Molecular Mechanisms of Breast Cancer Metastasis and Potential Anti-metastatic Compounds.

Science.gov (United States)

Tungsukruthai, Sucharat; Petpiroon, Nalinrat; Chanvorachote, Pithi

2018-05-01

Throughout the world, breast cancer is among the major causes of cancer-related death and is the most common cancer found in women. The development of cancer molecular knowledge has surpassed the novel concept of cancer biology and unraveled principle targets for anticancer drug developments and treatment strategies. Metastatic breast cancer cells acquire their aggressive features through several mechanisms, including augmentation of survival, proliferation, tumorigenicity, and motility-related cellular pathways. Clearly, natural product-derived compounds have since long been recognized as an important source for anticancer drugs, several of which have been shown to have promising anti-metastasis activities by suppressing key molecular features supporting such cell aggressiveness. This review provides the essential details of breast cancer, the molecular-based insights into metastasis, as well as the effects and mechanisms of potential compounds for breast cancer therapeutic approaches. As the abilities of cancer cells to invade and metastasize are addressed as the hallmarks of cancer, compounds possessing anti-metastatic effects, together with their defined molecular drug action could benefit the development of new drugs as well as treatment strategies. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Coupling Matched Molecular Pairs with Machine Learning for Virtual Compound Optimization.

Science.gov (United States)

Turk, Samo; Merget, Benjamin; Rippmann, Friedrich; Fulle, Simone

2017-12-26

Matched molecular pair (MMP) analyses are widely used in compound optimization projects to gain insights into structure-activity relationships (SAR). The analysis is traditionally done via statistical methods but can also be employed together with machine learning (ML) approaches to extrapolate to novel compounds. The here introduced MMP/ML method combines a fragment-based MMP implementation with different machine learning methods to obtain automated SAR decomposition and prediction. To test the prediction capabilities and model transferability, two different compound optimization scenarios were designed: (1) "new fragments" which occurs when exploring new fragments for a defined compound series and (2) "new static core and transformations" which resembles for instance the identification of a new compound series. Very good results were achieved by all employed machine learning methods especially for the new fragments case, but overall deep neural network models performed best, allowing reliable predictions also for the new static core and transformations scenario, where comprehensive SAR knowledge of the compound series is missing. Furthermore, we show that models trained on all available data have a higher generalizability compared to models trained on focused series and can extend beyond chemical space covered in the training data. Thus, coupling MMP with deep neural networks provides a promising approach to make high quality predictions on various data sets and in different compound optimization scenarios.

Statistical molecular design of balanced compound libraries for QSAR modeling.

Science.gov (United States)

Linusson, A; Elofsson, M; Andersson, I E; Dahlgren, M K

2010-01-01

A fundamental step in preclinical drug development is the computation of quantitative structure-activity relationship (QSAR) models, i.e. models that link chemical features of compounds with activities towards a target macromolecule associated with the initiation or progression of a disease. QSAR models are computed by combining information on the physicochemical and structural features of a library of congeneric compounds, typically assembled from two or more building blocks, and biological data from one or more in vitro assays. Since the models provide information on features affecting the compounds' biological activity they can be used as guides for further optimization. However, in order for a QSAR model to be relevant to the targeted disease, and drug development in general, the compound library used must contain molecules with balanced variation of the features spanning the chemical space believed to be important for interaction with the biological target. In addition, the assays used must be robust and deliver high quality data that are directly related to the function of the biological target and the associated disease state. In this review, we discuss and exemplify the concept of statistical molecular design (SMD) in the selection of building blocks and final synthetic targets (i.e. compounds to synthesize) to generate information-rich, balanced libraries for biological testing and computation of QSAR models.

Solubility of crystalline organic compounds in high and low molecular weight amorphous matrices above and below the glass transition by zero enthalpy extrapolation.

Science.gov (United States)

Amharar, Youness; Curtin, Vincent; Gallagher, Kieran H; Healy, Anne Marie

2014-09-10

Pharmaceutical applications which require knowledge of the solubility of a crystalline compound in an amorphous matrix are abundant in the literature. Several methods that allow the determination of such data have been reported, but so far have only been applicable to amorphous polymers above the glass transition of the resulting composites. The current work presents, for the first time, a reliable method for the determination of the solubility of crystalline pharmaceutical compounds in high and low molecular weight amorphous matrices at the glass transition and at room temperature (i.e. below the glass transition temperature), respectively. The solubilities of mannitol and indomethacin in polyvinyl pyrrolidone (PVP) K15 and PVP K25, respectively were measured at different temperatures. Mixtures of undissolved crystalline solute and saturated amorphous phase were obtained by annealing at a given temperature. The solubility at this temperature was then obtained by measuring the melting enthalpy of the crystalline phase, plotting it as a function of composition and extrapolating to zero enthalpy. This new method yielded results in accordance with the predictions reported in the literature. The method was also adapted for the measurement of the solubility of crystalline low molecular weight excipients in amorphous active pharmaceutical ingredients (APIs). The solubility of mannitol, glutaric acid and adipic acid in both indomethacin and sulfadimidine was experimentally determined and successfully compared with the difference between their respective calculated Hildebrand solubility parameters. As expected from the calculations, the dicarboxylic acids exhibited a high solubility in both amorphous indomethacin and sulfadimidine, whereas mannitol was almost insoluble in the same amorphous phases at room temperature. This work constitutes the first report of the methodology for determining an experimentally measured solubility for a low molecular weight crystalline solute

Molecular docking for thrombolytic activity of some isolated compounds from Clausena lansium.

Directory of Open Access Journals (Sweden)

Arkajyoti Paul

2017-03-01

Full Text Available Clausena lansium (Family- Rutaceae is commonly known as wampee, is found in fallow lands throughout Bangladesh. Our aim of the study to performed molecular docking studies to identify potential binding affinities of the phytocompounds from Clausena lansium, namely Clausemarin B, Clausenaline C, Clausenaline E, Murrayanine, vanillic acid and Xanthotoxol for searching of lead molecule for thrombolytic activity. A wide range of docking score found during molecular docking by Schrodinger. Clausemarin B , Clausenaline C , Clausenaline E, Murrayanine , vanillic acid and Xanthotoxol showed the docking score -6.926, -4.041, -4.889 , -4.356, -3.007 and -5.816 respectively. Among all the compounds Clausemarin B showed the best docking score. So, Clausemarin B is the best compounds for thrombolytic activity, as it possessed the best value in Molecular docking. Further in vivo investigation need to identify the thrombolytic activity of isolated compounds from Clausena lansium.

Review on Molecular Mechanisms of Antifouling Compounds: An Update since 2012.

Science.gov (United States)

Chen, Lianguo; Qian, Pei-Yuan

2017-08-28

Better understanding of the mechanisms of antifouling compounds is recognized to be of high value in establishing sensitive biomarkers, allowing the targeted optimization of antifouling compounds and guaranteeing environmental safety. Despite vigorous efforts to find new antifouling compounds, information about the mechanisms of antifouling is still scarce. This review summarizes the progress into understanding the molecular mechanisms underlying antifouling activity since 2012. Non-toxic mechanisms aimed at specific targets, including inhibitors of transmembrane transport, quorum sensing inhibitors, neurotransmission blockers, adhesive production/release inhibitors and enzyme/protein inhibitors, are put forward for natural antifouling products or shelf-stable chemicals. Several molecular targets show good potential for use as biomarkers in future mechanistic screening, such as acetylcholine esterase for neurotransmission, phenoloxidase/tyrosinase for the formation of adhesive plaques, N -acyl homoserine lactone for quorum sensing and intracellular Ca 2+ levels as second messenger. The studies on overall responses to challenges by antifoulants can be categorized as general targets, including protein expression/metabolic activity regulators, oxidative stress inducers, neurotransmission blockers, surface modifiers, biofilm inhibitors, adhesive production/release inhibitors and toxic killing. Given the current situation and the knowledge gaps regarding the development of alternative antifoulants, a basic workflow is proposed that covers the indispensable steps, including preliminary mechanism- or bioassay-guided screening, evaluation of environmental risks, field antifouling performance, clarification of antifouling mechanisms and the establishment of sensitive biomarkers, which are combined to construct a positive feedback loop.

Environmental Chemistry Compound Identification Using High ...

Science.gov (United States)

There is a growing need for rapid chemical screening and prioritization to inform regulatory decision-making on thousands of chemicals in the environment. We have previously used high-resolution mass spectrometry to examine household vacuum dust samples using liquid chromatography time-of-flight mass spectrometry (LC-TOF/MS). Using a combination of exact mass, isotope distribution, and isotope spacing, molecular features were matched with a list of chemical formulas from the EPA’s Distributed Structure-Searchable Toxicity (DSSTox) database. This has further developed our understanding of how openly available chemical databases, together with the appropriate searches, could be used for the purpose of compound identification. We report here on the utility of the EPA’s iCSS Chemistry Dashboard for the purpose of compound identification using searches against a database of over 720,000 chemicals. We also examine the benefits of QSAR prediction for the purpose of retention time prediction to allow for alignment of both chromatographic and mass spectral properties. This abstract does not reflect U.S. EPA policy presentation at the Eastern Analytical Symposium.

Intra-molecular selectivity of muonium towards chlorinated aromatic compounds

International Nuclear Information System (INIS)

Venkateswaran, K.; Stadlbauer, J.M.; Laing, M.E.; Klugkist, J.; Chong, D.P.; Porter, G.B.; Walker, D.C.

1994-01-01

Muon resonance studies show that muonium atoms (Mu) in ethanol add selectively to certain C-sites of aromatic compounds containing -Cl and -OH substituents. The sites chosen seem to be those carrying the lowest electron density. This helps to characterize Mu as a nucleophile in addition reactions and, in this respect, Mu differs from ordinary H-atoms. The study shows no apparent inter-molecular selectivity between a pair of aromatic solutes in an equimolar mixture, but strong intra-molecular selectivity in an ether composed of those two aromatic rings. This difference between intra- and inter-molecular selectivity is interpreted as kinetic in origin - arising from the 'caging effect' of the solvent and peculiar to reactions close to the diffusion-controlled limit. (orig.)

Oxidation of refractory sulfur compounds over Ti-containing mesoporous molecular sieves prepared by using a fluorosilicon compound.

Science.gov (United States)

Jeong, Kwang-Eun; Cho, Chin-Soo; Chae, Ho-Jeong; Kim, Chul-Ung; Jeong, Soon-Yong

2010-05-01

Titanium containing mesoporous molecular sieve (Ti-MMS) catalysts were studied for the oxidative desulfurization of refractory sulfur compounds. Ti-MMS catalysts were synthesized from fluorosilicon compounds and Ti with the hydrolysis reaction of H2SiF6 in an ammonia-surfactant mixed solution. The solid products were characterized by XRD, XRF, nitrogen adsorption, and diffuse reflectance UV-vis spectroscopy. Effects of Ti loading and oxidant/sulfur mole ratio, and sulfur species on ODS activity were investigated.

Demonstration of molecular beam epitaxy and a semiconducting band structure for I-Mn-V compounds

International Nuclear Information System (INIS)

Jungwirth, T.; Novak, V.; Cukr, M.; Zemek, J.; Marti, X.; Horodyska, P.; Nemec, P.; Holy, V.; Maca, F.; Shick, A. B.; Masek, J.; Kuzel, P.; Nemec, I.; Gallagher, B. L.; Campion, R. P.; Foxon, C. T.; Wunderlich, J.

2011-01-01

Our ab initio theory calculations predict a semiconducting band structure of I-Mn-V compounds. We demonstrate on LiMnAs that high-quality materials with group-I alkali metals in the crystal structure can be grown by molecular beam epitaxy. Optical measurements on the LiMnAs epilayers are consistent with the theoretical electronic structure. Our calculations also reproduce earlier reports of high antiferromagnetic ordering temperature and predict large, spin-orbit-coupling-induced magnetic anisotropy effects. We propose a strategy for employing antiferromagnetic semiconductors in high-temperature semiconductor spintronics.

Understanding the molecular behavior of organotin compounds to design their effective use as agrochemicals: exploration via quantum chemistry and experiments.

Science.gov (United States)

Ramalho, Teodorico C; Rocha, Marcus V J; da Cunha, Elaine F F; Oliveira, Luiz C A; Carvalho, Kele T C

2010-10-01

The high frequency of contamination by herbicides suggests the need for more active and selective agrochemicals. Organotin compounds are the active component of some herbicides, such as Du-Ter and Brestan, which is also a potent inhibitor of the F1Fo ATP Synthase. That is a key enzyme, because the ATP production is one of the major chemical reactions in living organisms. Thus ATP Synthase is regarded as a prime target for organotin compounds. In this line, molecular modeling studies and DFT calculations were performed in order to understand the molecular behavior of those compounds in solution. In addition, we investigated the reaction mechanism by ESI-MS analyses of the diphenyltin dichloride. Our findings indicate that an unstable key-intermediate generated in situ might take place in the reaction with ATP Synthase.

High-molecular products analysis of VOC destruction in atmospheric pressure discharge

International Nuclear Information System (INIS)

Grossmannova, Hana; Ciganek, Miroslav; Krcma, Frantisek

2007-01-01

We investigate the issue of applicability of the solid phase microextraction (SPME) in the analysis of volatile organic compounds (VOCs) destruction products in the gliding arc discharge. Our research is focused on the measurements with the simple one stage gliding arc reactor, applied voltage was varied in the range of 3.5-4 kV. As a carrier gas, the dry air and its mixtures with nitrogen and oxygen, enriched by toluene, with flow rate of 1000-3500 ml/min was used. Total decomposition of toluene of 97 % was achieved at the oxygen content in carrier gas of 60 %. For measurements with air as a carrier gas, the highest efficiency was 95 %. We also tested the SPME technique suitability for the quantitative analysis of exhausts gases and if this technique can be used efficiently in the field to extract byproducts. Carbowax/divinylbenzene and Carboxen/polydimethylsiloxane/divinylbenzene fibres were chosen for sampling. Tens of various high-molecular substances were observed, especially a large number of oxygenous compounds and further several nitrogenous and C x H y compounds. The concentrations of various generated compounds strongly depend on the oxygen content in gas mixture composition. The results showed that the fiber coated by Carbowax/divinylbenzene can extract more products independently on the used VOC compound. The Carboxen/polydimethylsiloxane/divinylbenzene fiber is useful for the analysis of oxygenous compounds and its use will be recommended especially when the destruction is done in the oxygen rich atmosphere. With the higher ratio of oxygen in the carrier gas a distinctive decline of C x H y compounds amount have been observed. We also tried to describe the significant production of some compounds like benzyl alcohol, benzeneacetaldehyde, even in oxygen content is proximate 0 %. Experimental data demonstrated that it is necessary to use several SPME fibres for full-scale high-molecular products analysis

MALDI matrices for low molecular weight compounds: an endless story?

Science.gov (United States)

Calvano, Cosima Damiana; Monopoli, Antonio; Cataldi, Tommaso R I; Palmisano, Francesco

2018-04-23

Since its introduction in the 1980s, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has gained a prominent role in the analysis of high molecular weight biomolecules such as proteins, peptides, oligonucleotides, and polysaccharides. Its application to low molecular weight compounds has remained for long time challenging due to the spectral interferences produced by conventional organic matrices in the low m/z window. To overcome this problem, specific sample preparation such as analyte/matrix derivatization, addition of dopants, or sophisticated deposition technique especially useful for imaging experiments, have been proposed. Alternative approaches based on second generation (rationally designed) organic matrices, ionic liquids, and inorganic matrices, including metallic nanoparticles, have been the object of intense and continuous research efforts. Definite evidences are now provided that MALDI MS represents a powerful and invaluable analytical tool also for small molecules, including their quantification, thus opening new, exciting applications in metabolomics and imaging mass spectrometry. This review is intended to offer a concise critical overview of the most recent achievements about MALDI matrices capable of specifically address the challenging issue of small molecules analysis. Graphical abstract An ideal Book of matrices for MALDI MS of small molecules.

Monolithic poly(1,2-bis(p-vinylphenyl)ethane) capillary columns for simultaneous separation of low- and high-molecular-weight compounds.

Science.gov (United States)

Greiderer, Andreas; Ligon, S Clark; Huck, Christian W; Bonn, Günther K

2009-08-01

Monolithic poly(1,2-bis(p-vinylphenyl)ethane (BVPE)) capillary columns were prepared by thermally initiated free radical polymerisation of 1,2-bis(p-vinylphenyl)ethane in the presence of inert diluents (porogens) and alpha,alpha'-azoisobutyronitrile (AIBN) as initiator. Polymerisations were accomplished in 200 microm ID fused silica capillaries at 65 degrees C and for 60 min. Mercury intrusion porosimetry measurements of the polymeric RP support showed a broad bimodal pore-size-distribution of mesopores and small macropores in the range of 5-400 nm and flow-channels in the mum range. N(2)-adsorption (BET) analysis resulted in a tremendous enhancement of surface area (101 m(2)/g) of BVPE stationary phases compared to typical organic monoliths (approximately 20 m(2)/g), indicating the presence of a considerable amount of mesopores. Consequently, the adequate proportion of both meso- and (small) macropores allowed the rapid and high-resolution separation of low-molecular-weight compounds as well as biomolecules on the same monolithic support. At the same time, the high fraction of flow-channels provided enhanced column permeability. The chromatographic performance of poly(1,2-bis(p-vinylphenyl)ethane) capillary columns for the separation of biomolecules (proteins, oligonucleotides) and small molecules (alkyl benzenes, phenols, phenons) are demonstrated in this article. Additionally, pressure drop versus flow rate measurements of novel poly(1,2-bis(p-vinylphenyl)ethane) capillary columns confirmed high mechanical robustness, low swelling in organic solvents and high permeability. Due to the simplicity of monolith fabrication, comprehensive studies of the retention and separation behaviour of monolithic BVPE columns resulted in high run-to-run and batch-to-batch reproducibilities. All these attributes prove the excellent applicability of monolithic poly(1,2-bis(p-vinylphenyl)ethane) capillary columns for micro-HPLC towards a huge range of analytes of different

Molecular basis of biodegradation of chloroaromatic compounds

Energy Technology Data Exchange (ETDEWEB)

Sangodkar, U M.X.; Aldrich, T L; Haugland, R A; Johnson, J; Rothmel, R K; Chakrabarty, A M [Illinois Univ., Chicago (USA). Coll. of Medicine; Chapman, P J [Environmental Protection Agency, Gulf Breeze, FL (USA). Microbial Ecology and Biotechnology

1989-01-01

Chlorinated aromatic hydrocarbons are widely used in industry and agriculture, and comprise the bulk of environmental pollutants. Although simple aromatic compounds are biodegradable by a variety of degradative pathways, their halogenated counterparts are more resistant to bacterial attack and often necessitate evolution of novel pathways. An understanding of such evolutionary processes is essential for developing genetically improved strains capable of mineralizing highly chlorinated compounds. This article provides an overview of the genetic aspects of dissimilation of chloroaromatic compounds and discusses the potential of gene manipulation to promote enhanced evolution of the degradation pathways. (orig.).

Screening alpha-glucosidase and alpha-amylase inhibitors from natural compounds by molecular docking in silico.

Science.gov (United States)

Jhong, Chien-Hung; Riyaphan, Jirawat; Lin, Shih-Hung; Chia, Yi-Chen; Weng, Ching-Feng

2015-01-01

The alpha-glucosidase inhibitor is a common oral anti-diabetic drug used for controlling carbohydrates normally converted into simple sugars and absorbed by the intestines. However, some adverse clinical effects have been observed. The present study seeks an alternative drug that can regulate the hyperglycemia by down-regulating alpha-glucosidase and alpha-amylase activity by molecular docking approach to screen the hyperglycemia antagonist against alpha-glucosidase and alpha-amylase activities from the 47 natural compounds. The docking data showed that Curcumin, 16-hydroxy-cleroda-3,13-dine-16,15-olide (16-H), Docosanol, Tetracosanol, Antroquinonol, Berberine, Catechin, Quercetin, Actinodaphnine, and Rutin from 47 natural compounds had binding ability towards alpha-amylase and alpha-glucosidase as well. Curcumin had a better biding ability of alpha-amylase than the other natural compounds. Analyzed alpha-glucosidase activity reveals natural compound inhibitors (below 0.5 mM) are Curcumin, Actinodaphnine, 16-H, Quercetin, Berberine, and Catechin when compared to the commercial drug Acarbose (3 mM). A natural compound with alpha-amylase inhibitors (below 0.5 mM) includes Curcumin, Berberine, Docosanol, 16-H, Actinodaphnine/Tetracosanol, Catechin, and Quercetin when compared to Acarbose (1 mM). When taken together, the implication is that molecular docking is a fast and effective way to screen alpha-glucosidase and alpha-amylase inhibitors as lead compounds of natural sources isolated from medicinal plants. © 2015 International Union of Biochemistry and Molecular Biology.

The association of low-molecular-weight hydrophobic compounds with native casein micelles in bovine milk.

Science.gov (United States)

Cheema, M; Mohan, M S; Campagna, S R; Jurat-Fuentes, J L; Harte, F M

2015-08-01

The agreed biological function of the casein micelles in milk is to carry minerals (calcium, magnesium, and phosphorus) from mother to young along with amino acids for growth and development. Recently, native and modified casein micelles were used as encapsulating and delivery agents for various hydrophobic low-molecular-weight probes. The ability of modified casein micelles to bind certain probes may derive from the binding affinity of native casein micelles. Hence, a study with milk from single cows was conducted to further elucidate the association of hydrophobic molecules into native casein micelles and further understand their biological function. Hydrophobic and hydrophilic extraction followed by ultraperformance liquid chromatography-high resolution mass spectrometry analysis were performed over protein fractions obtained from size exclusion fractionation of raw skim milk. Hydrophobic compounds, including phosphatidylcholine, lyso-phosphatidylcholine, phosphatidylethanolamine, and sphingomyelin, showed strong association exclusively to casein micelles as compared with whey proteins, whereas hydrophilic compounds did not display any preference for their association among milk proteins. Further analysis using liquid chromatography-tandem mass spectrometry detected 42 compounds associated solely with the casein-micelles fraction. Mass fragments in tandem mass spectrometry identified 4 of these compounds as phosphatidylcholine with fatty acid composition of 16:0/18:1, 14:0/16:0, 16:0/16:0, and 18:1/18:0. These results support that transporting low-molecular-weight hydrophobic molecules is also a biological function of the casein micelles in milk. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Molecular structure descriptors in the computer-aided design of biologically active compounds

International Nuclear Information System (INIS)

Raevsky, Oleg A

1999-01-01

The current state of description of molecular structure in computer-aided molecular design of biologically active compounds by means of descriptors is analysed. The information contents of descriptors increases in the following sequence: element-level descriptors-structural formulae descriptors-electronic structure descriptors-molecular shape descriptors-intermolecular interaction descriptors. Each subsequent class of descriptors normally covers information contained in the previous-level ones. It is emphasised that it is practically impossible to describe all the features of a molecular structure in terms of any single class of descriptors. It is recommended to optimise the number of descriptors used by means of appropriate statistical procedures and characteristics of structure-property models based on these descriptors. The bibliography includes 371 references.

Copper-catalyzed oxidative desulfurization-oxygenation of thiocarbonyl compounds using molecular oxygen: an efficient method for the preparation of oxygen isotopically labeled carbonyl compounds.

Science.gov (United States)

Shibahara, Fumitoshi; Suenami, Aiko; Yoshida, Atsunori; Murai, Toshiaki

2007-06-21

A novel copper-catalyzed oxidative desulfurization reaction of thiocarbonyl compounds, using molecular oxygen as an oxidant and leading to formation of carbonyl compounds, has been developed, and the utility of the process is demonstrated by its application to the preparation of a carbonyl-18O labeled sialic acid derivative.

Use of high-molecular compounds in plastic lubricants for geological exploratory drilling

Energy Technology Data Exchange (ETDEWEB)

Smyk, Z.I.; Kuz' michev, S.P.; Mnishchenko, V.G.; Smertenko, M.I.

1982-01-01

The existing lubricants in the series KAVS (OST 81-4-70) do not correspond to the conditions of high-rotational diamond drilling for a number of operating properties. Results are presented of studying the hydrated calcium lubricants with high molecular additives (polyisobutylene KP-10, polyethylene of high density of low pressure and atactic propylene in a quantity of 1-6%) improving their operating properties. Selection of the additives is governed by their compatability with the base and the capacity to improve the adhesion-cohesion properties with relative constancy of other characteristics. As a result of the studies it was established that the use in the lubricant of polymers of the carbon-chain type of amorphous structure in a quantity of 1-2% depending on the molecular weight noticeably improves the stickiness, resistance to erosion by water, colloidal stability, and lubricant properties. When they are added in a large quantity, a sharp weakening of the lubricants is observed and in individual cases, formation of unstable systems. Polymers of the hetero-chain type because of the presence of polar groups are highly effective adhesives. Protective and packing lubricants are developed which contain rubbers. Alkyl-phenol-amine resins (octophor-N), the bottoms from the production of phenol formaldehyde resin, rosin and lignite wax introduced at the stage of cooling have a positive effect on the lubricant properties. The best operating properties with satisfactory other indicators (viscosity, colloidal stability, antiwear properties) are found in the samples containing polyisobutylene KP-10, lignite wax and rosin. Operating tests of an experimental batch of this lubricant under conditions of real drilling indicated that its use as compared to KEVS-45 makes it possible to increase the drilling rate by 40%, reduce the outlays of power to 50%, reduce the service time and the outlays of energy resources for applying the lubricant layer to the pipe surface.

Molecular simulation of receptors of physiologically active compounds for purposes of medical chemistry

Science.gov (United States)

Baskin, Igor I.; Palyulin, Vladimir A.; Zefirov, Nikolai S.

2009-06-01

The general strategy of the molecular simulation of biological receptors and their interaction with ligands is considered. The procedures for construction of 3D protein models, molecular docking, evaluation of model quality, determination of the free energy of protein binding with ligands are discussed. The methods of molecular design of new medicaments based on molecular models of biological targets: virtual screening and de novo design, are presented. Examples of the above-listed approaches for the simulation of a number of pharmacologically significant receptors, analysis of receptor-ligand interactions and design of new biologically active organic compounds are given.

Molecular simulation of receptors of physiologically active compounds for purposes of medical chemistry

International Nuclear Information System (INIS)

Baskin, Igor I; Palyulin, Vladimir A; Zefirov, Nikolai S

2009-01-01

The general strategy of the molecular simulation of biological receptors and their interaction with ligands is considered. The procedures for construction of 3D protein models, molecular docking, evaluation of model quality, determination of the free energy of protein binding with ligands are discussed. The methods of molecular design of new medicaments based on molecular models of biological targets: virtual screening and de novo design, are presented. Examples of the above-listed approaches for the simulation of a number of pharmacologically significant receptors, analysis of receptor-ligand interactions and design of new biologically active organic compounds are given.

Molecular simulation of receptors of physiologically active compounds for purposes of medical chemistry

Energy Technology Data Exchange (ETDEWEB)

Baskin, Igor I; Palyulin, Vladimir A; Zefirov, Nikolai S [Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow (Russian Federation)

2009-06-30

The general strategy of the molecular simulation of biological receptors and their interaction with ligands is considered. The procedures for construction of 3D protein models, molecular docking, evaluation of model quality, determination of the free energy of protein binding with ligands are discussed. The methods of molecular design of new medicaments based on molecular models of biological targets: virtual screening and de novo design, are presented. Examples of the above-listed approaches for the simulation of a number of pharmacologically significant receptors, analysis of receptor-ligand interactions and design of new biologically active organic compounds are given.

Mass Spectrometry Imaging of low Molecular Weight Compounds in Garlic (Allium sativum L.) with Gold Nanoparticle Enhanced Target.

Science.gov (United States)

Misiorek, Maria; Sekuła, Justyna; Ruman, Tomasz

2017-11-01

Garlic (Allium sativum) is the subject of many studies due to its numerous beneficial properties. Although compounds of garlic have been studied by various analytical methods, their tissue distributions are still unclear. Mass spectrometry imaging (MSI) appears to be a very powerful tool for the identification of the localisation of compounds within a garlic clove. Visualisation of the spatial distribution of garlic low-molecular weight compounds with nanoparticle-based MSI. Compounds occurring on the cross-section of sprouted garlic has been transferred to gold-nanoparticle enhanced target (AuNPET) by imprinting. The imprint was then subjected to MSI analysis. The results suggest that low molecular weight compounds, such as amino acids, dipeptides, fatty acids, organosulphur and organoselenium compounds are distributed within the garlic clove in a characteristic manner. It can be connected with their biological functions and metabolic properties in the plant. New methodology for the visualisation of low molecular weight compounds allowed a correlation to be made between their spatial distribution within a sprouted garlic clove and their biological function. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Effects of molecular weight of PVA on formation, stability and deformation of compound droplets for ICF polymer shells

Science.gov (United States)

Liu, Meifang; Zheng, Yueqing; Li, Jie; Chen, Sufen; Liu, Yiyang; Li, Jing; Li, Bo; Zhang, Zhanwen

2017-01-01

Sphericity and wall thickness uniformity are some of the hardest specifications to fulfill, as required by inertial confined fusion (ICF) research for polymer shells prepared by the microencapsulation technique. Driven by the need to control the deformation of compound droplets, the effects of the molecular weight of poly(vinyl alcohol) (PVA) on the formation and stability of the droplets, as well as the sphericity and wall thickness uniformity of the resulting shells, were investigated. On increasing the molecular weight of the PVA, the densities of the external water phases (W2) are almost the same, but the viscosity of the W2 phase increases more quickly than the interfacial tension. This makes the detaching force increase more quickly than the upward one, causing the formation of compound droplets and detachment from the oil tube. On the other hand, the increase in interfacial tension makes the maximum pressures ( P max) in the O phase (O) of the compound droplets increase, causing them to rupture easily and decreasing their stability. However, for PVA with the same molecular weight, the viscous shear force in the flowing field reduces the role of gravity and makes the inner water droplet move towards the center of the compound droplet, decreasing its P max in the flowing field and improving its stability. Moreover, during the solidifying process, the viscous shear force increases more quickly than the interfacial tension force due to the quicker increase in viscosity with an increase in the molecular weight of the PVA. The increase in the viscous shear force can make the droplets deform, resulting in a decrease in their sphericity. However, the appropriate viscous shear force can also center the compound droplet—although they become decentered when the viscous shear force is too large, leading to the wall thickness uniformity increasing at first before decreasing quickly. The results presented in this work provide a more in-depth understanding of the

Reaction of low-molecular-mass organoselenium compounds (and their sulphur analogues) with inflammation-associated oxidants

DEFF Research Database (Denmark)

Carroll, L.; Davies, Michael J.; Pattison, D. I.

2015-01-01

Selenium is an essential trace element in mammals, with the majority specifically encoded as seleno-L-cysteine into a range of selenoproteins. Many of these proteins play a key role in modulating oxidative stress, via either direct detoxification of biological oxidants, or repair of oxidised...... the chemistry of low-molecular-mass organoselenium compounds (e.g. selenoethers, diselenides and selenols) with inflammatory oxidants, with a particular focus on the reaction kinetics and product studies, with the differences in reactivity between selenium and sulphur analogues described in the selected...... examples. These data provide insight into the therapeutic potential of low-molecular-mass selenium-containing compounds to modulate the activity of both radical and molecular oxidants and provide protection against inflammation-induced damage. Progress in their therapeutic development (including modulation...

Separation of rare earths by means of acid organophosphorous compounds. Structure-activity study by molecular simulation

International Nuclear Information System (INIS)

Fourcot, Fabrice

1991-01-01

The increasing number of industrial applications of rare earths has resulted in an increased demand in purified rare earths whereas their separation is difficult due to their high chemical similarity. The search for a better separation leads to the search for more selective extraction agents. Organophosphorous compounds appear to be the most selective. As the search for new extraction agents resulting in high lanthanide extraction efficiency or in a better selectivity between rare earths has been mainly empiric, this research thesis aims at developing a molecular simulation method which allows the number of molecules to be synthesized and tested to be reduced. After having briefly recalled general knowledge on liquid-liquid extraction and on rare earths, and described calculation methods (quantum methods, methods based on molecular mechanics, conformational analysis, methods of charge calculation), the author proposes a critical review of literature related to rare earth liquid-liquid extraction by organophosphorous acids with respect to the used extraction agent. The molecular modelling issue is then addressed by describing ways to apply it to extraction problems, faced problems, brought solutions and obtained results

CFTR chloride channel as a molecular target of anthraquinone compounds in herbal laxatives

Science.gov (United States)

Yang, Hong; Xu, Li-na; He, Cheng-yan; Liu, Xin; Fang, Rou-yu; Ma, Tong-hui

2011-01-01

Aim: To clarify whether CFTR is a molecular target of intestinal fluid secretion caused by the anthraquinone compounds from laxative herbal plants. Methods: A cell-based fluorescent assay to measure I− influx through CFTR chloride channel. A short-circuit current assay to measure transcellular Cl− current across single layer FRT cells and freshly isolated colon mucosa. A closed loop experiment to measure colon fluid secretion in vivo. Results: Anthraquinone compounds rhein, aloe-emodin and 1,8-dihydroxyanthraquinone (DHAN) stimulated I− influx through CFTR chloride channel in a dose-dependent manner in the presence of physiological concentration of cAMP. In the short-circuit current assay, the three compound enhanced Cl− currents in epithelia formed by CFTR-expressing FRT cells with EC50 values of 73±1.4, 56±1.7, and 50±0.5μmol/L, respectively, and Rhein also enhanced Cl− current in freshly isolated rat colonic mucosa with a similar potency. These effects were completely reversed by the CFTR selective blocker CFTRinh-172. In in vivo closed loop experiments, rhein 2 mmol/L stimulated colonic fluid accumulation that was largely blocked by CFTRinh-172. The anthraquinone compounds did not elevate cAMP level in cultured FRT cells and rat colonic mucosa, suggesting a direct effect on CFTR activity. Conclusion: Natural anthraquinone compounds in vegetable laxative drugs are CFTR potentiators that stimulated colonic chloride and fluid secretion. Thus CFTR chloride channel is a molecular target of vegetable laxative drugs. PMID:21602836

Sudden venting test of an emergency bearing for the magnet bearing type compound molecular pump

International Nuclear Information System (INIS)

Hiroki, Seiji; Abe, Tetsuya; Murakami, Yoshio; Okamoto, Masatomo; Iguchi, Masashi; Nakamura, Jyunichi; Nakazeki, Tsugito.

1995-01-01

The vacuum evacuation system for nuclear fusion reactors bears the role of exhausting hydrogen isotopes in large quantity together with helium continuously for long hours, and as the high vacuum pumps for this purpose, the mechanical pumps which can do continuous evacuation and decrease the quantity of staying radioactive tritium, such as turbo molecular pumps and compound molecular pumps, are promising. Because of the compatibility with tritium, oil lubrication is not desirable, accordingly, the pumps with ceramic rotating vanes and magnetic bearings are demanded. As a part of the development of a magnetic bearing type mechanical pump which can be used for nuclear fusion reactors, the compound molecular pump, in which emergency bearings were incorporated, was made for trial, and the test of sudden air intrusion was carried out, as the results, various knowledges were obtained. The constitution of the testing setup, and the test results are reported. When air was injected at the pressure rise of 3.3x10 4 Pa/s from exhaust port side, after about 2.5 s, the maximum lift of 4.2x10 3 N arose. When air was injected at the pressure rise of 2.7x10 5 Pa/s from the suction part side, after about 0.4s, the maximum lift of 6.9x10 3 N arose. In the air injection alternately from the suction port and exhaust port sides, the emergency bearings functioned normally in 10 times of the test. (K.I.)

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

EFFECT OF MOLECULAR WEIGHT ON THE YIELD BEHAVIOUR OF EPY EPOXY COMPOUND

Directory of Open Access Journals (Sweden)

Magdalena Urbaniak

2016-12-01

Full Text Available A series of epoxy networks with molecular weight between crosslinks (Mc ranging from 117 to 508 g/mol were investigated by employing as DSC and DMA methods and compression testing over a broad range of test temperatures (from 20 to 120 °C and strain rates (from 0.0208 to 20.8 min–1. Mechanical characteristics vs. testing temperature and strain rate developed in relation to working conditions of EPY compound applied for machine foundation chocks as well as effect of crosslinking on glass transition temperature (Tg presented in this paper let to find out the effect of molecular architecture composed chiefly by Mc on the thermal and mechanical properties that govern yield behaviour of the material. The investigations carried out in a.m. ranges of testing temperatures and strain rates showed that whichever change of Mc is related to the change in crosslink density causing relative shift in the Tg of the compound. However, a sensitivity of the polymer material on changes in strain rate falls down with growth of testing temperature. Obtained results prove that yielding in EPY compound can be examined in categories of the Eyring’s plastic flow model in which yielding is described.

Distinct high molecular weight organic compound (HMW-OC) types in aerosol particles collected at a coastal urban site

Science.gov (United States)

Dall'Osto, M.; Healy, R. M.; Wenger, J. C.; O'Dowd, C.; Ovadnevaite, J.; Ceburnis, D.; Harrison, Roy M.; Beddows, D. C. S.

2017-12-01

Organic oligomers were discovered in laboratory-generated atmospheric aerosol over a decade ago. However, evidence for the presence of oligomers in ambient aerosols is scarce and mechanisms for their formation have yet to be fully elucidated. In this work, three unique aerosol particle types internally mixed with High molecular weight organic compounds (HMW-OC) species - likely oligomers - were detected in ambient air using single particle Aerosol Time-Of-Flight Mass Spectrometry (ATOFMS) in Cork (Ireland) during winter 2009. These particle types can be described as follows: (1) HMW-OCs rich in organic nitrogen - possibly containing nitrocatechols and nitroguaiacols - originating from primary emissions of biomass burning particles during evening times; (2) HMW-OCs internally mixed with nitric acid, occurring in stagnant conditions during night time; and (3) HMW-OCs internally mixed with sea salt, likely formed via photochemical reactions during day time. The study exemplifies the power of methodologies capable of monitoring the simultaneous formation of organic and inorganic particle-phase reaction products. Primary emissions and atmospheric aging of different types of HMW-OC contributes to aerosol with a range of acidity, hygroscopic and optical properties, which can have different impacts on climate and health.

Effects of low molecular weight fungal compounds on inflammatory gene transcription and expression in mouse alveolar macrophages.

Science.gov (United States)

Rand, Thomas G; Dipenta, J; Robbins, C; Miller, J D

2011-04-25

The inflammatory potential and molecular mechanisms underscoring inflammatory responses of lung cells to compounds from fungi that grow on damp building materials is poorly understood in vitro. In this study we evaluated the effect of pure fungal compounds on potentiating acute inflammatory response in primary mouse alveolar macrophages (AMs) and tested the hypothesis that AM responses to low molecular weight fungal compounds exhibit temporal and compound specificity that mimic that observed in the whole lung. Transcriptional responses of 13 inflammation/respiratory burst-associated genes (KC=Cxcl1, Cxcl2, Cxcl5, Cxcl10, Ccl3, Ccl112, Ccl20, IL-1β, Il-6, ifi27 Tnfα, iNOS and Blvrb) were evaluated in mouse AMs exposed to a 1ml (10(-8)mol) dose of either pure atranone C, brevianimide, cladosporin, curdlan, LPS, neoechinulin A & B, sterigmatocystin or TMC-120A for 2h, 4h and 12h PE using customized reverse transcription (RT)-PCR based arrays. Multianalyte ELISA was used to measure expression of 6 pro-inflammatory cytokines common to the transcriptional assays (Cxcl1, Cxcl10, Ccl3, IL1β, Ifn-λ and Tnf-α) to determine whether gene expression corresponded to the transcription data. Compared to controls, all of these compounds induced significant (≥2.5-fold or ≤-2.5-fold change at p≤0.05) time- and compound-specific transcriptional gene alterations in treatment AMs. The highest number of transcribed genes were in LPS treatment AMs at 12h PE (12/13) followed by neoechinulin B at 4h PE (11/13). Highest fold change values (>30) were associated with KC, Cxcl2, Cxcl5 and IL1β genes in cells exposed to LPS. Compound exposures also induced significant (p≤0.05) time- and compound-specific pro-inflammatory responses manifest as differentially elevated Cxcl1, Cxcl10, Ccl3, Ifn-λ and Tnf-α concentrations in culture supernatant of treatment AMs. Dissimilarity in transcriptional responses in AMs and our in vivo model of lung disease is likely attributable to whole lung

Molecular Properties of Red Wine Compounds and Cardiometabolic Benefits.

