacity change) and ΔH m (van't Hoff enthalpy change at T m were calculated to be 41.25±0.2°C, 1.3±0.07kcalmol -1 K -1 and 61±2kcalmol -1 respectively for thermally denatured ASPI earlier. The reversibility of the protein was confirmed for both thermally and chemically denatured ASPI. The results obtained from trypsin inhibitory activity assay and structural studies are found to be in a significant correlation and hence established structure-function relationship of ASPI. Copyright © 2017 Elsevier B.V. All rights reserved.

Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

Science.gov (United States)

Otero, Toribio F

2017-01-18

In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

[Influence of surface chemical properties and pore structure characteristics of activated carbon on the adsorption of nitrobenzene from aqueous solution].

Science.gov (United States)

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).

Chemical Analysis of Cellular and Extracellular Carbohydrates of a Biofilm-Forming Strain Pseudomonas aeruginosa PA14

Science.gov (United States)

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

Analysis of Structural Units and Their Influence on Thermal Degradation of Alkali Lignins

Directory of Open Access Journals (Sweden)

Wen Hua

2016-01-01

Full Text Available The chemical structures of four alkali lignins isolated from poplar, fir, straw, and bagasse were investigated. To explore the relationship between the structural units and the thermal decomposition behavior, the system was tested by elemental analysis, Fourier transform infrared spectrometry, thermogravimetric analysis (TGA, and pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS. The results indicated that the carbon content of poplar lignin (PL was higher than that of others. Fir lignin (FL exhibited the highest guaiacol units, while the other three lignins were abundant in syringol units. The thermal decomposition characteristics and pyrolysis products of the four lignins were influenced by the material structural and composition. The DTG curves showed that the initial temperatures and major degradation temperatures of woody lignins（FL and PL） with complex inherent structures were shifted to the high temperature zoom compared with that of non-woody （BL and SL）lignins. Py-GC/MS analysis showed that guaiacol-type phenolic compounds were predominant pyrolysis products derived from the four lignins. The yield of guaiacol-type phenols could reach 82.87%. Moreover, the BL had selectively on phenol-type compounds with yield of 27.89%.

A Comprehensive Approach for Pectin Chemical and Functional Characterization

DEFF Research Database (Denmark)

de Sousa, António Felipe Gomes Teixeira

In this work, a comprehensive approach for the chemical and functional analysis of pectin was used in order to relate the different extraction conditions used to the polymer structure and the final functional (mainly gelling) properties. A wide range of methods were utilized including chemical an...

Modelling of structural effects on chemical reactions in turbulent flows

Energy Technology Data Exchange (ETDEWEB)

Gammelsaeter, H.R.

1997-12-31

Turbulence-chemistry interactions are analysed using algebraic moment closure for the chemical reaction term. The coupling between turbulence and chemical length and time scales generate a complex interaction process. This interaction process is called structural effects in this work. The structural effects are shown to take place on all scales between the largest scale of turbulence and the scales of the molecular motions. The set of equations describing turbulent correlations involved in turbulent reacting flows are derived. Interactions are shown schematically using interaction charts. Algebraic equations for the turbulent correlations in the reaction rate are given using the interaction charts to include the most significant couplings. In the frame of fundamental combustion physics, the structural effects appearing on the small scales of turbulence are proposed modelled using a discrete spectrum of turbulent scales. The well-known problem of averaging the Arrhenius law, the specific reaction rate, is proposed solved using a presumed single variable probability density function and a sub scale model for the reaction volume. Although some uncertainties are expected, the principles are addressed. Fast chemistry modelling is shown to be consistent in the frame of algebraic moment closure when the turbulence-chemistry interaction is accounted for in the turbulent diffusion. The modelling proposed in this thesis is compared with experimental data for an laboratory methane flame and advanced probability density function modelling. The results show promising features. Finally it is shown a comparison with full scale measurements for an industrial burner. All features of the burner are captured with the model. 41 refs., 33 figs.

The collection and field chemical analysis of water samples

International Nuclear Information System (INIS)

Korte, N.E.; Ealey, D.T.; Hollenbach, M.H.

1984-01-01

A successful water sampling program requires a clear understanding of appropriate measurement and sampling procedures in order to obtain reliable field data and representative samples. It is imperative that the personnel involved have a thorough knowledge of the limitations of the techniques being used. Though this seems self-evident, many sampling and field-chemical-analysis programs are still not properly conducted. Recognizing these problems, the Department of Energy contracted with Bendix Field Engineering Corporation through the Technical Measurements Center to develop and select procedures for water sampling and field chemical analysis at waste sites. The fundamental causese of poor field programs are addressed in this paper, largely through discussion of specific field-measurement techniques and their limitations. Recommendations for improvement, including quality-assurance measures, are also presented

Chemical analysis quality assurance at the ICPP

International Nuclear Information System (INIS)

Hand, R.L.

1990-01-01

This document discusses the chemical analysis quality assurance program at the ICPP which involves records management, analytical methods quality control, analysis procedures and training and qualification. Since 1979, the major portion of the quality assurance program has been implemented on a central analytical computer system. The individual features provided by the system are storage, retrieval, and search capabilities over all general request and sample analysis information, automatic method selection for all process streams, automation of all method calculations, automatic assignment of bias and precision estimates at all analysis levels, with-method-use requalification, untrained or unqualified analyst method lockout, statistical testing of all process stream results for replicate agreement, automatic testing of process results against pre- established operating, safety, or failure limits at varying confidence levels, and automatic transfer and report of all analysis data plus all statistical testing to the Production Department

Synchrotron x-ray fluorescence and extended x-ray absorption fine structure analysis

International Nuclear Information System (INIS)

Chen, J.R.; Gordon, B.M.; Hanson, A.L.; Jones, K.W.; Kraner, H.W.; Chao, E.C.T.; Minkin, J.A.

1984-01-01

The advent of dedicated synchrotron radiation sources has led to a significant increase in activity in many areas of science dealing with the interaction of x-rays with matter. Synchrotron radiation provides intense, linearly polarized, naturally collimated, continuously tunable photon beams, which are used to determine not only the elemental composition of a complex, polyatomic, dilute material but also the chemical form of the elements with improved accuracy. Examples of the application of synchrotron radiation include experiments in synchrotron x-ray fluorescence (SXRF) analysis and extended x-ray absorption fine structure (EXAFS) analysis. New synchrotron radiation x-ray microprobes for elemental analysis in the parts per billion range are under construction at several laboratories. 76 references, 24 figures

Fatty acid composition and its association with chemical and sensory analysis of boar taint.

Science.gov (United States)

Liu, Xiaoye; Trautmann, Johanna; Wigger, Ruth; Zhou, Guanghong; Mörlein, Daniel

2017-09-15

A certain level of disagreement between the chemical analysis of androstenone and skatole and the human perception of boar taint has been found in many studies. Here we analyze whether the fatty acid composition can explain such inconsistency between sensory evaluation and chemical analysis of boar taint compounds. Therefore, back fat samples (n=143) were selected according to their sensory evaluation by a 10-person sensory panel, and the chemical analysis (stable isotope dilution analysis with headspace solid-phase microextraction and gas chromatography-mass spectrometry) of androstenone and skatole. Subsequently a quantification of fatty acids using gas chromatography-flame ionization detection was conducted. The correlation analyses revealed that several fatty acids are significantly correlated with androstenone, skatole, and the sensory rating. However, multivariate analyses (principal component analysis) revealed no explanation of the fatty acid composition with respect to the (dis-)agreement between sensory and chemical analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors

Science.gov (United States)

Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.