Science.gov (United States)

Markoski, Melissa M; Garavaglia, Juliano; Oliveira, Aline; Olivaes, Jessica; Marcadenti, Aline

2016-01-01

Wine has been used since the dawn of human civilization. Despite many health benefits, there is still a lot of discussion about the real properties of its components and its actions on cells and molecular interactions. A large part of these issues permeate the fine line between the amount of alcohol that causes problems to organic systems and the amount that could be beneficial for the health. However, even after the process of fermentation, wine conserves different organic compounds from grapes, such as polysaccharides, acids, and phenolic compounds, such as flavonoids and nonflavonoids. These substances have known anti-inflammatory and antioxidant capacities, and are considered as regulatory agents in cardiometabolic process. In this study, the main chemical components present in the wine, its interaction with molecules and biological mechanisms, and their interference with intra- and extracellular signaling are reviewed. Finally, the properties of wine that may benefit cardiovascular system are also revised.

Molecular Properties of Red Wine Compounds and Cardiometabolic Benefits

Science.gov (United States)

Markoski, Melissa M.; Garavaglia, Juliano; Oliveira, Aline; Olivaes, Jessica; Marcadenti, Aline

2016-01-01

Wine has been used since the dawn of human civilization. Despite many health benefits, there is still a lot of discussion about the real properties of its components and its actions on cells and molecular interactions. A large part of these issues permeate the fine line between the amount of alcohol that causes problems to organic systems and the amount that could be beneficial for the health. However, even after the process of fermentation, wine conserves different organic compounds from grapes, such as polysaccharides, acids, and phenolic compounds, such as flavonoids and nonflavonoids. These substances have known anti-inflammatory and antioxidant capacities, and are considered as regulatory agents in cardiometabolic process. In this study, the main chemical components present in the wine, its interaction with molecules and biological mechanisms, and their interference with intra- and extracellular signaling are reviewed. Finally, the properties of wine that may benefit cardiovascular system are also revised. PMID:27512338

Molecular Properties of Red Wine Compounds and Cardiometabolic Benefits

Directory of Open Access Journals (Sweden)

Melissa M. Markoski

2016-01-01

Full Text Available Wine has been used since the dawn of human civilization. Despite many health benefits, there is still a lot of discussion about the real properties of its components and its actions on cells and molecular interactions. A large part of these issues permeate the fine line between the amount of alcohol that causes problems to organic systems and the amount that could be beneficial for the health. However, even after the process of fermentation, wine conserves different organic compounds from grapes, such as polysaccharides, acids, and phenolic compounds, such as flavonoids and nonflavonoids. These substances have known anti-inflammatory and antioxidant capacities, and are considered as regulatory agents in cardiometabolic process. In this study, the main chemical components present in the wine, its interaction with molecules and biological mechanisms, and their interference with intra- and extracellular signaling are reviewed. Finally, the properties of wine that may benefit cardiovascular system are also revised.

Spatial distributions of and diurnal variations in low molecular weight carbonyl compounds in coastal seawater, and the controlling factors

Energy Technology Data Exchange (ETDEWEB)

Takeda, Kazuhiko, E-mail: takedaq@hiroshima-u.ac.jp [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Katoh, Shinya; Mitsui, Yumi; Nakano, Shinichi [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Nakatani, Nobutake [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Department of Environmental and Symbiotic Sciences, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501 (Japan); Sakugawa, Hiroshi [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan)

2014-09-15

We studied the spatial distributions of and the diurnal variations in four low molecular weight (LMW) carbonyl compounds, formaldehyde, acetaldehyde, propionaldehyde, and glyoxal, in coastal seawater. The samples were taken from the coastal areas of Hiroshima Bay, the Iyo Nada, and the Bungo Channel, western Japan. The formaldehyde, acetaldehyde, and glyoxal concentrations were higher in the northern part of Hiroshima Bay than at offshore sampling points in the Iyo Nada and the Bungo Channel. These three compounds were found at much higher concentrations in the surface water than in deeper water layers in Hiroshima Bay. It is noteworthy that propionaldehyde was not detected in any of the seawater samples, the concentrations present being lower than the detection limit (1 nanomole per liter (nM)) of the high performance liquid chromatography (HPLC) system we used. Photochemical and biological experiments were performed in the laboratory to help understand the characteristic distributions and fates of the LMW carbonyl compounds. The primary process controlling their fate in the coastal environment appears to be their biological consumption. The direct photo degradation of propionaldehyde, initiated by ultraviolet (UV) absorption, was observed, although formaldehyde and acetaldehyde were not degraded by UV irradiation. Our results suggest that the degradation of the LMW carbonyl compounds by photochemically formed hydroxyl radicals is relatively insignificant in the study area. Atmospheric deposition is a possible source of soluble carbonyl compounds in coastal surface seawater, but it may not influence the carbonyl concentrations in offshore waters. - Highlights: • Low molecular weight (LMW) carbonyl compounds in coastal seawater were determined. • Photochemical productions of LMW carbonyl compounds in seawater were observed. • LMW carbonyl compounds were largely consumed biologically. • Photochemical degradation was relatively insignificant in the study area.

Spatial distributions of and diurnal variations in low molecular weight carbonyl compounds in coastal seawater, and the controlling factors

International Nuclear Information System (INIS)

Takeda, Kazuhiko; Katoh, Shinya; Mitsui, Yumi; Nakano, Shinichi; Nakatani, Nobutake; Sakugawa, Hiroshi

2014-01-01

We studied the spatial distributions of and the diurnal variations in four low molecular weight (LMW) carbonyl compounds, formaldehyde, acetaldehyde, propionaldehyde, and glyoxal, in coastal seawater. The samples were taken from the coastal areas of Hiroshima Bay, the Iyo Nada, and the Bungo Channel, western Japan. The formaldehyde, acetaldehyde, and glyoxal concentrations were higher in the northern part of Hiroshima Bay than at offshore sampling points in the Iyo Nada and the Bungo Channel. These three compounds were found at much higher concentrations in the surface water than in deeper water layers in Hiroshima Bay. It is noteworthy that propionaldehyde was not detected in any of the seawater samples, the concentrations present being lower than the detection limit (1 nanomole per liter (nM)) of the high performance liquid chromatography (HPLC) system we used. Photochemical and biological experiments were performed in the laboratory to help understand the characteristic distributions and fates of the LMW carbonyl compounds. The primary process controlling their fate in the coastal environment appears to be their biological consumption. The direct photo degradation of propionaldehyde, initiated by ultraviolet (UV) absorption, was observed, although formaldehyde and acetaldehyde were not degraded by UV irradiation. Our results suggest that the degradation of the LMW carbonyl compounds by photochemically formed hydroxyl radicals is relatively insignificant in the study area. Atmospheric deposition is a possible source of soluble carbonyl compounds in coastal surface seawater, but it may not influence the carbonyl concentrations in offshore waters. - Highlights: • Low molecular weight (LMW) carbonyl compounds in coastal seawater were determined. • Photochemical productions of LMW carbonyl compounds in seawater were observed. • LMW carbonyl compounds were largely consumed biologically. • Photochemical degradation was relatively insignificant in the study area

Formation of high-molecular-weight compounds via the heterogeneous reactions of gaseous C8-C10 n-aldehydes in the presence of atmospheric aerosol components

Science.gov (United States)

Han, Yuemei; Kawamura, Kimitaka; Chen, Qingcai; Mochida, Michihiro

2016-02-01

A laboratory study on the heterogeneous reactions of straight-chain aldehydes was performed by exposing n-octanal, nonanal, and decanal vapors to ambient aerosol particles. The aerosol and blank filters were extracted using methanol. The extracts were nebulized and the resulting compositions were examined using a high-resolution time-of-flight aerosol mass spectrometer. The mass spectral analysis showed that the exposures of the aldehydes to aerosol samples increased the peak intensities in the high mass range. The peaks in the mass spectra of the aerosol samples after exposure to different aldehydes were characterized by a homologous series of peak shifts due to the addition of multiple CH2 units. This result is explained by the formation of high-molecular-weight (HMW) compounds that contain single or multiple aldehyde moieties. The HMW fragment peaks for the blank filters exposed to n-aldehydes were relatively weak, indicating an important contribution from the ambient aerosol components to the formation of the HMW compounds. Among the factors affecting the overall interaction of aldehydes with atmospheric aerosol components, gas phase diffusion possibly limited the reactions under the studied conditions; therefore, their occurrence to a similar degree in the atmosphere is not ruled out, at least for the reactions involving n-nonanal and decanal. The major formation pathways for the observed HMW products may be the self-reactions of n-aldehydes mediated by atmospheric aerosol components and the reactions of n-aldehydes with organic aerosol components. The observed formation of HMW compounds encourages further investigations into their effects on the aerosol properties as well as the organic aerosol mass in the atmosphere.

Approaches for the analysis of low molecular weight compounds with laser desorption/ionization techniques and mass spectrometry.

Science.gov (United States)

Bergman, Nina; Shevchenko, Denys; Bergquist, Jonas

2014-01-01

This review summarizes various approaches for the analysis of low molecular weight (LMW) compounds by different laser desorption/ionization mass spectrometry techniques (LDI-MS). It is common to use an agent to assist the ionization, and small molecules are normally difficult to analyze by, e.g., matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) using the common matrices available today, because the latter are generally small organic compounds themselves. This often results in severe suppression of analyte peaks, or interference of the matrix and analyte signals in the low mass region. However, intrinsic properties of several LDI techniques such as high sensitivity, low sample consumption, high tolerance towards salts and solid particles, and rapid analysis have stimulated scientists to develop methods to circumvent matrix-related issues in the analysis of LMW molecules. Recent developments within this field as well as historical considerations and future prospects are presented in this review.

High energy radiation effects on mechanical properties of butyl rubber compounds

International Nuclear Information System (INIS)

Pozenato, Cristina A.; Scagliusi, Sandra R.; Cardoso, Elisabeth C.L.; Lugao, Ademar B.

2013-01-01

The high energy radiation on butyl rubber compounds causes a number of chemical reactions that occur after initial ionization and excitation events. These reactions lead to changes in molecular mass of the polymer through scission and crosslinking of the molecules, being able to affect the physical and mechanical properties. Butyl rubber has excellent mechanical properties and oxidation resistance as well as low gas and water vapor permeability. Due to all these properties butyl rubber is widely used industrially and particularly in tires manufacturing. In accordance with various authors, the major effect of high energy, such as gamma rays in butyl rubber, is the yielding of free-radicals along with changes in mechanical properties. There were evaluated effects imparted from high energy radiation on mechanical properties of butyl rubber compounds, non-irradiated and irradiated with 25 kGy, 50 kGy, 150 kGy and 200 kGy. It was also observed a sharp reducing in stress rupture and elongation at break for doses higher than 50 kGy, pointing toward changes in polymeric chain along build-up of free radicals and consequent degradation. (author)

SGC method for predicting the standard enthalpy of formation of pure compounds from their molecular structures

International Nuclear Information System (INIS)

Albahri, Tareq A.; Aljasmi, Abdulla F.

2013-01-01

Highlights: • ΔH° f is predicted from the molecular structure of the compounds alone. • ANN-SGC model predicts ΔH° f with a correlation coefficient of 0.99. • ANN-MNLR model predicts ΔH° f with a correlation coefficient of 0.90. • Better definition of the atom-type molecular groups is presented. • The method is better than others in terms of combined simplicity, accuracy and generality. - Abstract: A theoretical method for predicting the standard enthalpy of formation of pure compounds from various chemical families is presented. Back propagation artificial neural networks were used to investigate several structural group contribution (SGC) methods available in literature. The networks were used to probe the structural groups that have significant contribution to the overall enthalpy of formation property of pure compounds and arrive at the set of groups that can best represent the enthalpy of formation for about 584 substances. The 51 atom-type structural groups listed provide better definitions of group contributions than others in the literature. The proposed method can predict the standard enthalpy of formation of pure compounds with an AAD of 11.38 kJ/mol and a correlation coefficient of 0.9934 from only their molecular structure. The results are further compared with those of the traditional SGC method based on MNLR as well as other methods in the literature

Disorder-induced amorphization of intermetallic compounds: A molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Massobrio, C. (Ecole Polytechnique Federale, Lausanne (Switzerland). Inst. de Physique Experimentale); Pontikis, V.; Doan, N.V.; Martin, G. (CEA Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France). Dept. de Physique des Particules Elementaires)

The reaction of the crystalline compound NiZr{sub 2} to imposed chemical disorder has been studied by molecular dynamics in the isobaric canonical ensemble. The cohesive energy used is inspired by the second moment apporoximation of the local density of states in the tight binding model. Imposed chemical disorder induced swelling (3% for full disorder, 1% for 10% disorder). Above 10% disorder, the crystalline structure athermally collapses to an amorphous state which retains much of the local chemical order. (orig.).

Disorder-induced amorphization of intermetallic compounds: A molecular dynamics study

International Nuclear Information System (INIS)

Massobrio, C.; Pontikis, V.; Doan, N.V.; Martin, G.

1991-01-01

The reaction of the crystalline compound NiZr 2 to imposed chemical disorder has been studied by molecular dynamics in the isobaric canonical ensemble. The cohesive energy used is inspired by the second moment apporoximation of the local density of states in the tight binding model. Imposed chemical disorder induced swelling (3% for full disorder, 1% for 10% disorder). Above 10% disorder, the crystalline structure athermally collapses to an amorphous state which retains much of the local chemical order. (orig.)

Photocatalytic oxidation of organic compounds in a hybrid system composed of a molecular catalyst and visible light-absorbing semiconductor.

Science.gov (United States)

Zhou, Xu; Li, Fei; Li, Xiaona; Li, Hua; Wang, Yong; Sun, Licheng

2015-01-14

Photocatalytic oxidation of organic compounds proceeded efficiently in a hybrid system with ruthenium aqua complexes as catalysts, BiVO4 as a light absorber, [Co(NH3)5Cl](2+) as a sacrificial electron acceptor and water as an oxygen source. The photogenerated holes in the semiconductor are used to oxidize molecular catalysts into the high-valent Ru(IV)=O intermediates for 2e(-) oxidation.

High-throughput phytochemical characterization of non-cannabinoid compounds of cannabis plant and seed, from Pakistan

International Nuclear Information System (INIS)

Ahmad, F.; Abbasi, T.; Farman, K.; Akrem, A.; Asif, M.; Mahmood, S.; Iqbal, M.U.

2018-01-01

The herbs are the natural resources for the infinite phenolic compounds that are used in pharmaceutical industry. These herbs are of significant importance due to their beneficial usage for the human health. Here, we studied a common herbs Cannabis sativa, an important member of the family Cannabaceae for phytochemical characterization. The methanol extract of whole Cannabis plant and seed was analyzed for the identification of non-cannabinoid compounds through High Performance Liquid Chromatography (HPLC) technique, because the non-cannabinoid compounds have not been much studied in C. sativa. These compounds are very useful in different diseases, used in cosmetics and as antioxidant agent. HPLC analysis revealed the presence of a variety of non-cannabinoid compounds including Quercetin, Gallic acid, p-Coumaric acid, m-Coumaric acid, Caffeic acid, Cinnamic acid, Ferulic acid, Benzoic acid and Kampferol. Furthermore, Quercetin was observed with high concentration in whole plant sample, whereas high Gallic acid and absence of m-coumaric acid was noted in the Cannabis seed. It was also observed that plant samples were with higher concentration of cinnamic acid as compared to seed. The Caffeic acid, Benzoic acid and Ferulic acid were in low concentration in both Cannabis plant and seed samples. Kampferol is another important non-cannabinoid compound that was also quantified in both samples. This research will be providing a foundation for further molecular characterization of Cannabis plant and seed for their beneficial usage. (author)

Mesoporous thin films of ``molecular squares'' as sensors for volatile organic compounds

Energy Technology Data Exchange (ETDEWEB)

Keefe, M.H.; Slone, R.V.; Hupp, J.T.; Czaplewski, K.F.; Snurr, R.Q.; Stern, C.L.

2000-04-18

Mesoporous thin films of rhenium-based molecular squares, [Re(CO){sub 3}Cl(L)]{sub 4} (L = pyrazine, 4,4{prime}-bipyridine), have been utilized as sensors for volatile organic compounds (VOCs). The sensing was conducted using a quartz crystal microbalance with the target compounds present in the gas phase at concentrations ranging from 0.05 to 1 mM. Quartz crystal microbalance studies with these materials allowed for distinction between the following VOCs: (1) small aromatic versus aliphatic molecules of almost identical size and volatility and (2) an array of benzene molecules derivatized with electron donating/withdrawing substituents. The experiments suggest that the mesoporous host materials interact with VOC guest molecules through both van der Waals and weak charge-transfer interactions. In addition, size selectivity is shown by exposure of the molecular squares to cyclic ethers of differing size.

Homozygous and compound heterozygous mutations in the FBN1 gene: unexpected findings in molecular diagnosis of Marfan syndrome.

Science.gov (United States)

Arnaud, Pauline; Hanna, Nadine; Aubart, Mélodie; Leheup, Bruno; Dupuis-Girod, Sophie; Naudion, Sophie; Lacombe, Didier; Milleron, Olivier; Odent, Sylvie; Faivre, Laurence; Bal, Laurence; Edouard, Thomas; Collod-Beroud, Gwenaëlle; Langeois, Maud; Spentchian, Myrtille; Gouya, Laurent; Jondeau, Guillaume; Boileau, Catherine

2017-02-01

Marfan syndrome (MFS) is an autosomal-dominant connective tissue disorder usually associated with heterozygous mutations in the gene encoding fibrillin-1 (FBN1). Homozygous and compound heterozygous cases are rare events and have been associated with a clinical severe presentation. Report unexpected findings of homozygosity and compound heterozygosity in the course of molecular diagnosis of heterozygous MFS and compare the findings with published cases. In the context of molecular diagnosis of heterozygous MFS, systematic sequencing of the FBN1 gene was performed in 2500 probands referred nationwide. 1400 probands carried a heterozygous mutation in this gene. Unexpectedly, among them four homozygous cases (0.29%) and five compound heterozygous cases (0.36%) were identified (total: 0.64%). Interestingly, none of these cases carried two premature termination codon mutations in the FBN1 gene. Clinical features for these carriers and their families were gathered and compared. There was a large spectrum of severity of the disease in probands carrying two mutated FBN1 alleles, but none of them presented extremely severe manifestations of MFS in any system compared with carriers of only one mutated FBN1 allele. This observation is not in line with the severe clinical features reported in the literature for four homozygous and three compound heterozygous probands. Homozygotes and compound heterozygotes were unexpectedly identified in the course of molecular diagnosis of MFS. Contrary to previous reports, the presence of two mutated alleles was not associated with severe forms of MFS. Although homozygosity and compound heterozygosity are rarely found in molecular diagnosis, they should not be overlooked, especially among consanguineous families. However, no predictive evaluation of severity should be provided. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Next generation offline approaches to trace organic compound speciation: Approaching comprehensive speciation with soft ionization and very high resolution tandem mass spectrometry

Science.gov (United States)

Khare, P.; Marcotte, A.; Sheu, R.; Ditto, J.; Gentner, D. R.

2017-12-01

Intermediate- and semi-volatile organic compounds (IVOCs and SVOCs) have high secondary organic aerosol (SOA) yields, as well as significant ozone formation potentials. Yet, their emission sources and oxidation pathways remain largely understudied due to limitations in current analytical capabilities. Online mass spectrometers are able to collect real time data but their limited mass resolving power renders molecular level characterization of IVOCs and SVOCs from the unresolved complex mixture unfeasible. With proper sampling techniques and powerful analytical instrumentation, our offline tandem mass spectrometry (i.e. MS×MS) techniques provide molecular-level and structural identification over wide polarity and volatility ranges. We have designed a novel analytical system for offline analysis of gas-phase SOA precursors collected on custom-made multi-bed adsorbent tubes. Samples are desorbed into helium via a gradual temperature ramp and sample flow is split equally for direct-MS×MS analysis and separation via gas chromatography (GC). The effluent from GC separation is split again for analysis via atmospheric pressure chemical ionization quadrupole time-of-flight mass spectrometry (APCI-Q×TOF) and traditional electron ionization mass spectrometry (EI-MS). The compounds for direct-MS×MS analysis are delivered via a transfer line maintained at 70ºC directly to APCI-Q×TOF, thus preserving the molecular integrity of thermally-labile, or other highly-reactive, organic compounds. Both our GC-MS×MS and direct-MS×MS analyses report high accuracy parent ion masses as well as information on molecular structure via MS×MS, which together increase the resolution of unidentified complex mixtures. We demonstrate instrument performance and present preliminary results from urban atmospheric samples collected from New York City with a wide range of compounds including highly-functionalized organic compounds previously understudied in outdoor air. Our work offers new

CALCULATION OF COEFFICIENT OF SHARING OCTANOL-WATER OF ORGANIC COMPOUNDS USING MOLECULAR DESCRIPTORS

Directory of Open Access Journals (Sweden)

B. Souyei

2010-12-01

Full Text Available A quantitative structure-property relationship (QSPR study is carried out to develop correlations that relate the molecular structures of organic compounds to their Octanol- Water partition coefficients, Kow , using molecular descriptors. The correlations are simple in application with good accuracy, which provide an easy, direct and relatively accurate way to calculate Kow. Such calculation gives us a model that gives results in remarkable correlation with the descriptors of blocks fragments of the atom-centered and functional groups (R2 = 0.949, δ = 0477 (R2 = 0.926,δ = 0,548 respectively.

Structural elucidation and molecular docking of a novel antibiotic compound from cyanobacterium Nostoc sp. MGL001

Directory of Open Access Journals (Sweden)

Niveshika No Name

2016-11-01

Full Text Available Cyanobacteria are rich source of array of bioactive compounds. The present study reports a novel antibacterial bioactive compound purified from cyanobacterium Nostoc sp. MGL001 using various chromatographic techniques viz. thin layer chromatography (TLC and high performance liquid chromatography (HPLC. Further characterization was done using electrospray ionisation mass spectroscopy (ESIMS and nuclear magnetic resonance (NMR and predicted structure of bioactive compound was 9-Ethyliminomethyl-12-(morpholin - 4 - ylmethoxy -5, 8, 13, 16 – tetraaza – hexacene - 2, 3 dicarboxylic acid (EMTAHDCA. Structure of EMTAHDCA clearly indicated that it is a novel compound that was not reported in literature or natural product database. The compound exhibited growth inhibiting effects mainly against the gram negative bacterial strains and produced maximum zone of inhibition at 150 μg/mL concentration. The compound was evaluated through in silico studies for its ability to bind 30S ribosomal fragment (PDB ID: 1YRJ, 1MWL, 1J7T and 1LC4 and OmpF porin protein (4GCP, 4GCQ and 4GCS which are the common targets of various antibiotic drugs. Comparative molecular docking study revealed that EMTAHDCA has strong binding affinity for these selected targets in comparison to a number of most commonly used antibiotics. The ability of EMTAHDCA to bind the active sites on the proteins and 30S ribosomal fragments where the antibiotic drugs generally bind indicated that it is functionally similar to the commercially available drugs.

Correlations and adsorption mechanisms of aromatic compounds on a high heat temperature treated bamboo biochar

International Nuclear Information System (INIS)

Yang, Kun; Yang, Jingjing; Jiang, Yuan; Wu, Wenhao; Lin, Daohui

2016-01-01

Adsorption of aromatic compounds, including polycyclic aromatic hydrocarbons, nitrobenzenes, phenols, and anilines, on a bamboo biochar produced at 700 °C (Ba700) was investigated with the mechanism discussion by isotherm fitting using the Polanyi-theory based Dubinin–Ashtakhov (DA) model. Correlations of adsorption capacity (Q 0 ) of organic compounds with their molecular sizes and melting points, as well as correlations of adsorption affinity (E) with their solvatochromic parameters (i.e., π* and α m ), on the biochar, were developed and indicating that adsorption is captured by the pore filling mechanism and derived from the hydrophobic effects of organic compounds and the forming of π-π electron donor-acceptor (EDA) interactions and hydrogen bonding interactions of organic molecules with surface sites of the biochar. The effects of organic molecular sizes and melting points on adsorption capacity are ascribed to the molecular sieving effect and the packing efficiency of the organic molecules in the biochar pores, respectively. These correlations can be used to quantitatively estimate the adsorption of organic compounds on biochars from their commonly physicochemical properties including solvatochromic parameters, melting points and molecular cross-sectional area. The prediction using these correlations is important for assessing the unknown adsorption behaviors of new organic compounds and also helpful to guide the surface modification of biochars and make targeted selection in the environmental applications of biochars as adsorbents. - Highlights: • Adsorption of organic chemicals on biochars are captured by pore filling mechanism. • Adsorption is derived from Van der Waals force, π-π EDA and H-bonding interactions. • Adsorption capacity is negatively correlated with organic molecular sizes/melting points. • Adsorption capacity is restricted by molecular sieving effect and packing efficiency. • Adsorption affinity has a LSER with chemical

Rapid Determination of Six Low Molecular Carbonyl Compounds in Tobacco Smoke by the APCI-MS/MS Coupled to Data Mining

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Wuduo Zhao

2017-01-01

Full Text Available A simple method was established for the rapid determination of low molecular carbonyl compounds by the combination of atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS/MS and data mining. The ionization was carried out in positive mode, and six low molecular carbonyl compounds of acrolein, acetone, propionaldehyde, crotonaldehyde, butanone, and butyraldehyde were analyzed by both full scan mode and daughter scan mode. To overcome the quantitative difficulties from isomer of acetone/propionaldehyde and butanone/butyraldehyde, the quantitation procedure was performed with the characteristic ion of [CH3O]+ under CID energy of 5 and 15 eV. Subsequently, the established method was successfully applied to analysis of six low molecular carbonyl compounds in tobacco smoke with analytical period less than four minutes. The contents of acrolein, acetone, propionaldehyde, crotonaldehyde, butanone, and butyraldehyde for a cigarette were about 63±5.8, 325±82, 55±9.7, 11±1.4, 67±5.9, and 12±1.8 μg/cig, respectively. The experimental results indicated that the established method had the potential application in rapid determination of low molecular carbonyl compounds.

Molecular analysis of petroleum derived compounds that adsorb onto gas hydrate surfaces

International Nuclear Information System (INIS)

Borgund, Anna E.; Hoiland, Sylvi; Barth, Tanja; Fotland, Per; Askvik, Kjell M.

2009-01-01

Field observations have shown that some streams of water, gas and crude oil do not form gas hydrate plugs during petroleum production even when operating within thermodynamic conditions for hydrate formation. Also, when studied under controlled laboratory conditions, some oils are found to form hydrate dispersed systems whereas others form plugs. Oils with low tendency to form hydrate plugs are believed to contain natural hydrate plug inhibiting components (NICs) that adsorb onto the hydrate surface, making them less water-wet and preventing the particles from agglomerating into large hydrate clusters. The molecular structure of the NICs is currently unknown. In this work, hydrate adsorbing components were extracted from crude oils using freon hydrates as an extraction phase. The fractions were found to be enriched in polar material, and more polar material is associated with hydrates generated in biodegraded crude oils than in non-biodegraded oils. Various fractionation schemes and analytical techniques have been applied in the search for molecular characterisation. The average molecular weights were found to be approximately 500 g/mole. GC-MS chromatograms show a large UCM (Unresolved Complex Mixture). Thus, GC-MS has a limited potential for identification of compounds. A commercial biosurfactant was used as a model compound in the search for similar structures in the extracts. The results from analysis of the hydrate adsorbing components suggest that the type and structure are more important for hydrate morphology than the amount of material adsorbed.

Machine learning of molecular electronic properties in chemical compound space

International Nuclear Information System (INIS)

Montavon, Grégoire; Müller, Klaus-Robert; Rupp, Matthias; Gobre, Vivekanand; Hansen, Katja; Tkatchenko, Alexandre; Vazquez-Mayagoitia, Alvaro; Anatole von Lilienfeld, O

2013-01-01

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure–property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine’ is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost. (paper)

Machine learning of molecular electronic properties in chemical compound space

Science.gov (United States)

Montavon, Grégoire; Rupp, Matthias; Gobre, Vivekanand; Vazquez-Mayagoitia, Alvaro; Hansen, Katja; Tkatchenko, Alexandre; Müller, Klaus-Robert; Anatole von Lilienfeld, O.

2013-09-01

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine’ is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost.

Determination of high molecular mass compounds from Amazonian plant's leaves

International Nuclear Information System (INIS)

Siqueira, Denilson Soares de; Pereira, Alberto dos Santos; Aquino Neto, Francisco Radler de; Simoneit, Bernd R.T.

2003-01-01

The fractions of dichloromethane extracts of leaves from andiroba (Carapa guianensis - Meliaceae), caapi (Banisteriopsis caapi - Malpighiaceae), cocoa (Theobroma cacao - Sterculiaceae), Brazil nut (Bertholletia excelsa - Lecytidaceae), cupuacu (Theobroma grandiflorum - Sterculiaceae), marupa (Simaruba amara - Simaroubaceae) and rubber tree (Hevea brasiliensis - Euphorbiaceae), were analyzed by HT-HRGC and HT-HRGC-MS. Esters of homologous series of fatty acids and long chain alcohols, phytol, amyrines and tocopherols were characterized. The characterization of the compounds was based mainly in mass spectra data and in addition by usual spectrometric data ( 1 H and 13 C NMR, IR). (author)

Dependence of negative muon depolarization on molecular weight and temperature in organic compounds

International Nuclear Information System (INIS)

Djuraev, A.A.; Evseev, V.S.; Obukhov, Yu.V.; Roganov, V.S.

2009-01-01

An atomic capture of negative muons in the aliphatic spirit series, the dependence of muon rest polarization on the molecular weight of spirit have been studied. The temperature dependence of depolarization in benzole and styrene has been obtained. The results on depolarization are being interpreted basing on notions about chemical interactions of mesic atoms in organic compounds. (author)

New 1,2,4-triazine bearing compounds: molecular modeling, synthesis and biotesting

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Negrutska V. V.

2009-12-01

Full Text Available Aim. To enlarge a spectrum of biologically active compounds in the series of the 1,2,4-triazino[5,6-b] [1,4]benzothiazine (1,2,4-TBT derivatives and reveal among them efficient inhibitors of RNA synthesis Methods. The methods of structure optimization of the 3-oxo-1,2,4-TBT by fragment-oriented substitution, the molecular doking of new structures in a virtual target, the rational chemical synthesis of the theoretically predicted compounds and their testing in the system of transcription in vitro. Results. The series of 1,2,4-TBT derivatives with substituents in the benzene and triazine cycles of a base molecule were synthesized. The testing of synthesized compounds in the in vitro transcription system directed by T7 RNA polymerase revealed the structure- and concentration-dependent inhibition of the RNA synthesis by some of these compounds. The experimental and virtual screening data for all investigated compounds have a good correlation. It was found that most effective derivative is the 3-oxo-8-butyl-1,2,4-TBT which completely inhibited transcription at the concentration of 6 mg/ml. Conclusions. The biotesting results allow us to assume that the inhibition of RNA synthesis is caused by binding of the 3-oxo- 8-butyl-1,2,4-TBT to both free RNA polymerase molecules and those including in a transcriptional complex with DNA

MOLECULAR DOCKING OF COMPOUNDS FROM Chaetomium Sp. AGAINST HUMAN ESTROGEN RECEPTOR ALPHA IN SEARCHING ANTI BREAST CANCER

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Maywan Hariono

2016-05-01

Full Text Available A study on molecular docking-based virtual screening has been conducted to select virtual hit of compounds, reported its existence in fungal endophytes of Chaetomium sp. as cytotoxic agent of breast cancer. The ligands were docked into Human Estrogen Receptor alpha (HERa as the protein which regulates the breast cancer growth via estradiol-estrogen receptor binding intervention. The results showed that two compounds bearing xanthone and two compounds bearing benzonaphtyridinedione scaffolds were selected as virtual hit ligands for HERa leading to the conclusion that these compounds were good to be developed as anti breast cancer.

Prediction of the Fate of Organic Compounds in the Environment From Their Molecular Properties: A Review.

Science.gov (United States)

Mamy, Laure; Patureau, Dominique; Barriuso, Enrique; Bedos, Carole; Bessac, Fabienne; Louchart, Xavier; Martin-Laurent, Fabrice; Miege, Cecile; Benoit, Pierre

2015-06-18

A comprehensive review of quantitative structure-activity relationships (QSAR) allowing the prediction of the fate of organic compounds in the environment from their molecular properties was done. The considered processes were water dissolution, dissociation, volatilization, retention on soils and sediments (mainly adsorption and desorption), degradation (biotic and abiotic), and absorption by plants. A total of 790 equations involving 686 structural molecular descriptors are reported to estimate 90 environmental parameters related to these processes. A significant number of equations was found for dissociation process (pK a ), water dissolution or hydrophobic behavior (especially through the K OW parameter), adsorption to soils and biodegradation. A lack of QSAR was observed to estimate desorption or potential of transfer to water. Among the 686 molecular descriptors, five were found to be dominant in the 790 collected equations and the most generic ones: four quantum-chemical descriptors, the energy of the highest occupied molecular orbital (E HOMO ) and the energy of the lowest unoccupied molecular orbital (E LUMO ), polarizability (α) and dipole moment (μ), and one constitutional descriptor, the molecular weight. Keeping in mind that the combination of descriptors belonging to different categories (constitutional, topological, quantum-chemical) led to improve QSAR performances, these descriptors should be considered for the development of new QSAR, for further predictions of environmental parameters. This review also allows finding of the relevant QSAR equations to predict the fate of a wide diversity of compounds in the environment.

Aromatic C-Nitroso Compounds and Their Dimers: A Model for Probing the Reaction Mechanisms in Crystalline Molecular Solids

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Ivana Biljan

2017-12-01

Full Text Available This review is focused on the dimerization and dissociation of aromatic C-nitroso compounds and their dimers, the reactions that could be used as a convenient model for studying the thermal organic solid-state reaction mechanisms. This molecular model is simple because it includes formation or breaking of only one covalent bond between two nitrogen atoms. The crystalline molecular solids of nitroso dimers (azodioxides dissociate by photolysis under the cryogenic conditions, and re-dimerize by slow warming. The thermal re-dimerization reaction is examined under the different topotactic conditions in crystals: disordering, surface defects, and phase transformations. Depending on the conditions, and on the molecular structure, aromatic C-nitroso compounds can associate to form one-dimensional polymeric structures and are able to self-assemble on gold surfaces.

Research of operational properties of compound based on high viscosity styrene-butadiene rubber SSBR-2560 TDAE HV

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M. I. Falyakhov

2016-01-01

Full Text Available The article consider the influence of replacement of SSBR-2560 TDAE batch production on high viscosity SSBR-2560-TDAE HV in the tread recipe on the tire performance properties. Obtained samples were highly viscosity styrene butadiene rubber did not differ in the microstructure of the SSBR-2560 TDAE batch production. Increasing the molecular weight possible to increase the Mooney viscosity of the rubber, however, is known to one of adverse factors is the deterioration of processability of rubber compounds based on polymers. In this connection, investigated the behavior in the step mixing compound based on high viscosity SSBR rubber. We chose recipes tread of the tire with a high content of organic silicon filler. It is established that the equivalent replacement of the polymer in the tread recipe does not lead to significant changes in the basic parameters of rubber mixing. We observed a slight increase in the energy consumption for the preparation of the rubber compounds, as well as the discharge temperature at each stage. It was shown to improve the distribution of the filler in the polymer matrix for the compound based on SSBR-2560 TDAE HV. The results showed that compound based on high viscosity SSBR improves rolling resistance and traction characteristics, while maintaining abrasion in comparison with the SSBR-2560-M27 batch production. Recommended use this brand in the production of rubber car tires.

Chemosensors for detection of nitroaromatic compounds (explosives)

Science.gov (United States)

Zyryanov, G. V.; Kopchuk, D. S.; Kovalev, I. S.; Nosova, E. V.; Rusinov, V. L.; Chupakhin, O. N.

2014-09-01

The key types of low-molecular-mass chemosensors for the detection of nitroaromatic compounds representing energetic substances (explosives) are analyzed. The coordination and chemical properties of these chemosensors and structural features of their complexes with nitroaromatic compounds are considered. The causes and methods for attaining high selectivity of recognition are demonstrated. The primary attention is paid to the use of low-molecular-mass chemosensors for visual detection of explosives of this class by colorimetric and photometric methods. Examples of using photo- and chemiluminescence for this purpose are described. A separate section is devoted to electrochemical methods of detection of nitroaromatic compounds. Data published from 2000 to 2014 are mainly covered. The bibliography includes 245 references.

Chemosensors for detection of nitroaromatic compounds (explosives)

International Nuclear Information System (INIS)

Zyryanov, G V; Kopchuk, D S; Rusinov, V L; Chupakhin, O N; Kovalev, I S; Nosova, E V

2014-01-01

The key types of low-molecular-mass chemosensors for the detection of nitroaromatic compounds representing energetic substances (explosives) are analyzed. The coordination and chemical properties of these chemosensors and structural features of their complexes with nitroaromatic compounds are considered. The causes and methods for attaining high selectivity of recognition are demonstrated. The primary attention is paid to the use of low-molecular-mass chemosensors for visual detection of explosives of this class by colorimetric and photometric methods. Examples of using photo- and chemiluminescence for this purpose are described. A separate section is devoted to electrochemical methods of detection of nitroaromatic compounds. Data published from 2000 to 2014 are mainly covered. The bibliography includes 245 references

Molecules and Models The molecular structures of main group element compounds

CERN Document Server

Haaland, Arne

2008-01-01

This book provides a systematic description of the molecular structures and bonding in simple compounds of the main group elements with particular emphasis on bond distances, bond energies and coordination geometries. The description includes the structures of hydrogen, halogen and methyl derivatives of the elements in each group, some of these molecules are ionic, some polar covalent. The survey of molecules whose structures conform to well-established trends is followed byrepresentative examples of molecules that do not conform. We also describe electron donor-acceptor and hydrogen bonded co

Selective adsorption of volatile organic compounds in micropore aluminum methylphosphonate-alpha: a combined molecular simulation-experimental approach.

Science.gov (United States)

Herdes, Carmelo; Valente, Anabela; Lin, Zhi; Rocha, João; Coutinho, João A P; Medina, Francisco; Vega, Lourdes F

2007-06-19

Results concerning the adsorption capacity of aluminum methylphosphonate polymorph alpha (AlMePO-alpha) for pure ethyl chloride and vinyl chloride by measured individual adsorption isotherms of these pure compounds are presented and discussed here. The experimental data supports the idea of using these materials as selective adsorbents for separating these compounds in mixtures. To explore this possibility further, we have performed grand canonical Monte Carlo simulations using a recently proposed molecular simulation framework for gas adsorption on AlMePO, and the results are presented here. The molecular model of the material was used in a purely transferable manner from a previous work (Herdes, C.; Lin, Z.; Valente, A.; Coutinho, J. A. P.; Vega, L. F. Langmuir 2006, 22, 3097). Regarding the molecular model of the fluids, an existing model for ethyl chloride was improved to capture the experimental dipole value better; an equivalent force field for the vinyl chloride molecule was also developed for simulation purposes. Simulations of the pure compounds were found to be in excellent agreement with the measured experimental data at the three studied temperatures. Simulations were also carried out in a purely predictive manner as a tool to find the optimal conditions for the selective adsorption of these compounds prior experimental measurements are carried out. The influence of the temperature and the bulk composition on the adsorption selectivity was also investigated. Results support the use of AlMePO-alpha as an appropriate adsorbent for the purification process of vinyl chloride, upholding the selective adsorption of ethyl chloride.