2008-06-01

A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

Evaluation of the influence of fluoroquinolone chemical structure on stability: forced degradation and in silico studies

Directory of Open Access Journals (Sweden)

André Valle de Bairros

2018-05-01

Full Text Available ABSTRACT Fluoroquinolones are a known antibacterial class commonly used around the world. These compounds present relative stability and they may show some adverse effects according their distinct chemical structures. The chemical hydrolysis of five fluoroquinolones was studied using alkaline and photolytic degradation aiming to observe the differences in molecular reactivity. DFT/B3LYP-6.31G* was used to assist with understanding the chemical structure degradation. Gemifloxacin underwent degradation in alkaline medium. Gemifloxacin and danofloxacin showed more degradation perceptual indices in comparison with ciprofloxacin, enrofloxacin and norfloxacin in photolytic conditions. Some structural features were observed which may influence degradation, such as the presence of five member rings attached to the quinolone ring and the electrostatic positive charges, showed in maps of potential electrostatic charges. These measurements may be used in the design of effective and more stable fluoroquinolones as well as the investigation of degradation products from stress stability assays.

Structural and Chemical Analysis of Gadolinium Halides Encapsulated within WS 2 Nanotubes

KAUST Repository

Anumol, E A

2016-05-18

The hollow cavities of nanotubes could serve as templates for the growth of size- and shape-confined functional nanostructures, giving rise to novel materials and properties. In this work, considering their potential application as MRI contrast agents, gadolinium halides are encapsulated within the hollow cavities of inorganic nanotubes of WS2 by capillary filling to obtain GdX3@WS2 nanotubes (where X = Cl, Br or I and @ means encapsulated in). Aberration corrected scanning/transmission electron microscopy (S/TEM) and spectroscopy is employed to understand the morphology and composition of the GdI3@WS2 nanotubes. The three dimensional morphology is studied with STEM tomography but understanding the compositional information is a non-trivial matter due to the presence of multiple high atomic number elements. Therefore, energy dispersive X-ray spectroscopy (EDS) tomography was employed revealing the three dimensional chemical composition. Molecular dynamics simulations of the filling procedure shed light into the mechanics behind the formation of the confined gadolinium halide crystals. The quasi-1D system employed here serves as an example of a TEM-based chemical nanotomography method that could be extended to other materials, including beam-sensitive soft materials.

Structural and Chemical Analysis of Gadolinium Halides Encapsulated within WS 2 Nanotubes

KAUST Repository

Anumol, E A; Enyashin, Andrey; Batra, Nitin M; Da Costa, Pedro M. F. J.; Francis, Leonard Deepak

2016-01-01

The hollow cavities of nanotubes could serve as templates for the growth of size- and shape-confined functional nanostructures, giving rise to novel materials and properties. In this work, considering their potential application as MRI contrast agents, gadolinium halides are encapsulated within the hollow cavities of inorganic nanotubes of WS2 by capillary filling to obtain GdX3@WS2 nanotubes (where X = Cl, Br or I and @ means encapsulated in). Aberration corrected scanning/transmission electron microscopy (S/TEM) and spectroscopy is employed to understand the morphology and composition of the GdI3@WS2 nanotubes. The three dimensional morphology is studied with STEM tomography but understanding the compositional information is a non-trivial matter due to the presence of multiple high atomic number elements. Therefore, energy dispersive X-ray spectroscopy (EDS) tomography was employed revealing the three dimensional chemical composition. Molecular dynamics simulations of the filling procedure shed light into the mechanics behind the formation of the confined gadolinium halide crystals. The quasi-1D system employed here serves as an example of a TEM-based chemical nanotomography method that could be extended to other materials, including beam-sensitive soft materials.

Analysis of the structural quality of the CASD-NMR 2013 entries

Energy Technology Data Exchange (ETDEWEB)

Ragan, Timothy J.; Fogh, Rasmus H. [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom); Tejero, Roberto [Universidad de Valencia, Departamento de Química Física (Spain); Vranken, Wim [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Montelione, Gaetano T. [Rutgers, The State University of New Jersey, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium (United States); Rosato, Antonio [University of Florence, Magnetic Resonance Center, Department of Chemistry (Italy); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom)

2015-08-15

We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and quality to those generated by a skilled researcher, at least for small, single domain proteins such as the ten targets tested. The most robust results appear to be obtained when NOESY peak lists are used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from the same data showed a surprisingly low degree of overlap. Additionally, we found that there was no significant correlation between the extent of the NOE restraint overlap and the accuracy of the structure. This result was surprising given the importance of NOE data in producing good quality structures. We suggest that this could be explained by the information redundancy present in NOEs between atoms contained within a fixed covalent network.

Chemical synthesis, 3D structure, and ASIC binding site of the toxin mambalgin-2.

Science.gov (United States)

Schroeder, Christina I; Rash, Lachlan D; Vila-Farrés, Xavier; Rosengren, K Johan; Mobli, Mehdi; King, Glenn F; Alewood, Paul F; Craik, David J; Durek, Thomas

2014-01-20

Mambalgins are a novel class of snake venom components that exert potent analgesic effects mediated through the inhibition of acid-sensing ion channels (ASICs). The 57-residue polypeptide mambalgin-2 (Ma-2) was synthesized by using a combination of solid-phase peptide synthesis and native chemical ligation. The structure of the synthetic toxin, determined using homonuclear NMR, revealed an unusual three-finger toxin fold reminiscent of functionally unrelated snake toxins. Electrophysiological analysis of Ma-2 on wild-type and mutant ASIC1a receptors allowed us to identify α-helix 5, which borders on the functionally critical acidic pocket of the channel, as a major part of the Ma-2 binding site. This region is also crucial for the interaction of ASIC1a with the spider toxin PcTx1, thus suggesting that the binding sites for these toxins substantially overlap. This work lays the foundation for structure-activity relationship (SAR) studies and further development of this promising analgesic peptide. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Physical and chemical processes for the generation of 1-μm-structures

International Nuclear Information System (INIS)

Mader, L.

1979-01-01

The following processes for the realization of fine structures in isolator and metal layers on silicon wafers have been studied: Wet chemical etching of silicon dioxide and aluminum layers; plasma etching of polysilicon layers; ion beam etching of silicon dioxide and polysilicon layers, lift-off technique for metal pattern generation. Test structures and functioning integrated circuits (memory cells, CCDs) with minimum dimensions of 1.5 μm were realized using these methods of pattern generation. (orig.) 891 ORU/orig. 892 MB [de

Plant Sterols: Chemical and Enzymatic Structural Modifications and Effects on Their Cholesterol-Lowering Activity.

Science.gov (United States)

He, Wen-Sen; Zhu, Hanyue; Chen, Zhen-Yu

2018-03-28

Plant sterols have attracted increasing attention due to their excellent cholesterol-lowering activity. However, free plant sterols have some characteristics of low oil solubility, water insolubility, high melting point, and low bioavailability, which greatly limit their application in foods. Numerous studies have been undertaken to modify their chemical structures to improve their chemical and physical properties in meeting the needs of various applications. The present review is to summarize the literature and update the progress on structural modifications of plant sterols in the following aspects: (i) synthesis of plant sterol esters by esterification and transesterification with hydrophobic fatty acids and triacylglycerols to improve their oil solubility, (ii) synthesis of plant sterol derivatives by coupling with various hydrophilic moieties to enhance their water solubility, and (iii) mechanisms by which plant sterols reduce plasma cholesterol and the effect of structural modifications on plasma cholesterol-lowering activity of plant sterols.

ANALYSIS OF DEPENDENCE OF THE FLOW TEMPERATURE OF THE PLASTICIZED POLYMER ON THE CHEMICAL STRUCTURE AND CONCENTRATION OF THE POLYMER AND THE PLASTICIZER

Directory of Open Access Journals (Sweden)

Askadskiy Andrey Aleksandrovich

2012-10-01

Full Text Available Polymeric materials are widely used in construction. The properties of polymeric construction materials vary to a substantial extent; their durability, thermal stability, frost resistance, waterproof and dielectric properties are particularly pronounced. Their properties serve as the drivers of the high market demand for these products. These materials are applied as finishing materials, molded sanitary engineering products and effective thermal insulation and water proofing materials. The authors analyze the influence of the chemical structure and structural features of polymers on their properties. The authors consider flow and vitrification temperatures of polymers. These temperatures determine the parameters of polymeric products, including those important for the construction process. The analysis of influence of concentration of the plasticizer on the vitrification temperature is based on the two basic theories. In accordance with the first one, reduction of the vitrification temperature is proportionate to the molar fraction of the injected plasticizer. According to the second concept, reduction of the vitrification temperature is proportionate to the volume fraction of the injected solvent. Dependencies of the flow temperature on the molecular weight and the molar fraction of the plasticizer are derived for PVC. As an example, two plasticizers were considered, including dibutyl sebacate and dioctylftalatalate. The basic parameters of all mixtures were calculated through the employment of "Cascade" software programme (A.N. Nesmeyanov Institute of Organoelemental Connections, Russian Academy of Sciences.

Endocrine-disrupting Chemicals: Review of Toxicological Mechanisms Using Molecular Pathway Analysis

Science.gov (United States)

Yang, Oneyeol; Kim, Hye Lim; Weon, Jong-Il; Seo, Young Rok

2015-01-01

Endocrine disruptors are known to cause harmful effects to human through various exposure routes. These chemicals mainly appear to interfere with the endocrine or hormone systems. As importantly, numerous studies have demonstrated that the accumulation of endocrine disruptors can induce fatal disorders including obesity and cancer. Using diverse biological tools, the potential molecular mechanisms related with these diseases by exposure of endocrine disruptors. Recently, pathway analysis, a bioinformatics tool, is being widely used to predict the potential mechanism or biological network of certain chemicals. In this review, we initially summarize the major molecular mechanisms involved in the induction of the above mentioned diseases by endocrine disruptors. Additionally, we provide the potential markers and signaling mechanisms discovered via pathway analysis under exposure to representative endocrine disruptors, bisphenol, diethylhexylphthalate, and nonylphenol. The review emphasizes the importance of pathway analysis using bioinformatics to finding the specific mechanisms of toxic chemicals, including endocrine disruptors. PMID:25853100

Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations

Science.gov (United States)

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.

Chemical analysis as production guide

International Nuclear Information System (INIS)

Bouzigues, H.; Fontaine, A.; Patigny, P.

1975-01-01

All piloting data of chemical processing plants are based on the results of analysis. The first part of this article describes a system of analysers adapted to the needs of the Pierrelatte plant, with management of signals collected by the factory computer. Part two shows the influence of analytical development in the establishment of material balance sheets for the Marcoule spent fuel processing plant. Part three stresses the contribution of the automation of analytical test processes at the La Hague spent fuel processing plant. In all three cases the progress in analytical methods greatly improves the safety, reliability and response time of the various operations [fr

Chemical and structural properties of polymorphous silicon thin films grown from dichlorosilane

Energy Technology Data Exchange (ETDEWEB)

Álvarez-Macías, C.; Monroy, B.M.; Huerta, L.; Canseco-Martínez, M.A. [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, A.P. 70-360, Coyoacán, C.P. 04510 México, D.F. (Mexico); Picquart, M. [Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, A.P. 55-534, 09340 México, D.F. (Mexico); Santoyo-Salazar, J. [Departamento de Física, CINVESTAV-IPN, A.P. 14-740, C.P. 07000 México, D.F. (Mexico); Sánchez, M.F. García [Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional, Av. I.P.N. 2580, Gustavo A. Madero, 07340 México .D.F. (Mexico); Santana, G., E-mail: gsantana@iim.unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, A.P. 70-360, Coyoacán, C.P. 04510 México, D.F. (Mexico)

2013-11-15

We have examined the effects of hydrogen dilution (R{sub H}) and deposition pressure on the morphological, structural and chemical properties of polymorphous silicon thin films (pm-Si:H), using dichlorosilane as silicon precursor in the plasma enhanced chemical vapor deposition (PECVD) process. The use of silicon chlorinated precursors enhances the crystallization process in as grown pm-Si:H samples, obtaining crystalline fractions from Raman spectra in the range of 65–95%. Atomic Force Microscopy results show the morphological differences obtained when the chlorine chemistry dominates the growth process and when the plasma–surface interactions become more prominent. Augmenting R{sub H} causes a considerable reduction in both roughness and topography, demonstrating an enhancement of ion bombardment and attack of the growing surface. X-ray Photoelectron Spectroscopy results show that, after ambient exposure, there is low concentration of oxygen inside the films grown at low R{sub H}, present in the form of Si-O, which can be considered as structural defects. Instead, oxidation increases with deposition pressure and dilution, along with film porosity, generating a secondary SiO{sub x} phase. For higher pressure and dilution, the amount of chlorine incorporated to the film decreases congruently with HCl chlorine extraction processes involving atomic hydrogen interactions with the surface. In all cases, weak silicon hydride (Si-H) bonds were not detected by infrared spectroscopy, while bonding configurations associated to the silicon nanocrystal surface were clearly observed. Since these films are generally used in photovoltaic devices, analyzing their chemical and structural properties such as oxygen incorporation to the films, along with chlorine and hydrogen, is fundamental in order to understand and optimize their electrical and optical properties.

SWOT analysis for safer carriage of bulk liquid chemicals in tankers.

Science.gov (United States)

Arslan, Ozcan; Er, Ismail Deha

2008-06-15

The application of strengths, weaknesses, opportunities and threats (SWOT) analysis to formulation of strategy concerned with the safe carriage of bulk liquid chemicals in maritime tankers was examined in this study. A qualitative investigation using SWOT analysis has been implemented successfully for ships that are designed to carry liquid chemicals in bulk. The originality of this study lies in the use of SWOT analysis as a management tool to formulate strategic action plans for ship management companies, ship masters and officers for the carriage of dangerous goods in bulk. With this transportation-based SWOT analysis, efforts were made to explore the ways and means of converting possible threats into opportunities, and changing weaknesses into strengths; and strategic plans of action were developed for safer tanker operation.

[Relativity of commercial specification of Menthae Herba based on chemical analysis].

Science.gov (United States)

Ye, Dan; Zhao, Ming; Shao, Yang; Ouyang, Zhen; Peng, Hua-sheng; Han Bang-xing; Zhang, Wei-wan-qi; Gu, Xue-mei

2015-01-01

In order to compare the differences of 35 Menthae Herba samples collected on the market and at producing areas, the contents of six total terpenoids, the essential oil and chromatographic fingerprints were analyzed, which provided evidences for drawing up the commodity specifications and grading criteria of Menthae Herba. GC-MS method was used to analyze the chemical constituents of 35 different samples. The chromatographic fingerprints obtained by using GC were then evaluated by similarity analysis, hierarchical clustering analysis and principal component analysis. The relativity between the content of six terpenoids and the essential oil were studied. In this study, the chemical profiles of 35 samples from different producing areas had significant disparity. All samples collected in the report could be categorized into four chemical types, L-menthol, pulegone, carvone and L-menthone, but the chemical profiles had no relationship with the areas. The chromatographic fingerprints of the samples from different types were dissimilar, while the different producing areas were difficult to be separated. It was indicated that the content of volatile oil was positively correlated with the content of L-menthol and the sum of six total terpenoids. The content of the essential oil, L-menthol and the sum of six total terpenoids of Menthae Herba were considered as one of the commercial specifications and grading criteria. These results in the research could be helpful to draw up the commercial specification and grading criteria of Menthae Herba from a view of chemical information.