Novel Anthra[1,2-c][1,2,5]Thiadiazole-6,11-Diones as Promising Anticancer Lead Compounds: Biological Evaluation, Characterization & Molecular Targets Determination.

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Ahmed Atef Ahmed Ali

Full Text Available The novel compounds NSC745885 and NSC757963 developed at our laboratory were tested against a panel of 60 cancer cell lines at the National Cancer Institute, USA, and a panel of 39 cancer cell lines at the Japanese Foundation of Cancer Research. Both compounds demonstrated selective unique multi-log differential patterns of activity, with GI50 values in the sub-micro molar range against cancer cells rather than normal cardiac cells. NSC757963 showed high selectivity towards the leukemia subpanel. Activities of both compounds strongly correlated to expression of NFKB1 and CSNK2B genes, implying that they may inhibit the NF-κB pathway. Immunocytochemical microscopy of OVCAR-3 cells showed clear cytosolic accumulation of the NF-κB p65 subunit following treatment. Western blotting showed dose dependent inhibition of the nuclear expression of the NF-κB p65 subunit with subsequent accumulation in the cytosol following treatment. Docking experiments showed binding of both compounds to the NF-κB activator IKKβ subunit preventing its translocation to the nucleus. Collectively, these results confirm the ability of our compounds to inhibit the constitutively active NF-κB pathway of OVCAR-3 cells. Furthermore, COMPARE analysis indicated that the activity of NSC757963 is similar to the antituberculosis agent rifamycin SV, this was confirmed by testing the antimycobacterial activity of NSC757963 against Mycobacterium tuberculosis, results revealed potent activity suitable for use in clinical practice. Molecular properties and Lipinski's parameters predicted acceptable bioavailability properties with no indication of mutagenicity, tumorigenicity, irritability and reproductive effects. Oral absorption experiments using the human Caco-2 model showed high intestinal absorption of NSC745885 by passive transport mechanism with no intestinal efflux or active transport mechanisms. The unique molecular characterization as well as the illustrated anticancer

MALDI-TOF mass spectrometry analysis of small molecular weight compounds (under 10 KDa) as biomarkers of rat hearts undergoing arecoline challenge.

Science.gov (United States)

Chen, Tung-Sheng; Chang, Mu-Hsin; Kuo, Wei-Wen; Lin, Yueh-Min; Yeh, Yu-Lan; Day, Cecilia Hsuan; Lin, Chien-Chung; Tsai, Fuu-Jen; Tsai, Chang-Hai; Huang, Chih-Yang

2013-04-01

Statistical and clinical reports indicate that betel nut chewing is strongly associated with progression of oral cancer because some ingredients in betel nuts are potential cancer promoters, especially arecoline. Early diagnosis for cancer biomarkers is the best strategy for prevention of cancer progression. Several methods are suggested for investigating cancer biomarkers. Among these methods, gel-based proteomics approach is the most powerful and recommended tool for investigating biomarkers due to its high-throughput. However, this proteomics approach is not suitable for screening biomarkers with molecular weight under 10 KDa because of the characteristics of gel electrophoresis. This study investigated biomarkers with molecular weight under 10 KDa in rats with arecoline challenge. The centrifuging vials with membrane (10 KDa molecular weight cut-off) played a crucial role in this study. After centrifuging, the filtrate (containing compounds with molecular weight under 10 KDa) was collected and spotted on a sample plate for MALDI-TOF mass spectrometry analysis. Compared to control, three extra peaks (m/z values were 1553.1611, 1668.2097 and 1740.1832, respectively) were found in sera and two extra peaks were found in heart tissue samples (408.9719 and 524.9961, respectively). These small compounds should play important roles and may be potential biomarker candidates in rats with arecoline. This study successfully reports a mass-based method for investigating biomarker candidates with small molecular weight in different types of sample (including serum and tissue). In addition, this reported method is more time-efficient (1 working day) than gel-based proteomics approach (5~7 working days).

Photo-oxidation of 6-thioguanine by UVA: the formation of addition products with low molecular weight thiol compounds.

Science.gov (United States)

Ren, Xiaolin; Xu, Yao-Zhong; Karran, Peter

2010-01-01

The thiopurine, 6-thioguanine (6-TG) is present in the DNA of patients treated with the immunosuppressant and anticancer drugs azathioprine or mercaptopurine. The skin of these patients is selectively sensitive to UVA radiation-which comprises >90% of the UV light in incident sunlight-and they suffer high rates of skin cancer. UVA irradiation of DNA 6-TG produces DNA lesions that may contribute to the development of cancer. Antioxidants can protect 6-TG against UVA but 6-TG oxidation products may undergo further reactions. We characterize some of these reactions and show that addition products are formed between UVA-irradiated 6-TG and N-acetylcysteine and other low molecular weight thiol compounds including β-mercaptoethanol, cysteine and the cysteine-containing tripeptide glutathione (GSH). GSH is also adducted to 6-TG-containing oligodeoxynucleotides in an oxygen- and UVA-dependent nucleophilic displacement reaction that involves an intermediate oxidized 6-TG, guanine sulfonate (G(SO3) ). These photochemical reactions of 6-TG, particularly the formation of a covalent oligodeoxynucleotide-GSH complex, suggest that crosslinking of proteins or low molecular weight thiol compounds to DNA may be a previously unrecognized hazard in sunlight-exposed cells of thiopurine-treated patients. © 2010 The Authors. Journal Compilation. The American Society of Photobiology.

Synthesis and stability of hydrogen selenide compounds at high pressure

Energy Technology Data Exchange (ETDEWEB)

Pace, Edward J.; Binns, Jack; Alvarez, Miriam Pena; Dalladay-Simpson, Philip; Gregoryanz, Eugene; Howie, Ross T. (Edinburgh); (CHPSTAR- China)

2017-11-14

The observation of high-temperature superconductivity in hydride sulfide (H2S) at high pressures has generated considerable interest in compressed hydrogen-rich compounds. High-pressure hydrogen selenide (H2Se) has also been predicted to be superconducting at high temperatures; however, its behaviour and stability upon compression remains unknown. In this study, we synthesize H2Se in situ from elemental Se and molecular H2 at pressures of 0.4 GPa and temperatures of 473 K. On compression at 300 K, we observe the high-pressure solid phase sequence (I-I'-IV) of H2Se through Raman spectroscopy and x-ray diffraction measurements, before dissociation into its constituent elements. Through the compression of H2Se in H2 media, we also observe the formation of a host-guest structure, (H2Se)2H2, which is stable at the same conditions as H2Se, with respect to decomposition. These measurements show that the behaviour of H2Se is remarkably similar to that of H2S and provides further understanding of the hydrogen chalcogenides under pressure.

Feasibility of high-resolution continuum source molecular absorption spectrometry in flame and furnace for sulphur determination in petroleum products

Science.gov (United States)

Kowalewska, Zofia

2011-07-01

For the first time, high-resolution molecular absorption spectrometry with a high-intensity xenon lamp as radiation source has been applied for the determination of sulphur in crude oil and petroleum products. The samples were analysed as xylene solutions using vaporisation in acetylene-air flame or in an electrothermally heated graphite furnace. The sensitive rotational lines of the CS molecule, belonging to the ∆ν = 0 vibrational sequence within the electronic transition X 1∑ + → A 1П, were applied. For graphite furnace molecular absorption spectrometry, the Pd + Mg organic modifier was selected. Strong interactions with Pd atoms enable easier decomposition of sulphur-containing compounds, likely through the temporal formation of Pd xS y molecules. At the 258.056 nm line, with the wavelength range covering central pixel ± 5 pixels and with application of interactive background correction, the detection limit was 14 ng in graphite furnace molecular absorption spectrometry and 18 mg kg -1 in flame molecular absorption spectrometry. Meanwhile, application of 2-points background correction found a characteristic mass of 12 ng in graphite furnace molecular absorption spectrometry and a characteristic concentration of 104 mg kg -1 in flame molecular absorption spectrometry. The range of application of the proposed methods turned out to be significantly limited by the properties of the sulphur compounds of interest. In the case of volatile sulphur compounds, which can be present in light petroleum products, severe difficulties were encountered. On the contrary, heavy oils and residues from distillation as well as crude oil could be analysed using both flame and graphite furnace vaporisation. The good accuracy of the proposed methods for these samples was confirmed by their mutual consistency and the results from analysis of reference samples (certified reference materials and home reference materials with sulphur content determined by X-ray fluorescence

Feasibility of high-resolution continuum source molecular absorption spectrometry in flame and furnace for sulphur determination in petroleum products

Energy Technology Data Exchange (ETDEWEB)

Kowalewska, Zofia, E-mail: zofia.kowalewska@obr.pl

2011-07-15

For the first time, high-resolution molecular absorption spectrometry with a high-intensity xenon lamp as radiation source has been applied for the determination of sulphur in crude oil and petroleum products. The samples were analysed as xylene solutions using vaporisation in acetylene-air flame or in an electrothermally heated graphite furnace. The sensitive rotational lines of the CS molecule, belonging to the {Delta}{nu} = 0 vibrational sequence within the electronic transition X{sup 1}{Sigma}{sup +} {yields} A{sup 1}{Pi}, were applied. For graphite furnace molecular absorption spectrometry, the Pd + Mg organic modifier was selected. Strong interactions with Pd atoms enable easier decomposition of sulphur-containing compounds, likely through the temporal formation of Pd{sub x}S{sub y} molecules. At the 258.056 nm line, with the wavelength range covering central pixel {+-} 5 pixels and with application of interactive background correction, the detection limit was 14 ng in graphite furnace molecular absorption spectrometry and 18 mg kg{sup -1} in flame molecular absorption spectrometry. Meanwhile, application of 2-points background correction found a characteristic mass of 12 ng in graphite furnace molecular absorption spectrometry and a characteristic concentration of 104 mg kg{sup -1} in flame molecular absorption spectrometry. The range of application of the proposed methods turned out to be significantly limited by the properties of the sulphur compounds of interest. In the case of volatile sulphur compounds, which can be present in light petroleum products, severe difficulties were encountered. On the contrary, heavy oils and residues from distillation as well as crude oil could be analysed using both flame and graphite furnace vaporisation. The good accuracy of the proposed methods for these samples was confirmed by their mutual consistency and the results from analysis of reference samples (certified reference materials and home reference materials with

Capture compound mass spectrometry sheds light on the molecular mechanisms of liver toxicity of two Parkinson drugs.

Science.gov (United States)

Fischer, Jenny J; Michaelis, Simon; Schrey, Anna K; Graebner, Olivia Graebner nee; Glinski, Mirko; Dreger, Mathias; Kroll, Friedrich; Koester, Hubert

2010-01-01

Capture compound mass spectrometry (CCMS) is a novel technology that helps understand the molecular mechanism of the mode of action of small molecules. The Capture Compounds are trifunctional probes: A selectivity function (the drug) interacts with the proteins in a biological sample, a reactivity function (phenylazide) irreversibly forms a covalent bond, and a sorting function (biotin) allows the captured protein(s) to be isolated for mass spectrometric analysis. Tolcapone and entacapone are potent inhibitors of catechol-O-methyltransferase (COMT) for the treatment of Parkinson's disease. We aimed to understand the molecular basis of the difference of both drugs with respect to side effects. Using Capture Compounds with these drugs as selectivity functions, we were able to unambiguously and reproducibly isolate and identify their known target COMT. Tolcapone Capture Compounds captured five times more proteins than entacapone Capture Compounds. Moreover, tolcapone Capture Compounds isolated mitochondrial and peroxisomal proteins. The major tolcapone-protein interactions occurred with components of the respiratory chain and of the fatty acid beta-oxidation. Previously reported symptoms in tolcapone-treated rats suggested that tolcapone might act as decoupling reagent of the respiratory chain (Haasio et al., 2002b). Our results demonstrate that CCMS is an effective tool for the identification of a drug's potential off targets. It fills a gap in currently used in vitro screens for drug profiling that do not contain all the toxicologically relevant proteins. Thereby, CCMS has the potential to fill a technological need in drug safety assessment and helps reengineer or to reject drugs at an early preclinical stage.

Unraveling the Molecular Mechanism of Benzothiophene and Benzofuran scaffold merged compounds binding to anti-apoptotic Myeloid cell leukemia 1.

Science.gov (United States)

Marimuthu, Parthiban; Singaravelu, Kalaimathy

2018-05-10

Myeloid cell leukemia 1 (Mcl1), is an anti-apoptotic member of the Bcl-2 family proteins, has gained considerable importance due to its overexpression activity prevents the oncogenic cells to undergo apoptosis. This overexpression activity of Mcl1 eventually develops strong resistance to a wide variety of anticancer agents. Therefore, designing novel inhibitors with potentials to elicit higher binding affinity and specificity to inhibit Mcl1 activity is of greater importance. Thus, Mcl1 acts as an attractive cancer target. Despite recent experimental advancement in the identification and characterization of Benzothiophene and Benzofuran scaffold merged compounds the molecular mechanisms of their binding to Mcl1 are yet to be explored. The current study demonstrates an integrated approach -pharmacophore-based 3D-QSAR, docking, Molecular Dynamics (MD) simulation and free-energy estimation- to access the precise and comprehensive effects of current inhibitors targeting Mcl1 together with its known activity values. The pharmacophore -ANRRR.240- based 3D-QSAR model from the current study provided high confidence (R 2 =0.9154, Q 2 =0.8736, and RMSE=0.3533) values. Furthermore, the docking correctly predicted the binding mode of highly active compound 42. Additionally, the MD simulation for docked complex under explicit-solvent conditions together with free-energy estimation exhibited stable interaction and binding strength over the time period. Also, the decomposition analysis revealed potential energy contributing residues -M231, M250, V253, R265, L267, and F270- to the complex stability. Overall, the current investigation might serve as a valuable insight, either to (i) improve the binding affinity of the current compounds or (ii) discover new generation anti-cancer agents that can effectively downregulate Mcl1 activity.

Hydrogen bonded supra-molecular framework in inorganic-organic hybrid compounds: Syntheses, structures, and photoluminescent properties

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Yan, Li; Liu, Wei; Li, Chuanbi; Wang, Yifei; Ma, Li; Dong, Qinqin

2013-03-01

Two novel compounds constructed from aromatic acid and N-Heterocyclic ligands have been synthesized by hydrothermal reaction: [Cd(mip)(1,8-NDC)(H2O)]2 (1) [mip = 2-(3-methoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline, 1,8-NDC = naphthalene-1,8-dicarboxylic acid] and Cd(mip)2(NTC)2 (2) [NTC = nicotinic acid]. Compounds 1 and 2 are characterized by elemental analysis, IR, single crystal X-ray diffraction and thermogravimetric analysis (TGA). Single-crystal X-ray investigation reveals that compounds 1-2 are 0 dimensional (0D) structures, and the existence of hydrogen bonds and π-π interactions lead the 0D to 2D novel framework. Hydrogen bonds and π-π interactions are powerful non-covalent intermolecular interactions for directing supra-molecular architectures. TG analysis shows clear courses of weight loss, which corresponds to the decomposition of different ligands. At room temperature, compound 1 exhibits emission at 449 nm upon excitation at 325 nm, and compound 2 shows a strong emission at 656 nm upon excitation at 350 nm. Fluorescent spectrum displays that compounds 1 and 2 are potential luminescent materials.

Molecular descriptor data explain market prices of a large commercial chemical compound library

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Polanski, Jaroslaw; Kucia, Urszula; Duszkiewicz, Roksana; Kurczyk, Agata; Magdziarz, Tomasz; Gasteiger, Johann

2016-06-01

The relationship between the structure and a property of a chemical compound is an essential concept in chemistry guiding, for example, drug design. Actually, however, we need economic considerations to fully understand the fate of drugs on the market. We are performing here for the first time the exploration of quantitative structure-economy relationships (QSER) for a large dataset of a commercial building block library of over 2.2 million chemicals. This investigation provided molecular statistics that shows that on average what we are paying for is the quantity of matter. On the other side, the influence of synthetic availability scores is also revealed. Finally, we are buying substances by looking at the molecular graphs or molecular formulas. Thus, those molecules that have a higher number of atoms look more attractive and are, on average, also more expensive. Our study shows how data binning could be used as an informative method when analyzing big data in chemistry.

Structure-based virtual screening and characterization of a novel IL-6 antagonistic compound from synthetic compound database

Directory of Open Access Journals (Sweden)

Wang J

2016-12-01

Full Text Available Jing Wang,1,* Chunxia Qiao,1,* He Xiao,1 Zhou Lin,1 Yan Li,1 Jiyan Zhang,1 Beifen Shen,1 Tinghuan Fu,2 Jiannan Feng1 1Department of Molecular Immunology, Beijing Institute of Basic Medical Sciences, 2First Affiliated Hospital of PLA General Hospital, Beijing, People’s Republic of China *These authors contributed equally to this work Abstract: According to the three-dimensional (3D complex structure of (hIL-6·hIL-6R·gp 1302 and the binding orientation of hIL-6, three compounds with high affinity to hIL-6R and bioactivity to block hIL-6 in vitro were screened theoretically from the chemical databases, including 3D-Available Chemicals Directory (ACD and MDL Drug Data Report (MDDR, by means of the computer-guided virtual screening method. Using distance geometry, molecular modeling and molecular dynamics trajectory analysis methods, the binding mode and binding energy of the three compounds were evaluated theoretically. Enzyme-linked immunosorbent assay analysis demonstrated that all the three compounds could block IL-6 binding to IL-6R specifically. However, only compound 1 could effectively antagonize the function of hIL-6 and inhibit the proliferation of XG-7 cells in a dose-dependent manner, whereas it showed no cytotoxicity to SP2/0 or L929 cells. These data demonstrated that the compound 1 could be a promising candidate of hIL-6 antagonist. Keywords: virtual screening, structural optimization, human interlukin-6, small molecular antagonist, XG-7 cells, apoptosis

Benchmarking the DFT+U method for thermochemical calculations of uranium molecular compounds and solids.

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Beridze, George; Kowalski, Piotr M

2014-12-18

Ability to perform a feasible and reliable computation of thermochemical properties of chemically complex actinide-bearing materials would be of great importance for nuclear engineering. Unfortunately, density functional theory (DFT), which on many instances is the only affordable ab initio method, often fails for actinides. Among various shortcomings, it leads to the wrong estimate of enthalpies of reactions between actinide-bearing compounds, putting the applicability of the DFT approach to the modeling of thermochemical properties of actinide-bearing materials into question. Here we test the performance of DFT+U method--a computationally affordable extension of DFT that explicitly accounts for the correlations between f-electrons - for prediction of the thermochemical properties of simple uranium-bearing molecular compounds and solids. We demonstrate that the DFT+U approach significantly improves the description of reaction enthalpies for the uranium-bearing gas-phase molecular compounds and solids and the deviations from the experimental values are comparable to those obtained with much more computationally demanding methods. Good results are obtained with the Hubbard U parameter values derived using the linear response method of Cococcioni and de Gironcoli. We found that the value of Coulomb on-site repulsion, represented by the Hubbard U parameter, strongly depends on the oxidation state of uranium atom. Last, but not least, we demonstrate that the thermochemistry data can be successfully used to estimate the value of the Hubbard U parameter needed for DFT+U calculations.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

KAUST Repository

Wang, Zhandong

2017-11-28

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

KAUST Repository

Wang, Zhandong; Popolan-Vaida, Denisia M.; Chen, Bingjie; Moshammer, Kai; Mohamed, Samah; Wang, Heng; Sioud, Salim; Raji, Misjudeen; Kohse-Hö inghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Leone, Stephen R.; Sarathy, Mani

2017-01-01

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

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Daniel Petras

2017-12-01

Full Text Available Dissolved organic matter (DOM is arguably one of the most complex exometabolomes on earth, and is comprised of thousands of compounds, that together contribute more than 600 × 1015 g carbon. This reservoir is primarily the product of interactions between the upper ocean's microbial food web, yet abiotic processes that occur over millennia have also modified many of its molecules. The compounds within this reservoir play important roles in determining the rate and extent of element exchange between inorganic reservoirs and the marine biosphere, while also mediating microbe-microbe interactions. As such, there has been a widespread effort to characterize DOM using high-resolution analytical methods including nuclear magnetic resonance spectroscopy (NMR and mass spectrometry (MS. To date, molecular information in DOM has been primarily obtained through calculated molecular formulas from exact mass. This approach has the advantage of being non-targeted, accessing the inherent complexity of DOM. Molecular structures are however still elusive and the most commonly used instruments are costly. More recently, tandem mass spectrometry has been employed to more precisely identify DOM components through comparison to library mass spectra. Here we describe a data acquisition and analysis workflow that expands the repertoire of high-resolution analytical approaches available to access the complexity of DOM molecules that are amenable to electrospray ionization (ESI MS. We couple liquid chromatographic separation with tandem MS (LC-MS/MS and a data analysis pipeline, that integrates peak extraction from extracted ion chromatograms (XIC, molecular formula calculation and molecular networking. This provides more precise structural characterization. Although only around 1% of detectable DOM compounds can be annotated through publicly available spectral libraries, community-wide participation in populating and annotating DOM datasets could rapidly increase the

Using Molecular Modeling in Teaching Group Theory Analysis of the Infrared Spectra of Organometallic Compounds

Science.gov (United States)

Wang, Lihua

2012-01-01

A new method is introduced for teaching group theory analysis of the infrared spectra of organometallic compounds using molecular modeling. The main focus of this method is to enhance student understanding of the symmetry properties of vibrational modes and of the group theory analysis of infrared (IR) spectra by using visual aids provided by…

Transformations in refractory compounds, caused by high pressures and temperatures

International Nuclear Information System (INIS)

Zajnulin, Yu.G.; Alyamovskij, S.I.; Shvejkin, G.P.

1979-01-01

Considered is the effect of high pressures and temperatures on structural features of refractory carbides, nitrides and monooxides of transition metals. The results are discussed on the basis of one component of the theory on daltonides and bertollides by N.S. Kurnakov - the theory of imaginary compounds, developed by G.B. Bokij. Several new ideas, resulting from this consideration, are formulated, It is shown that at high pressures and temperatures it is possible to obtain new electron modifications of compounds and to expand sufficiently the region of the existance of variable composition phases. The concept on imaginary compounds is shown to be true. A supposition is made on realization of numerous imaginary compounds at high pressures and temperatures. Other ways of production of imaginary compounds are recommended

Rapid profiling of antimicrobial compounds characterising B. subtilis TR50 cell-free filtrate by high-performance liquid chromatography coupled to high-resolution Orbitrap™ mass spectrometry.

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Monaci, Linda; Quintieri, Laura; Caputo, Leonardo; Visconti, Angelo; Baruzzi, Federico

2016-01-15

Several Bacillus strains, typically isolated from different food sources, represent renowned producers of a multitude of low and high molecular weight compounds, including lipopeptides and macrolactones, with an importance for their antimicrobial activity. The high homology shared by many of these compounds also occurring as closely related isoforms poses a challenge in their prompt detection. Identification and structural elucidation is generally achieved by matrix-assisted laser desorption/ionization (MALDI) or liquid chromatography (LC) coupled to mass spectrometry (MS) after a pre-fractionation and/or purification step of the extract. In this paper we report the application of a method based on LC separation and high-resolution Orbitrap™-based MS for the rapid screening of raw filtrate of the strain Bacillus subtilis TR50 endowed with antimicrobial activity, without requiring any sample pre-treatment. Upon direct analysis of the cell-free filtrate of Bacillus subtilis TR50 by high-resolution mass spectrometry (HRMS), different compounds families, that proved to exert a remarked antimicrobial activity against several foodborne pathogens, can be readily displayed along the chromatographic run. Among them, three different classes were identified and characterized belonging to the iturin, fengycin and surfactin groups. The high resolving power and accurate mass accuracy provided by the HRMS system in use ensured an enhanced selectivity compared to other mass spectrometers. In addition, after activation of the HCD cell, the HR-MS/MS spectra can provide insights in the structural elucidation of several compounds. The acquisition of HRMS spectra of raw filtrates of subtilis strains allows untargeted analysis of the major classes of compounds produced to be performed, thus facilitating identification of other unknown bioactive molecules after retrospective analysis. These features make this approach a fast tool applicable to the rapid screening and further

Block of the Mevalonate Pathway Triggers Oxidative and Inflammatory Molecular Mechanisms Modulated by Exogenous Isoprenoid Compounds

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Paola Maura Tricarico

2014-04-01

Full Text Available Deregulation of the mevalonate pathway is known to be involved in a number of diseases that exhibit a systemic inflammatory phenotype and often neurological involvements, as seen in patients suffering from a rare disease called mevalonate kinase deficiency (MKD. One of the molecular mechanisms underlying this pathology could depend on the shortage of isoprenoid compounds and the subsequent mitochondrial damage, leading to oxidative stress and pro-inflammatory cytokines’ release. Moreover, it has been demonstrated that cellular death results from the balance between apoptosis and pyroptosis, both driven by mitochondrial damage and the molecular platform inflammasome. In order to rescue the deregulated pathway and decrease inflammatory markers, exogenous isoprenoid compounds were administered to a biochemical model of MKD obtained treating a murine monocytic cell line with a compound able to block the mevalonate pathway, plus an inflammatory stimulus. Our results show that isoprenoids acted in different ways, mainly increasing the expression of the evaluated markers [apoptosis, mitochondrial dysfunction, nucleotide-binding oligomerization-domain protein-like receptors 3 (NALP3, cytokines and nitric oxide (NO]. Our findings confirm the hypothesis that inflammation is triggered, at least partially, by the shortage of isoprenoids. Moreover, although further studies are necessary, the achieved results suggest a possible role for exogenous isoprenoids in the treatment of MKD.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

International Nuclear Information System (INIS)

Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

2013-01-01

A new approach is presented that allows the efficient localization and orientation of heavy-atom cluster compounds used in experimental phasing by a molecular replacement procedure. This permits the calculation of meaningful phases up to the highest resolution of the diffraction data. Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome

NATURAL POLYACETYLENE COMPOUNDS

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A. M. Nasukhova

2014-01-01

Full Text Available In article the review of the initial stage of researches of natural polyacetylene compounds is resulted. The high reactionary ability leading to fast oxidation and degradation of these compounds, especially at influence of Uf-light, oxygen of air, pH and other factors, has caused the serious difficulties connected with an establishment of structure and studying of their physical and chemical properties. Therefore the greatest quantity of works of this stage is connected with studying of essential oils of plants from families Apiaceae, Araliaceae, Asteraceae, Campanulaceae, Olacaceae, Pittosporaceae and Santalaceae where have been found out, basically, diacetylene compounds. About development of physical and chemical methods of the analysis of possibility of similar researches have considerably extended. More than 2000 polyacetylenes are known today, from them more than 1100 are found out in plants fam. Asteraceae. Revolution in the field of molecular biology has allowed to study processes of biosynthesis of these compounds intensively.

Atomic and molecular physics of plasma-based environmental technologies for abatement of volatile organic compounds

International Nuclear Information System (INIS)

Penetrante, B. M.; Hsiao, M. C.; Bardsley, J. N.; Merritt, B. T.; Vogtin, G. E.; Kuthi, A.; Burkhart, C. P.; Bayless, J. R.

1997-01-01

Non-thermal plasma techniques represent a new generation of air emission control technology that potentially could treat large-volume emissions containing dilute concentrations of volatile organic compounds. In order to apply non-thermal plasmas in an industrial scale, it is important to establish the electrical power requirements and byproducts of the process.There is a need for reliable data concerning the primary decomposition mechanisms and subsequent chemical kinetics associated with non- thermal plasma processing of volatile organic compounds. There are many basic atomic and molecular physics issues that are essential in evaluating the economic performance of non-thermal plasma reactors. These studies are important in understanding how the input electrical power is dissipated in the plasma and how efficiently it is converted to the production of the plasma species (radicals, ions or electrons) responsible for the decomposition of the volatile organic compounds. This paper will present results from basic experimental and theoretical studies aimed at identifying the reaction mechanisms responsible for the primary decomposition of various types of volatile organic compounds. (authors)

Molecular Mobility of an Amorphous Chiral Pharmaceutical Compound: Impact of Chirality and Chemical Purity.

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Viel, Quentin; Delbreilh, Laurent; Coquerel, Gérard; Petit, Samuel; Dargent, Eric

2017-08-17

A dielectric relaxation spectroscopy (DRS) study was performed to investigate the molecular mobility of amorphous chiral diprophylline (DPL). For this purpose, both racemic DPL and a single enantiomer of DPL were considered. After fast cooling from the melt at very low temperature (-140 °C), progressive heating below and above the glass transition (T g ≈ 37 °C) induces two secondary relaxations (γ- and δ-) and primary relaxations (α-) for both enantiomeric compositions. After chemical purification of our samples by means of cooling recrystallization, no γ-process could be detected by DRS. Hence, it was highlighted that the molecular mobility in the glassy state is influenced by the presence of theophylline (TPH), the main impurity in DPL samples. We also proved that the dynamic behavior of a single enantiomer and the racemic mixture of the same purified compound are quasi-identical. This study demonstrates that the relative stability and the molecular mobility of chiral amorphous drugs are strongly sensitive to chemical purity.

Effect of Nitrooxy Compounds with Different Molecular Structures on the Rumen Methanogenesis, Metabolic Profile, and Methanogenic Community.

Science.gov (United States)

Jin, Wei; Meng, Zhenxiang; Wang, Jing; Cheng, Yanfen; Zhu, Weiyun

2017-08-01

Rumen in vitro fermentation was used to evaluate the capacity of nitrooxy compounds to mitigate rumen methane production. The following three nitrooxy compounds, each with different molecular structures, were evaluated: 2,2-dimethyl-3-(nitrooxy) propanoic (DNP), N-[2-(Nitrooxy)ethyl]-3-pyridinecarboxamide (NPD), and nitroglycerin (NG). All three compounds substantially decreased the total gas production, methane production, and the acetate:propionate ratio, while increasing hydrogen production. The growth of methanogens was specifically inhibited by all three compounds, without affecting the abundance of bacteria, anaerobic fungi, or protozoa. However, inhibition of methanogenesis required a much higher dose of DNP when compared to NPD or NG. Further investigations were conducted on NG to determine its effects on the methanogenic community. NG reduced the relative abundance of Methanomassiliicoccales, while increasing the relative abundance of Methanobrevibacter and Methanosphaera. Overall, the results suggested that all three of these nitrooxy compounds could specifically inhibit rumen methanogenesis, but NPD and NG were much more efficient than DNP at rumen methane mitigation.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

Science.gov (United States)

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

UTILIZATION OF ACTIVATED ZEOLITE AS MOLECULAR SIEVE IN CHROMATOGRAPHIC COLUMN FOR SEPARATION OF COAL TAR COMPOUNDS

Directory of Open Access Journals (Sweden)

Dwi Retno Nurotul Wahidiyah

2010-06-01

Full Text Available Application of activated zeolite (ZAA as molecular sieve to separate compounds of coal tar from vaccum fractional distillation, have been done. The size of zeolite was 10-20 mesh and used as solid phase in column chromatography with length of 30 cm. The first step of the research was coal pyrolisis and the product (tar was distillated by fractional column and vaccum system at reduced pressure 44 cmHg and maximum temperature at 200 oC. The distillate from this procedure was flowed to the column chromatography of zeolite (ZAA. The compound absorbed by zeolite was eluted with varying solvents, i.e: CCl4, acetone and ethanol. Each fraction was then analyzed by gas chromatography. The results showed, zeolite have a capability to separate the compounds of tar and it tends to absorb medium hydrocarbon. The nonpolar eluent [CCl4] gives the better result in eluting tar compound than polar (ethanol or medium polar eluents (acetone.   Keywords: zeolite, coal tar, column chromatography

Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes

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Andreoli, Federico; Del Rio, Alberto

2015-01-01

Growing evidences show that epigenetic mechanisms play crucial roles in the genesis and progression of many physiopathological processes. As a result, research in epigenetic grew at a fast pace in the last decade. In particular, the study of histone post-translational modifications encountered an extraordinary progression and many modifications have been characterized and associated to fundamental biological processes and pathological conditions. Histone modifications are the catalytic result of a large set of enzyme families that operate covalent modifications on specific residues at the histone tails. Taken together, these modifications elicit a complex and concerted processing that greatly contribute to the chromatin remodeling and may drive different pathological conditions, especially cancer. For this reason, several epigenetic targets are currently under validation for drug discovery purposes and different academic and industrial programs have been already launched to produce the first pre-clinical and clinical outcomes. In this scenario, computer-aided molecular design techniques are offering important tools, mainly as a consequence of the increasing structural information available for these targets. In this mini-review we will briefly discuss the most common types of known histone modifications and the corresponding operating enzymes by emphasizing the computer-aided molecular design approaches that can be of use to speed-up the efforts to generate new pharmaceutically relevant compounds. PMID:26082827

Molecular Dynamics Simulation Study on the Binding and Stabilization Mechanism of Antiprion Compounds to the "Hot Spot" Region of PrPC.

Science.gov (United States)

Zhou, Shuangyan; Liu, Xuewei; An, Xiaoli; Yao, Xiaojun; Liu, Huanxiang

2017-11-15

Structural transitions in the prion protein from the cellular form, PrP C , into the pathological isoform, PrP Sc , are regarded as the main cause of the transmissible spongiform encephalopathies, also known as prion diseases. Hence, discovering and designing effective antiprion drugs that can inhibit PrP C to PrP Sc conversion is regarded as a promising way to cure prion disease. Among several strategies to inhibit PrP C to PrP Sc conversion, stabilizing the native PrP C via specific binding is believed to be one of the valuable approaches and many antiprion compounds have been reported based on this strategy. However, the detailed mechanism to stabilize the native PrP C is still unknown. As such, to unravel the stabilizing mechanism of these compounds to PrP C is valuable for the further design and discovery of antiprion compounds. In this study, by molecular dynamics simulation method, we investigated the stabilizing mechanism of several antiprion compounds on PrP C that were previously reported to have specific binding to the "hot spot" region of PrP C . Our simulation results reveal that the stabilization mechanism of specific binding compounds can be summarized as (I) to stabilize both the flexible C-terminal of α2 and the hydrophobic core, such as BMD42-29 and GN8; (II) to stabilize the hydrophobic core, such as J1 and GJP49; (III) to stabilize the overall structure of PrP C by high binding affinity, as NPR-056. In addition, as indicated by the H-bond analysis and decomposition analysis of binding free energy, the residues N159 and Q160 play an important role in the specific binding of the studied compounds and all these compounds interact with PrP C in a similar way with the key interacting residues L130 in the β1 strand, P158, N159, Q160, etc. in the α1-β2 loop, and H187, T190, T191, etc. in the α2 C-terminus although the compounds have large structural difference. As a whole, our obtained results can provide some insights into the specific binding

High mobility n-type organic thin-film transistors deposited at room temperature by supersonic molecular beam deposition

Energy Technology Data Exchange (ETDEWEB)

Chiarella, F., E-mail: fabio.chiarella@spin.cnr.it; Barra, M.; Ciccullo, F.; Cassinese, A. [CNR-SPIN and Physics Department, University of Naples, Piazzale Tecchio 80, I-80125 Naples (Italy); Toccoli, T.; Aversa, L.; Tatti, R.; Verucchi, R. [IMEM-CNR-FBK Division of Trento, Via alla Cascata 56/C, I-38123 Povo (Italy); Iannotta, S. [IMEM-CNR, Parco Area delle Scienze 37/A, I-43124 Parma (Italy)

2014-04-07

In this paper, we report on the fabrication of N,N′-1H,1H-perfluorobutil dicyanoperylenediimide (PDIF-CN{sub 2}) organic thin-film transistors by Supersonic Molecular Beam Deposition. The devices exhibit mobility up to 0.2 cm{sup 2}/V s even if the substrate is kept at room temperature during the organic film growth, exceeding by three orders of magnitude the electrical performance of those grown at the same temperature by conventional Organic Molecular Beam Deposition. The possibility to get high-mobility n-type transistors avoiding thermal treatments during or after the deposition could significantly extend the number of substrates suitable to the fabrication of flexible high-performance complementary circuits by using this compound.

Molecular and compound-specific hydrogen isotope analyses of insoluble organic matter from different carbonaceous chondrite groups

Science.gov (United States)

Wang, Yi; Huang, Yongsong; Alexander, Conel M. O.'D.; Fogel, Marilyn; Cody, George

2005-07-01

We have conducted the first systematic analyses of molecular distribution and δD values of individual compounds in pyrolysates of insoluble organic matter (IOM) from different carbonaceous chondrite groups, using flash pyrolysis coupled to gas chromatography-mass spectrometry and compound-specific D/H analysis. IOM samples from six meteorites of different classifications, Elephant Moraine (EET) 92042 (CR2), Orgueil (CI1), Allan Hills (ALH) 83100 (CM1/2), Murchison (CM2), ALH 85013 (CM2), and Tagish Lake (C2) were isolated and studied. Except for the pyrolysate of Tagish Lake IOM, pyrolysates of all five meteorite IOM samples were dominated by an extensive series of aromatic (C 1 to C 7 alkyl-substituted benzenes, C 0 to C 2 alkyl-substituted naphthalenes), with aliphatic (straight chain and branched C 10 to C 15 alkanes) hydrocarbons and several S- and O- containing compounds (C 1 to C 2 alkylthiophenes, benzothiophene, benzaldehyde) being also present. The strong similarity in the pyrolysates of different carbonaceous chondrites suggests certain common characteristics in the formation mechanisms of IOM from different meteorites. The Tagish Lake IOM sample is unique in that its pyrolysate lacks most of the alkyl-substituted aromatic hydrocarbons detected in other meteorite IOM samples, suggesting distinctively different formation processes. Both bulk δD values of meteorite IOMs and weighted-average δD values of individual compounds in pyrolysates show a decreasing trend: CR2 > CI1 > CM2 > C2 (Tagish Lake), with the EET 92042 (CR2) IOM having the highest δD values (˜2000‰ higher than other samples). We attribute the high D contents in the IOM to primitive interstellar organic sources.

The cytotoxicity of organobismuth compounds with certain molecular structures can be diminished by replacing the bismuth atom with an antimony atom in the molecules.

Science.gov (United States)

Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki

2015-06-01

Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.

Generation of standard gas mixtures of halogenated, aliphatic, and aromatic compounds and prediction of the individual output rates based on molecular formula and boiling point.

Science.gov (United States)

Thorenz, Ute R; Kundel, Michael; Müller, Lars; Hoffmann, Thorsten

2012-11-01

In this work, we describe a simple diffusion capillary device for the generation of various organic test gases. Using a set of basic equations the output rate of the test gas devices can easily be predicted only based on the molecular formula and the boiling point of the compounds of interest. Since these parameters are easily accessible for a large number of potential analytes, even for those compounds which are typically not listed in physico-chemical handbooks or internet databases, the adjustment of the test gas source to the concentration range required for the individual analytical application is straightforward. The agreement of the predicted and measured values is shown to be valid for different groups of chemicals, such as halocarbons, alkanes, alkenes, and aromatic compounds and for different dimensions of the diffusion capillaries. The limits of the predictability of the output rates are explored and observed to result in an underprediction of the output rates when very thin capillaries are used. It is demonstrated that pressure variations are responsible for the observed deviation of the output rates. To overcome the influence of pressure variations and at the same time to establish a suitable test gas source for highly volatile compounds, also the usability of permeation sources is explored, for example for the generation of molecular bromine test gases.

Diazo Compounds as Highly Tunable Reactants in 1,3-Dipolar Cycloaddition Reactions with Cycloalkynes†

Science.gov (United States)

McGrath, Nicholas A.

2012-01-01

Diazo compounds, which can be accessed directly from azides by deimidogenation, are shown to be extremely versatile dipoles in 1,3-dipolar cycloaddition reactions with a cyclooctyne. The reactivity of a diazo compound can be much greater or much less than its azide analog, and is enhanced markedly in polar-protic solvents. These reactivities are predictable from frontier molecular orbital energies. The most reactive diazo compound exhibited the highest known second-order rate constant to date for a dipolar cycloaddition with a cycloalkyne. These data provide a new modality for effecting chemoselective reactions in a biological context. PMID:23227302

Modification of polyelectrolyte microcapsules into a container for the low molecular weight compounds

Science.gov (United States)

Goryacheva, O. A.; Gao, H.; Sukhorukov, G. B.

2018-04-01

Polyelectrolyte microcapsules are one of the most successful developments in the direction of target drug delivery. Nevertheless, to encapsulate low molecular weight compounds and to deliver the targeted drugs it is necessary to modify the surface of the microcapsules. Silica nanostructures obtained as result of hydrolysis of (3-Aminopropyl)- triethoxysilane (APTES) were used for the modification of the microcapsules. This material shows no toxic effect on cells and is capable of biodegradation. Amino-groups in the structure of APTES make it possible for further direct bioconjugation.

Characterization of aromatic organosulfur model compounds relevant to fossil fuels by using atmospheric pressure chemical ionization with CS2 and high-resolution tandem mass spectrometry.

Science.gov (United States)

Tang, Weijuan; Sheng, Huaming; Jin, Chunfen; Riedeman, James S; Kenttämaa, Hilkka I

2016-04-15

The chemistry of desulfurization involved in processing crude oil is greatly dependent on the forms of sulfur in the oil. Sulfur exists in different chemical bonding environments in fossil fuels, including those in thiophenes and benzothiophenes, thiols, sulfides, and disulfides. In this study, the fragmentation behavior of the molecular ions of 17 aromatic organosulfur compounds with various functionalities was systematically investigated by using high-resolution tandem mass spectrometry. Multiple-stage tandem mass spectrometric experiments were carried out using a linear quadrupole ion trap (LQIT) equipped with an atmospheric pressure chemical ionization (APCI) source. (+)APCI/CS2 was used to generate stable dominant molecular ions for all the compounds studied except for three sulfides that also showed abundant fragment ions. The LQIT coupled with an orbitrap mass spectrometer was used for elemental composition analysis, which facilitated the identification of the neutral molecules lost during fragmentation. The characteristic fragment ions generated in MS(2) and MS(3) experiments provide clues for the chemical bonding environment of sulfur atoms in the examined compounds. Upon collision-induced dissociation (CID), the molecular ions can lose the sulfur atom in a variety of ways, including as S (32 Da), HS(•) (33 Da), H2 S (34 Da), CS (44 Da), (•) CHS (45 Da) and CH2 S (46 Da). These neutral fragments are not only indicative of the presence of sulfur, but also of the type of sulfur present in the compound. Generally, losses of HS(•) and H2 S were found to be associated with compounds containing saturated sulfur functionalities, while losses of S, CS and (•) CHS were more common for heteroaromatic sulfur compounds. High-resolution tandem mass spectrometry with APCI/CS2 ionization is a viable approach to determining the types of organosulfur compounds. It can potentially be applied to analysis of complex mixtures, which is beneficial to improving the

Synthesis of Heteroaromatic Compounds by Oxidative Aromatization Using an Activated Carbon/Molecular Oxygen System

Directory of Open Access Journals (Sweden)

Masahiko Hayashi

2009-08-01

Full Text Available A variety of heteroaromatic compounds, such as substituted pyridines, pyrazoles, indoles, 2-substituted imidazoles, 2-substituted imidazoles, 2-arylbenzazoles and pyrimidin-2(1H-ones are synthesized by oxidative aromatization using the activated carbon and molecular oxygen system. Mechanistic study focused on the role of activated carbon in the synthesis of 2-arylbenzazoles is also discussed. In the final section, we will disclose the efficient synthesis of substituted 9,10-anthracenes via oxidative aromatization.

Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds.

Science.gov (United States)

Prosdocimi, Tommaso; Mollica, Luca; Donini, Stefano; Semrau, Marta S; Lucarelli, Anna Paola; Aiolfi, Egidio; Cavalli, Andrea; Storici, Paola; Alfei, Silvana; Brullo, Chiara; Bruno, Olga; Parisini, Emilio

2018-05-01

Selected members of the large rolipram-related GEBR family of type 4 phosphodiesterase (PDE4) inhibitors have been shown to facilitate long-term potentiation and to improve memory functions without causing emetic-like behavior in rodents. Despite their micromolar-range binding affinities and their promising pharmacological and toxicological profiles, few if any structure-activity relationship studies have been performed to elucidate the molecular bases of their action. Here, we report the crystal structure of a number of GEBR library compounds in complex with the catalytic domain of PDE4D as well as their inhibitory profiles for both the long PDE4D3 isoform and the catalytic domain alone. Furthermore, we assessed the stability of the observed ligand conformations in the context of the intact enzyme using molecular dynamics simulations. The longer and more flexible ligands appear to be capable of forming contacts with the regulatory portion of the enzyme, thus possibly allowing some degree of selectivity between the different PDE4 isoforms.

Photoionization mass spectrometric studies of selected compounds in a molecular beam

Energy Technology Data Exchange (ETDEWEB)

Trott, W.M.

1979-03-01

Photoionization efficiency curves have been measured at moderate to high resolution for several species produced in supersonic molecular beams of acetone, acetone-d/sub 6/ and CS/sub 2/. The molecular beam photoionization mass spectrometer which has been assembled for this work is described. The performance of this instrument has been characterized by a number of experiments and calculations.

Photoionization mass spectrometric studies of selected compounds in a molecular beam

International Nuclear Information System (INIS)

Trott, W.M.

1979-03-01

Photoionization efficiency curves have been measured at moderate to high resolution for several species produced in supersonic molecular beams of acetone, acetone-d 6 and CS 2 . The molecular beam photoionization mass spectrometer which has been assembled for this work is described. The performance of this instrument has been characterized by a number of experiments and calculations

Charged hydrogels for post-loading, release, and molecular imprinting of proteins

NARCIS (Netherlands)

Schillemans, J.P.|info:eu-repo/dai/nl/304835137

2010-01-01

Molecular imprinting is a technique to create template-shaped cavities in polymer matrices with memory of the template molecules, to be used in molecular recognition. Molecular imprinting of low molecular weight compounds is a well established technique used to create high affinity materials. On the

Superconductivity of ternary metal compounds prepared at high pressures

CERN Document Server

Shirotani, I

2003-01-01

Various ternary metal phosphides, arsenides, antimonides, silicides and germanides have been prepared at high temperatures and high pressures. These ternary metal compounds can be classified into four groups: [1] metal-rich compounds MM' sub 4 X sub 2 and [2] MM'X, [3] non-metal-rich compounds MXX' and [4] MM' sub 4 X sub 1 sub 2 (M and M' = metal element; X and X' = non-metal element). We have studied the electrical and magnetic properties of these materials at low temperatures, and found many new superconductors with the superconducting transition temperature (T sub c) of above 10 K. The metal-rich compound ZrRu sub 4 P sub 2 with a tetragonal structure showed the superconducting transition at around 11 K, and had an upper critical field (H sub c sub 2) of 12.2 tesla (T) at 0 K. Ternary equiatomic compounds ZrRuP and ZrRuSi crystallize in two modifications, a hexagonal Fe sub 2 P-type structure [h-ZrRuP(Si)] and an orthorhombic Co sub 2 P-type structure [o-ZrRuP(Si)]. Both h-ZrRuP and h-ZrRuSi have rather h...

Optic and electro-optic investigations on SmQ, SmCA* and L phases in highly chiral compounds

International Nuclear Information System (INIS)

Manai, M.; Gharbi, A.; Marcerou, J.P.; Nguyen, H.T.; Rouillon, J.C.

2005-01-01

Chiral molecules give rise to a large variety of mesophases. Well-known examples are cholesteric or ferroelectric smectic phases where the chirality tends to favor a macroscopic twist. Furthermore, the molecular core length (l) plays an important role on the range of the mesophases and on the temperature (T NI ) for the onset of orientational order. The tendency for T NI is to increase (going over 200 - bar C for some compounds) with increasing l. We report in this paper on a selection of compounds which have been designed in order to favor an anticlinic smectic ordering together with high chirality. As a common feature, they have a long rigid core with four benzene rings and a chiral chain (usually the same) at each end. They display a locally anisotropic liquid phase referred to as ''L phase'' in a large temperature range between T NI and the low temperature SmQ or SmC A * phase. Optical rotatory power (ORP), birefringence and electro-optic studies have been performed with these compounds

Antimicrobial compounds of porcine mucosa

Science.gov (United States)

Kotenkova, E. A.; Lukinova, E. A.; Fedulova, L. V.

2017-09-01

The aim of the study was to investigate porcine oral cavity mucosa (OCM), nasal cavity mucosa (NCM), rectal mucosa (RM) and tongue mucosa (TM) as sources of antimicrobial compounds. Ultrafiltrates with MW >30 kDa, MW 5-30 kDa and MW 30 kDa, the zone of microbial growth inhibition was 7.5 mm, for the MW<5 kDa fraction, it was 7 mm, and for MW 5-30 kDa fraction, it was 4.5 mm. No significant differences were found in high molecular weight proteomic profile, while qualitative and quantitative differences were observed in the medium and low molecular weight areas, especially in OCM and NCM. HPLC showed 221 tissue-specific peptides in OCM, 156 in NCM, 225 in RM, but only 5 in TM. The results observed confirmed porcine mucous tissues as a good source of antimicrobial compounds, which could be an actual alternative for reduction of microbial spoilage of foods.

Organically bound sulphur in coal: A molecular approach

NARCIS (Netherlands)

Sinninghe Damsté, J.S.; Leeuw, J.W. de

1992-01-01

A critical review of literature concerning the molecular characterization of low and high molecular weight organosulphur constitutents present in coal as well as a detailed analysis of organic sulphur compounds present in flash evaporates and pyrolysates of a suite of coals ranging in sulphur

Molecularly imprinted solid phase extraction using stable isotope labeled compounds as template and liquid chromatography-mass spectrometry for trace analysis of bisphenol A in water sample

International Nuclear Information System (INIS)

Kawaguchi, Migaku; Hayatsu, Yoshio; Nakata, Hisao; Ishii, Yumiko; Ito, Rie; Saito, Koichi; Nakazawa, Hiroyuki

2005-01-01

We have developed a molecularly imprinted polymer (MIP) using a stable isotope labeled compound as the template molecule and called it the ''isotope molecularly imprinted polymer'' (IMIP). In this study, bisphenol A (BPA) was used as the model compound. None imprinted polymer (NIP), MIP, dummy molecularly imprinted polymer (DMIP) and IMIP were prepared by the suspension polymerization method using without template, BPA, 4-tert-butylphenol (BP) and bisphenol A-d 16 (BPA-d 16 ), respectively. The polymers were subjected to molecularly imprinted solid phase extraction (MI-SPE), and the extracted samples were subjected to liquid chromatography-mass spectrometry (LC-MS). Although the leakage of BPA-d 16 from the IMIP was observed and that of BPA was not observed. The selectivity factors of MIP and IMIP for BPA were 4.45 and 4.43, respectively. Therefore, IMIP had the same molecular recognition ability as MIP. When MI-SPE with IMIP was used and followed by LC-MS in the analysis of river water sample, the detection limit of BPA was 1 ppt with high sensitivity. Moreover, the average recovery was higher than 99.8% (R.S.D.: 3.7%) by using bisphenol A- 13 C 12 (BPA- 13 C 12 ) as the surrogate standard. In addition, the IMIP were employed in MI-SPE of BPA in river water sample by LC-MS. The concentration of BPA in the river water sample was determined to be 32 pg ml -1 . We confirmed that it was possible to measure trace amounts of a target analyte by MI-SPE using IMIP

Quantification of low molecular weight compounds by MALDI imaging mass spectrometry - A tutorial review.

Science.gov (United States)

Rzagalinski, Ignacy; Volmer, Dietrich A

2017-07-01

Matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry imaging (MSI) permits label-free in situ analysis of chemical compounds directly from the surface of two-dimensional biological tissue slices. It links qualitative molecular information of compounds to their spatial coordinates and distribution within the investigated tissue. MALDI-MSI can also provide the quantitative amounts of target compounds in the tissue, if proper calibration techniques are performed. Obviously, as the target molecules are embedded within the biological tissue environment and analysis must be performed at their precise locations, there is no possibility for extensive sample clean-up routines or chromatographic separations as usually performed with homogenized biological materials; ion suppression phenomena therefore become a critical side effect of MALDI-MSI. Absolute quantification by MALDI-MSI should provide an accurate value of the concentration/amount of the compound of interest in relatively small, well-defined region of interest of the examined tissue, ideally in a single pixel. This goal is extremely challenging and will not only depend on the technical possibilities and limitations of the MSI instrument hardware, but equally on the chosen calibration/standardization strategy. These strategies are the main focus of this article and are discussed and contrasted in detail in this tutorial review. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2016 Elsevier B.V. All rights reserved.

New concepts for molecular magnets

Science.gov (United States)

Pilawa, Bernd

1999-03-01

Miller and Epstein (1994) define molecular magnets as magnetic materials which are prepared by the low-temperature methods of the preparative chemistry. This definition includes molecular crystals of neutral radicals, radical salts and charge transfer complexes as well as metal complexes and polymers with unpaired spins (Dormann 1995). The challenge of molecular magnets consists in tailoring magnetic properties by specific modifications of the molecular units. The combination of magnetism with mechanical or electrical properties of molecular compounds promise materials of high technical interest (Gatteschi 1994a and 1994b, Möhwald 1996) and both the chemical synthesis of new molecular materials with magnetic properties as well as the physical investigation and explanation of these properties is important, in order to achieve any progress. This work deals with the physical characterization of the magnetic properties of molecular materials. It is organized as follows. In the first part molecular crystals of neutral radicals are studied. After briefly discussing the general magnetic properties of these materials and after an overview over the physical principles of exchange interaction between organic radicals I focus on the interplay between the crystallographic structure and the magnetic properties of various derivatives of the verdazyl and nitronyl nitroxide radicals. The magnetic properties of metal complexes are the subject of the second part. After an overview over the experimental and theoretical tools which are used for the investigation of the magnetic properties I shortly discuss the exchange coupling of transition metal ions and the magnetic properties of complexes of two and three metal ions. Special emphasis is given to spin cluster compounds. Spin cluster denote complexes of many magnetic ions. They are attractive as building blocks of molecular magnets as well as magnetic model compounds for the study of spin frustration, molecular super

High sensitivity optical molecular imaging system

Science.gov (United States)

An, Yu; Yuan, Gao; Huang, Chao; Jiang, Shixin; Zhang, Peng; Wang, Kun; Tian, Jie

2018-02-01

Optical Molecular Imaging (OMI) has the advantages of high sensitivity, low cost and ease of use. By labeling the regions of interest with fluorescent or bioluminescence probes, OMI can noninvasively obtain the distribution of the probes in vivo, which play the key role in cancer research, pharmacokinetics and other biological studies. In preclinical and clinical application, the image depth, resolution and sensitivity are the key factors for researchers to use OMI. In this paper, we report a high sensitivity optical molecular imaging system developed by our group, which can improve the imaging depth in phantom to nearly 5cm, high resolution at 2cm depth, and high image sensitivity. To validate the performance of the system, special designed phantom experiments and weak light detection experiment were implemented. The results shows that cooperated with high performance electron-multiplying charge coupled device (EMCCD) camera, precision design of light path system and high efficient image techniques, our OMI system can simultaneously collect the light-emitted signals generated by fluorescence molecular imaging, bioluminescence imaging, Cherenkov luminance and other optical imaging modality, and observe the internal distribution of light-emitting agents fast and accurately.

Inclusion Compound Based Approach to Forming Arrays of Artificial Dipolar Molecular Rotors: A Search for Optimal Rotor Structures

Czech Academy of Sciences Publication Activity Database

Kobr, L.; Zhao, K.; Shen, X.; Shoemaker, R. K.; Rogers, C. T.; Michl, Josef

2013-01-01

Roč. 25, č. 3 (2013), s. 443-448 ISSN 0935-9648 EU Projects: European Commission(XE) 227756 - DIPOLAR ROTOR ARRAY Grant - others:NSF(US) CHE 0848663 Institutional support: RVO:61388963 Keywords : inclusion compounds * molecular rotors * ferroelectricity * two-dimensional arrays Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 15.409, year: 2013

Molecular-beam epitaxial growth and characterization of quaternary III-nitride compounds

International Nuclear Information System (INIS)

Monroy, E.; Gogneau, N.; Enjalbert, F.; Fossard, F.; Jalabert, D.; Bellet-Amalric, E.; Dang, Le Si; Daudin, B.

2003-01-01

We report on the controlled growth and characterization of quaternary AlGaInN compounds by plasma-assisted molecular beam epitaxy. Two-dimensional growth is achieved with a monolayer of In segregating at the growth front. In incorporation is hindered by increasing growth temperature and Al mole fraction, which is explained by the lower binding energy of InN compared to GaN and AlN. The mosaicity of the layers is determined by the substrate quality, whereas the alloy disorder increases with the Al content, independent of the In mole fraction. Room temperature photoluminescence is dominated by a narrow band-edge emission, whose Stokes shift and activation energy increase with the In content. This behavior is interpreted in terms of carrier localization in self-formed alloy inhomogeneities. An In-related band bowing parameter of 2.5 eV has been estimated

Calcium binding to low molecular weight compounds and health promoting products

DEFF Research Database (Denmark)

Vavrusova, Martina

absorption. Therefore, calcium as an essential nutrient should not be underestimated in our diet. Milk and dairy products are good sources of bioavailable calcium due to specific protein binding. Other sources of calcium, apart from a balanced and healthy diet, are calcium supplements and calcium fortified...... food. Therefore, an understanding of the basic chemistry of calcium binding to low molecular weight compounds can contribute to a general knowledge about calcium bioavailability and also to product improvement. Calcium precipitation with palmitate was described by a first-order reaction for conditions...... of excess calcium in neutral aqueous solutions with a stoichiometry Ca:Pal lower than 1:2. Increasing pH during aging of the precipitate and solubility product determination lead to a suggestion of an initial precipitation of calcium hydroxy palmitate as a possible precursor phase. The binding of calcium...

Identification of compounds that selectively target highly chemotherapy refractory neuroblastoma cancer stem cells.

Science.gov (United States)

Díaz-Carballo, David; Acikelli, Ali Haydar; Bardenheuer, Walter; Gustmann, Sebastian; Malak, Sascha; Stoll, Raphael; Kedziorski, Thorsten; Nazif, Mhd Ali; Jastrow, Holger; Wennemuth, Gunter; Dammann, Philip; Feigel, Martin; Strumberg, Dirk

2014-09-01

Relapse of cancer months or years after an apparently successful therapy is probably caused by cancer stem cells (CSCs) due to their intrinsic features like dormant periods, radiorefraction, and acquired multidrug resistance (MDR) phenotypes, among other mechanisms of cellular drug evasiveness. Thus, the lack of currently efficacious interventions remains a major problem in the treatment of malignancies, together with the inability of existing drugs to destroy specifically CSCs. Neuroblastomas per se are highly chemotherapy-refractory extracranial tumors in infants with very low survival rates. So far, no effective cytostatics against this kind of tumors are clinically available. Therefore, we have put much effort into the development of agents to efficiently combat this malignancy. For this purpose, we tested several compounds isolated from Cuban propolis on induced CSCs (iCSC) derived from LAN-1 neuroblastoma cells which expressed several characteristics of tumor-initiating cells both in in-vitro and in-vivo models. Some small molecules such as flavonoids and polycyclic polyprenylated acylphloroglucinols (PPAP) were isolated using successive RT-HPLC cycles and identified employing mass spectrometry and NMR spectroscopic techniques. Their cytotoxicity was first screened in sensitive cell systems by MTT proliferation assays and afterwards studied in less sensitive neuroblastoma iCSC models. We found several compounds with considerable anti-iCSC activity, most of them belonging to the PPAP class. The majority of the compounds act in a pleiotropic manner on the molecular biology of tumors although their specific targets remain unclear. Nevertheless, two substances, one of them a flavonoid, induced a strong disruption of tubulin polymerization. In addition, an unknown compound strongly inhibited replicative enzymes like toposimerases I/II and DNA polymerase. Here, we report for the first time cytotoxic activities of small molecules isolated from Caribbean propolis

Molecular corridors and parameterizations of volatility in the chemical evolution of organic aerosols

Directory of Open Access Journals (Sweden)

Y. Li

2016-03-01

Full Text Available The formation and aging of organic aerosols (OA proceed through multiple steps of chemical reaction and mass transport in the gas and particle phases, which is challenging for the interpretation of field measurements and laboratory experiments as well as accurate representation of OA evolution in atmospheric aerosol models. Based on data from over 30 000 compounds, we show that organic compounds with a wide variety of functional groups fall into molecular corridors, characterized by a tight inverse correlation between molar mass and volatility. We developed parameterizations to predict the saturation mass concentration of organic compounds containing oxygen, nitrogen, and sulfur from the elemental composition that can be measured by soft-ionization high-resolution mass spectrometry. Field measurement data from new particle formation events, biomass burning, cloud/fog processing, and indoor environments were mapped into molecular corridors to characterize the chemical nature of the observed OA components. We found that less-oxidized indoor OA are constrained to a corridor of low molar mass and high volatility, whereas highly oxygenated compounds in atmospheric water extend to high molar mass and low volatility. Among the nitrogen- and sulfur-containing compounds identified in atmospheric aerosols, amines tend to exhibit low molar mass and high volatility, whereas organonitrates and organosulfates follow high O : C corridors extending to high molar mass and low volatility. We suggest that the consideration of molar mass and molecular corridors can help to constrain volatility and particle-phase state in the modeling of OA particularly for nitrogen- and sulfur-containing compounds.

Investigation of Interactions between Thrombin and Ten Phenolic Compounds by Affinity Capillary Electrophoresis and Molecular Docking

Directory of Open Access Journals (Sweden)

Qiao-Qiao Li

2018-01-01

Full Text Available Thrombin plays a vital role in blood coagulation, which is a key process involved in thrombosis by promoting platelet aggregation and converting fibrinogen to form the fibrin clot. In the receptor concept, drugs produce their therapeutic effects via interactions with the targets. Therefore, investigation of interaction between thrombin and small molecules is important to find out the potential thrombin inhibitor. In this study, affinity capillary electrophoresis (ACE and in silico molecular docking methods were developed to study the interaction between thrombin and ten phenolic compounds (p-hydroxybenzoic acid, protocatechuic acid, vanillic acid, gallic acid, catechin, epicatechin, dihydroquercetin, naringenin, apigenin, and baicalein. The ACE results showed that gallic acids and six flavonoid compounds had relative strong interactions with thrombin. In addition, the docking results indicated that all of optimal conformations of the six flavonoid compounds were positioned into the thrombin activity centre and had interaction with the HIS57 or SER195 which was the key residue to bind thrombin inhibitors such as argatroban. Herein, these six flavonoid compounds might have the potential of thrombin inhibition activity. In addition, the developed method in this study can be further applied to study the interactions of other molecules with thrombin.

Simplified Production of Organic Compounds Containing High Enantiomer Excesses

Science.gov (United States)

Cooper, George W. (Inventor)

2015-01-01

The present invention is directed to a method for making an enantiomeric organic compound having a high amount of enantiomer excesses including the steps of a) providing an aqueous solution including an initial reactant and a catalyst; and b) subjecting said aqueous solution simultaneously to a magnetic field and photolysis radiation such that said photolysis radiation produces light rays that run substantially parallel or anti-parallel to the magnetic field passing through said aqueous solution, wherein said catalyst reacts with said initial reactant to form the enantiomeric organic compound having a high amount of enantiomer excesses.

Molecular sensors and molecular logic gates

International Nuclear Information System (INIS)

Georgiev, N.; Bojinov, V.

2013-01-01

Full text: The rapid grow of nanotechnology field extended the concept of a macroscopic device to the molecular level. Because of this reason the design and synthesis of (supra)-molecular species capable of mimicking the functions of macroscopic devices are currently of great interest. Molecular devices operate via electronic and/or nuclear rearrangements and, like macroscopic devices, need energy to operate and communicate between their elements. The energy needed to make a device work can be supplied as chemical energy, electrical energy, or light. Luminescence is one of the most useful techniques to monitor the operation of molecular-level devices. This fact determinates the synthesis of novel fluorescence compounds as a considerable and inseparable part of nanoscience development. Further miniaturization of semiconductors in electronic field reaches their limit. Therefore the design and construction of molecular systems capable of performing complex logic functions is of great scientific interest now. In semiconductor devices the logic gates work using binary logic, where the signals are encoded as 0 and 1 (low and high current). This process is executable on molecular level by several ways, but the most common are based on the optical properties of the molecule switches encoding the low and high concentrations of the input guest molecules and the output fluorescent intensities with binary 0 and 1 respectively. The first proposal to execute logic operations at the molecular level was made in 1988, but the field developed only five years later when the analogy between molecular switches and logic gates was experimentally demonstrated by de Silva. There are seven basic logic gates: AND, OR, XOR, NOT, NAND, NOR and XNOR and all of them were achieved by molecules, the fluorescence switching as well. key words: fluorescence, molecular sensors, molecular logic gates

Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening.

Science.gov (United States)

Paricharak, Shardul; IJzerman, Adriaan P; Jenkins, Jeremy L; Bender, Andreas; Nigsch, Florian

2016-09-26

Despite the usefulness of high-throughput screening (HTS) in drug discovery, for some systems, low assay throughput or high screening cost can prohibit the screening of large numbers of compounds. In such cases, iterative cycles of screening involving active learning (AL) are employed, creating the need for smaller "informer sets" that can be routinely screened to build predictive models for selecting compounds from the screening collection for follow-up screens. Here, we present a data-driven derivation of an informer compound set with improved predictivity of active compounds in HTS, and we validate its benefit over randomly selected training sets on 46 PubChem assays comprising at least 300,000 compounds and covering a wide range of assay biology. The informer compound set showed improvement in BEDROC(α = 100), PRAUC, and ROCAUC values averaged over all assays of 0.024, 0.014, and 0.016, respectively, compared to randomly selected training sets, all with paired t-test p-values agnostic fashion. This approach led to a consistent improvement in hit rates in follow-up screens without compromising scaffold retrieval. The informer set is adjustable in size depending on the number of compounds one intends to screen, as performance gains are realized for sets with more than 3,000 compounds, and this set is therefore applicable to a variety of situations. Finally, our results indicate that random sampling may not adequately cover descriptor space, drawing attention to the importance of the composition of the training set for predicting actives.

Geometrically and conformationally restrained cinnamoyl compounds as inhibitors of HIV-1 integrase: synthesis, biological evaluation, and molecular modeling.

Science.gov (United States)

Artico, M; Di Santo, R; Costi, R; Novellino, E; Greco, G; Massa, S; Tramontano, E; Marongiu, M E; De Montis, A; La Colla, P

1998-10-08

Various cinnammoyl-based structures were synthesized and tested in enzyme assays as inhibitors of the HIV-1 integrase (IN). The majority of compounds were designed as geometrically or conformationally constrained analogues of caffeic acid phenethyl ester (CAPE) and were characterized by a syn disposition of the carbonyl group with respect to the vinylic double bond. Since the cinnamoyl moiety present in flavones such as quercetin (inactive on HIV-1-infected cells) is frozen in an anti arrangement, it was hoped that fixing our compounds in a syn disposition could favor anti-HIV-1 activity in cell-based assays. Geometrical and conformational properties of the designed compounds were taken into account through analysis of X-ray structures available from the Cambridge Structural Database. The polyhydroxylated analogues were prepared by reacting 3,4-bis(tetrahydropyran-2-yloxy)benzaldehyde with various compounds having active methylene groups such as 2-propanone, cyclopentanone, cyclohexanone, 1,3-diacetylbenzene, 2, 4-dihydroxyacetophenone, 2,3-dihydro-1-indanone, 2,3-dihydro-1, 3-indandione, and others. While active against both 3'-processing and strand-transfer reactions, the new compounds, curcumin included, failed to inhibit the HIV-1 multiplication in acutely infected MT-4 cells. Nevertheless, they specifically inhibited the enzymatic reactions associated with IN, being totally inactive against other viral (HIV-1 reverse transcriptase) and cellular (RNA polymerase II) nucleic acid-processing enzymes. On the other hand, title compounds were endowed with remarkable antiproliferative activity, whose potency correlated neither with the presence of catechols (possible source of reactive quinones) nor with inhibition of topoisomerases. The SARs developed for our compounds led to novel findings concerning the molecular determinants of IN inhibitory activity within the class of cinnamoyl-based structures. We hypothesize that these compounds bind to IN featuring the

Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis

DEFF Research Database (Denmark)

Damgaard, Ida; Bjerg, Poul Løgstrup; Bælum, Jacob

2013-01-01

subsampling of the clay till cores. The study demonstrates that an integrated approach combining chemical analysis, molecular microbial tools and compound specific isotope analysis (CSIA) was required in order to document biotic and abiotic degradations in the clay till system. © 2013 Elsevier B.V.......The degradation of chlorinated ethenes and ethanes in clay till was investigated at a contaminated site (Vadsby, Denmark) by high resolution sampling of intact cores combined with groundwater sampling. Over decades of contamination, bioactive zones with degradation of trichloroethene (TCE) and 1...

In situ synthesis of molecularly imprinted nanoparticles in porous support membranes using high-viscosity polymerization solvents.

Science.gov (United States)

Renkecz, Tibor; László, Krisztina; Horváth, Viola

2012-06-01

There is a growing need in membrane separations for novel membrane materials providing selective retention. Molecularly imprinted polymers (MIPs) are promising candidates for membrane functionalization. In this work, a novel approach is described to prepare composite membrane adsorbers incorporating molecularly imprinted microparticles or nanoparticles into commercially available macroporous filtration membranes. The polymerization is carried out in highly viscous polymerization solvents, and the particles are formed in situ in the pores of the support membrane. MIP particle composite membranes selective for terbutylazine were prepared and characterized by scanning electron microscopy and N₂ porosimetry. By varying the polymerization solvent microparticles or nanoparticles with diameters ranging from several hundred nanometers to 1 µm could be embedded into the support. The permeability of the membranes was in the range of 1000 to 20,000 Lm⁻²  hr⁻¹  bar⁻¹. The imprinted composite membranes showed high MIP/NIP (nonimprinted polymer) selectivity for the template in organic media both in equilibrium-rebinding measurements and in filtration experiments. The solid phase extraction of a mixture of the template, its analogs, and a nonrelated compound demonstrated MIP/NIP selectivity and substance selectivity of the new molecularly imprinted membrane. The synthesis technique offers a potential for the cost-effective production of selective membrane adsorbers with high capacity and high throughput. Copyright © 2012 John Wiley & Sons, Ltd.

Compound Structure-Independent Activity Prediction in High-Dimensional Target Space.

Science.gov (United States)

Balfer, Jenny; Hu, Ye; Bajorath, Jürgen

2014-08-01

Profiling of compound libraries against arrays of targets has become an important approach in pharmaceutical research. The prediction of multi-target compound activities also represents an attractive task for machine learning with potential for drug discovery applications. Herein, we have explored activity prediction in high-dimensional target space. Different types of models were derived to predict multi-target activities. The models included naïve Bayesian (NB) and support vector machine (SVM) classifiers based upon compound structure information and NB models derived on the basis of activity profiles, without considering compound structure. Because the latter approach can be applied to incomplete training data and principally depends on the feature independence assumption, SVM modeling was not applicable in this case. Furthermore, iterative hybrid NB models making use of both activity profiles and compound structure information were built. In high-dimensional target space, NB models utilizing activity profile data were found to yield more accurate activity predictions than structure-based NB and SVM models or hybrid models. An in-depth analysis of activity profile-based models revealed the presence of correlation effects across different targets and rationalized prediction accuracy. Taken together, the results indicate that activity profile information can be effectively used to predict the activity of test compounds against novel targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-throughput Molecular Docking Now in Reach for a Wider Biochemical Community

NARCIS (Netherlands)

Balan, D.M.; Malinauskas, T.; Prins, J.C.P.; Moller, S.

2012-01-01

In silico molecular docking is used to predict how a small molecule, the ligand, interacts with a target protein, its receptor. Together with experimental methods like NMR or X-ray crystallography, industrial and academic groups use it for their investigation of compounds with the potential to

Synthesis, pharmacological activity evaluation and molecular modeling of new polynuclear heterocyclic compounds containing benzimidazole derivatives.

Science.gov (United States)

Bassyouni, Fatma A; Saleh, Tamer S; ElHefnawi, Mahmoud M; Abd El-Moez, Sherein I; El-Senousy, Waled M; Abdel-Rehim, Mohamed E

2012-12-01

Novel heterocyclic compounds containing benzimidazole derivatives were synthesized from 2-(1H-benzimidazol-2-yl) acetonitrile (1) and arylhydrazononitrile derivative 2 was obtained via coupling of 1 with 4-methyl phenyldiazonium salt, which was then reacted with hydroxylamine hydrochloride to give amidooxime derivative 3. This product was cyclized into the corresponding oxadiazole derivative 4 upon reflux in acetic anhydride. Compound 4 was refluxed in DMF in the presence of triethylamine to give the corresponding 5-(1H-benzimidazol-2-yl)-2-p-tolyl-2H-1,2,3-triazol-4-amine 6. Treatment of compound 6 with ethyl chloroformate afforded 2,6-dihydro-2-(4-methylphenyl)-1,2,3-triazolo[4",5"-4',5']pyrimido[1,6-a]benzimidazole-5(4H)-one (8). 1,2-bis(2-cyanomethyl-1H-benzimidazol-1-yl)ethane-1,2-dione (10) was synthesized via the condensation reaction of 2-(1H-benzimidazol-2-yl) acetonitrile (1) and diethyloxalate. The reactivity of compound 10 towards some diamine reagents was studied. The in vitro antimicrobial activity of the synthesized compounds was investigated against several pathogenic bacterial strains such as Escherichia coli O157, Salmonella typhimurium, E. coli O119, S. paratyphi, Pseudomonas aeruginosa, Staphylococcus aureus, Listeria monocytogenes and Bacillus cereus. The results of MIC revealed that compounds 12a-c showed the most effective antimicrobial activity against tested strains. On the other hand, compounds 12a, b exhibited high activity against rotavirus Wa strain while compounds 12b, c exhibited high activity against adenovirus type 7. In silico target prediction, docking and validation of the compounds 12a-c were performed. The dialkylglycine decarboxylase bacterial enzyme was predicted as a potential bacterial target receptor using pharmacophore-based correspondence with previous leads; giving the highest normalized scores and a high correlation docking score with mean inhibition concentrations. A novel binding mechanism was predicted after docking

Assembled microneedle arrays enhance the transport of compounds varying over a large range of molecular weight across human dermatomed skin

NARCIS (Netherlands)

Verbaan, F.J.; Bal, S.M.; van den Berg, D.J.; Groenink, W.H.H.; Verpoorten, H.; Lüttge, Regina; Bouwstra, J.A.

2007-01-01

In this study, we demonstrate the feasibility to use microneedle arrays manufactured from commercially available 30G hypodermal needles to enhance the transport of compounds up to a molecular weight of 72 kDa. Piercing of human dermatomed skin with microneedle arrays was studied by Trypan Blue

Laser ablation of molecular carbon nitride compounds

Energy Technology Data Exchange (ETDEWEB)

Fischer, D., E-mail: d.fischer@fkf.mpg.de [Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart (Germany); Schwinghammer, K. [Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart (Germany); Department of Chemistry, University of Munich, LMU, Butenandtstr. 5-13, 81377 Munich (Germany); Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), 80799 Munich (Germany); Sondermann, C. [Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart (Germany); Department of Chemistry, University of Munich, LMU, Butenandtstr. 5-13, 81377 Munich (Germany); Lau, V.W.; Mannhart, J. [Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart (Germany); Lotsch, B.V. [Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart (Germany); Department of Chemistry, University of Munich, LMU, Butenandtstr. 5-13, 81377 Munich (Germany); Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), 80799 Munich (Germany)

2015-09-15

We present a method for the preparation of thin films on sapphire substrates of the carbon nitride precursors dicyandiamide (C{sub 2}N{sub 4}H{sub 4}), melamine (C{sub 3}N{sub 6}H{sub 6}), and melem (C{sub 6}N{sub 10}H{sub 6}), using the femtosecond-pulsed laser deposition technique (femto-PLD) at different temperatures. The depositions were carried out under high vacuum with a femtosecond-pulsed laser. The focused laser beam is scanned on the surface of a rotating target consisting of the pelletized compounds. The resulting polycrystalline, opaque films were characterized by X-ray powder diffraction, infrared, Raman, and X-ray photoelectron spectroscopy, photoluminescence, SEM, and MALDI-TOF mass spectrometry measurements. The crystal structures and optical/spectroscopic results of the obtained rough films largely match those of the bulk materials.

The effect of high pressure on nitrogen compounds of milk

International Nuclear Information System (INIS)

Kielczewska, Katarzyna; Czerniewicz, Maria; Michalak, Joanna; Brandt, Waldemar

2004-01-01

The effect of pressurization at different pressures (from 200 to 1000 MPa, at 200 MPa intervals, t const. = 15 min) and periods of time (from 15 to 35 min, at 10 min intervals, p const. = 800 MPa) on the changes of proteins and nitrogen compounds of skimmed milk was studied. The pressurization caused an increase in the amount of soluble casein and denaturation of whey proteins. The level of nonprotein nitrogen compounds and proteoso-peptone nitrogen compounds increased as a result of the high-pressure treatment. These changes increased with an increase in pressure and exposure time. High-pressure treatment considerably affected the changes in the conformation of milk proteins, which was reflected in the changes in the content of proteins sedimenting and an increase in their degree of hydration

Molecular dynamics in high electric fields

International Nuclear Information System (INIS)

Apostol, M.; Cune, L.C.

2016-01-01

Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.

Semiconducting compounds and devices incorporating same

Science.gov (United States)

Marks, Tobin J.; Facchetti, Antonio; Boudreault, Pierre-Luc; Miyauchi, Hiroyuki

2016-01-19

Disclosed are molecular and polymeric compounds having desirable properties as semiconducting materials. Such compounds can exhibit desirable electronic properties and possess processing advantages including solution-processability and/or good stability. Organic transistor and photovoltaic devices incorporating the present compounds as the active layer exhibit good device performance.

High Molecular Weight Polybenzimidazole Membranes for High Temperature PEMFC

DEFF Research Database (Denmark)

Yang, Jingshuai; Cleemann, Lars Nilausen; Steenberg, T.

2014-01-01

High temperature operation of proton exchange membrane fuel cells under ambient pressure has been achieved by using phosphoric acid doped polybenzimidazole (PBI) membranes. To optimize the membrane and fuel cells, high performance polymers were synthesized of molecular weights from 30 to 94 kDa w...

Binding affinity toward human prion protein of some anti-prion compounds - Assessment based on QSAR modeling, molecular docking and non-parametric ranking.