Double-Layer Structured CO2 Adsorbent Functionalized with Modified Polyethyleneimine for High Physical and Chemical Stability.

Science.gov (United States)

Jeon, Sunbin; Jung, Hyunchul; Kim, Sung Hyun; Lee, Ki Bong

2018-06-18

CO 2 capture using polyethyleneimine (PEI)-impregnated silica adsorbents has been receiving a lot of attention. However, the absence of physical stability (evaporation and leaching of amine) and chemical stability (urea formation) of the PEI-impregnated silica adsorbent has been generally established. Therefore, in this study, a double-layer impregnated structure, developed using modified PEI, is newly proposed to enhance the physical and chemical stabilities of the adsorbent. Epoxy-modified PEI and diepoxide-cross-linked PEI were impregnated via a dry impregnation method in the first and second layers, respectively. The physical stability of the double-layer structured adsorbent was noticeably enhanced when compared to the conventional adsorbents with a single layer. In addition to the enhanced physical stability, the result of simulated temperature swing adsorption cycles revealed that the double-layer structured adsorbent presented a high potential working capacity (3.5 mmol/g) and less urea formation under CO 2 -rich regeneration conditions. The enhanced physical and chemical stabilities as well as the high CO 2 working capacity of the double-layer structured adsorbent were mainly attributed to the second layer consisting of diepoxide-cross-linked PEI.

Structural characterization of chemically deposited PbS thin films

International Nuclear Information System (INIS)

Fernandez-Lima, F.A.; Gonzalez-Alfaro, Y.; Larramendi, E.M.; Fonseca Filho, H.D.; Maia da Costa, M.E.H.; Freire, F.L.; Prioli, R.; Avillez, R.R. de; Silveira, E.F. da; Calzadilla, O.; Melo, O. de; Pedrero, E.; Hernandez, E.

2007-01-01

Polycrystalline thin films of lead sulfide (PbS) grown using substrate colloidal coating chemical bath depositions were characterized by RBS, XPS, AFM and GIXRD techniques. The films were grown on glass substrates previously coated with PbS colloidal particles in a polyvinyl alcohol solution. The PbS films obtained with the inclusion of the polymer showed non-oxygen-containing organic contamination. All samples maintained the Pb:S 1:1 stoichiometry throughout the film. The amount of effective nucleation centers and the mean grain size have being controlled by the substrate colloidal coating. The analysis of the polycrystalline PbS films showed that a preferable (1 0 0) lattice plane orientation parallel to the substrate surface can be obtained using a substrate colloidal coating chemical bath deposition, and the orientation increases when a layer of colloid is initially dried on the substrate

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Comparative analysis of pharmaceuticals versus industrial chemicals acute aquatic toxicity classification according to the United Nations classification system for chemicals. Assessment of the (Q)SAR predictability of pharmaceuticals acute aquatic toxicity and their predominant acute toxic mode-of-action

DEFF Research Database (Denmark)

Sanderson, Hans; Thomsen, Marianne

2009-01-01

data. Pharmaceuticals were found to be more frequent than industrial chemicals in GHS category III. Acute toxicity was predictable (>92%) using a generic (Q)SAR ((Quantitative) Structure Activity Relationship) suggesting a narcotic MOA. Analysis of model prediction error suggests that 68...

THE CHEMICAL EVOLUTION OF THE MONOCEROS RING/GALACTIC ANTICENTER STELLAR STRUCTURE

International Nuclear Information System (INIS)

Chou Meiyin; Majewski, Steven R.; Patterson, Richard J.; Cunha, Katia; Smith, Verne V.; MartInez-Delgado, David

2010-01-01

The origin of the Galactic Anticenter Stellar Structure (GASS) or 'Monoceros Ring' - a low-latitude overdensity at the edge of the Galactic disk spanning at least the second and third Galactic quadrants-remains controversial. Models for the origin of GASS generally fall into scenarios where either it is a part (e.g., warp) of the Galactic disk or it represents tidal debris from the disruption of a Milky Way (MW) satellite galaxy. To further constrain models for the origin of GASS, we derive chemical abundance patterns from high-resolution spectra for 21 M giants spatially and kinematically identified with it. The abundances of the (mostly) α-element, titanium, and s-process elements, yttrium and lanthanum, for these GASS stars are found to be lower at the same [Fe/H] than those for MW stars, but similar to those of stars in the Sagittarius stream, other dwarf spheroidal galaxies, and the Large Magellanic Cloud. This demonstrates that GASS stars have a chemical enrichment history typical of dwarf galaxies-and unlike those of typical MW stars (at least MW stars near the Sun). Nevertheless, these abundance results cannot definitively rule out the possibility that GASS was dynamically created out of a previously formed, outer MW disk because ΛCDM-based structure formation models show that galactic disks grow outward by accretion of dwarf galaxies. On the other hand, the chemical patterns seen in GASS stars do provide striking verification that accretion of dwarf galaxies has indeed happened at the edge of the MW disk.

Computational singular perturbation analysis of stochastic chemical systems with stiffness

Science.gov (United States)

Wang, Lijin; Han, Xiaoying; Cao, Yanzhao; Najm, Habib N.

2017-04-01

Computational singular perturbation (CSP) is a useful method for analysis, reduction, and time integration of stiff ordinary differential equation systems. It has found dominant utility, in particular, in chemical reaction systems with a large range of time scales at continuum and deterministic level. On the other hand, CSP is not directly applicable to chemical reaction systems at micro or meso-scale, where stochasticity plays an non-negligible role and thus has to be taken into account. In this work we develop a novel stochastic computational singular perturbation (SCSP) analysis and time integration framework, and associated algorithm, that can be used to not only construct accurately and efficiently the numerical solutions to stiff stochastic chemical reaction systems, but also analyze the dynamics of the reduced stochastic reaction systems. The algorithm is illustrated by an application to a benchmark stochastic differential equation model, and numerical experiments are carried out to demonstrate the effectiveness of the construction.

Analysis of chemical constituents in medicinal plants of selected ...

African Journals Online (AJOL)

Analysis of chemical constituents in medicinal plants of selected districts of Pakhtoonkhwa, Pakistan. I Hussain, R Ullah, J Khan, N Khan, M Zahoor, N Ullah, MuR Khattak, FA Khan, A Baseer, M Khurram ...

Probabilistic Structural Analysis Program

Science.gov (United States)

Pai, Shantaram S.; Chamis, Christos C.; Murthy, Pappu L. N.; Stefko, George L.; Riha, David S.; Thacker, Ben H.; Nagpal, Vinod K.; Mital, Subodh K.