Science.gov (United States)

Kovačević, Strahinja; Karadžić, Milica; Podunavac-Kuzmanović, Sanja; Jevrić, Lidija

2018-01-01

The present study is based on the quantitative structure-activity relationship (QSAR) analysis of binding affinity toward human prion protein (huPrP C ) of quinacrine, pyridine dicarbonitrile, diphenylthiazole and diphenyloxazole analogs applying different linear and non-linear chemometric regression techniques, including univariate linear regression, multiple linear regression, partial least squares regression and artificial neural networks. The QSAR analysis distinguished molecular lipophilicity as an important factor that contributes to the binding affinity. Principal component analysis was used in order to reveal similarities or dissimilarities among the studied compounds. The analysis of in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) parameters was conducted. The ranking of the studied analogs on the basis of their ADMET parameters was done applying the sum of ranking differences, as a relatively new chemometric method. The main aim of the study was to reveal the most important molecular features whose changes lead to the changes in the binding affinities of the studied compounds. Another point of view on the binding affinity of the most promising analogs was established by application of molecular docking analysis. The results of the molecular docking were proven to be in agreement with the experimental outcome. Copyright © 2017 Elsevier B.V. All rights reserved.

Organic compounds in radiation fogs in Davis (California)

Science.gov (United States)

Herckes, Pierre; Hannigan, Michael P.; Trenary, Laurie; Lee, Taehyoung; Collett, Jeffrey L.

New stainless steel active fogwater collectors were designed and used in Davis (CA, USA) to collect fogwater for the speciation of organic matter. Organic compounds in fog samples were extracted by liquid-liquid extraction and analyzed by gas chromatography coupled to mass spectrometry. Numerous organic compounds, including various alkanes, polycyclic aromatic hydrocarbons (PAH) and alkanoic acids, have been identified in the fogwater samples. Higher molecular weight (MW) compounds are preferentially associated with an insoluble phase inside the fog drops, whereas lower molecular weight and more polar compounds are found predominantly in the dissolved phase. Concentrations in the dissolved phase were sometimes much higher than estimated by the compounds' aqueous solubilities.

Synthesis, biological evaluation and molecular modeling of a novel series of 7-azaindole based tri-heterocyclic compounds as potent CDK2/Cyclin E inhibitors.

Science.gov (United States)

Baltus, Christine B; Jorda, Radek; Marot, Christophe; Berka, Karel; Bazgier, Václav; Kryštof, Vladimír; Prié, Gildas; Viaud-Massuard, Marie-Claude

2016-01-27

From four molecules, inspired by the structural features of fascaplysin, with an interesting potential to inhibit cyclin-dependent kinases (CDKs), we designed a new series of tri-heterocyclic derivatives based on 1H-pyrrolo[2,3-b]pyridine (7-azaindole) and triazole heterocycles. Using a Huisgen type [3 + 2] cycloaddition as the convergent key step, 24 derivatives were synthesized and their biological activities were evaluated. Comparative molecular field analysis (CoMFA), based on three-dimensional quantitative structure-activity relationship (3D-QSAR) studies, was conducted on a series of 30 compounds from the literature with high to low known inhibitory activity towards CDK2/cyclin E and was validated by a test set of 5 compounds giving satisfactory predictive r(2) value of 0.92. Remarkably, it also gave a good prediction of pIC50 for our tri-heterocyclic series which reinforce the validation of this model for the pIC50 prediction of external set compounds. The most promising compound, 43, showed a micro-molar range inhibitory activity against CDK2/cyclin E and also an antiproliferative and proapoptotic activity against a panel of cancer cell lines. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Skin: Major target organ of allergic reactions to small molecular weight compounds

International Nuclear Information System (INIS)

Merk, Hans F.; Baron, Jens M.; Neis, Mark M.; Obrigkeit, Daniela Hoeller; Karlberg, Ann-Therese

2007-01-01

Skin is a major target organ for allergic reactions to small molecular weight compounds. Drug allergic reactions may be life-threatening such as in the case of anaphylactic reactions or bullous drug reactions and occur in about 5% of all hospitalized patients. Allergic contact dermatitis has an enormous influence on the social life of the patient because it is the most frequent reason for occupational skin diseases and the treatment and prevention of this disease cost approximately Euro 3 billion per year in Germany. The different proposed pathophysiological pathways leading to a drug eruption are discussed in this paper. All major enzymes which are involved in the metabolism of xenobiotica were shown to be present in skin. Evidence supporting the role of metabolism in the development of drug allergy and allergic contact dermatitis is demonstrated in the example of sulphonamides and fragrances

X-ray photoelectron spectra structure of actinide compounds stipulated by electrons of the inner valence molecular orbitals (IVMO)

International Nuclear Information System (INIS)

Teterin, Yu. A.; Ivanov, K. E.

1997-01-01

Development of precise X-ray photoelectron spectroscopy using X-ray radiation hν< 1.5 KeV allowed to carry out immediate investigations of fine spectra structure of both weakly bond and deep electrons. Based on the experiments and the obtained results it may be concluded: 1. Under favourable conditions the inner valence molecular orbitals (IVMO) may form in all actinide compounds. 2. The XPS spectra fine structure stipulated by IVMO electrons allows to judge upon the degree of participation of the filled AO electrons in the chemical bond, on the structure o considered atom close environment and the bond lengths in compounds. For amorphous compounds the obtaining of such data based on X-ray structure analysis is restricted. 3. The summary contribution of IVMO electrons to the absolute value of the chemical bonding is comparable with the corresponding value of OMO electrons contribution to the atomic bonding. This fact is very important and new in chemistry. (author)

Molecular Electronics

DEFF Research Database (Denmark)

Jennum, Karsten Stein

This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

Molecular docking, QSAR and ADMET based mining of natural compounds against prime targets of HIV.

Science.gov (United States)

Vora, Jaykant; Patel, Shivani; Sinha, Sonam; Sharma, Sonal; Srivastava, Anshu; Chhabria, Mahesh; Shrivastava, Neeta

2018-01-07

AIDS is one of the multifaceted diseases and this underlying complexity hampers its complete cure. The toxicity of existing drugs and emergence of multidrug-resistant virus makes the treatment worse. Development of effective, safe and low-cost anti-HIV drugs is among the top global priority. Exploration of natural resources may give ray of hope to develop new anti-HIV leads. Among the various therapeutic targets for HIV treatment, reverse transcriptase, protease, integrase, GP120, and ribonuclease are the prime focus. In the present study, we predicted potential plant-derived natural molecules for HIV treatment using computational approach, i.e. molecular docking, quantitative structure activity relationship (QSAR), and ADMET studies. Receptor-ligand binding studies were performed using three different software for precise prediction - Discovery studio 4.0, Schrodinger and Molegrow virtual docker. Docking scores revealed that Mulberrosides, Anolignans, Curcumin and Chebulic acid are promising candidates that bind with multi targets of HIV, while Neo-andrographolide, Nimbolide and Punigluconin were target-specific candidates. Subsequently, QSAR was performed using biologically proved compounds which predicted the biological activity of compounds. We identified Anolignans, Curcumin, Mulberrosides, Chebulic acid and Neo-andrographolide as potential natural molecules for HIV treatment from results of molecular docking and 3D-QSAR. In silico ADMET studies showed drug-likeness of these lead molecules. Structure similarities of identified lead molecules were compared with identified marketed drugs by superimposing both the molecules. Using in silico studies, we have identified few best fit molecules of natural origin against identified targets which may give new drugs to combat HIV infection after wet lab validation.

Wild Roman chamomile extracts and phenolic compounds: enzymatic assays and molecular modelling studies with VEGFR-2 tyrosine kinase.

Science.gov (United States)

Guimarães, Rafaela; Calhelha, Ricardo C; Froufe, Hugo J C; Abreu, Rui M V; Carvalho, Ana Maria; Queiroz, Maria João R P; Ferreira, Isabel C F R

2016-01-01

Angiogenesis is a process by which new blood vessels are formed from the pre-existing vasculature, and it is a key process that leads to tumour development. Some studies have recognized phenolic compounds as chemopreventive agents; flavonoids, in particular, seem to suppress the growth of tumor cells modifying the cell cycle. Herein, the antiangiogenic activity of Roman chamomile (Chamaemelum nobile L.) extracts (methanolic extract and infusion) and the main phenolic compounds present (apigenin, apigenin-7-O-glucoside, caffeic acid, chlorogenic acid, luteolin, and luteolin-7-O-glucoside) was evaluated through enzymatic assays using the tyrosine kinase intracellular domain of the Vascular Endothelium Growth Factor Receptor-2 (VEGFR-2), which is a transmembrane receptor expressed fundamentally in endothelial cells involved in angiogenesis, and molecular modelling studies. The methanolic extract showed a lower IC50 value (concentration that provided 50% of VEGFR-2 inhibition) than the infusion, 269 and 301 μg mL(-1), respectively. Regarding phenolic compounds, luteolin and apigenin showed the highest capacity to inhibit the phosphorylation of VEGFR-2, leading us to believe that these compounds are involved in the activity revealed by the methanolic extract.

High-Tc Superconductors Based on FeAs Compounds

CERN Document Server

Izyumov, Yuri

2010-01-01

Physical properties and models of electronic structure are analyzed for a new class of high-TC superconductors which belong to iron-based layered compounds. Despite their variable chemical composition and differences in the crystal structure, these compounds possess similar physical characteristics, due to electron carriers in the FeAs layers and the interaction of these carriers with fluctuations of the magnetic order. A tremendous interest towards these materials is explained by the prospects of their practical use. In this monograph, a full picture of the formation of physical properties of these materials, in the context of existing theory models and electron structure studies, is given. The book is aimed at a broad circle of readers: physicists who study electronic properties of the FeAs compounds, chemists who synthesize them and specialists in the field of electronic structure calculations in solids. It is helpful not only to researchers active in the fields of superconductivity and magnetism, but also...

High-performance liquid chromatographic method for guanylhydrazone compounds.

Science.gov (United States)

Cerami, C; Zhang, X; Ulrich, P; Bianchi, M; Tracey, K J; Berger, B J

1996-01-12

A high-performance liquid chromatographic method has been developed for a series of aromatic guanylhydrazones that have demonstrated therapeutic potential as anti-inflammatory agents. The compounds were separated using octadecyl or diisopropyloctyl reversed-phase columns, with an acetonitrile gradient in water containing heptane sulfonate, tetramethylammonium chloride, and phosphoric acid. The method was used to reliably quantify levels of analyte as low as 785 ng/ml, and the detector response was linear to at least 50 micrograms/ml using a 100 microliters injection volume. The assay system was used to determine the basic pharmacokinetics of a lead compound, CNI-1493, from serum concentrations following a single intravenous injection in rats.

A QSPR STUDY OF NORMAL BOILING POINT OF ORGANIC COMPOUNDS (ALIPHATIC ALKANES USING MOLECULAR DESCRIPTORS

Directory of Open Access Journals (Sweden)

B. Souyei

2013-12-01

Full Text Available A quantitative structure–property relationship (QSPR study is carried out to develop correlations that relate the molecular structures of organic compounds (Aliphatic Alkanes to their normal boiling point (NBP and two correlations were proposed for constitutionals and connectivity indices Models. The correlations are simple in application with good accuracy, which provide an easy, direct and relatively accurate way to calculate NBP. Such calculation gives us a model that gives results in remarkable correlations with the descriptors of blokes constitutionals (CON, and connectivity indices (CI (R2 = 0.950, δ = 0.766 (R2 = 0.969, δ = 0.782 respectively.

Molecular Determinants of Dissolved Organic Matter Reactivity in Lake Water

Directory of Open Access Journals (Sweden)

Alina Mostovaya

2017-12-01

Full Text Available Lakes in the boreal region have been recognized as the biogeochemical hotspots, yet many questions regarding the regulators of organic matter processing in these systems remain open. Molecular composition can be an important determinant of dissolved organic matter (DOM fate in freshwater systems, but many aspects of this relationship remain unclear due to the complexity of DOM and its interactions in the natural environment. Here, we combine ultrahigh resolution mass spectrometry (FT-ICR-MS with kinetic modeling of decay of >1,300 individual DOM molecular formulae identified by mass spectrometry, to evaluate the role of specific molecular characteristics in decomposition of lake water DOM. Our data is derived from a 4 months microbial decomposition experiment, carried out on water from three Swedish lakes, with the set-up including natural lake water, as well as the lake water pretreated with UV light. The relative decay rate of every molecular formula was estimated by fitting a single exponential model to the change in FT-ICR-MS signal intensities over decomposition time. We found a continuous range of exponential decay coefficients (kexp within different groups of compounds and show that for highly unsaturated and phenolic compounds the distribution of kexp was shifted toward the lowest values. Contrary to this general trend, plant-derived polyphenols and polycondensed aromatics were on average more reactive than compounds with an intermediate aromaticity. The decay rate of aromatic compounds increased with increasing nominal oxidation state of carbon, and molecular mass in some cases showed an inverse relationship with kexp in the UV-manipulated treatment. Further, we observe an increase in formulae-specific kexp as a result of the UV pretreatment. General trends in reactivity identified among major compound groups emphasize the importance of the intrinsic controllers of lake water DOM decay. However, we additionally indicate that each

Studies about behavior of microbial degradation of organic compounds

International Nuclear Information System (INIS)

Ohtsuka, Makiko

2003-02-01

Some of TRU waste include organic compounds, thus these organic compounds might be nutrients for microbial growth at disposal site. This disposal system might be exposed to high alkali condition by cement compounds as engineering barrier material. In the former experimental studies, it has been supposed that microbial exist under pH = 12 and the microbial activity acclimated to high alkali condition are able to degrade asphalt under anaerobic condition. Microbes are called extremophile that exist in cruel habitat as high alkali or reductive condition. We know less information about the activity of extremophile, though any recent studies reveal them. In this study, the first investigation is metabolic pathway as microbial activity, the second is microbial degradation of aromatic compounds in anaerobic condition, and the third is microbial activity under high alkali. Microbial metabolic pathway consist of two systems that fulfill their function each other. One system is to generate energy for microbial activities and the other is to convert substances for syntheses of organisms' structure materials. As these systems are based on redox reaction between substances, it is made chart of the microbial activity region using pH, Eh, and depth as parameter, There is much report that microbe is able to degrade aromatic compounds under aerobic or molecular O 2 utilizing condition. For degradation of aromatic compounds in anaerobic condition, supplying electron acceptor is required. Co-metabolism and microbial consortia has important role, too. Alcalophile has individual transporting system depending Na + and acidic compounds contained in cell wall. Generating energy is key for survival and growth under high alkali condition. Co-metabolism and microbial consortia are effective for microbial degradation of aromatic compounds under high alkali and reductive condition, and utilizable electron acceptor and degradable organic compounds are required for keeping microbial activity and

[Chromatographic mass spectrometric determination of low-molecular-weight aromatic compounds of microbial origin in the serum from patients with sepsis].

Science.gov (United States)

Beloborodova, N V; Arkhipova, A S; Beloborodov, D M; Boĭko, N B; Mel'ko, A I; Olenin, A Iu

2006-02-01

The investigation quantitatively determined the content of low-molecular-weight aromatic compounds of microbial origin in the sera of 34 individuals by chromatographic mass spectrometry. An "Agilent Technogies 6890N" gas chromatograph with a 5973 mass selective detector was applied; chromatographic separation of components was effected on an Hp-5MS quartz capillary column. Aromatic small molecules originating from microbes (SMOM) were determined in the sera of 7 patients with sepsis. The diagnosis of sepsis was documented by the presence of the systemic inflammation syndrome and by that of bacteriemia and/or artificial ventilation-associated pneumonia along with the level of procalcitonin of higher than 10 ng/ml. The levels of aromatic SMOM were compared in 10 healthy donors, 8 preoperative cardiosurgical patients, and 9 patients with different abnormalities without sepsis treated in an intensive care unit (ICU). Serum phenylacetic and 3-phenylpropionic acids were found to be prevalent in the healthy donors and postoperative cardiosurgical patients. In ICU patients with different complications without sepsis, more than half the compounds under study were undetectable, the others were found in very low concentrations, which may be accounted for by antibiotic therapy. At the same time, almost the whole spectrum of the test compounds (other than 3-phenylpropionic acid) with the highest concentrations of 3-phenyllactic, p-hydroxyphenylacetic, 3-(p-hydroxyphenyl)lactic and 2-hydroxybutanic acids, was detectable in septic patients receiving a more intensive therapy. The differences were statistically significant (by the Mann-Whitney U-test; p < 0.05). By taking into account the potentially high biological activity of the test compounds, studies are to be continued in this area.

A Multi-step and Multi-level approach for Computer Aided Molecular Design

DEFF Research Database (Denmark)

. The problem formulation step incorporates a knowledge base for the identification and setup of the design criteria. Candidate compounds are identified using a multi-level generate and test CAMD solution algorithm capable of designing molecules having a high level of molecular detail. A post solution step...... using an Integrated Computer Aided System (ICAS) for result analysis and verification is included in the methodology. Keywords: CAMD, separation processes, knowledge base, molecular design, solvent selection, substitution, group contribution, property prediction, ICAS Introduction The use of Computer...... Aided Molecular Design (CAMD) for the identification of compounds having specific physic...

High-energy neutron irradiation of superconducting compounds

International Nuclear Information System (INIS)

Sweedler, A.R.; Snead, C.L.; Newkirk, L.; Valencia, F.; Geballe, T.H.; Schwall, R.H.; Matthias, B.T.; Corenswit, E.

1975-01-01

The effect of high-energy neutron irradiation (E greater than 1 MeV) at ambient reactor temperatures on the superconducting properties of a variety of superconducting compounds is reported. The materials studied include the A-15 compounds Nb 3 Sn, Nb 3 Al, Nb 3 Ga, Nb 3 Ge and V 3 Si, the C-15 Laves phase HfV 2 , the ternary molybdenum sulfide Mo 3 Pb 0 . 5 S 4 and the layered dichalcogenide NbSe 2 . The superconducting transition temperature has been measured for all of the above materials for neutron fluences up to 5 x 10 19 n/cm 2 . The critical current for multifilamentary Nb 3 Sn has also been determined for fields up to 16 T and fluences between 3 x 10 17 n/cm 2 and 1.1 x 10 19 n/cm 2

High-Resolution Mass Spectrometry and Molecular Characterization of Aqueous Photochemistry Products of Common Types of Secondary Organic Aerosols

Energy Technology Data Exchange (ETDEWEB)

Romonosky, Dian E.; Laskin, Alexander; Laskin, Julia; Nizkorodov, Sergey

2015-03-19

A significant fraction of atmospheric organic compounds is predominantly found in condensed phases, such as aerosol particles and cloud droplets. Many of these compounds are photolabile and can degrade through direct photolysis or indirect photooxidation processes on time scales that are comparable to the typical lifetimes of aqueous droplets (hours) and particles (days). This paper presents a systematic investigation of the molecular level composition and the extent of aqueous photochemical processing in different types of secondary organic aerosol (SOA) from biogenic and anthropogenic precursors including α-pinene, β-pinene, β-myrcene, d- limonene, α-humulene, 1,3,5-trimethylbenzene, and guaiacol, oxidized by ozone (to simulate a remote atmosphere) or by OH in the presence of NOx (to simulate an urban atmosphere). Chamber- and flow tube-generated SOA samples were collected, extracted in a methanol/water solution, and photolyzed for 1 h under identical irradiation conditions. In these experiments, the irradiation was equivalent to about 3-8 h of exposure to the sun in its zenith. The molecular level composition of the dissolved SOA was probed before and after photolysis with direct-infusion electrospray ionization high-resolution mass spectrometry (ESI-HR-MS). The mass spectra of unphotolyzed SOA generated by ozone oxidation of monoterpenes showed qualitatively similar features, and contained largely overlapping subsets of identified compounds. The mass spectra of OH/NOx generated SOA had more unique visual appearance, and indicated a lower extent of products overlap. Furthermore, the fraction of nitrogen containing species (organonitrates and nitroaromatics) was highly sensitive to the SOA precursor. These observations suggest that attribution of high-resolution mass spectra in field SOA samples to specific SOA precursors should be more straightforward under OH/NOx oxidation conditions compared to the ozone driven oxidation. Comparison of the SOA constituents

High- and low-molecular-mass microbial surfactants.

Science.gov (United States)

Rosenberg, E; Ron, E Z

1999-08-01

Microorganisms synthesize a wide variety of high- and low-molecular-mass bioemulsifiers. The low-molecular-mass bioemulsifiers are generally glycolipids, such as trehalose lipids, sophorolipids and rhamnolipids, or lipopeptides, such as surfactin, gramicidin S and polymyxin. The high-molecular-mass bioemulsifiers are amphipathic polysaccharides, proteins, lipopolysaccharides, lipoproteins or complex mixtures of these biopolymers. The low-molecular-mass bioemulsifiers lower surface and interfacial tensions, whereas the higher-molecular-mass bioemulsifiers are more effective at stabilizing oil-in-water emulsions. Three natural roles for bioemulsifiers have been proposed: (i) increasing the surface area of hydrophobic water-insoluble growth substrates; (ii) increasing the bioavailability of hydrophobic substrates by increasing their apparent solubility or desorbing them from surfaces; (iii) regulating the attachment and detachment of microorganisms to and from surfaces. Bioemulsifiers have several important advantages over chemical surfactants, which should allow them to become prominent in industrial and environmental applications. The potential commercial applications of bioemulsifiers include bioremediation of oil-polluted soil and water, enhanced oil recovery, replacement of chlorinated solvents used in cleaning-up oil-contaminated pipes, vessels and machinery, use in the detergent industry, formulations of herbicides and pesticides and formation of stable oil-in-water emulsions for the food and cosmetic industries.

Versatile piezoelectric pulsed molecular beam source for gaseous compounds and organic molecules with femtomole accuracy for UHV and surface science applications

International Nuclear Information System (INIS)

Schiesser, Alexander; Schaefer, Rolf

2009-01-01

This note describes the construction of a piezoelectric pulsed molecular beam source based upon a design presented in an earlier work [D. Proch and T. Trickl, Rev. Sci. Instrum. 60, 713 (1988)]. The design features significant modifications that permit the determination of the number of molecules in a beam pulse with an accuracy of 1x10 11 molecules per pulse. The 21 cm long plunger-nozzle setup allows the molecules to be brought to any point of the UHV chamber with very high intensity. Furthermore, besides typical gaseous compounds, also smaller organic molecules with a vapor pressure higher than 0.1 mbar at room temperature may serve as feed material. This makes the new design suitable for various applications in chemical and surface science studies.

Molecular docking.

Science.gov (United States)

Morris, Garrett M; Lim-Wilby, Marguerita

2008-01-01

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

High temperature and high resolution uv photoelectron spectroscopy using supersonic molecular beams

International Nuclear Information System (INIS)

Wang, Lai-Sheng; Reutt-Robey, J.E.; Niu, B.; Lee, Y.T.; Shirley, D.A.

1989-07-01

A high temperature molecular beam source with electron bombardment heating has been built for high resolution photoelectron spectroscopic studies of high temperature species and clusters. This source has the advantages of: producing an intense, continuous, seeded molecular beam, eliminating the interference of the heating mechanism from the photoelectron measurement. Coupling the source with our hemispherical electron energy analyzer, we can obtain very high resolution HeIα (584 angstrom) photoelectron spectra of high temperature species. Vibrationally-resolved photoelectron spectra of PbSe, As 2 , As 4 , and ZnCl 2 are shown to demonstrate the performance of the new source. 25 refs., 8 figs., 1 tab

Measurement of loss rates of organic compounds in snow using in situ experiments and isotopically labelled compounds

Directory of Open Access Journals (Sweden)

Erika von Schneidemesser

2012-07-01

Full Text Available Organic molecular marker compounds are widely used to identify emissions from anthropogenic and biogenic air pollution sources in atmospheric samples and in deposition. Specific organic compounds have been detected in polar regions, but their fate after deposition to snow is poorly characterized. Within this context, a series of exposure experiments were carried out to observe the post-depositional processing of organic compounds under real-world conditions in snow on the surface of the Greenland Ice Sheet, at the Summit research station. Snow was prepared from water spiked with isotopically labelled organic compounds, representative of typical molecular marker compounds emitted from anthropogenic activities. Reaction rate constants and reaction order were determined based on a decrease in concentration to a stable, non-zero, threshold concentration. Fluoranthene-d10, docosane-d46, hexadecanoic acid-d31, docosanoic acid-d43 and azelaic acid-d14 were estimated to have first order loss rates within surface snow with reaction rate constants of 0.068, 0.040, 0.070, 0.067 and 0.047 h−1, respectively. No loss of heptadecane-d36 was observed. Overall, these results suggest that organic contaminants are archived in polar snow, although significant post-depositional losses of specific organic compounds occur. This has implications for the environmental fate of organic contaminants, as well as for ice-core studies that seek to use organic molecular markers to infer past atmospheric loadings, and source emissions.

HIV-1 entry inhibition by small-molecule CCR5 antagonists: A combined molecular modeling and mutant study using a high-throughput assay

International Nuclear Information System (INIS)

Labrecque, Jean; Metz, Markus; Lau, Gloria; Darkes, Marilyn C.; Wong, Rebecca S.Y.; Bogucki, David; Carpenter, Bryon; Chen Gang; Li Tongshuang; Nan, Susan; Schols, Dominique; Bridger, Gary J.; Fricker, Simon P.; Skerlj, Renato T.

2011-01-01

Based on the attrition rate of CCR5 small molecule antagonists in the clinic the discovery and development of next generation antagonists with an improved pharmacology and safety profile is necessary. Herein, we describe a combined molecular modeling, CCR5-mediated cell fusion, and receptor site-directed mutagenesis approach to study the molecular interactions of six structurally diverse compounds (aplaviroc, maraviroc, vicriviroc, TAK-779, SCH-C and a benzyloxycarbonyl-aminopiperidin-1-yl-butane derivative) with CCR5, a coreceptor for CCR5-tropic HIV-1 strains. This is the first study using an antifusogenic assay, a model of the interaction of the gp120 envelope protein with CCR5. This assay avoids the use of radioactivity and HIV infection assays, and can be used in a high throughput mode. The assay was validated by comparison with other established CCR5 assays. Given the hydrophobic nature of the binding pocket several binding models are suggested which could prove useful in the rational drug design of new lead compounds.

Alternative CHCA-based matrices for the analysis of low molecular weight compounds by UV-MALDI-tandem mass spectrometry.

Science.gov (United States)

Porta, Tiffany; Grivet, Chantal; Knochenmuss, Richard; Varesio, Emmanuel; Hopfgartner, Gérard

2011-02-01

Analysis of low molecular weight compounds (LMWC) in complex matrices by vacuum matrix-assisted laser desorption/ionization (MALDI) often suffers from matrix interferences, which can severely degrade limits of quantitation. It is, therefore, useful to have available a range of suitable matrices, which exhibit complementary regions of interference. Two newly synthesized α-cyanocinnamic acid derivatives are reported here; (E)-2-cyano-3-(naphthalen-2-yl)acrylic acid (NpCCA) and (2E)-3-(anthracen-9-yl)-2-cyanoprop-2enoic acid (AnCCA). Along with the commonly used α-cyano-4-hydroxycinnamic acid (CHCA), and the recently developed 4-chloro-α-cyanocinnamic acid (Cl-CCA) matrices, these constitute a chemically similar series of matrices covering a range of molecular weights, and with correspondingly differing ranges of spectral interference. Their performance was compared by measuring the signal-to-noise ratios (S/N) of 47 analytes, mostly pharmaceuticals, with the different matrices using the selected reaction monitoring (SRM) mode on a triple quadrupole instrument equipped with a vacuum MALDI source. AnCCA, NpCCA and Cl-CCA were found to offer better signal-to-noise ratios in SRM mode than CHCA, but Cl-CCA yielded the best results for 60% of the compounds tested. To better understand the relative performance of this matrix series, the proton affinities (PAs) were measured using the kinetic method. Their relative values were: AnCCA > CHCA > NpCCA > Cl-CCA. This ordering is consistent with the performance data. The synthesis of the new matrices is straightforward and they provide (1) tunability of matrix background interfering ions and (2) enhanced analyte response for certain classes of compounds. Copyright © 2011 John Wiley & Sons, Ltd.

Insight into the binding interactions of CYP450 aromatase inhibitors with their target enzyme: a combined molecular docking and molecular dynamics study.

Science.gov (United States)

Galeazzi, Roberta; Massaccesi, Luca

2012-03-01

CYP450 aromatase catalyzes the terminal and rate-determining step in estrogen synthesis, the aromatization of androgens, and its inhibition is an efficient approach to treating estrogen-dependent breast cancer. Insight into the molecular basis of the interaction at the catalytic site between CYP450 aromatase inhibitors and the enzyme itself is required in order to design new and more active compounds. Hence, a combined molecular docking-molecular dynamics study was carried out to obtain the structure of the lowest energy association complexes of aromatase with some third-generation aromatase inhibitors (AIs) and with other novel synthesized letrozole-derived compounds which showed high in vitro activity. The results obtained clearly demonstrate the role of the pharmacophore groups present in the azaheterocyclic inhibitors (NSAIs)-namely the triazolic ring and highly functionalized aromatic moieties carrying H-bond donor or acceptor groups. In particular, it was pointed out that all of them can contribute to inhibition activity by interacting with residues of the catalytic cleft, but the amino acids involved are different for each compound, even if they belong to the same class. Furthermore, the azaheterocyclic group strongly coordinates with the Fe(II) of heme cysteinate in the most active NSAI complexes, while it prefers to adopt another orientation in less active ones.

Phosphate incorporation in organic compounds in roots of maize

Energy Technology Data Exchange (ETDEWEB)

Michalik, I; Ivanko, S [Vysoka Skola Polnohospodarska, Nitra (Czechoslovakia)

1976-01-01

/sup 32/P incorporation and metabolism was investigated for short exposure times of 1 sec, 10 sec and 1, 10, 30 and 120 min. By stepwise extraction with a methanol-chloroform-formic acid-water mixture, various fractions of P compounds were obtained. Low-molecular acid-soluble P compounds were separated by one-dimensional paper chromatography. Of the total amount of /sup 32/P absorbed by the roots of maize in the form of phosphate ions during the short incubation time of 1 sec, more than 33% was incorporated into organic compounds. With increasing incubation time, the proportion of /sup 32/P in low-molecular organic compounds increased with the decreasing proportion of inorganic phosphorus. In the 1 sec, exposure incorporation was found in 3 low-molecular organic compounds only, namely ATP, ADP and diphosphoglyceric acid. The /sup 32/P incorporation into ATP and ADP, in contrast with incorporation into diphosphoglyceric acid, increased markedly with increased exposure time.

Phosphate incorporation in organic compounds in roots of maize

International Nuclear Information System (INIS)

Michalik, I.; Ivanko, S.

1976-01-01

32 P incorporation and metabolism was investigated for short exposure times of 1 sec, 10 sec and 1, 10, 30 and 120 min. By stepwise extraction with a methanol-chloroform-formic acid-water mixture, various fractions of P compounds were obtained. Low-molecular acid-soluble P compounds were separated by one-dimensional paper chromatography. Of the total amount of 32 P absorbed by the roots of maize in the form of phosphate ions during the short incubation time of 1 sec, more than 33% was incorporated into organic compounds. With increasing incubation time, the proportion of 32 P in low-molecular organic compounds increased with the decreasing proportion of inorganic phosphorus. In the 1 sec, exposure incorporation was found in 3 low-molecular organic compounds only, namely ATP, ADP and diphosphoglyceric acid. The 32 P incorporation into ATP and ADP, in contrast with incorporation into diphosphoglyceric acid, increased markedly with increased exposure time. (author)

Development of radiation-resisting high molecular-weight materials

International Nuclear Information System (INIS)

Nakagawa, Tsutomu

1976-01-01

The excellent radiation-resisting polyvinyl chloride developed at the opportunity of the research on the relationships between the protection of living body and the polymer-technological protection from radiation is reviewed. The report is divided into four main parts, namely 1) the change in the molecular arrangement of market-available, high molecular-weight materials by gamma-ray irradiation, 2) the protection of high molecular-weight materials from radiation, 3) the relationships between the biological radiation-protective substances and the change to radiation-resisting property of synthesized high molecular-weight substances, and 4) the development of the radiation-resisting high molecular-weight materials as metal-collecting agents. Attention is paid to the polyvinyl chloride having N-methyl-dithio-carbamate radical (PMD), synthesized by the author et. al., that has excellent radiation-resisting property. PMD has some possibility to form thiol- and amino-radicals necessary to protect living things from radiation. It is believed that the protection effects of N-methyl-dithio-carbamate radical are caused by the relatively stable S radical produced by the energy transfer. PMD film is suitable for the irradiation of foods, because it hardly changes the permeability of oxygen and carbon dioxide. PMD produces mercaptide or chelate. A new metal-collecting agent (PSDC) having reactivity with the metallic ions with radiation-resisting property was developed, which is derived from polyvinyl chloride and sodium N-methyl-N-carboxy-methyl-dithio-carbamate. (Iwakiri, K.)

Using microwave heating to improve the desorption efficiency of high molecular weight VOC from beaded activated carbon.

Science.gov (United States)

Fayaz, Mohammadreza; Shariaty, Pooya; Atkinson, John D; Hashisho, Zaher; Phillips, John H; Anderson, James E; Nichols, Mark

2015-04-07

Incomplete regeneration of activated carbon loaded with organic compounds results in heel build-up that reduces the useful life of the adsorbent. In this study, microwave heating was tested as a regeneration method for beaded activated carbon (BAC) loaded with n-dodecane, a high molecular weight volatile organic compound. Energy consumption and desorption efficiency for microwave-heating regeneration were compared with conductive-heating regeneration. The minimum energy needed to completely regenerate the adsorbent (100% desorption efficiency) using microwave regeneration was 6% of that needed with conductive heating regeneration, owing to more rapid heating rates and lower heat loss. Analyses of adsorbent pore size distribution and surface chemistry confirmed that neither heating method altered the physical/chemical properties of the BAC. Additionally, gas chromatography (with flame ionization detector) confirmed that neither regeneration method detectably altered the adsorbate composition during desorption. By demonstrating improvements in energy consumption and desorption efficiency and showing stable adsorbate and adsorbent properties, this paper suggests that microwave heating is an attractive method for activated carbon regeneration particularly when high-affinity VOC adsorbates are present.

Engineering biosynthesis of high-value compounds in photosynthetic organisms.

Science.gov (United States)

O'Neill, Ellis C; Kelly, Steven

2017-09-01

The photosynthetic, autotrophic lifestyle of plants and algae position them as ideal platform organisms for sustainable production of biomolecules. However, their use in industrial biotechnology is limited in comparison to heterotrophic organisms, such as bacteria and yeast. This usage gap is in part due to the challenges in generating genetically modified plants and algae and in part due to the difficulty in the development of synthetic biology tools for manipulating gene expression in these systems. Plant and algal metabolism, pre-installed with multiple biosynthetic modules for precursor compounds, bypasses the requirement to install these pathways in conventional production organisms, and creates new opportunities for the industrial production of complex molecules. This review provides a broad overview of the successes, challenges and future prospects for genetic engineering in plants and algae for enhanced or de novo production of biomolecules. The toolbox of technologies and strategies that have been used to engineer metabolism are discussed, and the potential use of engineered plants for industrial manufacturing of large quantities of high-value compounds is explored. This review also discusses the routes that have been taken to modify the profiles of primary metabolites for increasing the nutritional quality of foods as well as the production of specialized metabolites, cosmetics, pharmaceuticals and industrial chemicals. As the universe of high-value biosynthetic pathways continues to expand, and the tools to engineer these pathways continue to develop, it is likely plants and algae will become increasingly valuable for the biomanufacturing of high-value compounds.

Mini-review: Molecular mechanisms of antifouling compounds

KAUST Repository

Qian, Pei-Yuan; Chen, Lianguo; Xu, Ying

2013-01-01

Various antifouling (AF) coatings have been developed to protect submerged surfaces by deterring the settlement of the colonizing stages of fouling organisms. A review of the literature shows that effective AF compounds with specific targets

Molecular dynamics simulation of radiation-induced amorphization of the ordered compound NiZr2

International Nuclear Information System (INIS)

Devanathan, R.; Meshii, M.

1992-12-01

We have studied the electron irradiation-induced amorphization of the ordered intermetallic compound NiZr 2 by molecular dynamics simulations in conjunction with embedded-atom potentials. Randomly chosen Frenkel pairs and chemical disorder were introduced into the system in separate processes. In both cases, the energy and volume of the system rose above the corresponding levels of a quenched liquid and the calculated diffraction patterns indicated the occurrence of a crystalline-to-amorphous transition. In addition, the average shear elastic constant fell to about 50% of its value in the perfect crystal and the system became elastically isotropic. These results indicate that NiZr 2 can be amorphized by chemical disorder as well as Frenkel pairs and are in good agreement with experimental observations

Identification and preclinical testing of novel antiepileptic compounds.

Science.gov (United States)

Meldrum, B S

1997-01-01

Procedures for identifying novel antiepileptic drugs (AEDs) are changing and need to change more. Widespread reliance on two primary screens has led to the identification of novel compounds that resemble either phenytoin (suppressing high-frequency repetitive firing in cultured neurons and prolonging inactivation of voltage-dependent sodium channels identified by the maximal electroshock test) or benzodiazepines (potentiating the inhibitory effect of gamma-aminobutyric acid (GABA), identified by the threshold pentylenetetrazol test). Advances in molecular neurobiology have identified specific molecular targets (subunits of ion channels, neurotransmitter receptors, and transporters) and have made them available in a form permitting high-throughput screening. AEDs can be designed to interact with specific sites on the target molecules. Alternatively, the molecular screens can be used to identify active components in natural products, including folk remedies. Preclinical in vivo screens can be improved by using animals with genetic or acquired epilepsies that have similar modifications in the properties of the target molecules as do human epilepsy syndromes. Future work is likely to define molecular targets for AEDs that will block or reverse chronic epileptogenesis.

Ion implantation in compound semiconductors for high-performance electronic devices

International Nuclear Information System (INIS)

Zolper, J.C.; Baca, A.G.; Sherwin, M.E.; Klem, J.F.

1996-01-01

Advanced electronic devices based on compound semiconductors often make use of selective area ion implantation doping or isolation. The implantation processing becomes more complex as the device dimensions are reduced and more complex material systems are employed. The authors review several applications of ion implantation to high performance junction field effect transistors (JFETs) and heterostructure field effect transistors (HFETs) that are based on compound semiconductors, including: GaAs, AlGaAs, InGaP, and AlGaSb

Molecular evaluation of herbal compounds as potent inhibitors of acetylcholinesterase for the treatment of Alzheimer's disease.

Science.gov (United States)

Chen, Yan-Xiu; Li, Guan-Zeng; Zhang, Bin; Xia, Zhang-Yong; Zhang, Mei

2016-07-01

Alzheimer's disease (AD) is a progressive disease and the predominant cause of dementia. Common symptoms include short-term memory loss, and confusion with time and place. Individuals with AD depend on their caregivers for assistance, and may pose a burden to them. The acetylcholinesterase (AChE) enzyme is a key target in AD and inhibition of this enzyme may be a promising strategy in the drug discovery process. In the present study, an inhibitory assay was carried out against AChE using total alkaloidal plants and herbal extracts commonly available in vegetable markets. Subsequently, molecular docking simulation analyses of the bioactive compounds present in the plants were conducted, as well as a protein‑ligand interaction analysis. The stability of the docked protein‑ligand complex was assessed by 20 ns molecular dynamics simulation. The inhibitory assay demonstrated that Uncaria rhynchophylla and Portulaca oleracea were able to inhibit AChE. In addition, molecular docking simulation analyses indicated that catechin present in Uncaria rhynchophylla, and dopamine and norepinephrine present in Portulaca oleracea, had the best docking scores and interaction energy. In conclusion, catechin in Uncaria rhynchophylla, and dopamine and norepinephrine in Portulaca oleracea may be used to treat AD.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.

Science.gov (United States)

Dahms, Sven O; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E

2013-02-01

Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome.

Identification of novel synthetic organic compounds with supersonic gas chromatography-mass spectrometry.