2010-01-01

NASA/NESSUS 6.2c is a general-purpose, probabilistic analysis program that computes probability of failure and probabilistic sensitivity measures of engineered systems. Because NASA/NESSUS uses highly computationally efficient and accurate analysis techniques, probabilistic solutions can be obtained even for extremely large and complex models. Once the probabilistic response is quantified, the results can be used to support risk-informed decisions regarding reliability for safety-critical and one-of-a-kind systems, as well as for maintaining a level of quality while reducing manufacturing costs for larger-quantity products. NASA/NESSUS has been successfully applied to a diverse range of problems in aerospace, gas turbine engines, biomechanics, pipelines, defense, weaponry, and infrastructure. This program combines state-of-the-art probabilistic algorithms with general-purpose structural analysis and lifting methods to compute the probabilistic response and reliability of engineered structures. Uncertainties in load, material properties, geometry, boundary conditions, and initial conditions can be simulated. The structural analysis methods include non-linear finite-element methods, heat-transfer analysis, polymer/ceramic matrix composite analysis, monolithic (conventional metallic) materials life-prediction methodologies, boundary element methods, and user-written subroutines. Several probabilistic algorithms are available such as the advanced mean value method and the adaptive importance sampling method. NASA/NESSUS 6.2c is structured in a modular format with 15 elements.

Three-dimensionality of space in the structure of the periodic table of chemical elements

International Nuclear Information System (INIS)

Veremeichik, T. F.

2006-01-01

The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the number of stable systems of electrons at different levels of the periodic table of chemical elements and some characteristics of the systems. The conditions for the stability of systems of electrons and the electron system of an atom as a whole are considered. On the basis of the results obtained, comparison with other hierarchical systems (nanostructures and biological structures) is performed

Nanostructured PLD-grown gadolinia doped ceria: Chemical and structural characterization by transmission electron microscopy techniques

DEFF Research Database (Denmark)

Rodrigo, Katarzyna Agnieszka; Wang, Hsiang-Jen; Heiroth, Sebastian

2011-01-01

The morphology as well as the spatially resolved elemental and chemical characterization of 10 mol% gadolinia doped ceria (CGO10) structures prepared by pulsed laser deposition (PLD) technique are investigated by scanning transmission electron microscopy accompanied with electron energy loss spec......, indicate apparent variation of the ceria valence state across and along the film. No element segregation to the grain boundaries is detected. These results are discussed in the context of solid oxide fuel cell applications.......The morphology as well as the spatially resolved elemental and chemical characterization of 10 mol% gadolinia doped ceria (CGO10) structures prepared by pulsed laser deposition (PLD) technique are investigated by scanning transmission electron microscopy accompanied with electron energy loss...... spectroscopy and energy dispersive X-ray spectroscopy. A dense, columnar and structurally inhomogeneous CGO10 film, i.e. exhibiting grain size refinement across the film thickness, is obtained in the deposition process. The cerium M4,5 edges, used to monitor the local electronic structure of the grains...

The Virtual Product-Process Design Laboratory for Structured Chemical Product Design and Analysis

DEFF Research Database (Denmark)

Mattei, Michele; Yunus, Nor Alafiza Binti; Kalakul, Sawitree

2014-01-01

The objective of this paper is to present new methods for design of chemicals based formulated products and their implementation in the software, the Virtual Product-Process Design Laboratory. The new products are tailor-made blended liquid products and emulsion-based products. The new software...

Collapse Analysis of Timber Structures

DEFF Research Database (Denmark)

Kirkegaard, Poul Henning; Sørensen, John Dalsgaard

2008-01-01

of Structures and a probabilistic modelling of the timber material proposed in the Probabilistic Model Code (PMC) of the Joint Committee on Structural Safety (JCSS). Due to the framework in the Danish Code the timber structure has to be evaluated with respect to the following criteria where at least one shall...... to criteria a) and b) the timber frame structure has one column with a reliability index a bit lower than an assumed target level. By removal three columns one by one no significant extensive failure of the entire structure or significant parts of it are obtained. Therefore the structure can be considered......A probabilistic based collapse analysis has been performed for a glulam frame structure supporting the roof over the main court in a Norwegian sports centre. The robustness analysis is based on the framework for robustness analysis introduced in the Danish Code of Practice for the Safety...

On the thermal phase structure of QCD at vanishing chemical potentials

CERN Document Server

Kabana, S

2011-01-01

The hypothesis is investigated, that the thermal structure of QCD phases at and near zero chemical potentials is determined by long range coherence, inducing the gauge boson pair condensate. The latter reflects the dynamical nature of gauge boson Bogoliubov transformations at the origin of localization of all color fields inside hadrons at low temperature in contrast to loss of such localization above a unique critical temperature.

Chemical Analysis of Plants that Poison Livestock: Successes, Challenges, and Opportunities.

Science.gov (United States)

Welch, Kevin D; Lee, Stephen T; Cook, Daniel; Gardner, Dale R; Pfister, James A

2018-04-04

Poisonous plants have a devastating impact on the livestock industry as well as human health. To fully understand the effects of poisonous plants, multiple scientific disciplines are required. Chemical analysis of plant secondary compounds is key to identifying the responsible toxins, characterizing their metabolism, and understanding their effects on animals and humans. In this review, we highlight some of the successes in studying poisonous plants and mitigating their toxic effects. We also highlight some of the remaining challenges and opportunities with regards to the chemical analysis of poisonous plants.

Physico-chemical analysis and sensory evaluation of bread ...

African Journals Online (AJOL)

This study carried out the physico-chemical analysis and sensory evaluation of bread produced using different indigenous yeast isolates in order to offer an insight into the overall quality of the bread. Four (4) different yeast species were isolated from sweet orange, pineapple and palm wine. The yeasts were characterized ...

Modeling the binding affinity of structurally diverse industrial chemicals to carbon using the artificial intelligence approaches.

Science.gov (United States)

Gupta, Shikha; Basant, Nikita; Rai, Premanjali; Singh, Kunwar P

2015-11-01

Binding affinity of chemical to carbon is an important characteristic as it finds vast industrial applications. Experimental determination of the adsorption capacity of diverse chemicals onto carbon is both time and resource intensive, and development of computational approaches has widely been advocated. In this study, artificial intelligence (AI)-based ten different qualitative and quantitative structure-property relationship (QSPR) models (MLPN, RBFN, PNN/GRNN, CCN, SVM, GEP, GMDH, SDT, DTF, DTB) were established for the prediction of the adsorption capacity of structurally diverse chemicals to activated carbon following the OECD guidelines. Structural diversity of the chemicals and nonlinear dependence in the data were evaluated using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation procedures performed employing a wide series of statistical checks. In complete dataset, the qualitative models rendered classification accuracies between 97.04 and 99.93%, while the quantitative models yielded correlation (R(2)) values of 0.877-0.977 between the measured and the predicted endpoint values. The quantitative prediction accuracies for the higher molecular weight (MW) compounds (class 4) were relatively better than those for the low MW compounds. Both in the qualitative and quantitative models, the Polarizability was the most influential descriptor. Structural alerts responsible for the extreme adsorption behavior of the compounds were identified. Higher number of carbon and presence of higher halogens in a molecule rendered higher binding affinity. Proposed QSPR models performed well and outperformed the previous reports. A relatively better performance of the ensemble learning models (DTF, DTB) may be attributed to the strengths of the bagging and boosting algorithms which enhance the predictive accuracies. The

Dynamic analysis program for frame structure

International Nuclear Information System (INIS)

Ando, Kozo; Chiba, Toshio

1975-01-01

A general purpose computer program named ISTRAN/FD (Isub(HI) STRucture ANalysis/Frame structure, Dynamic analysis) has been developed for dynamic analysis of three-dimensional frame structures. This program has functions of free vibration analysis, seismic response analysis, graphic display by plotter and CRT, etc. This paper introduces ISTRAN/FD; examples of its application are shown with various problems : idealization of the cantilever, dynamic analysis of the main tower of the suspension bridge, three-dimensional vibration in the plate girder bridge, seismic response in the boiler steel structure, and dynamic properties of the underground LNG tank. In this last example, solid elements, in addition to beam elements, are especially used for the analysis. (auth.)