Science.gov (United States)

Fialkov, Alexander B; Amirav, Aviv

2004-11-26

Several novel synthetic organic compounds were successfully analyzed with a unique type of GC-MS titled Supersonic GC-MS following a failure in their analysis with standard GC-MS. Supersonic GC-MS is based on interfacing GC and MS with a supersonic molecular beam (SMB) and on electron ionization of sample compounds as vibrationally cold molecules while in the SMB, or by cluster chemical ionization. The analyses of novel synthetic organic compounds significantly benefited from the extended range of compounds amenable to analyses with the Supersonic GC-MS. The Supersonic GC-MS enabled the analysis of thermally labile compounds that usually degrade in the GC injector, column and/or ion source. Due to the high carrier gas flow rate at the injector liner and column these compounds eluted without degradation at significantly lower elution temperatures and the use of fly-through EI ion source eliminated any sample degradation at the ion source. The cold EI feature of providing trustworthy enhanced molecular ion (M+), complemented by its optional further confirmation with cluster CI was highly valued by the synthetic organic chemists that were served by the Supersonic GC-MS. Furthermore, the provision of extended mass spectral structural, isomer and isotope information combined with short (a few minutes) GC-MS analysis times also proved beneficial for the analysis of unknown synthetic organic compounds. As a result, the synthetic organic chemists were provided with both qualitative and quantitative data on the composition of their synthetic mixture, and could better follow the path of their synthetic chemistry. Ten cases of such analyses are demonstrated in figures and discussed.

Vapor pressure and evaporation rate of certain heat-resistant compounds in a vacuum at high temperatures

Science.gov (United States)

Bolgar, A. S.; Verkhoglyadova, T. S.; Samsonov, G. V.

1985-01-01

The vapor pressure and evaporation rate of borides of titanium, zirconium, and chrome; and of strontium and carbides of titanium, zirconium, and chrome, molybdenum silicide; and nitrides of titanium, niobium, and tantalum in a vacuum were studied. It is concluded that all subject compounds evaporate by molecular structures except AlB sub 12' which dissociates, losing the aluminum.

A Molecularly Imprinted Polymer on a Plasmonic Plastic Optical Fiber to Detect Perfluorinated Compounds in Water

Directory of Open Access Journals (Sweden)

Nunzio Cennamo

2018-06-01

Full Text Available A novel Molecularly Imprinted Polymer (MIP able to bind perfluorinated compounds, combined with a surface plasmon resonance (SPR optical fiber platform, is presented. The new MIP receptor has been deposited on a D-shaped plastic optical fiber (POF covered with a photoresist buffer layer and a thin gold film. The experimental results have shown that the developed SPR-POF-MIP sensor makes it possible to selectively detect the above compounds. In this work, we present the results obtained with perfluorooctanoate (PFOA compound, and they hold true when obtained with a perfluorinated alkylated substances (PFAs mixture sample. The sensor’s response is the same for PFOA, perfluorooctanesulfonate (PFOS or PFA contaminants in the C4–C11 range. We have also tested a sensor based on a non-imprinted polymer (NIP on the same SPR in a D-shaped POF platform. The limit of detection (LOD of the developed chemical sensor was 0.13 ppb. It is similar to the one obtained by the configuration based on a specific antibody for PFOA/PFOS exploiting the same SPR-POF platform, already reported in literature. The advantage of an MIP receptor is that it presents a better stability out of the native environment, very good reproducibility, low cost and, furthermore, it can be directly deposited on the gold layer, without modifying the metal surface by functionalizing procedures.

Hydrophilic interaction chromatography coupled matrix assisted laser desorption/ionization mass spectrometry for molecular analysis of organic compounds in medicines, tea, and coffee.

Science.gov (United States)

Wang, Ren-Qi; Bao, Kai; Croué, Jean-Philippe; Ng, Siu Choon

2013-11-21

Natural occurring organic compounds from food, natural organic matter, as well as metabolic products have received intense attention in current chemical and biological studies. Examination of unknown compounds in complex sample matrices is hampered by the limited choices for data readout and molecular elucidation. Herein, we report a generic method of hydrophilic interaction chromatography (HILIC) coupled with matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the rapid characterization of ingredients in pharmaceutical compounds, tea, and coffee. The analytes were first fractionated using a cationic HILIC column prior to MALDI-MS analyses. It was found that the retention times of a compound arising from different samples were consistent under the same conditions. Accordingly, molecules can be readily characterized by both the mass and chromatographic retention time. The retention behaviors of acidic and basic compounds on the cationic HILIC column were found to be significantly influenced by the pH of mobile phases, whereas neutral compounds depicted a constant retention time at different pH. The general HILIC-MALDI-MS method is feasible for fast screening of naturally occurring organic compounds. A series of homologs can be determined if they have the same retention behavior. Their structural features can be elucidated by considering their mass differences and hydrophilic properties as determined by HILIC chromatogram.

Highly oxidized superconductors

Science.gov (United States)

Morris, Donald E.

1994-01-01

Novel superconducting materials in the form of compounds, structures or phases are formed by performing otherwise known syntheses in a highly oxidizing atmosphere rather than that created by molecular oxygen at atmospheric pressure or below. This leads to the successful synthesis of novel superconducting compounds which are thermodynamically stable at the conditions under which they are formed.

Radiation-induced amorphization of intermetallic compounds: A molecular-dynamics study of CuTi and Cu4Ti3

International Nuclear Information System (INIS)

Lam, N.Q.; Okamoto, P.R.; Sabochick, M.J.

1991-06-01

In the present paper, important results of our recent computer simulation of radiation-induced amorphization in the ordered compounds CuTi and Cu 4 Ti 3 are summarized. The energetic, structural, thermodynamic and mechanical responses of these intermetallics during chemical disordering, point-defect production and heating were simulated, using molecular dynamics and embedded-atom potentials. From the atomistic details obtained, the critical role of radiation-induced structural disorder in driving the crystalline-to-amorphous phase transformation is discussed. 25 refs., 4 figs

Molecular screening of compounds to the predicted Protein-Protein Interaction site of Rb1-E7 with p53- E6 in HPV

Science.gov (United States)

Shaikh, Faraz; Sanehi, Parvish; Rawal, Rakesh

2012-01-01

Cervical cancer is malignant neoplasm of the cervix uteri or cervical area. Human Papillomaviruses (HPVs) which are heterogeneous groups of small double stranded DNA viruses are considered as the primary cause of cervical cancer, involved in 90% of all Cervical Cancers. Two early HPV genes, E6 and E7, are known to play crucial role in tumor formation. E6 binds with p53 and prevents its translocation and thereby inhibit the ability of p53 to activate or repress target genes. E7 binds to hypophosphorylated Rb and thereby induces cells to enter into premature S-phase by disrupting Rb-E2F complexes. The strategy of the research work was to target the site of interaction of Rb1 -E7 & p53-E6. A total of 88 compounds were selected for molecular screening, based on comprehensive literature survey for natural compounds with anti-cancer activity. Molecular docking analysis was carried out with Molegro Virtual Docker, to screen the 88 chosen compounds and rank them according to their binding affinity towards the site of interaction of the viral oncoproteins and human tumor suppressor proteins. The docking result revealed that Nicandrenone a member of Withanolides family of chemical compounds as the most likely molecule that can be used as a candidate drug against HPV induced cervical cancer. Abbreviations HPV - Human Papiloma Virus, HTSP - Human Tumor Suppressor Proteins, VOP - Viral oncoproteins. PMID:22829740

Dendritic azo compounds as a new type amorphous molecular material with quick photoinduced surface-relief-grating formation ability

Science.gov (United States)

He, Yaning; Gu, Xinyu; Guo, Miaocai; Wang, Xiaogong

2008-09-01

A series of dendritic azobenzene-containing compounds have been synthesized as a new type amorphous molecular material, which can show quick surface-relief-grating (SRG) formation ability upon light irradiation. For the synthesis, the dendritic precursor tris(2-(ethyl(phenyl)amino)ethyl)benzene-1,3,5-tricarboxylate and tris(3,5-bis(2-(ethyl(phenyl)amino)ethoxy)benzyl)benzene-1,3,5-tricarboxylate were prepared by esterification reactions between 1,3,5-benzenetricarbonyl chloride and N-ethyl- N-hydroxyethyl-aniline and 3,5-bis[2-( N-ethylanilino)ethoxy] benzylalcohol. The precursors were, respectively reacted with the diazonium salts of 4-nitroaniline, 4-aminobenzoic acid, and 4-aminobenzonitrile to introduce different types of donor-acceptor azo chromophores at the peripheral positions. The structure and properties of the dendritic azo compounds were characterized by the spectroscopic methods and thermal analysis. The surface-relief-grating (SRG) formation behavior of the dendritic azo compounds was studied by exposing the spin-coated thin films to an interference pattern of laser beams (532 nm) at modest intensity (100 mW/cm 2). The results show that the azo compounds can form stable amorphous glasses in a broad temperature range. The glass transition temperatures ( Tgs) depend on the backbone structures and the type of the peripheral azo chromophors. The type of the electron withdrawing groups in the p-positions of the terminal azobenzene units shows a significant influence on the SRG inscription rate. For the compounds containing the same type azo chromophores, the SRG inscription rate is also affected by the backbone structure.

Bisindeno-annulated pentacenes with exceptionally high photo-stability and ordered molecular packing: Simple synthesis by a regio-selective Scholl reaction

KAUST Repository

Naibi Lakshminarayana, Arun; Chang, Jingjing; Luo, Jie; Zheng, Bin; Huang, Kuo-Wei; Chi, Chunyan

2015-01-01

Bisindeno-annulated pentacenes 3a and 3b were synthesized by a simple regio-selective, FeCl3-mediated Scholl reaction from the corresponding 6,13-diaryl pentacene precursors. The fusion of two indeno-units dramatically changes the electronic properties and chemical reactivity of pentacene and the obtained compounds exhibited exceptionally high photo-stability in the solution, with a half-life time of 11.2 (3a) and 32.0 (3b) days under ambient light and air conditions. Ordered molecular packing with a small π-π stacking distance was observed in the single crystals of 3a and 3b. Our research provides a promising strategy to access stable higher order acenes with controlled molecular order. This journal is

Synthesis and properties of bis(pentamethylcyclopentadienyl) actinide hydrocarbyls and hydrides. A new class of highly reactive f-element organometallic compounds

International Nuclear Information System (INIS)

Fagan, P.J.; Manriquez, J.M.; Maatta, E.A.; Seyam, A.M.; Marks, T.J.

1981-01-01

The synthesis and chemical and physcochemical properties of Th and U bis(pentamethylcyclopentadienyl) chlorides, hydrocarbyls, chlorohydrocarbyls, and hydrides are reported. The reaction of the precursor compounds M[eta 5 -(CH 3 ) 5 C 5 ] 2 Cl 2 with 2 equiv of lithium reagent RLi produces M[eta 5 -(CH 3 ) 5 ] 2 R 2 compounds where R = CH 3 , CH 2 Si(CH 3 ) 3 , CH 2 C(CH 3 ) 3 , CH 2 C 6 H 5 , and C 6 H 5 (M = Th) and R = CH 3 , CH 2 Si(CH 3 ) 3 , CH 2 C 6 H 5 , and C 6 H 5 (M = U) in good yield. With 1 equiv of lithium reagent, M[eta 5 -(CH 3 ) 5 C 5 ] 2 (R)Cl compounds where R = CH 2 C(CH 3 ) 3 , CH 2 Si(CH 3 ) 3 , CH 2 C 6 H 5 , and C 6 H 5 (M = Th) and R = CH 2 C(CH 3 ) 3 CH 2 Si(C 3 ) 3 , CH 2 C 6 H 5 , and C 6 H 5 , and C 6 H 5 (M = U) are formed in high yield. The M[eta 5 -(CH 3 ) 5 C 52 (C 3 )Cl compounds can be synthesized by redistribution between the corresponding dimethyl and dichloro complexes. The new organoactinides were thoroughly characterized by elemental analysis, 1 H NMR and vibrational spectroscopy, and in many cases cryoscopic molecular weight measurements. The hydrocarbyls and chlorohydrocarbyls generally exhibit high thermal stability. However, the diphenyl compounds react readily with C 6 D 6 to yield, via a benzyne complex, the corresponding M(C 6 D 5 ) 2 compounds. The Th bis(neopentyl) complex reacts with benzene to produce the corresponding diphenyl complex. Competition experiments at -78 0 C indicate that the Th complexes are more reactive than those of U. The M[eta 5 -(CH 3 ) 5

Environmentally Friendly Procedure Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking for the Discovery of Potent Antiviral Compounds from Euphorbia semiperfoliata.

Science.gov (United States)

Nothias, Louis-Félix; Boutet-Mercey, Stéphanie; Cachet, Xavier; De La Torre, Erick; Laboureur, Laurent; Gallard, Jean-François; Retailleau, Pascal; Brunelle, Alain; Dorrestein, Pieter C; Costa, Jean; Bedoya, Luis M; Roussi, Fanny; Leyssen, Pieter; Alcami, José; Paolini, Julien; Litaudon, Marc; Touboul, David

2017-10-27

A supercritical fluid chromatography-based targeted purification procedure using tandem mass spectrometry and molecular networking was developed to analyze, annotate, and isolate secondary metabolites from complex plant extract mixture. This approach was applied for the targeted isolation of new antiviral diterpene esters from Euphorbia semiperfoliata whole plant extract. The analysis of bioactive fractions revealed that unknown diterpene esters, including jatrophane esters and phorbol esters, were present in the samples. The purification procedure using semipreparative supercritical fluid chromatography led to the isolation and identification of two new jatrophane esters (13 and 14) and one known (15) and three new 4-deoxyphorbol esters (16-18). The structure and absolute configuration of compound 16 were confirmed by X-ray crystallography. This compound was found to display antiviral activity against Chikungunya virus (EC 50 = 0.45 μM), while compound 15 proved to be a potent and selective inhibitor of HIV-1 replication in a recombinant virus assay (EC 50 = 13 nM). This study showed that a supercritical fluid chromatography-based protocol and molecular networking can facilitate and accelerate the discovery of bioactive small molecules by targeting molecules of interest, while minimizing the use of toxic solvents.

Molecular gas in dusty high-redshift galaxies

Science.gov (United States)

Sharon, Chelsea Electra

2013-12-01

We present high-resolution observations of carbon monoxide (CO) emission lines for three high-redshift galaxies in order to determine their molecular gas and star formation properties. These galaxies (SMM J14011+0252, SMM J00266+1708, and SDSS J0901+1814) have large infrared luminosities, which imply high dust enshrouded star formation rates and substantial molecular gas masses. We observed these sources using the Robert C. Byrd Green Bank Telescope, the Karl G. Jansky Very Large Array, the Plateau de Bure Interferometer, and the Submillimeter Array in order to obtain measurements of multiple CO spectral lines, allowing us to determine the physical conditions of the molecular gas. Our high resolution and multi-line CO mapping of SMM J00266+1708 reveals that it is a pair of merging galaxies, whose two components have different gas excitation conditions and different gas kinematics. For SMM J14011+0252 (J14011), we find a near-unity CO(3--2)/CO(1--0) intensity ratio, consistent with a single phase (i.e., a single temperature and density) of molecular gas and different from the average population value for dusty galaxies selected at submillimeter wavelengths. Our radiative transfer modeling (using the large velocity gradient approximation) indicates that converting the CO line luminosity to molecular gas mass requires a Galactic (disk-like) scale factor rather than the typical conversion factor assumed for starbursts. Despite this choice of conversion factor, J14011 falls in the same region of star formation rate surface density and gas mass surface density (the Schmidt-Kennicutt relation) as other starburst galaxies. SDSS J0901+1814 (J0901) was initially selected as a star-forming galaxy at ultraviolet wavelengths, but also has a large infrared luminosity. We use the magnification provided by the strong gravitational lensing affecting this system to examine the spatial variation of the CO excitation within J0901. We find that the CO(3--2)/CO(1--0) line ratio is

High-content, high-throughput screening for the identification of cytotoxic compounds based on cell morphology and cell proliferation markers.

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Heather L Martin

Full Text Available Toxicity is a major cause of failure in drug discovery and development, and whilst robust toxicological testing occurs, efficiency could be improved if compounds with cytotoxic characteristics were identified during primary compound screening. The use of high-content imaging in primary screening is becoming more widespread, and by utilising phenotypic approaches it should be possible to incorporate cytotoxicity counter-screens into primary screens. Here we present a novel phenotypic assay that can be used as a counter-screen to identify compounds with adverse cellular effects. This assay has been developed using U2OS cells, the PerkinElmer Operetta high-content/high-throughput imaging system and Columbus image analysis software. In Columbus, algorithms were devised to identify changes in nuclear morphology, cell shape and proliferation using DAPI, TOTO-3 and phosphohistone H3 staining, respectively. The algorithms were developed and tested on cells treated with doxorubicin, taxol and nocodazole. The assay was then used to screen a novel, chemical library, rich in natural product-like molecules of over 300 compounds, 13.6% of which were identified as having adverse cellular effects. This assay provides a relatively cheap and rapid approach for identifying compounds with adverse cellular effects during screening assays, potentially reducing compound rejection due to toxicity in subsequent in vitro and in vivo assays.

The Formation of Organic Compounds of Astrobiological Interest by the Irradiation Processing of Astrophysical Ices

Science.gov (United States)

Sandford, Scott A.

2015-01-01

Many environments in space contain very low temperature mixed molecular ices that are exposed to ionizing radiation in the form of cosmic rays and high-energy photons. While traditional chemistry would not be expected to occur at the temperatures typical of these ices (T compounds. Many of these new products are of direct interest to astrobiology. For example, the irradiation of mixed molecular ices has been shown to produce amino acids, amphiphiles, quinones, sugars, heterocyclic compounds, and nucleobases, all molecular building blocks used by terrestrial life. Insofar as the presence of these materials plays a role in the origin of life on planets, this has profound implications for the potential abundance of life in the universe since these experiments simulate universal conditions that are expected to be found wherever new stars and planets form.

Sintering of ultra high molecular weight polyethylene

Indian Academy of Sciences (India)

Abstract. Ultra high molecular weight polyethylene (UHMWPE) is a high performance polymer having low coefficient of friction, good abrasion resistance, good chemical ... In this study, we report our results on compaction and sintering behaviour of two grades of UHMWPE with reference to the powder morphology, sintering ...

A new multidimensional stoichiometric classification of compounds: moving beyond the van Krevelen diagram.

Science.gov (United States)

Rivas-Ubach, A.; Liu, Y.; Bianchi, T. S.; Tolic, N.; Jansson, C.; Paša-Tolić, L.

2017-12-01

The role of nutrients in organisms, especially primary producers, has been a topic of special interest in ecosystem research for understanding the ecosystem structure and function. The majority of macro-elements in organisms, such as C, H, O, N and P, do not act as single elements but are components of organic compounds (lipids, peptides, carbohydrates, etc), which are more directly related to the physiology of organisms and thus to the ecosystem function. However, accurately deciphering the overall content of the main compound classes (lipids, proteins, carbohydrates,…) in organisms is still a major challenge. van Krevelen (vK) diagrams have been widely used as an estimation of the main compound categories present in environmental samples based on O:C vs H:C molecular ratios, but a stoichiometric classification based exclusively on O:C and H:C ratios is feeble. Different compound classes show large O:C and H:C ratio overlapping and other heteroatoms, such as N and P, should be considered to robustly distinguish the different classes. We propose a new compound classification for biological/environmental samples based on the C:H:O:N:P stoichiometric ratios of thousands of molecular formulas of characterized compounds from 6 different main categories: lipids, peptides, amino-sugars, carbohydrates, nucleotides and phytochemical compounds (oxy-aromatic compounds). This new multidimensional stoichiometric compound constraints classification (MSCC) can be applied to data obtained with high resolution mass spectrometry (HRMS), allowing an accurate overview of the relative abundances of the main compound categories present in organismal samples. The MSCC has been optimized for plants, but it could be also applied to different organisms and serve as a strong starting point to further investigate other environmental complex matrices (soils, aerosols, etc). The proposed MSCC advances environmental research, especially eco-metabolomics, ecophysiology and ecological

Functional Molecular Diversity of Marine Dissolved Organic Matter Is Reduced during Degradation

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Andrea Mentges

2017-06-01

Full Text Available Dissolved organic matter (DOM is a highly diverse mixture of compounds, accounting for one of the world's largest active carbon pools. The surprising recalcitrance of some DOM compounds to bacterial degradation has recently been associated with its diversity. However, little is known about large-scale patterns of marine DOM diversity and its change through degradation, in particular considering the functional diversity of DOM. Here, we analyze the development of marine DOM diversity during degradation in two data sets comprising DOM of very different ages: a three-year mesocosm experiment and highly-resolved field samples from the Atlantic and Southern Ocean. The DOM molecular composition was determined using ultra-high resolution mass spectrometry. We quantify DOM diversity using three conceptually different diversity measures, namely richness of molecular formulas, abundance-based diversity, and functional molecular diversity. Using these measures we find stable molecular richness of DOM with age >1 year, systematic changes in the molecules' abundance distribution with degradation state, and increasing homogeneity with respect to chemical properties for more degraded DOM. Coinciding with differences in sea water density, the spatial field data separated clearly into regions of high and low diversity. The joint application of different diversity measures yields a comprehensive overview on temporal and spatial patterns of molecular diversity, valuable for general conclusions on drivers and consequences of marine DOM diversity.

Research for molecular magnetic theory

International Nuclear Information System (INIS)

Kuang Xiaoyu; Zhou Kangwei; Gou Qingquan

2002-01-01

Recently, the authors have established a DSF theoretical method suitable for researching molecular magnetism of the compounds consisting of transition group elements. By this method, the authors have revealed that the ferromagnetism of molecules is due to the cross-interaction between d orbitals of adjacent transition-metal ions, and that the antiferromagnetism is due to the parallel interactions. Further more, the authors have also established a magnetism theory for hetero-dinuclear molecular systems and covalent molecular systems, respectively. With these theoretical methods, a systematical studies are performed for the magnetism origin and the magnetism variation rule of transition metal complex molecules in various inorganic compounds, organic compounds and biologic proteins, and a reasonable explanation is presented for the strong antiferromagnetic coupling phenomenon in the catalysis active center of ribonucleotide reductase. This indicates that the main physical mechanisms are the combined effect of the direct-exchange, kinetic exchange and the molecular covalent property

Sea cucumbers, the ocean of bioactive compounds

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Hadi Ebrahimi

2015-07-01

Full Text Available Sea cucumbers are one of the most echinoderms and from the class Holothuroidea. Some of their specific biological activities are including anti-cancer, anticoagulant, antihypertensive, anti-inflammatory, antimicrobial, antioxidant, anti-atherosclerosis and anti-tumor properties, as well as accelerate wound healing. The presence of different compounds such as saponins, chondroitin sulfates, glycosaminoglycans, sulfated Polysaccharides, glycoprotein, glycosphingolipids and essential and non essential fatty acids, are the causes of their biological properties. Saponins, which are produced for compatibility with the environment, are as theire secondary metabolites. These active compounds have biological properties like hemolytic, anti-tumor, anti-inflammatory, antibacterial, antiviral, ichthyotoxic, cytostatic, anti neogenic, antineoplastic, and uric acid lowering effects. Sea cucumber, have high economic value. In East Asia, Since ancient times, it have been traditionally used for the treatment of fatigue, sexual impotence, impotence caused by aging, constipation due to intestinal dryness, urinary incontinence, asthma, hypertension, arthritis and anemia. Also, toxins obtained from sea cucumber, have anti-viral, anti-tumor, anti-cancer and anti-pregnancy properties. According to literatures, the aqueous extract and high molecular weight compounds from sea cucumbers can inhibit tumor activity, via the apoptosis induction. Sea cucumbers because of the high percentage of protein and the absence of cholesterol, classified as an invigorating food. Because of different species of sea cucumbers in the Persian Gulf and Oman Sea the identification of compounds and biological properties of sea cucumber species in these regions is recommended to the researchers.

Molecular Dynamics: New Frontier in Personalized Medicine.

Science.gov (United States)

Sneha, P; Doss, C George Priya

2016-01-01

The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.

Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses

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Jinxiang Xi

2018-03-01

Full Text Available Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of

Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses.

Science.gov (United States)

Xi, Jinxiang; Hu, Qin; Zhao, Linlin; Si, Xiuhua April

2018-03-27

Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high

Hydrophilic interaction chromatography coupled matrix assisted laser desorption/ionization mass spectrometry for molecular analysis of organic compounds in medicines, tea, and coffee

KAUST Repository

Wang, Renqi

2013-01-01

Natural occurring organic compounds from food, natural organic matter, as well as metabolic products have received intense attention in current chemical and biological studies. Examination of unknown compounds in complex sample matrices is hampered by the limited choices for data readout and molecular elucidation. Herein, we report a generic method of hydrophilic interaction chromatography (HILIC) coupled with matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the rapid characterization of ingredients in pharmaceutical compounds, tea, and coffee. The analytes were first fractionated using a cationic HILIC column prior to MALDI-MS analyses. It was found that the retention times of a compound arising from different samples were consistent under the same conditions. Accordingly, molecules can be readily characterized by both the mass and chromatographic retention time. The retention behaviors of acidic and basic compounds on the cationic HILIC column were found to be significantly influenced by the pH of mobile phases, whereas neutral compounds depicted a constant retention time at different pH. The general HILIC-MALDI-MS method is feasible for fast screening of naturally occurring organic compounds. A series of homologs can be determined if they have the same retention behavior. Their structural features can be elucidated by considering their mass differences and hydrophilic properties as determined by HILIC chromatogram. © 2013 The Royal Society of Chemistry.

Natural Compounds Interacting with Nicotinic Acetylcholine Receptors: From Low-Molecular Weight Ones to Peptides and Proteins

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Denis Kudryavtsev

2015-05-01

Full Text Available Nicotinic acetylcholine receptors (nAChRs fulfill a variety of functions making identification and analysis of nAChR subtypes a challenging task. Traditional instruments for nAChR research are d-tubocurarine, snake venom protein α-bungarotoxin (α-Bgt, and α-conotoxins, neurotoxic peptides from Conus snails. Various new compounds of different structural classes also interacting with nAChRs have been recently identified. Among the low-molecular weight compounds are alkaloids pibocin, varacin and makaluvamines C and G. 6-Bromohypaphorine from the mollusk Hermissenda crassicornis does not bind to Torpedo nAChR but behaves as an agonist on human α7 nAChR. To get more selective α-conotoxins, computer modeling of their complexes with acetylcholine-binding proteins and distinct nAChRs was used. Several novel three-finger neurotoxins targeting nAChRs were described and α-Bgt inhibition of GABA-A receptors was discovered. Information on the mechanisms of nAChR interactions with the three-finger proteins of the Ly6 family was found. Snake venom phospholipases A2 were recently found to inhibit different nAChR subtypes. Blocking of nAChRs in Lymnaea stagnalis neurons was shown for venom C-type lectin-like proteins, appearing to be the largest molecules capable to interact with the receptor. A huge nAChR molecule sensible to conformational rearrangements accommodates diverse binding sites recognizable by structurally very different compounds.

High temperature superconductivity: Concept, preparation and testing of high Tc superconductor compounds, and applications

International Nuclear Information System (INIS)

Harara, Wafik

1992-06-01

Many studies have been carried out on high temperature superconductors with transition temperature above that of the liquid nitrogen. In this scientific study the concept and the mechanism of this phenomena are discussed, in addition the examples of preparation and testing of high temperature superconductors compounds are shown. Also the most important applications in industry are explained. (author). 15 refs., 2 tabs., 18 figs

Towards an understanding of the propensity for crystalline hydrate formation by molecular compounds

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Alankriti Bajpai

2016-11-01

Full Text Available Hydrates are technologically important and ubiquitous yet they remain a poorly understood and understudied class of molecular crystals. In this work, we attempt to rationalize propensity towards hydrate formation through crystallization studies of molecules that lack strong hydrogen-bond donor groups. A Cambridge Structural Database (CSD survey indicates that the statistical occurrence of hydrates in 124 molecules that contain five- and six-membered N-heterocyclic aromatic moieties is 18.5%. However, hydrate screening experiments on a library of 11 N-heterocyclic aromatic compounds with at least two acceptor moieties and no competing hydrogen-bond donors or acceptors reveals that over 70% of this group form hydrates, suggesting that extrapolation from CSD statistics might, at least in some cases, be deceiving. Slurrying in water and exposure to humidity were found to be the most effective discovery methods. Electrostatic potential maps and/or analysis of the crystal packing in anhydrate structures was used to rationalize why certain molecules did not readily form hydrates.

Harmonic force field for nitro compounds.

Science.gov (United States)

Bellido, Edson P; Seminario, Jorge M

2012-06-01

Molecular simulations leading to sensors for the detection of explosive compounds require force field parameters that can reproduce the mechanical and vibrational properties of energetic materials. We developed precise harmonic force fields for alanine polypeptides and glycine oligopeptides using the FUERZA procedure that uses the Hessian tensor (obtained from ab initio calculations) to calculate precise parameters. In this work, we used the same procedure to calculate generalized force field parameters of several nitro compounds. We found a linear relationship between force constant and bond distance. The average angle in the nitro compounds was 116°, excluding the 90° angle of the carbon atoms in the octanitrocubane. The calculated parameters permitted the accurate molecular modeling of nitro compounds containing many functional groups. Results were acceptable when compared with others obtained using methods that are specific for one type of molecule, and much better than others obtained using methods that are too general (these ignore the chemical effects of surrounding atoms on the bonding and therefore the bond strength, which affects the mechanical and vibrational properties of the whole molecule).

Understanding the Effectiveness of Natural Compound Mixtures in Cancer through Their Molecular Mode of Action

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Thazin Nwe Aung

2017-03-01

Full Text Available Many approaches to cancer management are often ineffective due to adverse reactions, drug resistance, or inadequate target specificity of single anti-cancer agents. In contrast, a combinatorial approach with the application of two or more anti-cancer agents at their respective effective dosages can achieve a synergistic effect that boosts cytotoxicity to cancer cells. In cancer, aberrant apoptotic pathways allow cells that should be killed to survive with genetic abnormalities, leading to cancer progression. Mutations in apoptotic mechanism arising during the treatment of cancer through cancer progression can consequently lead to chemoresistance. Natural compound mixtures that are believed to have multiple specific targets with minimal acceptable side-effects are now of interest to many researchers due to their cytotoxic and chemosensitizing activities. Synergistic interactions within a drug mixture enhance the search for potential molecular targets in cancer cells. Nonetheless, biased/flawed scientific evidence from natural products can suggest false positive therapeutic benefits during drug screening. In this review, we have taken these factors into consideration when discussing the evidence for these compounds and their synergistic therapeutic benefits in cancer. While there is limited evidence for clinical efficacy for these mixtures, in vitro data suggest that these preparations merit further investigation, both in vitro and in vivo.

The influence of compound admixtures on the properties of high-content slag cement

Energy Technology Data Exchange (ETDEWEB)

Dongxu, L.; Xuequan, W.; Jinlin, S.; Yujiang, W.

2000-01-01

Based on the activation theory of alkali and sulfate, the influence of compound admixtures on the properties of high-content slag cement was studied by testing the strength, pore structure, hydrates, and microstructure, Test results show that compound admixtures can obviously improve the properties of high-content slag cement. The emphasis of the present research is two-fold: substituting gypsum with anhydrite and calcining gypsum. These both can improve early and later performance.

3D-QSAR, molecular docking, and molecular dynamic simulations for prediction of new Hsp90 inhibitors based on isoxazole scaffold.

Science.gov (United States)

Abbasi, Maryam; Sadeghi-Aliabadi, Hojjat; Amanlou, Massoud

2018-05-01

Heat shock protein 90(Hsp90), as a molecular chaperone, play a crucial role in folding and proper function of many proteins. Hsp90 inhibitors containing isoxazole scaffold are currently being used in the treatment of cancer as tumor suppressers. Here in the present studies, new compounds based on isoxazole scaffold were predicted using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamic (MD) simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were also done. The steric and electrostatic contour map of CoMFA and CoMSIA were created. Hydrophobic, hydrogen bond donor and acceptor of CoMSIA model also were generated, and new compounds were predicted by CoMFA and CoMSIA contour maps. To investigate the binding modes of the predicted compounds in the active site of Hsp90, a molecular docking simulation was carried out. MD simulations were also conducted to evaluate the obtained results on the best predicted compound and the best reported Hsp90 inhibitors in the 3D-QSAR model. Findings indicate that the predicted ligands were stable in the active site of Hsp90.

Modeling of RO/NF membrane rejections of PhACs and organic compounds: a statistical analysis

Directory of Open Access Journals (Sweden)

G. Amy

2008-07-01

Full Text Available Rejections of pharmaceutical compounds (Ibuprofen, Diclofenac, Clofibric acid, Naproxen, Primidone, Phenacetin and organic compounds (Dichloroacetic acid, Trichloroacetic acid, Chloroform, Bromoform, Trichloroethene, Perchloroethene, Carbontetrachloride, Carbontetrabromide by NF (Filmtec, Saehan and RO (Filmtec, Saehan, Toray, Koch membranes were studied. Chloroform presented the lowest rejection due to small molar volume, equivalent width and length. Diclofenac and Primidone showed high rejections related to high molar volume and length. Dichloroacetic acid and Trichloroacetic acid presented good rejections caused by charge exclusion instead of steric hindrance mechanism influencing rejection. Bromoform and Trichloroethene showed low rejections due to small length and equivalent width. Carbontetrabromide, Perchloroethene and Carbontetrachloride with higher equivalent width than BF and TCE presented better rejections. A qualitative analysis of variables using Principal Component Analysis was successfully implemented for reduction of physical-chemical compound properties that influence membrane rejection of PhACs and organic compounds. Properties such as dipole moment, molar volume, hydrophobicity/hydrophilicity, molecular length and equivalent width were found to be important descriptors for simulation of membrane rejection. For membranes used in the experiments, we may conclude that charge repulsion was an important mechanism of rejection for ionic compounds. After analysis with Multiple Linear Regression, we also may conclude that membrane rejection of neutral compounds was well predicted by molar volume, length, equivalent width, hydrophobicity/hydrophilicity and dipole moment. Molecular weight was a poor descriptor variable for rejection modelling. We were able to provide acceptable statistical significance for important results.

Computer aided drug discovery of highly ligand efficient, low molecular weight imidazopyridine analogs as FLT3 inhibitors.

Science.gov (United States)

Frett, Brendan; McConnell, Nick; Smith, Catherine C; Wang, Yuanxiang; Shah, Neil P; Li, Hong-yu

2015-04-13

The FLT3 kinase represents an attractive target to effectively treat AML. Unfortunately, no FLT3 targeted therapeutic is currently approved. In line with our continued interests in treating kinase related disease for anti-FLT3 mutant activity, we utilized pioneering synthetic methodology in combination with computer aided drug discovery and identified low molecular weight, highly ligand efficient, FLT3 kinase inhibitors. Compounds were analyzed for biochemical inhibition, their ability to selectively inhibit cell proliferation, for FLT3 mutant activity, and preliminary aqueous solubility. Validated hits were discovered that can serve as starting platforms for lead candidates. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds

Science.gov (United States)

Mounet, Nicolas; Gibertini, Marco; Schwaller, Philippe; Campi, Davide; Merkys, Andrius; Marrazzo, Antimo; Sohier, Thibault; Castelli, Ivano Eligio; Cepellotti, Andrea; Pizzi, Giovanni; Marzari, Nicola

2018-02-01

Two-dimensional (2D) materials have emerged as promising candidates for next-generation electronic and optoelectronic applications. Yet, only a few dozen 2D materials have been successfully synthesized or exfoliated. Here, we search for 2D materials that can be easily exfoliated from their parent compounds. Starting from 108,423 unique, experimentally known 3D compounds, we identify a subset of 5,619 compounds that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van der Waals density functional theory, validated against experimental structural data and calculated random phase approximation binding energies, further allowed the identification of 1,825 compounds that are either easily or potentially exfoliable. In particular, the subset of 1,036 easily exfoliable cases provides novel structural prototypes and simple ternary compounds as well as a large portfolio of materials to search from for optimal properties. For a subset of 258 compounds, we explore vibrational, electronic, magnetic and topological properties, identifying 56 ferromagnetic and antiferromagnetic systems, including half-metals and half-semiconductors.

Decomposition and Ignition of the high-nitrogen compound triaminoguanidinium azotetrazolate (TAGzT)

Energy Technology Data Exchange (ETDEWEB)

Tappan, Bryce C.; Ali, Arif N.; Son, Steven F. [Dynamic Experimentation Division, DX-2 High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Brill, Thomas B. [Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716 (United States)

2006-06-15

The high-nitrogen compound triaminoguanidinium azotetrazolate (TAGzT) belongs to a class of C, H and N compounds that are free of both oxygen and metal, but retain energetic material properties as a result of their high heat of formation. Its decomposition thus lacks secondary oxidation reactions of carbon and hydrogen. The fact that TAGzT is over 80% nitrogen makes it potentially useful as a gas generant and energetic material with a low flame temperature to increase the impulse in gun or rocket propellants. The burning rate, laser ignition and flash pyrolysis (T-jump/FTIR spectroscopy) characteristics were determined. It was found that TAGzT exhibits one of the fastest low-pressure burning rates yet measured for an organic compound. Both the decomposition and ignition behavior of TAGzT are dominated by condensed phase reactions. T-Jump/FTIR spectroscopy indicates that condensed phase reactions release about 65% of the energy, which helps to explain the high burning rate at low pressure. (Abstract Copyright [2006], Wiley Periodicals, Inc.)

Nitrogen-rich higher-molecular soil organic compounds patterned by lignin degradation products: Considerations on the nature of soil organic nitrogen

Science.gov (United States)

Liebner, Falk; Bertoli, Luca; Pour, Georg; Klinger, Karl; Ragab, Tamer; Rosenau, Thomas

2016-04-01

and NMR spectroscopy (1H, 13C, 15N), respectively. The reactions of hydroquinone, methyl hydroquinone and p-benzoquinone with ammonia and dimethyl-ammonium dimethylcarbamate - a source of dimethyl amine - affording the respective (substituted) 2,5-diamino-[1,4]benzoquinones under aerobic conditions have been studied by EPR spectroscopy for both oxygen-free and oxygen-rich conditions. 15N CPMAS NMR and XPS spectra of ammoxidized technical lignins and of ammoxidized low-molecular polyphenolic and quinoid products of the aerobic, microbial lignin degradation using 15N labeled aqueous ammonium hydroxide share many similarities, highly indicative for reaction sequences proceeding via common key intermediates. It has been demonstrated that 2,5-dihydroxy-[1,4]benzoquinone which can be surprisingly formed from both lignin and cellulose reacts with N nucleophiles to the respective 2,5-amino derivatives. The latter are semi-stable and react further to nitrogenous compounds of higher molecular weight. Hydroquinone and methoxy hydroquinone react even faster affording the respective 2,5-diamino-[1,4]benzoquinones. EPR experiments revealed that the reaction of hydroquinone with dimethyl amine proceed via radical intermediates. The results of this study strongly support the polyphenol theory and is hoped to contribute to a better understanding of nitrogen accumulation in soil organic matter. Acknowledgement The financial support by the Austrian Research Promotion Agency FFG (project FLIPPR: Future Lignin and Pulp Processing Research, 836650) and by The Austrian Science Fund FWF (project I154-N19) is gratefully acknowledged.