High-Temperature Structural Analysis Model of the Process Heat Exchanger for Helium Gas Loop (II)

International Nuclear Information System (INIS)

Song, Kee Nam; Lee, Heong Yeon; Kim, Chan Soo; Hong, Seong Duk; Park, Hong Yoon

2010-01-01

PHE (Process Heat Exchanger) is a key component required to transfer heat energy of 950 .deg. C generated in a VHTR (Very High Temperature Reactor) to the chemical reaction that yields a large quantity of hydrogen. Korea Atomic Energy Research Institute established the helium gas loop for the performance test of components, which are used in the VHTR, and they manufactured a PHE prototype to be tested in the loop. In this study, as part of the high temperature structural-integrity evaluation of the PHE prototype, which is scheduled to be tested in the helium gas loop, we carried out high-temperature structural-analysis modeling, thermal analysis, and thermal expansion analysis of the PHE prototype. The results obtained in this study will be used to design the performance test setup for the PHE prototype

Analysis of Pumphouse RCC Frame Structure for Soil Structure Interaction

OpenAIRE

Mr A.S. Thombare; Prof. V.P. Kumbhar; Prof. A.H. Kumbhar

2016-01-01

When structure is built on ground some elements of structure are direct contact with soil. When loads are applied on structure internal forces are developed in both the structure as well as in soil. It results in deformation of both the components which are independent to each other. This are called soil structure interaction. The analysis is done by using (Bentley STAAD.Pro V8i Version 2007) software. The analysis carried out been pump house structure R.C.C. frame structure find ...

Chemical synthesis of porous web-structured CdS thin films for photosensor applications

Energy Technology Data Exchange (ETDEWEB)

Gosavi, S.R., E-mail: srgosavi.taloda@gmail.com [C. H. C. Arts, S. G. P. Commerce, and B. B. J. P. Science College, Taloda, Dist., Nandurbar 425413, M. S. (India); Nikam, C.P. [B.S.S.P.M.S. Arts, Commerce and Science College, Songir, Dist., Dhule 424309, M. S. (India); Shelke, A.R.; Patil, A.M. [Department of Physics, Shivaji University, Kolhapur 416004, M.S. (India); Ryu, S.-W. [Department of Physics, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Bhat, J.S. [Department of Physics, Karnatak University, Dharwad 580003 (India); Deshpande, N.G., E-mail: nicedeshpande@yahoo.co.in [Department of Physics, Shivaji University, Kolhapur 416004, M.S. (India)

2015-06-15

The photo-activity of chemically deposited cadmium sulphide (CdS) thin film has been studied. The simple chemical route nucleates the CdS films with size up to the mean free path of the electron. Growth Kinematics of crystalline hexagonal CdS phase in the thin film form was monitored using X-ray diffraction. The time limitation set for the formation of the amorphous/nano-crystalline material is 40 and 60 min. Thereafter enhancement of the crystalline orientation along the desired plane was identified. Web-like porous structured surface morphology of CdS thin film over the entire area is observed. With decrease in synthesis time, increase of band gap energy i.e., a blue spectral shift was seen. The activation energy of CdS thin film at low and high temperature region was examined. It is considered that this activation energy corresponds to the donor levels associated with shallow traps or surface states of CdS thin film. The photo-electrochemical performance of CdS thin films in polysulphide electrolyte showed diode-like characteristics. Exposure of light on the CdS electrode increases the photocurrent. This suggests the possibility of production of free carriers via excited ions and also the light harvesting mechanism due to porous web-structured morphology. These studies hint that the obtained CdS films can work as a photosensor. - Highlights: • Photoactivity of chemically synthesized cadmium sulphide (CdS) thin films was studied. • Web-like porous structured surface morphology of CdS thin film over the entire area was observed. • Blue spectral shift with lowering of the synthesis time suggests films can act as a window layer over the absorber layer. • Porous web-structured CdS thin films can be useful in light harvesting.

Chemical synthesis of porous web-structured CdS thin films for photosensor applications

International Nuclear Information System (INIS)

Gosavi, S.R.; Nikam, C.P.; Shelke, A.R.; Patil, A.M.; Ryu, S.-W.; Bhat, J.S.; Deshpande, N.G.

2015-01-01

The photo-activity of chemically deposited cadmium sulphide (CdS) thin film has been studied. The simple chemical route nucleates the CdS films with size up to the mean free path of the electron. Growth Kinematics of crystalline hexagonal CdS phase in the thin film form was monitored using X-ray diffraction. The time limitation set for the formation of the amorphous/nano-crystalline material is 40 and 60 min. Thereafter enhancement of the crystalline orientation along the desired plane was identified. Web-like porous structured surface morphology of CdS thin film over the entire area is observed. With decrease in synthesis time, increase of band gap energy i.e., a blue spectral shift was seen. The activation energy of CdS thin film at low and high temperature region was examined. It is considered that this activation energy corresponds to the donor levels associated with shallow traps or surface states of CdS thin film. The photo-electrochemical performance of CdS thin films in polysulphide electrolyte showed diode-like characteristics. Exposure of light on the CdS electrode increases the photocurrent. This suggests the possibility of production of free carriers via excited ions and also the light harvesting mechanism due to porous web-structured morphology. These studies hint that the obtained CdS films can work as a photosensor. - Highlights: • Photoactivity of chemically synthesized cadmium sulphide (CdS) thin films was studied. • Web-like porous structured surface morphology of CdS thin film over the entire area was observed. • Blue spectral shift with lowering of the synthesis time suggests films can act as a window layer over the absorber layer. • Porous web-structured CdS thin films can be useful in light harvesting

Recent Development in Optical Chemical Sensors Coupling with Flow Injection Analysis

Directory of Open Access Journals (Sweden)

Fuensanta Sánchez Rojas

2006-10-01

Full Text Available Optical techniques for chemical analysis are well established and sensors based on thesetechniques are now attracting considerable attention because of their importance in applications suchas environmental monitoring, biomedical sensing, and industrial process control. On the other hand,flow injection analysis (FIA is advisable for the rapid analysis of microliter volume samples and canbe interfaced directly to the chemical process. The FIA has become a widespread automatic analyticalmethod for more reasons; mainly due to the simplicity and low cost of the setups, their versatility, andease of assembling. In this paper, an overview of flow injection determinations by using opticalchemical sensors is provided, and instrumentation, sensor design, and applications are discussed. Thiswork summarizes the most relevant manuscripts from 1980 to date referred to analysis using opticalchemical sensors in FIA.

Flow Injection Analysis and Liquid Chromatography for Multifunctional Chemical Analysis (MCA) Systems

Science.gov (United States)

Mayo, Ana V.; Loegel, Thomas N.; Bretz, Stacey Lowery; Danielson, Neil D.

2013-01-01

The large class sizes of first-year chemistry labs makes it challenging to provide students with hands-on access to instrumentation because the number of students typically far exceeds the number of research-grade instruments available to collect data. Multifunctional chemical analysis (MCA) systems provide a viable alternative for large-scale…

Total Analysis System for Ship Structural Strength

OpenAIRE

Takuya, Yoneya; Hiroyuki, Kobayashi; Abdul M., Rahim; Yoshimichi, Sasaki; Masaki, Irisawa; Technical Investigation and Information Department, Research Center; Technical Investigation and Information Department, Research Center; Singapore Office; Technical Investigation and Information Department, Research Center; Technical Investigation and Information Department, Research Center

2001-01-01

This paper outlines a total analysis system for ship hull structures, which integrates a wide variety of analysis functions to realise practical applications of rational methods for assessing ship structural strength. It is based on direct calculation of wave-induced loads as well as three-dimensional structural analysis of an entire-ship or hold structure. Three major analysis functions of the total system are ship motion and wave load analysis, ship structural analysis and statistical analy...