Effect of Molecular Weight on the Properties of Liquid Epoxidized Natural Rubber Acrylate (LENRA)/ Silica Hybrid Composites

International Nuclear Information System (INIS)

Eda Yuhana Ariffin; Azizan Ahmad; Dahlan Mohd; Mahathir Mohamed

2011-01-01

This paper reports on the effect of molecular weight on the morphological and mechanical properties of liquid epoxidized natural rubber acrylate (LENRA)/ silica hybrid composites prepared by sol-gel technique. The sol-gel reaction was conducted at different concentration of tetraethyl orthosilicate (TEOS), used as a precursor of silica. TEOS were introduced in 10, 20, 30, 40 and 50 parts per hundred rubber (phr) in the composites. Two different molecular weights of ENR were used to study the effect of molecular weight on the mechanical and morphological properties of the compounds. These compounds were cured by ultraviolet (UV) irradiation. The mechanical properties were studied through pendulum hardness and scratch tests. Higher molecular weight of ENR showed better mechanical properties than lower molecular weight. Transmission electron microscope was used to determine the silica size and to study the distribution and dispersion of the silica particles. High molecular weight showed greater distribution and dispersion of silica particles with diameter of 13 - 256 nm. Morphological and mechanical properties of LENRA/ silica hybrid composites were improved by using high molecular weight of ENR. (author)

Application of molecular calcium compounds in catalysis and hydrogen storage; Anwendung von molekularen Calcium-Verbindungen in der Katalyse und der Wasserstoffspeicherung

Energy Technology Data Exchange (ETDEWEB)

Spielmann, Jan

2010-07-20

1. Applications in catalysis: In the course of this work new catalytic applications of calcium compounds and in particular hydrocarbon-soluble calcium hydride species have been investigated. The complex [(DIPP-nacnac)CaH(THF)]2 (1, DIPP-nacnac = HC[C(Me)N-2,6-(i-Pr)-C6H3]2) served as a model system to test reactivity of the calcium hydride in stoichiometric reactions on a molecular level. It has been found that the hydroboration of conjugated alkenes with catecholborane can be accelerated considerably by using catalytic amounts of calcium complexes. However it was shown that calcium hydride species catalyze the decomposition of catecholborane to BH3 which is probably the catalytically active species. Investigations on the catalytic hydrosilylation of ketones have demonstrated that calcium complexes are efficient catalysts for this reaction. In the proposed catalytic cycle of this reaction six-coordinate hypervalent silicon species play a crucial role. Furthermore it has been shown that molecular calcium compounds are catalysts for the hydrogenation of conjugated alkenes with H2 under relatively mild conditions (20 bar H2, 20 C). Both steps in the proposed catalytical cycle i.e. addition of a metal hydride to the C=C double bond and a heterolytic cleavage of H2 by a calcium alkyl compound have been confirmed experimentally. 2. Applications in hydrogen storage: Ligand stabilized metal amidoborane complexes in the form of (DIPP-nacnac)MNH(R)BH3(THF)x (M = Ca, Mg; R = H, Me, i-Pr, 2,6-(i-Pr)-C6H3; x = 0, 1, 2) have been synthesized and structurally characterized. These complexes are model systems for the metal amidoborane compounds M(NH2BH3)n (M = Li, Na, n = 1; M = Ca, n = 2), which are potential high capacity hydrogen storage materials. To get insights in their dehydrogenation mechanisms the thermal decomposition of the model compounds was investigated in solution. This allowed for the first isolation of well-defined dehydrogenated products which have been

Processing and properties of PCL/cotton linter compounds

Energy Technology Data Exchange (ETDEWEB)

Bezerra, Elieber Barros; Franca, Danyelle Campos; Morais, Dayanne Diniz de Souza; Araujo, Edcleide Maria [Universidade Federal de Campina Grande (UFCG), PB (Brazil). Departamento de Engenharia de Materiais; Rosa, Morsyleide de Freitas; Morais, Joao Paulo Saraiva [Embrapa Tropical Agroindustia, Fortaleza, CE (Brazil); Wellen, Renate Maria Ramos, E-mail: wellen.renate@gmail.com [Universidade Federal da Paraiaba (UFPB), Joao Pessoa, PB (Brazil)

2017-03-15

Biodegradable compounds of poly(ε-caprolactone) (PCL)/ cotton linter were melting mixed with filling content ranging from 1% to 5% w/w. Cotton linter is an important byproduct of textile industry; in this work it was used in raw state and after acid hydrolysis. According to the results of torque rheometry no decaying of viscosity took place during compounding, evidencing absence of breaking down in molecular weight. The thermal stability increased by 20% as observed in HDT for PCL/cotton nanolinter compounds. Adding cotton linter to PCL did not change its crystalline character as showed by XRD; however an increase in degree of crystallinity was observed by means of DSC. From mechanical tests in tension was observed an increase in ductility of PCL, and from mechanical tests in flexion an increase in elastic modulus upon addition of cotton linter, whereas impact strength presented lower values for PCL/cotton linter and PCL/cotton nanolinter compounds. SEM images showed that PCL presents plastic fracture and cotton linter has an interlacing fibril structure with high L/D ratio, which are in agreement with matrix/fibril morphology observed for PCL/cotton linter compounds. PCL/cotton linter compounds made in this work cost less than neat PCL matrix and presented improved properties making feasible its commercial use. (author)

MXene molecular sieving membranes for highly efficient gas separation.

Science.gov (United States)

Ding, Li; Wei, Yanying; Li, Libo; Zhang, Tao; Wang, Haihui; Xue, Jian; Ding, Liang-Xin; Wang, Suqing; Caro, Jürgen; Gogotsi, Yury

2018-01-11

Molecular sieving membranes with sufficient and uniform nanochannels that break the permeability-selectivity trade-off are desirable for energy-efficient gas separation, and the arising two-dimensional (2D) materials provide new routes for membrane development. However, for 2D lamellar membranes, disordered interlayer nanochannels for mass transport are usually formed between randomly stacked neighboring nanosheets, which is obstructive for highly efficient separation. Therefore, manufacturing lamellar membranes with highly ordered nanochannel structures for fast and precise molecular sieving is still challenging. Here, we report on lamellar stacked MXene membranes with aligned and regular subnanometer channels, taking advantage of the abundant surface-terminating groups on the MXene nanosheets, which exhibit excellent gas separation performance with H 2 permeability >2200 Barrer and H 2 /CO 2 selectivity >160, superior to the state-of-the-art membranes. The results of molecular dynamics simulations quantitatively support the experiments, confirming the subnanometer interlayer spacing between the neighboring MXene nanosheets as molecular sieving channels for gas separation.

Solid state synthesis, structural, physicochemical and optical properties of an inter-molecular compound: 2-hydroxy-1, 2-diphenylethanone-4-nitro-o-phenylenediamine system

Science.gov (United States)

Rai, U. S.; Singh, Manjeet; Rai, R. N.

2017-09-01

The phase diagram of 2-hydroxy-1, 2-diphenylethanone (HDPE)-4-nitro-o-phenylenediamine (NOPDA) system, determined by the thaw-melt method, gives two eutectics E1 (m p = 66.0 °C) and E2 (m p = 155.0 °C) with 0.30 and 0.55 mol fractions of NOPDA, respectively, and an 1:1 inter-molecular compound (IMC) (m p 162.0 °C). This IMC was synthesized by adopting the green synthetic method of solid state reaction. While its formation and structure were confirmed by the X-ray diffraction and spectroscopic methods, the ORTEP view gives mode of crystal packing, C‒H…O, C‒H…N, π-π stacking and the inter-molecular hydrogen bonding in the compound. The single crystal of the IMC shows 53% transmission and emits significantly higher dual fluorescence, and the band gap was computed to be 3.04 eV. The values of solubility of the IMC, measured in the temperature range 304-322 K, satisfy the mole fraction (X) and temperature equation: Xeq= 5.1324 × 10-7 e 0.01356T.

A new wire fabrication processing using high Ga content Cu-Ga compound in V3Ga compound superconducting wire

International Nuclear Information System (INIS)

Hishinuma, Yoshimitsu; Nishimura, Arata; Kikuchi, Akihiro; Iijima, Yasuo; Takeuchi, Takao

2007-01-01

A superconducting magnet system is also one of the important components in an advanced magnetic confinement fusion reactor. Then it is required to have a higher magnetic field property to confine and maintain steady-sate burning deuterium (D)-tritium (T) fusion plasma in the large interspace during the long term operation. Burning plasma is sure to generate 14 MeV fusion neutrons during deuterium-tritium reaction, and fusion neutrons will be streamed and penetrated to superconducting magnet through large ports with damping neutron energy. Therefore, it is necessary to consider carefully not only superconducting property but also neutron irradiation property in superconducting materials for use in a future fusion reactor, and a 'low activation and high field superconducting magnet' will be required to realize the fusion power plant beyond International Thermonuclear Experimental Reactor (ITER). V-based superconducting material has a much shorter decay time of induced radioactivity compared with the Nb-based materials. We thought that the V 3 Ga compound was one of the most promising materials for the 'low activation and higher field superconductors' for an advanced fusion reactor. However, the present critical current density (J c ) property of V 3 Ga compound wire is insufficient for apply to fusion magnet applications. We investigated a new route PIT process using a high Ga content Cu-Ga compound in order to improve the superconducting property of the V 3 Ga compound wire. (author)

High-Throughput Screening and Quantitation of Target Compounds in Biofluids by Coated Blade Spray-Mass Spectrometry.

Science.gov (United States)

Tascon, Marcos; Gómez-Ríos, Germán Augusto; Reyes-Garcés, Nathaly; Poole, Justen; Boyacı, Ezel; Pawliszyn, Janusz

2017-08-15

Most contemporary methods of screening and quantitating controlled substances and therapeutic drugs in biofluids typically require laborious, time-consuming, and expensive analytical workflows. In recent years, our group has worked toward developing microextraction (μe)-mass spectrometry (MS) technologies that merge all of the tedious steps of the classical methods into a simple, efficient, and low-cost methodology. Unquestionably, the automation of these technologies allows for faster sample throughput, greater reproducibility, and radically reduced analysis times. Coated blade spray (CBS) is a μe technology engineered for extracting/enriching analytes of interest in complex matrices, and it can be directly coupled with MS instruments to achieve efficient screening and quantitative analysis. In this study, we introduced CBS as a technology that can be arranged to perform either rapid diagnostics (single vial) or the high-throughput (96-well plate) analysis of biofluids. Furthermore, we demonstrate that performing 96-CBS extractions at the same time allows the total analysis time to be reduced to less than 55 s per sample. Aiming to validate the versatility of CBS, substances comprising a broad range of molecular weights, moieties, protein binding, and polarities were selected. Thus, the high-throughput (HT)-CBS technology was used for the concomitant quantitation of 18 compounds (mixture of anabolics, β-2 agonists, diuretics, stimulants, narcotics, and β-blockers) spiked in human urine and plasma samples. Excellent precision (∼2.5%), accuracy (≥90%), and linearity (R 2 ≥ 0.99) were attained for all the studied compounds, and the limits of quantitation (LOQs) were within the range of 0.1 to 10 ng·mL -1 for plasma and 0.25 to 10 ng·mL -1 for urine. The results reported in this paper confirm CBS's great potential for achieving subsixty-second analyses of target compounds in a broad range of fields such as those related to clinical diagnosis, food, the

Western blotting of high and low molecular weight proteins using heat.

Science.gov (United States)

Kurien, Biji T; Scofield, R Hal

2015-01-01

A method for the electrophoretic transfer of high and low molecular weight proteins to nitrocellulose membranes following sodium dodecyl sulfate (SDS) polyacrylamide gel is described here. The transfer was performed with heated (70-75 °C) normal transfer buffer from which methanol had been omitted. Complete transfer of high and low molecular weight antigens (molecular weight protein standards, a purified protein, and proteins from a human tissue extract) could be carried out in 10 min for a 7 % (0.75 mm) SDS polyacrylamide gel. For 10 and 12.5 % gels (0.75 mm) the corresponding time was 15 min. A complete transfer could be carried out in 20 min for 7, 10, and 12.5 % gels (1.5 mm gels). The permeability of the gel is increased by heat, such that the proteins trapped in the polyacrylamide gel matrix can be easily transferred to the membrane. The heat mediated transfer method was compared with a conventional transfer protocol, under similar conditions. The conventional method transferred minimal low molecular weight proteins while retaining most of the high molecular weight proteins in the gel. In summary, this procedure is particularly useful for the transfer of high molecular weight proteins, very rapid, and avoids the use of methanol.

Impact of molecular weight on the formation of electrosprayed chitosan microcapsules as delivery vehicles for bioactive compounds.

Science.gov (United States)

Gómez-Mascaraque, Laura G; Sanchez, Gloria; López-Rubio, Amparo

2016-10-05

The molecular weight of chitosan is one of its most determinant characteristics, which affects its processability and its performance as a biomaterial. However, information about the effect of this parameter on the formation of electrosprayed chitosan microcapsules is scarce. In this work, the impact of chitosan molecular weight on its electrosprayability was studied and correlated with its effect on the viscosity, surface tension and electrical conductivity of solutions. A Discriminant Function Analysis revealed that the morphology of the electrosprayed chitosan materials could be correctly predicted using these three parameters for almost 85% of the samples. The suitability of using electrosprayed chitosan capsules as carriers for bioactive agents was also assessed by loading them with a model active compound, (-)-epigallocatechin gallate (EGCG). This encapsulation, with an estimated efficiency of around 80% in terms of preserved antioxidant activity, showed the potential to prolong the antiviral activity of EGCG against murine norovirus via gradual bioactive release combined with its protection against degradation in simulated physiological conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Volatile compounds emitted by diverse phytopathogenic microorganisms promote plant growth and flowering through cytokinin action

Czech Academy of Sciences Publication Activity Database

Sanchez-Lopez, A.; Baslam, M.; De Diego, N.; Jose Munoz, F.; Bahaji, A.; Almagro, G.; Ricarte-Bermejo, A.; Garcia-Gomez, P.; Li, J.; Humplík, J.F.; Novák, Ondřej; Spíchal, L.; Doležal, Karel; Baroja-Fernandez, E.; Pozueta-Romero, J.

2016-01-01

Roč. 39, č. 12 (2016), s. 2592-2608 ISSN 0140-7791 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : exceptionally high-levels * tandem mass-spectrometry * arabidopsis-thaliana * nitric-oxide * bacterial volatiles * floral transition * anthocyanin biosynthesis * transgenic arabidopsis * liquid-chromatography * organic-compounds * cytokinin * flowering * growth promotion * microbial volatile compounds * photoregulation * photosynthesis * plant-microbe interaction * starch Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.173, year: 2016

Cantilever torque magnetometry on coordination compounds

DEFF Research Database (Denmark)

Perfetti, Mauro

2017-01-01

compounds, such as quantum computation or information storage. This review enlightens that CTM offers a unique combination of accuracy and precision to disentangle noncollinear contributions inside Single Crystals as well as the sensitivity to detect molecular order of thin films. CTM can also detect......Cantilever Torque Magnetometry (CTM) is one of the leading techniques to deeply understand magnetic anisotropy of coordination compounds. The knowledge of magnetic anisotropy is a mandatory requirement before proceeding with any future application related to the magnetic properties of coordination...... quantum phenomena such as magnetization steps and molecular hysteresis curves. Moreover, it can also provide the energy levels splitting and avefunctions composition, especially if coupled with microwave radiation....

Biologic activities of molecular chaperones and pharmacologic chaperone imidazole-containing dipeptide-based compounds: natural skin care help and the ultimate challenge: implication for adaptive responses in the skin.

Science.gov (United States)

Babizhayev, Mark A; Nikolayev, Gennady M; Nikolayeva, Juliana G; Yegorov, Yegor E

2012-03-01

Accumulation of molecular damage and increased molecular heterogeneity are hallmarks of photoaged skin and pathogenesis of human cutaneous disease. Growing evidence demonstrates the ability of molecular chaperone proteins and of pharmacologic chaperones to decrease the environmental stress and ameliorate the oxidation stress-related and glycation disease phenotypes, suggesting that the field of chaperone therapy might hold novel treatments for skin diseases and aging. In this review, we examine the evidence suggesting a role for molecular chaperone proteins in the skin and their inducer and protecting agents: pharmacologic chaperone imidazole dipeptide-based agents (carcinine and related compounds) in cosmetics and dermatology. Furthermore, we discuss the use of chaperone therapy for the treatment of skin photoaging diseases and other skin pathologies that have a component of increased glycation and/or free radical-induced oxidation in their genesis. We examine biologic activities of molecular and pharmacologic chaperones, including strategies for identifying potential chaperone compounds and for experimentally demonstrating chaperone activity in in vitro and in vivo models of human skin disease. This allows the protein to function and traffic to the appropriate location in the skin, thereby increasing protein activity and cellular function and reducing stress on skin cells. The benefits of imidazole dipeptide antioxidants with transglycating activity (such as carcinine) in skin care are that they help protect and repair cell membrane damage and help retain youthful, younger-looking skin. All skin types will benefit from daily, topical application of pharmacologic chaperone antioxidants, anti-irritants, in combination with water-binding protein agents that work to mimic the structure and function of healthy skin. General strategies are presented addressing ground techniques to improve absorption of usually active chaperone proteins and dipeptide compounds, include

Synthesis, spectroscopic investigations, DFT studies, molecular docking and antimicrobial potential of certain new indole-isatin molecular hybrids: Experimental and theoretical approaches

Science.gov (United States)

Almutairi, Maha S.; Zakaria, Azza S.; Ignasius, P. Primsa; Al-Wabli, Reem I.; Joe, Isaac Hubert; Attia, Mohamed I.

2018-02-01

Indole-isatin molecular hybrids 5a-i have been synthesized and characterized by different spectroscopic methods to be evaluated as new antimicrobial agents against a panel of Gram positive bacteria, Gram negative bacteria, and moulds. Compound 5h was selected as a representative example of the prepared compounds 5a-i to perform computational investigations. Its vibrational properties have been studied using FT-IR and FT-Raman with the aid of density functional theory approach. The natural bond orbital analysis as well as HOMO and LUMO molecular orbitals investigations of compound 5h were carried out to explore its possible intermolecular delocalization or hyperconjugation and its possible interactions with the target protein. Molecular docking of compound 5h predicted its binding mode with the fungal target protein.

Identification of high molecular weight nitroaromatic compounds from coal fly ash

International Nuclear Information System (INIS)

Harris, W.R.; Okamoto, D.J.; Chess, E.K.; Wilson, B.W.

1983-01-01

A large sample of stack-collected coal fly ash was extracted with 60:40 nu/nu benzene:methanol to remove as much of the soluble organic material as possible. This solution was concentrated by gentle evaporation, and was then fractionated on a series of high performance liquid chromatography columns to generate samples suitable for probe mass spectrometric analysis. A series of nitrated derivatives of C 21 H 12 polycyclic aromatic hydrocarbon have been tentatively identified by low and high resolution mass spectrometry and gas chromatography. The series includes a mononitro, two dinitro isomers, and a trinitro derivative

Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds

Directory of Open Access Journals (Sweden)

Shu-ichi Nakano

2014-01-01

Full Text Available Nucleic acids are useful for biomedical targeting and sensing applications in which the molecular environment is different from that of a dilute aqueous solution. In this study, the influence of various types of mixed solutions of water and water-soluble organic compounds on RNA was investigated by measuring the catalytic activity of the hammerhead ribozyme and the thermodynamic stability of an oligonucleotide duplex. The compounds with a net neutral charge, such as poly(ethylene glycol, small primary alcohols, amide compounds, and aprotic solvent molecules, added at high concentrations changed the ribozyme-catalyzed RNA cleavage rate, with the magnitude of the effect dependent on the NaCl concentration. These compounds also changed the thermodynamic stability of RNA base pairs of an oligonucleotide duplex and its dependence on the NaCl concentration. Specific interactions with RNA molecules and reduced water activity could account for the inhibiting effects on the ribozyme catalysis and destabilizing effects on the duplex stability. The salt concentration dependence data correlated with the dielectric constant, but not with water activity, viscosity, and the size of organic compounds. This observation suggests the significance of the dielectric constant effects on the RNA reactions under molecular crowding conditions created by organic compounds.

Exploring the physicochemical profile and the binding patterns of selected novel anticancer Himalayan plant derived active compounds with macromolecular targets

Directory of Open Access Journals (Sweden)

Arun Bahadur Gurung

Full Text Available Plants are vital source of compounds offering plethora of therapeutic effects against various ailments without much side effects. Due to wide spread prevalence and drug resistance in cancer; there is an urgent need for discovery of new anti-cancer drugs. In the present study, selected novel anti-cancer plants derived compounds (cmpd1 to cmpd15 from Himalayan region were docked with defined molecular targets that regulate cell proliferation and apoptosis. The binding energies of best docked compounds ranged between −8.0 kcal/mol and −11.71 kcal/mol. Further analysis revealed critical hydrogen bonds and hydrophobic interactions between compounds and targets. The best docked compounds viz., cmpd15 against cyclin-dependent kinase-2 (CDK-2, cmpd8 against CDK-6 and cmpd9 against Topoisomerase I and II showed higher binding affinities than the native co-crystal ligands. The root mean square deviation (RMSD and potential energy plot clearly indicates the stability of the complexes during 20 ns molecular dynamics (MD simulation. The Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA binding energy analysis revealed Van der Waals energy component which is the principal stabilizing energy for their interactions except CDK-2/cmpd15 complex. The polar solvation energy did not have favorable contribution to their stabilization. The binding energy decomposition analysis revealed per residue contribution for each docked complexes. Physicochemical profile studies showed that majority of the compounds conform to Lipinski's rule of five (ROF having low to high blood brain barrier (BBB penetration, human intestinal absorption, plasma binding protein inhibition and P glycoprotein inhibition. Keywords: ADMET, Anticancer, MM/PBSA, Molecular docking, Molecular dynamics simulation and plant derived compounds

Clinical and molecular features of high-grade osteosarcoma

NARCIS (Netherlands)

Anninga, Jakob Klaas

2013-01-01

It can be concluded from this thesis that high-grade osteosarcoma is at clinical, pathological and molecular level a heterogeneous disease. To treat high-grade osteosarcoma, neo-adjuvant chemotherapy should be combined with radical surgery, irrespective the localization. There are only 4 effective

Facile synthesis of upconversion nanoparticles with high purity using lanthanide oleate compounds

Science.gov (United States)

Kang, Ning; Ai, Chao-Chao; Zhou, Ya-Ming; Wang, Zuo; Ren, Lei

2018-02-01

A novel strategy for preparing highly pure NaYF4-based upconversion nanoparticles (UCNPs) was developed using lanthanide oleate compounds [Ln(OA)3] as the precursor, denoted as the Ln-OA preparation method. Compared to the conventional solvothermal method for synthesizing UCNPs using lanthanide chloride compounds (LnCl3) as the precursor (denoted as the Ln-Cl method), the Ln-OA strategy exhibited the merits of high purity, reduced purification process and a uniform size in preparing core and core-shell UCNPs excited by a 980 or 808 nm near infrared (NIR) laser. This work sheds new insight on the preparation of UCNPs and promotes their application in biomedical fields.

Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers

Directory of Open Access Journals (Sweden)

Rogier Christophe

2009-04-01

Full Text Available Abstract Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the

Identification of antifungal compounds active against Candida albicans using an improved high-throughput Caenorhabditis elegans assay.

Directory of Open Access Journals (Sweden)

Ikechukwu Okoli

2009-09-01

Full Text Available Candida albicans, the most common human pathogenic fungus, can establish a persistent lethal infection in the intestine of the microscopic nematode Caenorhabditis elegans. The C. elegans-C. albicans infection model was previously adapted to screen for antifungal compounds. Modifications to this screen have been made to facilitate a high-throughput assay including co-inoculation of nematodes with C. albicans and instrumentation allowing precise dispensing of worms into assay wells, eliminating two labor-intensive steps. This high-throughput method was utilized to screen a library of 3,228 compounds represented by 1,948 bioactive compounds and 1,280 small molecules derived via diversity-oriented synthesis. Nineteen compounds were identified that conferred an increase in C. elegans survival, including most known antifungal compounds within the chemical library. In addition to seven clinically used antifungal compounds, twelve compounds were identified which are not primarily used as antifungal agents, including three immunosuppressive drugs. This assay also allowed the assessment of the relative minimal inhibitory concentration, the effective concentration in vivo, and the toxicity of the compound in a single assay.

Some methods for labelling organic compounds by deuterium

International Nuclear Information System (INIS)

Moustapha, C.

1988-01-01

The rapid growth of knowledge in the fields of biochemistry, physiology, and molecular biology reflects to a considerable degree the utilization of stable isotopes (specially deuterium) in the study of chemical reactions and fragmentation mechanisms in mass spectrometry, as well as in the pharmacological and biological studies. Organic compounds maybe labelled by deuterium through classic organic reactions by using special deuterated solvents and reagents. This article discusses some reactions, with examples on how to prepare labelled compounds with high isotopic purety. These reactions are: exchange reactions in acid and alkaline media (the exchange in the chromatographic column in liquid and gas phases, the exchange in homogenous medium), reduction reactions of functional groups as well as saturation of the double bounds by deuterium using hydrogenation catalystes, electrochemical reactions using KOLBE, and photochemical reactions. This article also deals with spectroscopic properties of deuterium and the methods which are used to identify its compounds such as infrared, nuclear magnetic resonance, and mass spectroscopy. 37 refs., 2 figs

Geometric and electronic structures of molecular ions from high energy collisions

International Nuclear Information System (INIS)

Groeneveld, K.O.

1983-01-01

This chapter examines the characteristics of heavy ion collision and of beam foil spectroscopy. It discusses the kinematic consequences of the high energies and presents results from ''Coulomb explosion'' and structure determination of molecular ions. It demonstrates that studies of molecular ions with accelerators can provide electronic and geometric structure information of molecules or molecular ions and points out that the understanding of the microscopic processes at such high energies is incomplete and needs further experimental and theoretical efforts

Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

Energy Technology Data Exchange (ETDEWEB)

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15

The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

High Molecular Weight Melanoidins from Coffee Brew

NARCIS (Netherlands)

Bekedam, E.K.; Schols, H.A.; Boekel, van T.; Smit, G.

2006-01-01

The composition of high molecular weight (HMw) coffee melanoidin populations, obtained after ethanol precipitation, was studied. The specific extinction coefficient (Kmix) at 280, 325, 405 nm, sugar composition, phenolic group content, nitrogen content, amino acid composition, and non-protein

Mechanism of Corrosion by Naphthenic Acids and Organosulfur Compounds at High Temperatures

Science.gov (United States)

Jin, Peng

Due to the law of supply and demand, the last decade has witnessed a skyrocketing in the price of light sweet crude oil. Therefore, refineries are increasingly interested in "opportunity crudes", characterized by their discounted price and relative ease of procurement. However, the attractive economics of opportunity crudes come with the disadvantage of high acid/organosulfur compound content, which could lead to corrosion and even failure of facilities in refineries. However, it is generally accepted that organosulfur compounds may form protective iron sulfide layers on the metal surface and decrease the corrosion rate. Therefore, it is necessary to investigate the corrosive property of crudes at high temperatures, the mechanism of corrosion by acids (naphthenic acids) in the presence of organosulfur compounds, and methods to mitigate its corrosive effect. In 2004, an industrial project was initiated at the Institute for Corrosion and Multiphase Technology to investigate the corrosion by naphthenic acids and organosulfur compounds. In this project, for each experiment there were two experimentation phases: pretreatment and challenge. In the first pretreatment phase, a stirred autoclave was filled with a real crude oil fraction or model oil of different acidity and organosulfur compound concentration. Then, the stirred autoclave was heated to high temperatures to examine the corrosivity of the oil to different materials (specimens made from CS and 5% Cr containing steel were used). During the pretreatment, corrosion product layers were formed on the metal surface. In the second challenge phase, the steel specimens pretreated in the first phase were inserted into a rotating cylinder autoclave, called High Velocity Rig (HVR). The HVR was fed with a high-temperature oil solution of naphthenic acids to attack the iron sulfide layers. Based on the difference of specimen weight loss between the two steps, the net corrosion rate could be calculated and the protectiveness

Application of molecular sieves in the fractionation of lemongrass oil from high-pressure carbon dioxide extraction

Directory of Open Access Journals (Sweden)

L. Paviani

2006-06-01

Full Text Available The aim of this work was to study the feasibility of simultaneous process of high-pressure extraction and fractionation of lemongrass essential oil using molecular sieves. For this purpose, a high-pressure laboratory-scale extraction unit coupled with a column with four different stationary phases for fractionation: ZSM5 zeolite, MCM-41 mesoporous material, alumina and silica was employed. Additionally, the effect of carbon dioxide extraction variables on the global yield and chemical composition of the essential oil was also studied in a temperature range of 293 to 313 K and a pressure range of 100 to 200 bar. The volatile organic compounds of the extracts were identified by a gas chromatograph coupled with a mass spectrometer detector (GC/MS. The results indicated that the extraction process variables and the stationary phase exerted an effect on both the extraction yield and the chemical composition of the extracts.

Origin of organic sulphur compounds and sulphur-containing high molecular weight substances in sediments and immature crude oils

NARCIS (Netherlands)

Sinninghe Damsté, J.S.; Rijpstra, W.I.C.; Leeuw, J.W. de; Schenck, P.A.

1988-01-01

The distribution patterns of Organic Sulphur Compounds (OSC), occurring in certain sediments and immature crude oils, were compared with those of the corresponding hydrocarbons. Because of the complexity of the OSC mixtures, they were desulphurized to hydrocarbons (n-alkanes, isoprenoid alkanes,

Instant detection and identification of concealed explosive-related compounds: Induced Stokes Raman versus infrared.

Science.gov (United States)

Elbasuney, Sherif; El-Sherif, Ashraf F

2017-01-01

The instant detection of explosives and explosive-related compounds has become an urgent priority in recent years for homeland security and counter-terrorism applications. Modern techniques should offer enhancement in selectivity, sensitivity, and standoff distances. Miniaturisation, portability, and field-ruggedisation are crucial requirements. This study reports on instant and standoff identification of concealed explosive-related compounds using customized Raman technique. Stokes Raman spectra of common explosive-related compounds were generated and spectrally resolved to create characteristic finger print spectra. The scattered Raman emissions over the band 400:2000cm -1 were compared to infrared absorption using FTIR. It has been demonstrated that the two vibrational spectroscopic techniques were opposite and completing each other. Molecular vibrations with strong absorption in infrared (those involve strong change in dipole moments) induced weak signals in Raman and vice versa. The tailored Raman offered instant detection, high sensitivity, and standoff detection capabilities. Raman demonstrated characteristic fingerprint spectra with stable baseline and sharp intense peaks. Complete correlations of absorption/scattered signals to certain molecular vibrations were conducted to generate an entire spectroscopic profile of explosive-related compounds. This manuscript shades the light on Raman as one of the prevailing technologies for instantaneous detection of explosive-related compounds. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Molecular geometry

CERN Document Server

Rodger, Alison

1995-01-01

Molecular Geometry discusses topics relevant to the arrangement of atoms. The book is comprised of seven chapters that tackle several areas of molecular geometry. Chapter 1 reviews the definition and determination of molecular geometry, while Chapter 2 discusses the unified view of stereochemistry and stereochemical changes. Chapter 3 covers the geometry of molecules of second row atoms, and Chapter 4 deals with the main group elements beyond the second row. The book also talks about the complexes of transition metals and f-block elements, and then covers the organometallic compounds and trans

Subtype and pathway specific responses to anticancer compounds in breast cancer.

Science.gov (United States)

Heiser, Laura M; Sadanandam, Anguraj; Kuo, Wen-Lin; Benz, Stephen C; Goldstein, Theodore C; Ng, Sam; Gibb, William J; Wang, Nicholas J; Ziyad, Safiyyah; Tong, Frances; Bayani, Nora; Hu, Zhi; Billig, Jessica I; Dueregger, Andrea; Lewis, Sophia; Jakkula, Lakshmi; Korkola, James E; Durinck, Steffen; Pepin, François; Guan, Yinghui; Purdom, Elizabeth; Neuvial, Pierre; Bengtsson, Henrik; Wood, Kenneth W; Smith, Peter G; Vassilev, Lyubomir T; Hennessy, Bryan T; Greshock, Joel; Bachman, Kurtis E; Hardwicke, Mary Ann; Park, John W; Marton, Laurence J; Wolf, Denise M; Collisson, Eric A; Neve, Richard M; Mills, Gordon B; Speed, Terence P; Feiler, Heidi S; Wooster, Richard F; Haussler, David; Stuart, Joshua M; Gray, Joe W; Spellman, Paul T

2012-02-21

Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.

Surface passivation process of compound semiconductor material using UV photosulfidation

Science.gov (United States)

Ashby, Carol I. H.

1995-01-01

A method for passivating compound semiconductor surfaces by photolytically disrupting molecular sulfur vapor with ultraviolet radiation to form reactive sulfur which then reacts with and passivates the surface of compound semiconductors.

Radiation polymerization of acrylamide with super-high molecular weight in inverse emulsion

International Nuclear Information System (INIS)

Ye Qiang; Ge Xuewu; Xu Xiangling; Zhang Zhicheng

1998-01-01

The inverse emulsion polymerization of acrylamide has been studied with γ-ray initiation. Polyacrylamide with super high molecular weight over ten million (11 x 10 6 ), which is very important in application as flocculant, is obtained. In this work, some methods are taken to enhance the molecular weight as follows: (1) In order to prepare soluble polyacrylamide with super high molecular weight, the better conditions are: the emulsifier content is about 2% and the monomer concentration is about 20%∼24% in the composition of monomer emulsion, and the absorbed dose is about 500∼600 Gy. (2) Initiating with high dose rate and polymerizing with low dose rate can not only enhance the molecular weight of product, but also curtail the polymerizing time. (3) Stopping radiation when the conversion gets to about 10% and post-polymerizing outside the radiation source until the conversion gets to 82% can obtain polyacrylamide with super high molecular weight, and shorten the irradiation time as well

Prediction of Partition Coefficients of Organic Compounds for SPME/PDMS

OpenAIRE

Liao Hsuan-Yu; Huang Miao-Ling; Lu Yu-Ting; Chao Keh-Ping

2016-01-01

The partition coefficients of 51 organic compounds between SPME/PDMS and gas were compiled from the literature sources in this study. The effect of physicochemical properties and descriptors on the partitioning process of partition coefficients was explicated by the correlation analysis. The PDMS-gas partition coefficients were well correlated to the molecular weight of organic compounds (r = 0.832, p < 0.05). An empirical model, consisting of the molecular weight and the polarizability, was ...

Kirishites, a new type of natural high-carbon compounds

Science.gov (United States)

Marin, Yu. B.; Skublov, G. T.; Yushkin, N. P.

2010-01-01

On the right-hand bank of the Volkhov River, in the natural area of tektite-like glasses (Volkhovites), fragments of shungites and slags with bunches of hairlike dark brownish enclosures were found. The filament thickness ranged from 20 to 100 μm, and separate “hairlines” were 3 cm in length. The composition of shungites and “hairlines” was found to be identical, which allowed us to consider the latter as aposhungite carbon formations. The high-carbon hairline structures associated with volkhovites are called kirishites. Kirishites are a new type of high-carbon structures that formed simultaneously with volkhovites in the case of explosion-type delivery of carbon slag and shungite fragments to the daylight surface during Holocene explosive activity. Under sharply reductive conditions, the slags partially melted, the melts were segregated, and carbonaceous-silicate and carbonaceous-ferriferous glasses formed with subsequent decompression-explosive liberation of carbon-supersaturated structures, which were extruded from shungite and slag fragments in the form of a resinoid mass. The “hairlines” were found to be zonal in structure: the central axial zones are composed of high-nitrogen hydrocarbon compounds, and peripheral regions are essentially carbonaceous with a high content of organic-mineral compounds and numerous microanomalies of petrogenic, volatile, rare, and ore elements. Infrared spectroscopy identified in kirishites proteinlike compounds, diagnosed in absorption bands (in cm-1) 600-720 (Amid V), 1200-1300 (Amid III), 1480-1590 (Amid II), 1600-1700 (Amid I), 3000-3800 (vibrations in NH2 and II groups). Gas chromatography, with the possibility of differentiation of left- and right-handed forms, revealed a broad spectrum of amino acids in kirishites, with their total content found to be the absolutely highest record for natural bitumens, an order of magnitude higher than the largest amino acid concentrations ever revealed in fibrous high

NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds

DEFF Research Database (Denmark)

Nour-Eldin, Hussam Hassan; Andersen, Tonni Grube; Burow, Meike

2012-01-01

glucosinolates in seeds and had more than tenfold over-accumulation in source tissues such as leaves and silique walls, indicating that both plasma membrane-localized transporters are essential for long-distance transport of glucosinolates. We propose that GTR1 and GTR2 control the loading of glucosinolates from......In plants, transport processes are important for the reallocation of defence compounds to protect tissues of high value, as demonstrated in the plant model Arabidopsis, in which the major defence compounds, glucosinolates, are translocated to seeds on maturation. The molecular basis for long...

Molecular profiling of signalling proteins for effects induced by the anti-cancer compound GSAO with 400 antibodies

International Nuclear Information System (INIS)

Cadd, Verity A; Hogg, Philip J; Harris, Adrian L; Feller, Stephan M

2006-01-01

GSAO (4-[N-[S-glutathionylacetyl]amino] phenylarsenoxide) is a hydrophilic derivative of the protein tyrosine phosphatase inhibitor phenylarsine oxide (PAO). It inhibits angiogenesis and tumour growth in mouse models and may be evaluated in a phase I clinical trial in the near future. Initial experiments have implicated GSAO in perturbing mitochondrial function. Other molecular effects of GSAO in human cells, for example on the phosphorylation of proteins, are still largely unknown. Peripheral white blood cells (PWBC) from healthy volunteers were isolated and used to profile effects of GSAO vs. a control compound, GSCA. Changes in site-specific phosphorylations, other protein modifications and expression levels of many signalling proteins were analysed using more than 400 different antibodies in Western blots. PWBC were initially cultured in low serum conditions, with the aim to reduce basal protein phosphorylation and to increase detection sensitivity. Under these conditions pleiotropic intracellular signalling protein changes were induced by GSAO. Subsequently, PWBC were cultured in 100% donor serum to reflect more closely in vivo conditions. This eliminated detectable GSAO effects on most, but not all signalling proteins analysed. Activation of the MAP kinase Erk2 was still observed and the paxillin homologue Hic-5 still displayed a major shift in protein mobility upon GSAO-treatment. A GSAO induced change in Hic-5 mobility was also found in endothelial cells, which are thought to be the primary target of GSAO in vivo. Serum conditions greatly influence the molecular activity profile of GSAO in vitro. Low serum culture, which is typically used in experiments analysing protein phosphorylation, is not suitable to study GSAO activity in cells. The signalling proteins affected by GSAO under high serum conditions are candidate surrogate markers for GSAO bioactivity in vivo and can be analysed in future clinical trials. GSAO effects on Hic-5 in endothelial cells may

Reflectance spectroscopy of organic compounds: 1. Alkanes

Science.gov (United States)

Clark, R.N.; Curchin, J.M.; Hoefen, T.M.; Swayze, G.A.

2009-01-01

Reflectance spectra of the organic compounds comprising the alkane series are presented from the ultraviolet to midinfrared, 0.35 to 15.5 /??m. Alkanes are hydrocarbon molecules containing only single carbon-carbon bonds, and are found naturally on the Earth and in the atmospheres of the giant planets and Saturn's moon, Titan. This paper presents the spectral properties of the alkanes as the first in a series of papers to build a spectral database of organic compounds for use in remote sensing studies. Applications range from mapping the environment on the Earth, to the search for organic molecules and life in the solar system and throughout the. universe. We show that the spectral reflectance properties of organic compounds are rich, with major diagnostic spectral features throughout the spectral range studied. Little to no spectral change was observed as a function of temperature and only small shifts and changes in the width of absorption bands were observed between liquids and solids, making remote detection of spectral properties throughout the solar system simpler. Some high molecular weight organic compounds contain single-bonded carbon chains and have spectra similar to alkanes even ' when they fall into other families. Small spectral differences are often present allowing discrimination among some compounds, further illustrating the need to catalog spectral properties for accurate remote sensing identification with spectroscopy.