Physico-Chemical and Structural Properties of DeNOx and SO2 Oxidation Catalysts

DEFF Research Database (Denmark)

Masters, Stephen Grenville; Oehlers, Cord; Nielsen, Kurt

1996-01-01

Commercial catalysts for NOx removal and SO2 oxidation and their model systems have been investigated by spectroscopic, thermal, electrochemical and X-ray methods. Structural information on the vanadium complexes and compounds as well as physico-chemical properties for catalyst model systems have...

High-Temperature Structural Analysis of a Small-Scale Prototype of a Process Heat Exchanger (IV) - Macroscopic High-Temperature Elastic-Plastic Analysis -

International Nuclear Information System (INIS)

Song, Kee Nam; Hong, Sung Deok; Park, Hong Yoon

2011-01-01

A PHE (Process Heat Exchanger) is a key component required to transfer heat energy of 950 .deg. C generated in a VHTR (Very High Temperature Reactor) to a chemical reaction that yields a large quantity of hydrogen. A small-scale PHE prototype made of Hastelloy-X was scheduled for testing in a small-scale gas loop at the Korea Atomic Energy Research Institute. In this study, as a part of the evaluation of the high-temperature structural integrity of the PHE prototype, high-temperature structural analysis modeling, and macroscopic thermal and elastic-plastic structural analysis of the PHE prototype were carried out under the gas-loop test conditions as a preliminary qwer123$ study before carrying out the performance test in the gas loop. The results obtained in this study will be used to design the performance test setup for the modified PHE prototype

The development of chemical speciation analysis

International Nuclear Information System (INIS)

Martin, R.; Santana, J.L.; Lima, L.; De La Rosa, D.; Melchor, K.

2003-01-01

The knowledge of many metals species on the environmental, its bioaccumulation, quantification and its effect in human body has been studied by a wide researchers groups in the last two decades. The development of speciation analysis has an vertiginous advance close to the developing of novel analytical techniques. Separation and quantification at low level is a problem that's has been afford by a coupling of high resolution chromatographic techniques like HPLC and HRGC with a specific method of detection (ICP-MS or CV-AAS). This methodological approach make possible the success in chemical speciation nowadays

Laser chemical analysis: the recent developments

International Nuclear Information System (INIS)

Mauchien, P.

1997-01-01

This paper gives a general overview and describes the principles of the main laser-based techniques for physical and chemical analysis, and of their recent developments. Analytical techniques using laser radiations were actually developed at the end of the 1970's. The recent evolutions concern the 3 principal techniques of laser spectroscopy currently used: Raman, fluorescence (atomic and molecular) and ablation (ICP laser ablation-plasma coupling, optical emission spectroscopy on laser-induced plasma). The description of these different techniques is illustrated with some examples of applications. (J.S.)

Magnitude differences in agronomic, chemical, nutritional, and structural features among different varieties of forage corn grown on dry land and irrigated land.

Science.gov (United States)

Xin, Hangshu; Abeysekara, Samen; Zhang, Xuewei; Yu, Peiqiang

2015-03-11

In this study, eight varieties of corn forage grown in semiarid western Canada (including Pioneer P2501, Pioneer P39m26, Pioneer P7443, Hyland HL3085, Hyland HLBaxxos, Hyland HLR219, Hyland HLSR22, and Pickseed Silex BT) were selected to explore the effect of irrigation implementation in comparison with nonirrigation on (1) agronomic characteristics, (2) basic chemical profiles explored by using a near-infrared reflectance (NIR) system, and (3) protein and carbohydrate internal structural parameters revealed by using an attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) system. Also, principal component analysis (PCA) was performed on spectroscopic data for clarification of differences in molecular structural makeup among the varieties. The results showed that irrigation treatment significantly increased (P forages. Significant interactions of irrigation treatment and corn variety were observed on most agronomic characteristics (DM yield, T/ha, days to tasseling, days to silking) and crude fiber (CF) and ether extract (EE) contents as well as some spectral data such as cellulosic compounds (CELC) peak intensity, peak ratios of CHO third peak to CELC, α-helix to β-sheet, and CHO third peak to amide I. Additionally, the spectral ratios of chemical functional groups that related to structural and nonstructural carbohydrates and protein polymers in forages did not remain constant over corn varieties cultivated with and without water treatment. Moreover, different cultivars had different growth, structure, and nutrition performances in this study. Although significant differences could be found in peak intensities, PCA results indicated some structural similarities existed between two treated corn forages with the exception of HL3085 and HLBaxxos. In conclusion, irrigation and corn variety had interaction effects on agronomic, chemical, nutritional, and structural features. Further study on the optimum level of irrigation for corn forage

Structure soil structure interaction effects: Seismic analysis of safety related collocated concrete structures

International Nuclear Information System (INIS)

Joshi, J.R.

2000-01-01

The Process, Purification and Stack Buildings are collocated safety related concrete shear wall structures with plan dimensions in excess of 100 feet. An important aspect of their seismic analysis was the determination of structure soil structure interaction (SSSI) effects, if any. The SSSI analysis of the Process Building, with one other building at a time, was performed with the SASSI computer code for up to 50 frequencies. Each combined model had about 1500 interaction nodes. Results of the SSSI analysis were compared with those from soil structure interaction (SSI) analysis of the individual buildings, done with ABAQUS and SASSI codes, for three parameters: peak accelerations, seismic forces and the in-structure floor response spectra (FRS). The results may be of wider interest due to the model size and the potential applicability to other deep soil layered sites. Results obtained from the ABAQUS analysis were consistently higher, as expected, than those from the SSI and SSSI analyses using the SASSI. The SSSI effect between the Process and Purification Buildings was not significant. The Process and Stack Building results demonstrated that under certain conditions a massive structure can have an observable effect on the seismic response of a smaller and less stiff structure

Chemical analysis of refractories by plasma spectrometry

International Nuclear Information System (INIS)

Coutinho, C.A.

1990-01-01

X-ray spectrometry has been, since the last two or three decades, the traditional procedure for the chemical analysis of refractories, due to its high degree of accuracy and speed to produce analytical results. An interesting alternative to X-ray fluorescence is provided by the Inductively Coupled Plasma Spectrometry technique, for those laboratories where wet chemistry facilities are already available or process control is not required at high speed, or investiment costs have to be low. This paper presents results obtained by plasma spectroscopy for the analysis of silico - aluminous refractories, showing calibration curves, precion and detection limits. Considerations and comparisons with X-ray fluorescence are also made. (author) [pt

Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

Science.gov (United States)

Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

2010-03-01

Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

International Nuclear Information System (INIS)

Anantachaisilp, Suranan; Smith, Siwaporn Meejoo; Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong; Pratontep, Sirapat; Puttipipatkhachorn, Satit

2010-01-01

Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ( 1 H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1 H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1 H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

Replication of noise-sustained autocatalytic chemical structures.

Science.gov (United States)

Izús, Gonzalo G; Deza, Roberto R; Sánchez, Alejandro D

2010-06-21

Autocatalytic systems in a differential-flow reactor may undergo a differential-flow-induced chemical instability toward a convectively unstable regime, in which noise-sustained structures may appear. This is the case of a system with Gray-Scott kinetics in a packed-bed reactor, as reported in [B. von Haeften and G. Izus, Phys. Rev. E 67, 056207 (2003)]. In this work, two identical copies of such a system are coupled in master-slave configuration and submitted to independent spatiotemporal Gaussian white noise sources. Numerical simulation of two-dimensional reactors with uniform and Poiseuille flows reveals that the slave system replicates to a very high degree of precision and the convective patterns arising in the master one due to the presence of noise. The quality of this synchronization is assessed through several measures. A convective instability in the synchronization manifold is theoretically predicted and numerically confirmed.

Structural analysis of fuel handling systems

Energy Technology Data Exchange (ETDEWEB)

Lee, L S.S. [Atomic Energy of Canada Ltd., Mississauga, ON (Canada)

1997-12-31

The purpose of this paper has three aspects: (i) to review `why` and `what` types of structural analysis, testing and report are required for the fuel handling systems according to the codes, or needed for design of a product, (ii) to review the input requirements for analysis and the analysis procedures, and (iii) to improve the communication between the analysis and other elements of the product cycle. The required or needed types of analysis and report may be categorized into three major groups: (i) Certified Stress Reports for design by analysis, (ii) Design Reports not required for certification and registration, but are still required by codes, and (iii) Design Calculations required by codes or needed for design. Input requirements for structural analysis include: design, code classification, loadings, and jurisdictionary boundary. Examples of structural analysis for the fueling machine head and support structure are given. For improving communication between the structural analysis and the other elements of the product cycle, some areas in the specification of design requirements and load rating are discussed. (author). 6 refs., 1 tab., 4 figs.

Structural analysis of fuel handling systems

International Nuclear Information System (INIS)

Lee, L.S.S.

1996-01-01

The purpose of this paper has three aspects: (i) to review 'why' and 'what' types of structural analysis, testing and report are required for the fuel handling systems according to the codes, or needed for design of a product, (ii) to review the input requirements for analysis and the analysis procedures, and (iii) to improve the communication between the analysis and other elements of the product cycle. The required or needed types of analysis and report may be categorized into three major groups: (i) Certified Stress Reports for design by analysis, (ii) Design Reports not required for certification and registration, but are still required by codes, and (iii) Design Calculations required by codes or needed for design. Input requirements for structural analysis include: design, code classification, loadings, and jurisdictionary boundary. Examples of structural analysis for the fueling machine head and support structure are given. For improving communication between the structural analysis and the other elements of the product cycle, some areas in the specification of design requirements and load rating are discussed. (author). 6 refs., 1 tab., 4 figs

Quantum chemical studies on molecular structural conformations and hydrated forms of salicylamide and O-hydroxybenzoyl cyanide

Science.gov (United States)

Anandan, K.; Kolandaivel, P.; Kumaresan, R.

Ab initio and density functional theory (DFT) methods have been employed to study the molecular structural conformations and hydrated forms of both salicylamide (SAM) and O-hydroxybenzoyl cyanide (OHBC). Molecular geometries and energetics have been obtained in the gaseous phase by employing the Møller-Plesset type 2 MP2/6-311G(2d,2p) and B3LYP/6-311G(2d,2p) levels of theory. The presence of an electron-releasing group (SAM) leads to an increase in the energy of the molecular system, while the presence of an electron-withdrawing group (OHBC) drastically decreases the energy. Chemical reactivity parameters (η and μ) have been calculated using the energy values of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) obtained at the Hartree-Fock (HF)/6-311G(2d,2p) level of theory for all the conformers and the principle of maximum hardness (MHP) has been tested. The condensed Fukui functions have been calculated using the atomic charges obtained through the natural bond orbital (NBO) analysis scheme for all the optimized structures at the B3LYP/6-311G(2d,2p) level of theory, and the most reactive sites of the molecules have been identified. Nuclear magnetic resonance (NMR) studies have been carried out at the B3LYP/6-311G(2d,2p) level of theory for all the conformers in the gaseous phase on the basis of the method of Cheeseman and coworkers. The calculated chemical shift values have been used to discuss the delocalization activity of the electron clouds. The dimeric structures of the most stable conformers of both SAM and OHBC in the gaseous phase have been optimized at the B3LYP/6-311G(2d,2p) level of theory, and the interaction energies have been calculated. The most stable conformers of both compounds bear an intramolecular hydrogen bond, which gives rise to the formation of a pseudo-aromatic ring. These conformers have been allowed to interact with the water molecule. Special emphasis has been given to analysis of the

Hybrid carrageenans: isolation, chemical structure, and gel properties.

Science.gov (United States)

Hilliou, Loic

2014-01-01

Hybrid carrageenan is a special class of carrageenan with niche application in food industry. This polysaccharide is extracted from specific species of seaweeds belonging to the Gigartinales order. This chapter focuses on hybrid carrageenan showing the ability to form gels in water, which is known in the food industry as weak kappa or kappa-2 carrageenan. After introducing the general chemical structure defining hybrid carrageenan, the isolation of the polysaccharide will be discussed focusing on the interplay between seaweed species, extraction parameters, and the hybrid carrageenan chemistry. Then, the rheological experiments used to determine the small and large deformation behavior of gels will be detailed before reviewing the relationships between gel properties and hybrid carrageenan chemistry. © 2014 Elsevier Inc. All rights reserved.

Forecasting global developments in the basic chemical industry for environmental policy analysis

NARCIS (Netherlands)

Broeren, M.L.M.|info:eu-repo/dai/nl/371687438; Saygin, D.; Patel, M.K.

The chemical sector is the largest industrial energy user, but detailed analysis of its energy use developments lags behind other energy-intensive sectors. A cost-driven forecasting model for basic chemicals production is developed, accounting for regional production costs, demand growth and stock

Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

Directory of Open Access Journals (Sweden)

H. V. Lee

2014-01-01

Full Text Available Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate’s application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein.

Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

Science.gov (United States)

Lee, H. V.; Hamid, S. B. A.; Zain, S. K.

2014-01-01

Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate's application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein. PMID:25247208

Hydrogen fluoride (HF) substance flow analysis for safe and sustainable chemical industry.

Science.gov (United States)

Kim, Junbeum; Hwang, Yongwoo; Yoo, Mijin; Chen, Sha; Lee, Ik-Mo

2017-11-01

In this study, the chemical substance flow of hydrogen fluoride (hydrofluoric acid, HF) in domestic chemical industries in 2014 was analyzed in order to provide a basic material and information for the establishment of organized management system to ensure safety during HF applications. A total of 44,751 tons of HF was made by four domestic companies (in 2014); import amount was 95,984 tons in 2014 while 21,579 tons of HF was imported in 2005. The export amount of HF was 2180 tons, of which 2074 ton (China, 1422 tons, U.S. 524 tons, and Malaysia, 128 tons) was exported for the manufacturing of semiconductors. Based on the export and import amounts, it can be inferred that HF was used for manufacturing semiconductors. The industries applications of 161,123 tons of HF were as follows: manufacturing of basic inorganic chemical substance (27,937 tons), manufacturing of other chemical products such as detergents (28,208 tons), manufacturing of flat display (24,896 tons), and manufacturing of glass container package (22,002 tons). In this study, an analysis of the chemical substance flow showed that HF was mainly used in the semiconductor industry as well as glass container manufacturing. Combined with other risk management tools and approaches in the chemical industry, the chemical substance flow analysis (CSFA) can be a useful tool and method for assessment and management. The current CSFA results provide useful information for policy making in the chemical industry and national systems. Graphical abstract Hydrogen fluoride chemical substance flows in 2014 in South Korea.

Structure alerts for carcinogenicity, and the Salmonella assay system: a novel insight through the chemical relational databases technology.

Science.gov (United States)

Benigni, Romualdo; Bossa, Cecilia