Effect of Molecular Flexibility on the Nematic-to-Isotropic Phase Transition for Highly Biaxial Molecular Non-Symmetric Liquid Crystal Dimers

Science.gov (United States)

Sebastián, Nerea; López, David Orencio; Diez-Berart, Sergio; de la Fuente, María Rosario; Salud, Josep; Pérez-Jubindo, Miguel Angel; Ros, María Blanca

2011-01-01

In this work, a study of the nematic (N)–isotropic (I) phase transition has been made in a series of odd non-symmetric liquid crystal dimers, the α-(4-cyanobiphenyl-4’-yloxy)-ω-(1-pyrenimine-benzylidene-4’-oxy) alkanes, by means of accurate calorimetric and dielectric measurements. These materials are potential candidates to present the elusive biaxial nematic (NB) phase, as they exhibit both molecular biaxiality and flexibility. According to the theory, the uniaxial nematic (NU)–isotropic (I) phase transition is first-order in nature, whereas the NB–I phase transition is second-order. Thus, a fine analysis of the critical behavior of the N–I phase transition would allow us to determine the presence or not of the biaxial nematic phase and understand how the molecular biaxiality and flexibility of these compounds influences the critical behavior of the N–I phase transition. PMID:28824100

Development of High-Antifouling PPSU Ultrafiltration Membrane by Using Compound Additives: Preparation, Morphologies, and Filtration Resistant Properties

OpenAIRE

Jie Liu; Zhencheng Zhong; Rui Ma; Weichen Zhang; Jiding Li

2016-01-01

In this study, flat sheet asymmetric polyphenylsulfone (PPSU) ultrafiltration membranes with enhanced antifouling properties were prepared with a non-solvent induced phase separation (NIPS) method through compound additives containing a polymeric pore-forming agent, a small molecular non-solvent and a surfactant. The formation processes of the porous asymmetric membranes with different kinds of additives were studied in detail, and the microstructure controllable preparation of membrane was a...

Synthesis and characterization of phenylethynylcarbonyl terminated novel thermosetting imide compound

Directory of Open Access Journals (Sweden)

H. Kimura

2013-02-01

Full Text Available Phenylethynyl terminated novel imide compound based on 1,3-bis(3-aminophenoxybenzene (APB and phenylethynyl trimellitic anhydride (PETA were prepared. The curing behavior of phenylethynyl terminated imide compound was investigated by differential scanning calorimetry and Fourier transform infrared spectrometry. The curing reaction of phenylethynylcarbonyl end group completed at 220°C, and proceeded much faster than that of phenylethynyl end group. Glass transition temperature of the thermosetting resin from phenylethynylcarbonyl terminated novel imide compound determined by dynamic mechanical analysis was almost the same as that of o-cresolnovolac type epoxy resin. In addition, the thermosetting resin from phenylethynylcarbonyl terminated novel imide compound exhibited excellent thermal and dimensional stabilities. These excellent properties of these phenylethynyl terminated imide compound might be due to the incorporation of alkene group or aromatic ring substitutes in the backbones, which might enhance the chain interaction (molecular packing and reduce the molecular chain mobility.

From Chemical Topology to Molecular Machines (Nobel Lecture).

Science.gov (United States)

Sauvage, Jean-Pierre

2017-09-04

To a large extent, the field of "molecular machines" started after several groups were able to prepare, reasonably easily, interlocking ring compounds (named catenanes for compounds consisting of interlocking rings and rotaxanes for rings threaded by molecular filaments or axes). Important families of molecular machines not belonging to the interlocking world were also designed, prepared, and studied but, for most of them, their elaboration was more recent than that of catenanes or rotaxanes. Since the creation of interlocking ring molecules is so important in relation to the molecular machinery area, we will start with this aspect of our work. The second part will naturally be devoted to the dynamic properties of such systems and to the compounds for which motions can be directed in a controlled manner from the outside, that is, molecular machines. We will restrict our discussion to a very limited number of examples which we consider as particularly representative of the field. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Molecular-Level View of the Physical Stability of Amorphous Solid Dispersions

Science.gov (United States)

Yuan, Xiaoda

Many pharmaceutical compounds being developed in recent years are poorly soluble in water. This has led to insufficient oral bioavailability of many compounds in vitro. The amorphous formulation is one of the promising techniques to increase the oral bioavailability of these poorly water-soluble compounds. However, an amorphous drug substance is inherently unstable because it is a high energy form. In order to increase the physical stability, the amorphous drug is often formulated with a suitable polymer to form an amorphous solid dispersion. Previous research has suggested that the formation of an intimately mixed drug-polymer mixture contributes to the stabilization of the amorphous drug compound. The goal of this research is to better understand the role of miscibility, molecular interactions and mobility on the physical stability of amorphous solid dispersions. Methods were developed to detect different degrees of miscibility on nanometer scale and to quantify the extent of hydrogen-bonding interactions between the drug and the polymer. Miscibility, hydrogen-bonding interactions and molecular mobility were correlated with physical stability during a six-month period using three model systems. Overall, this research provides molecular-level insights into many factors that govern the physical stability of amorphous solid dispersions which can lead to a more effective design of stable amorphous formulations.

Study of the influence of the molecular structure of vinyl compounds on their ability to form polymer films by electro-polymerization under cathodic polarisation

International Nuclear Information System (INIS)

Deniau, Guy

1990-01-01

This research thesis addresses the study of new vinyl compounds, and aims at improving knowledge on the interaction between metal and a vinyl molecule under an intense electric field (the field of the double electrochemical layer), and more particularly at studying the influence of the molecular structure of the vinyl compound as well as the occurring reactions. After a first part presenting physical-chemical principles and knowledge which govern the whole set of reactions which are occurring within an electrolysis reactor, and a brief historical overview, this research thesis proposes a presentation of molecules which have been chosen for this study (vinyl compounds) and a justification of this choice. The author also presents the experimental device and describes the process implementation. Then, he presents and analyses experimental results. It appears that only some studied molecules result in the formation of polymer film [fr

Prediction of Partition Coefficients of Organic Compounds for SPME/PDMS

Directory of Open Access Journals (Sweden)

Liao Hsuan-Yu

2016-01-01

Full Text Available The partition coefficients of 51 organic compounds between SPME/PDMS and gas were compiled from the literature sources in this study. The effect of physicochemical properties and descriptors on the partitioning process of partition coefficients was explicated by the correlation analysis. The PDMS-gas partition coefficients were well correlated to the molecular weight of organic compounds (r = 0.832, p < 0.05. An empirical model, consisting of the molecular weight and the polarizability, was developed to appropriately predict the partition coefficients of organic compounds. The empirical model for estimating the PDMS-gas partition coefficient will contribute to the practical applications of the SPME technique.

Borides and vitreous compounds sintered as high-energy fuels

International Nuclear Information System (INIS)

Mota, J.M.; Abenojar, J.; Martinez, M.A.; Velasco, F.; Criado, A.J.

2004-01-01

Boron was chosen as fuel in view of its excellent thermodynamic values for combustion, as compared to traditional fuels. The problem of the boron in combustion is the formation of a surface layer of oxide, which delays the ignition process, reducing the performance of the rocket engine. This paper presents a high-energy fuel for rocket engines. It is composed of sintered boron (borides and carbides and vitreous compounds) with a reducing chemical agent. Borides and boron carbide were prepared since the combustion heat of the latter is similar to that of the amorphous boron (in: K.K. Kuo (Ed.), Boron-Based Solid Propellant and Solid Fuel, Vol. 427, CRC Press, Boca Raton, FL, 1993). Several chemical reducing elements were used, such as aluminum, magnesium, and coke. As the raw material for boron, different compounds were used: amorphous boron, boric acid and boron oxide

Gas Sensors Based on Molecular Imprinting Technology.

Science.gov (United States)

Zhang, Yumin; Zhang, Jin; Liu, Qingju

2017-07-04

Molecular imprinting technology (MIT); often described as a method of designing a material to remember a target molecular structure (template); is a technique for the creation of molecularly imprinted polymers (MIPs) with custom-made binding sites complementary to the target molecules in shape; size and functional groups. MIT has been successfully applied to analyze; separate and detect macromolecular organic compounds. Furthermore; it has been increasingly applied in assays of biological macromolecules. Owing to its unique features of structure specificity; predictability; recognition and universal application; there has been exploration of the possible application of MIPs in the field of highly selective gas sensors. In this present study; we outline the recent advances in gas sensors based on MIT; classify and introduce the existing molecularly imprinted gas sensors; summarize their advantages and disadvantages; and analyze further research directions.

Effects of organic compounds on actinoid transfer in natural environment

Energy Technology Data Exchange (ETDEWEB)

Hiraki, Keizo; Nakaguchi, Yuzuru; Suzuki, Yasuhiro [Kinki Univ., Higashi-Osaka, Osaka (Japan). Faculty of Science and Technology; Senoo, Muneaki; Nagao, Seiya; Sakamoto, Yoshiaki

1996-01-01

For safety evaluation of geological disposal of radioactive wastes, it seems necessary to elucidate the geological transfer of radioactive nuclides in the soil and the undersea sediments. It has been known that there exist various organic compounds highly potential to form a complex with TRU elements, uranium, copper etc. in the soil and the sediments and those compounds may play an important role for geological transfer of nuclides. In this study, fluorescent substances contained in underground and river water were focused as the measures to identify the molecular species of organic compounds in natural water and their interactions with radionuclides and minor metals, and their geological transfers were investigated. Spectrophotometric properties of humic acid obtained in the market were examined. Its fluorescent intensity was strongest at pH 10 and stable for 2 weeks or more. Then, highly polluted river water was taken from Yamato river to determine the contents of humic acid and other fluorescent substances. Further, the effects of the additions of Cu and Fe on the fluorescent intensity were examined. (M.N.)

Determination of the n-octanol/water partition coefficients of weakly ionizable basic compounds by reversed-phase high-performance liquid chromatography with neutral model compounds.

Science.gov (United States)

Liang, Chao; Han, Shu-ying; Qiao, Jun-qin; Lian, Hong-zhen; Ge, Xin

2014-11-01

A strategy to utilize neutral model compounds for lipophilicity measurement of ionizable basic compounds by reversed-phase high-performance liquid chromatography is proposed in this paper. The applicability of the novel protocol was justified by theoretical derivation. Meanwhile, the linear relationships between logarithm of apparent n-octanol/water partition coefficients (logKow '') and logarithm of retention factors corresponding to the 100% aqueous fraction of mobile phase (logkw ) were established for a basic training set, a neutral training set and a mixed training set of these two. As proved in theory, the good linearity and external validation results indicated that the logKow ''-logkw relationships obtained from a neutral model training set were always reliable regardless of mobile phase pH. Afterwards, the above relationships were adopted to determine the logKow of harmaline, a weakly dissociable alkaloid. As far as we know, this is the first report on experimental logKow data for harmaline (logKow = 2.28 ± 0.08). Introducing neutral compounds into a basic model training set or using neutral model compounds alone is recommended to measure the lipophilicity of weakly ionizable basic compounds especially those with high hydrophobicity for the advantages of more suitable model compound choices and convenient mobile phase pH control. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists

Directory of Open Access Journals (Sweden)

Yuwei Wang

2017-01-01

Full Text Available The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR, are the main endocrine therapies for prostate cancer (PCa. But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestosterones derivatives taken from PubChem, resulting in the finding of novel compounds CID_70128824, CID_70127147, and CID_70126881, whose in silico bioactivities are much higher than the published best one, even higher than bicalutamide. In addition, molecular docking, molecular dynamics (MD simulations, and MM/GBSA have been employed to analyze and compare the binding modes between the novel compounds and AR. Through the analysis of the binding free energy and residue energy decomposition, we concluded that the newly discovered chemicals can in silico bind to AR with similar position and mechanism to the reported active compound and the van der Waals interaction is the main driving force during the binding process.

Continuous extraction of phenolic compounds from pomegranate peel using high voltage electrical discharge.

Science.gov (United States)

Xi, Jun; He, Lang; Yan, Liang-Gong

2017-09-01

Pomegranate peel, a waste generated from fruit processing industry, is a potential source of phenolic compounds that are known for their anti-oxidative properties. In this study, a continuous high voltage electrical discharge (HVED) extraction system was for the first time designed and optimized for phenolic compounds from pomegranate peel. The optimal conditions for HVED were: flow rate of materials 12mL/min, electrodes gap distance 3.1mm (corresponding to 29kV/cm of electric field intensity) and liquid to solid ratio 35mL/g. Under these conditions, the experimental yield of phenolic compounds was 196.7±6.4mg/g, which closely agreed with the predicted value (199.83mg/g). Compared with the warm water maceration, HVED method possessed higher efficiency for the extraction of phenolic compounds. The results demonstrated that HVED technique could be a very effective method for continuous extraction of natural compounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

Laser-induced blurring of molecular structure information in high harmonic spectroscopy

DEFF Research Database (Denmark)

Risoud, Francois; Leveque, Camille; Labeye, Marie

2017-01-01

High harmonic spectroscopy gives access to molecular structure with Angstrom resolution. Such information is encoded in the destructive interferences occurring between the harmonic emissions from the different parts of the molecule. By solving the time-dependent Schrodinger equation, either....... These findings have important consequences for molecular imaging and orbital tomography using high harmonic spectroscopy....

Application of organic compounds for high-order harmonic generation of ultrashort pulses

Science.gov (United States)

Ganeev, R. A.

2016-02-01

The studies of the high-order nonlinear optical properties of a few organic compounds (polyvinyl alcohol, polyethylene, sugar, coffee, and leaf) are reported. Harmonic generation in the laser-produced plasmas containing the molecules and large particles of above materials is demonstrated. These studies showed that the harmonic distributions and harmonic cutoffs from organic compound plasmas were similar to those from the graphite ablation. The characteristic feature of observed harmonic spectra was the presence of bluesided lobes near the lower-order harmonics.

Biomimetic studies of wood decay: Simulating the effect of low molecular weight compounds and fungal enzymes

DEFF Research Database (Denmark)

Hastrup, Anne Christine Steenkjær; Howell, Caitlin; Jellison, Jody

The effect of FeCl3 (Fe3+), hydrogen peroxide (H2O2), a low molecular weight compound (2,3- Dihydroxybenzoic acid), and oxalic acid on wood were tested in a study designed to mimic wood degradation by brown rot fungi. Previous studies suggest that these components are involved in the early stages...... 50 ml of 40 mM acetate buffer (pH 4.5), white pine wood powder and varying combinations of the chemicals previously mentioned. Changes in cellulose crystallinity were analyzed by X-ray diffraction using a ¿-2¿ scan. Findings suggest that iron, H2O2, chelators and oxalic acid may affect over all...

Computation of Dielectric Response in Molecular Solids for High Capacitance Organic Dielectrics.

Science.gov (United States)

Heitzer, Henry M; Marks, Tobin J; Ratner, Mark A

2016-09-20

The dielectric response of a material is central to numerous processes spanning the fields of chemistry, materials science, biology, and physics. Despite this broad importance across these disciplines, describing the dielectric environment of a molecular system at the level of first-principles theory and computation remains a great challenge and is of importance to understand the behavior of existing systems as well as to guide the design and synthetic realization of new ones. Furthermore, with recent advances in molecular electronics, nanotechnology, and molecular biology, it has become necessary to predict the dielectric properties of molecular systems that are often difficult or impossible to measure experimentally. In these scenarios, it is would be highly desirable to be able to determine dielectric response through efficient, accurate, and chemically informative calculations. A good example of where theoretical modeling of dielectric response would be valuable is in the development of high-capacitance organic gate dielectrics for unconventional electronics such as those that could be fabricated by high-throughput printing techniques. Gate dielectrics are fundamental components of all transistor-based logic circuitry, and the combination high dielectric constant and nanoscopic thickness (i.e., high capacitance) is essential to achieving high switching speeds and low power consumption. Molecule-based dielectrics offer the promise of cheap, flexible, and mass producible electronics when used in conjunction with unconventional organic or inorganic semiconducting materials to fabricate organic field effect transistors (OFETs). The molecular dielectrics developed to date typically have limited dielectric response, which results in low capacitances, translating into poor performance of the resulting OFETs. Furthermore, the development of better performing dielectric materials has been hindered by the current highly empirical and labor-intensive pace of synthetic

High-latitude molecular clouds and infrared cirrus

International Nuclear Information System (INIS)

Vries, H.W. de.

1988-01-01

The high-latitude infrared cirrus detected by IRAS is identified with atomic and molecular clouds. These clouds are small (usually less than 1 sq. deg.) and show weak CO emission. On the basis of a distance of 100 pc they are characterized by a mass of a few solar masses and a radius of about 1 pc. Thermal radiation by dust as a results of heating by the diffuse interstellar radiation field is the most-plausible origin of the cirrus emission at far-infrared wavelengths. On the basis of plausible assumptions regarding the uniformity of both the gas-to-dust ratio and the heating and cooling of the dust, the flux density at 100 μm from regions with low visual extinction should be a good tracer of the gas column density. Indeed, the data show an approximately linear proportionality between N(HI), obtained from 21-cm observations, and I 100 (HI), the flux density from dust associated with HI. If the ratio of column density to flux density in high-latitude molecular clouds is equal to the corresponding relation in atomic ones, a value for the ratio of H 2 column density to CO velocity-integrated radiation temperature may be obtained. Although low-mass clouds may be large in number, the fraction of the Galactic molecular mass in the form of these clouds is probably no more than 1%

Electrochemical screening of biomembrane-active compounds in water

Energy Technology Data Exchange (ETDEWEB)

Mohamadi, Shahrzad, E-mail: cmsm@leeds.ac.uk; Tate, Daniel J.; Vakurov, Alexander; Nelson, Andrew

2014-02-01

Graphical abstract: - Highlights: • Analytical technology application with improvement allowing for on-line high-throughput water toxin screening is presented. • Compound classes of related structure and shape interact with DOPC coated Pt/Hg with a class specific response. • Predecessor membrane system proved as fragile, complex and for environmental application incompatible. - Abstract: Interactions of biomembrane-active compounds with phospholipid monolayers on microfabricated Pt/Hg electrodes in an on-line high throughput flow system are demonstrated by recording capacitance current peak changes as rapid cyclic voltammograms (RCV). Detection limits of the compounds’ effects on the layer have been estimated from the data. Compounds studied include steroids, polycyclic aromatic hydrocarbons, tricyclic antidepressants and tricyclic phenothiazines. The results show that the extent and type of interaction depends on the—(a) presence and number of aromatic rings and substituents, (b) presence and composition of side chains and, (c) molecular shape. Interaction is only indirectly related to compound hydrophobicity. For a selection of tricyclic antidepressants and tricyclic phenothiazines the detection limit in water is related to their therapeutic normal threshold. The sensing assay has been tested in the presence of humic acid as a potential interferent and in a tap water matrix. The system can be applied to the screening of putative hazardous substances and pharmaceuticals allowing for early detection thereof in the water supply. The measurements are made in real time which means that potentially toxic compounds are detected rapidly within <10 min per assay. This technology will contribute greatly to environment safety and health.

Electrochemical screening of biomembrane-active compounds in water

International Nuclear Information System (INIS)

Mohamadi, Shahrzad; Tate, Daniel J.; Vakurov, Alexander; Nelson, Andrew

2014-01-01

Graphical abstract: - Highlights: • Analytical technology application with improvement allowing for on-line high-throughput water toxin screening is presented. • Compound classes of related structure and shape interact with DOPC coated Pt/Hg with a class specific response. • Predecessor membrane system proved as fragile, complex and for environmental application incompatible. - Abstract: Interactions of biomembrane-active compounds with phospholipid monolayers on microfabricated Pt/Hg electrodes in an on-line high throughput flow system are demonstrated by recording capacitance current peak changes as rapid cyclic voltammograms (RCV). Detection limits of the compounds’ effects on the layer have been estimated from the data. Compounds studied include steroids, polycyclic aromatic hydrocarbons, tricyclic antidepressants and tricyclic phenothiazines. The results show that the extent and type of interaction depends on the—(a) presence and number of aromatic rings and substituents, (b) presence and composition of side chains and, (c) molecular shape. Interaction is only indirectly related to compound hydrophobicity. For a selection of tricyclic antidepressants and tricyclic phenothiazines the detection limit in water is related to their therapeutic normal threshold. The sensing assay has been tested in the presence of humic acid as a potential interferent and in a tap water matrix. The system can be applied to the screening of putative hazardous substances and pharmaceuticals allowing for early detection thereof in the water supply. The measurements are made in real time which means that potentially toxic compounds are detected rapidly within <10 min per assay. This technology will contribute greatly to environment safety and health

[Stability of physical state on compound hawthorn dropping pills].

Science.gov (United States)

Zhang, Wei; Chen, Hong-Yan; Jiang, Jian-Lan

2008-11-01

To evaluate the stability of physical state with accelerate test and dropping in process before and after on compound hawthorn dropping pills. Scanning electron microscope, TG-DTA, FT-IR and XRD were used. The active components presented amorphous, tiny crystal and molecular state in dropping pills, and it had no obvious reaction between PEG 4000 and active components. With time prolonging, a little of active components changed from amorphous state to tiny crystal or molecular state. Solid dispersion improved the stability and dissolution of compound hawthorn dropping pills.

Molecular docking and ADME-toxicity studies of potential compounds of medicinal plants grown in Indonesia as an anti-rheumatoid arthritis

Science.gov (United States)

Awaluddin, Rizki; Muhtadi, Wildan Khairi; Chabib, Lutfi; Ikawati, Zullies; Martien, Ronny; Ismail, Hilda

2017-03-01

Rheumatoid arthritis (RA) is an autoimmune disease with recurrent bone destruction around the joints that could lead to permanent joint damage. DMARDs (Disease Modifying Anti-Rheumatoid Drugs) and NSAIDs (Non-Steroid Anti-Inflammatory Drugs) are the RA therapies with many side effects on long term use. Based on the ethnomedicine, there are many plants that could be found in Indonesia that contain the potential compounds as alternative RA therapies. The aim of this study is to assess the potential of compounds of various medicinal plants against multiple proteins that play an important role on RA through the molecular docking study and pharmacokinetic prediction. Hesperidin, EGCG (Epigallocatechin gallate), and mangiferin showed higher activity compared to the other compounds against TACE (TNF-α converting enzyme) which play an important role in the inhibition of TNF-α. Inhibition on it could suppress macrophage cell and T-cell activity by suppressing the regulation of cytokine secretion against inflammation. Furthermore, hesperidin, EGCG, and mangiferin did not show effects on CYP450 (cytochrome P450). Modification of drug delivery system must be done to increase the bioavailability of the compounds. It can be concluded that hesperidin, EGCG, and mangiferin are potential to be developed as an RA therapy with a modification of drug delivery system. This study suggest the encapsulation method using liposome as the drug carrier, which is suitable with the charactheristic of hesperidine, EGCG, and mangiferin.

Low molecular weight components in an aquatic humic substance as characterized by membrane dialysis and orbitrap mass spectrometry.

Science.gov (United States)

Remucal, Christina K; Cory, Rose M; Sander, Michael; McNeill, Kristopher

2012-09-04

Suwannee River fulvic acid (SRFA) was dialyzed through a 100-500 molecular weight cutoff dialysis membrane, and the dialysate and retentate were analyzed by UV-visible absorption and high-resolution Orbitrap mass spectrometry (MS). A significant fraction (36% based on dissolved organic carbon) of SRFA passed through the dialysis membrane. The fraction of SRFA in the dialysate had a different UV-visible absorption spectrum and was enriched in low molecular weight molecules with a more aliphatic composition relative to the initial SRFA solution. Comparison of the SRFA spectra collected by Orbitrap MS and Fourier transform ion cyclotron resonance MS (FT-ICR MS) demonstrated that the mass accuracy of the Orbitrap MS is sufficient for determination of unique molecular formulas of compounds with masses masses detected by Orbitrap MS were found in the 100-200 Da mass range. Many of these low molecular masses corresponded to molecular formulas of previously identified compounds in organic matter, lignin, and plants, and the use of the standard addition method provided an upper concentration estimate of selected target compounds in SRFA. Collectively, these results provide evidence that SRFA contains low molecular weight components that are present individually or in loosely bound assemblies.

Determination of sulfur in bovine serum albumin and L-cysteine using high-resolution continuum source molecular absorption spectrometry of the CS molecule

Science.gov (United States)

Andrade-Carpente, Eva; Peña-Vázquez, Elena; Bermejo-Barrera, Pilar

2016-08-01

In this study, the content of sulfur in bovine serum albumin and L-cysteine was determined using high-resolution continuum source molecular absorption spectrometry of the CS molecule, generated in a reducing air-acetylene flame. Flame conditions (height above the burner, measurement time) were optimized using a 3.0% (v/v) sulfuric acid solution. A microwave lab station (Ethos Plus MW) was used for the digestion of both compounds. During the digestion step, sulfur was converted to sulfate previous to the determination. Good repeatability (4-10%) and analytical recovery (91-106%) was obtained.

Synthesis and chemical recycling of high polymers using C1 compounds; C1 kagobutsu ni yoru kobunshi no chemical recycle

Energy Technology Data Exchange (ETDEWEB)

Masuda, T. [National Institute of Materials and Chemical Research, Tsukuba (Japan)

1997-09-01

The paper outlined a study of the synthesis of high polymers using C1 compounds which are continuously usable chemical materials and the related compounds such as the derivatives, and also the chemical recycle. In the case of waste plastics mixed in urban refuse, effective is the chemical recycle where C1 compounds obtained by gasifying the mixed waste are used as high polymer material. For the synthesis and recycle of high polymers using C1 compounds, there are three routes: Route A (recycle via high polymer materials), Route B (recycle via C1 compounds and high polymer materials), and Route C including global-scale carbon recycle (recycle via carbon dioxide from biodegradable plastics using microorganism). Among high polymers, those that can be synthesized from C1 compounds, for example, polymethylene, polyacetal and polyketone can be chemically recycled by Route B. 30 refs., 2 figs., 1 tab.

3D molecular descriptors important for clinical success.

Science.gov (United States)

Kombo, David C; Tallapragada, Kartik; Jain, Rachit; Chewning, Joseph; Mazurov, Anatoly A; Speake, Jason D; Hauser, Terry A; Toler, Steve

2013-02-25

The pharmacokinetic and safety profiles of clinical drug candidates are greatly influenced by their requisite physicochemical properties. In particular, it has been shown that 2D molecular descriptors such as fraction of Sp3 carbon atoms (Fsp3) and number of stereo centers correlate with clinical success. Using the proteomic off-target hit rate of nicotinic ligands, we found that shape-based 3D descriptors such as the radius of gyration and shadow indices discriminate off-target promiscuity better than do Fsp3 and the number of stereo centers. We have deduced the relevant descriptor values required for a ligand to be nonpromiscuous. Investigating the MDL Drug Data Report (MDDR) database as compounds move from the preclinical stage toward the market, we have found that these shape-based 3D descriptors predict clinical success of compounds at preclinical and phase1 stages vs compounds withdrawn from the market better than do Fsp3 and LogD. Further, these computed 3D molecular descriptors correlate well with experimentally observed solubility, which is among well-known physicochemical properties that drive clinical success. We also found that about 84% of launched drugs satisfy either Shadow index or Fsp3 criteria, whereas withdrawn and discontinued compounds fail to meet the same criteria. Our studies suggest that spherical compounds (rather than their elongated counterparts) with a minimal number of aromatic rings may exhibit a high propensity to advance from clinical trials to market.

Development of High-Antifouling PPSU Ultrafiltration Membrane by Using Compound Additives: Preparation, Morphologies, and Filtration Resistant Properties.

Science.gov (United States)

Liu, Jie; Zhong, Zhencheng; Ma, Rui; Zhang, Weichen; Li, Jiding

2016-06-21

In this study, flat sheet asymmetric polyphenylsulfone (PPSU) ultrafiltration membranes with enhanced antifouling properties were prepared with a non-solvent induced phase separation (NIPS) method through compound additives containing a polymeric pore-forming agent, a small molecular non-solvent and a surfactant. The formation processes of the porous asymmetric membranes with different kinds of additives were studied in detail, and the microstructure controllable preparation of membrane was achieved by establishing a bridge between the membrane preparation parameters and separation performances. All prepared membranes were characterized by using a scanning electron microscope (SEM), contact angle analysis, porosity, maximum pore size, water and BSA solution permeability studies. The performance efficiency of the membrane was evaluated by using BSA as a model foulant in terms of permeability, solute rejection (R), Rm (membrane inherent resistance), Rc (cake layer resistance), and Rp (pore plugging resistance). The results showed that when the compound additives were used, the inter-connected pores were observed, maximum pore size, contact angle and membrane filtration resistance decreased, while the porosity increased. When PVP compound additives were added, the water flux increased from 80.4 to 148.1 L/(m²·h), the BSA rejection increased from 53.2% to 81.5%. A similar trend was observed for membranes with added PEG compound additives; the water flux and BSA rejection simultaneously increased. The filtration resistance decreased as a result of compound additives. The uniformity of membrane and the number of effective pores could be enhanced by adding compound additives through the cooperation of different additives.

Development of High-Antifouling PPSU Ultrafiltration Membrane by Using Compound Additives: Preparation, Morphologies, and Filtration Resistant Properties

Directory of Open Access Journals (Sweden)

Jie Liu

2016-06-01

Full Text Available In this study, flat sheet asymmetric polyphenylsulfone (PPSU ultrafiltration membranes with enhanced antifouling properties were prepared with a non-solvent induced phase separation (NIPS method through compound additives containing a polymeric pore-forming agent, a small molecular non-solvent and a surfactant. The formation processes of the porous asymmetric membranes with different kinds of additives were studied in detail, and the microstructure controllable preparation of membrane was achieved by establishing a bridge between the membrane preparation parameters and separation performances. All prepared membranes were characterized by using a scanning electron microscope (SEM, contact angle analysis, porosity, maximum pore size, water and BSA solution permeability studies. The performance efficiency of the membrane was evaluated by using BSA as a model foulant in terms of permeability, solute rejection (R, Rm (membrane inherent resistance, Rc (cake layer resistance, and Rp (pore plugging resistance. The results showed that when the compound additives were used, the inter-connected pores were observed, maximum pore size, contact angle and membrane filtration resistance decreased, while the porosity increased. When PVP compound additives were added, the water flux increased from 80.4 to 148.1 L/(m2·h, the BSA rejection increased from 53.2% to 81.5%. A similar trend was observed for membranes with added PEG compound additives; the water flux and BSA rejection simultaneously increased. The filtration resistance decreased as a result of compound additives. The uniformity of membrane and the number of effective pores could be enhanced by adding compound additives through the cooperation of different additives.

Tunability of photoswitchable ruthenium sulfoxide compounds on the basis of ligand substitution

Energy Technology Data Exchange (ETDEWEB)

Eicke, Sebastian; Dieckmann, Volker; Springfeld, Kristin; Imlau, Mirco [Deparment of Physics, University of Osnabrueck (Germany)

2010-07-01

Photoswitchable ruthenium sulfoxide compounds provide a light-induced linkage isomerization in combination with pronounced changes in characteristic optical properties. As representative of the ruthenium sulfoxide group the molecular compound [Ru(bpy){sub 2}(R-OSO)]{sup +} (OSO: 2-methylsulfinylbenzoate) can be tuned in its optical properties by the substitution of the photoswitchable ligands (R=Bn, BnCl, BnMe). These modified sulfoxides were studied in respect to their photochromic properties and kinetics of the generation and relaxation of the light-induced isomers. The kinetics were determined by pump-probe technique and show in each case two reversible thermal decay processes following Arrhenius law. The two photo-excited states offer lifetimes in the magnitude of {tau}{sub 1}{approx}10{sup 3} s and {tau}{sub 2}{approx}10{sup 4} s at room temperature with activation energies about E{sub A,I}=0.72 eV to 0.92 eV and E{sub A,II}=0.8 eV to 1.00 eV. Another respresentative of the photoswitchable sulfoxides is the [Ru(bpy){sub 2}(pySO)]{sup 2+} compound. This molecule is the first sulfoxide which allows for reversible switching between the ground and metastable states by light exposure. With this compound the sulfoxides are highly qualified for optical data storage on a molecular scale.

Selective determination of semi-volatile thiophene compounds in water by molecularly imprinted polymer thin films with direct headspace gas chromatography sulfur chemiluminescence detection.

Science.gov (United States)

Hijazi, Hassan Y; Bottaro, Christina S

2018-02-26

Water-compatible molecularly imprinted polymer (MIP) thin films are coupled with headspace gas chromatography sulfur chemiluminescence detection (HS-GC-SCD) to create a new approach for the determination of trace concentrations of thiophene compounds in water samples. Thiophene compounds are persistent, typically petrogenic, organic pollutants of concern due to their potential for biomagnification and bioaccumulation, mutagenicity, and carcinogenicity in terrestrial and aquatic fauna. Identification and quantitation in water, particularly following oil spills, is a priority. Following adsorption of the thiophenes to the MIPs, the MIP-bound analytes are analyzed directly by HS-GC-SCD, with minimal sample manipulation and virtually no organic solvent. Calibration curves of spiked seawater were linear from 5 μg L -1 to 100 μg L -1 and limits of detection (LOD) were in the range of 0.24-0.82 μg L -1 . Low matrix effects were observed in the analysis of thiophene compounds in seawater making the method suitable for use in fresh and saline waters without modification. Acceptable reproducibility was obtained for analysis of thiophene compounds from spiked seawater samples at RSDs ≤7.0% (n = 3).

High molecular somatostatin, an interfering factor in radioimmunoassay

International Nuclear Information System (INIS)

Diel, F.; Schneider, E.; Baumann, H.

1977-01-01

Cyclic Tyr 1 -somatostatin (Tyr 1 -SRIF) is radioiodinated by the lactoperoxidase method. Purification is achieved by Sephadex G-25 adsorption chromatography. Specific anti-SRIF serum (FA1) has been raised in rabbits. A dose response curve is obtained in the range of 5 - 5,000 pg per tube using an antiserum dilution of 1:2,000. There is little cross-reaction with linear somatostatin and none with ocytocin, (lys-, arg-) vasopressin, valinomycin, polymyxin, insulin, glucagon, human growth hormone (hGH), and thyrotropin-releasing hormone (TRH). For recovery tests, extraction procedures are necessary. Thin-layer chromatography (TLC) and polyacrylamide-disc-electrophoresis (Disc-PAGE) are performed to identify the presumed high molecular 125 I-Tyr 1 -SRIF associate. This high molecular associate may represent an interfering factor in the radioimmunoassay for cyclic SRIF. (orig./AJ) [de

Organic high ionic strength aqueous two-phase solvent system series for separation of ultra-polar compounds by spiral high-speed counter-current chromatography

Science.gov (United States)

Zeng, Yun; Liu, Gang; Ma, Ying; Chen, Xiaoyuan; Ito, Yoichiro

2011-01-01

Existing two-phase solvent systems for high-speed countercurrent chromatography cover the separation of hydrophobic to moderately polar compounds, but often fail to provide suitable partition coefficient values for highly polar compounds such as sulfonic acids, catecholamines and zwitter ions. The present paper introduces a new solvent series which can be applied for the separation of these polar compounds. It is composed of 1-butanol, ethanol, saturated ammonium sulfate and water at various volume ratios and consists of a series of 10 steps which are arranged according to the polarity of the solvent system so that the two-phase solvent system with suitable K values for the target compound(s) can be found in a few steps. Each solvent system gives proper volume ratio and high density difference between the two phases to provide a satisfactory level of retention of the stationary phase in the spiral column assembly. The method is validated by partition coefficient measurement of four typical polar compounds including methyl green (basic dye), tartrazine (sulfonic acid), tyrosine (zwitter ion) and epinephrine (a catecholamine), all of which show low partition coefficient values in the polar 1-butanol-water system. The capability of the method is demonstrated by separation of three catecholamines. PMID:22033108

Measurement of low molecular weight silicon AMC to protect UV optics in photo-lithography environments

Science.gov (United States)

Lobert, Jürgen M.; Miller, Charles M.; Grayfer, Anatoly; Tivin, Anne M.

2009-03-01

A new analytical method for semiconductor-specific applications is presented for the accurate measurement of low molecular weight, silicon-containing, organic compounds TMS, HMDSO and D3. Low molecular weight / low boiling point silicon-containing compounds are not captured for extended periods of time by traditional chemical filters but have the same potential to degrade exposure tool optical surfaces as their high molecular weight counterparts. Likewise, we show that capturing these compounds on sample traps that are commonly used for organic AMC analysis does not work for various reasons. Using the analytical method described here, TMS, HMDSO and D3 can be measured artifact-free, with at least a 50:1 peak-to-noise ratio at the method detection limit, determined through the Hubaux-Vos method and satisfying a conservative 99% statistical confidence. Method detection limits for the compounds are 1-6 ppt in air. We present calibration curve, capacity, capture efficiency, break-through and repeatability data to demonstrate robustness of method. Seventy-one real-world samples from 26 projects taken in several fab environments show that TMS is found in concentrations 100 times higher than those of HMDSO and D3. All compounds are found in all environments in concentrations ranging from zero to 12 ppm, but most concentrations were below 50 ppb. All compounds are noticeably higher in litho-bays than in sub-fabs and we found all three compounds inside of two exposure tools, suggesting cleanroom and/or tool-internal contamination sources.

High-throughput microfluidic mixing and multiparametric cell sorting for bioactive compound screening.

Science.gov (United States)

Young, Susan M; Curry, Mark S; Ransom, John T; Ballesteros, Juan A; Prossnitz, Eric R; Sklar, Larry A; Edwards, Bruce S

2004-03-01

HyperCyt, an automated sample handling system for flow cytometry that uses air bubbles to separate samples sequentially introduced from multiwell plates by an autosampler. In a previously documented HyperCyt configuration, air bubble separated compounds in one sample line and a continuous stream of cells in another are mixed in-line for serial flow cytometric cell response analysis. To expand capabilities for high-throughput bioactive compound screening, the authors investigated using this system configuration in combination with automated cell sorting. Peptide ligands were sampled from a 96-well plate, mixed in-line with fluo-4-loaded, formyl peptide receptor-transfected U937 cells, and screened at a rate of 3 peptide reactions per minute with approximately 10,000 cells analyzed per reaction. Cell Ca(2+) responses were detected to as little as 10(-11) M peptide with no detectable carryover between samples at up to 10(-7) M peptide. After expansion in culture, cells sort-purified from the 10% highest responders exhibited enhanced sensitivity and more sustained responses to peptide. Thus, a highly responsive cell subset was isolated under high-throughput mixing and sorting conditions in which response detection capability spanned a 1000-fold range of peptide concentration. With single-cell readout systems for protein expression libraries, this technology offers the promise of screening millions of discrete compound interactions per day.

Molecular Imprinting of Macromolecules for Sensor Applications.

Science.gov (United States)

Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

2017-04-19

Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting.

Design, synthesis, α-glucosidase inhibitory activity, molecular docking and QSAR studies of benzimidazole derivatives

Science.gov (United States)

Dinparast, Leila; Valizadeh, Hassan; Bahadori, Mir Babak; Soltani, Somaieh; Asghari, Behvar; Rashidi, Mohammad-Reza

2016-06-01

In this study the green, one-pot, solvent-free and selective synthesis of benzimidazole derivatives is reported. The reactions were catalyzed by ZnO/MgO containing ZnO nanoparticles as a highly effective, non-toxic and environmentally friendly catalyst. The structure of synthesized benzimidazoles was characterized using spectroscopic technics (FT-IR, 1HNMR, 13CNMR). Synthesized compounds were evaluated for their α-glucosidase inhibitory potential. Compounds 3c, 3e, 3l and 4n were potent inhibitors with IC50 values ranging from 60.7 to 168.4 μM. In silico studies were performed to explore the binding modes and interactions between enzyme and synthesized benzimidazoles. Developed linear QSAR model based on density and molecular weight could predict bioactivity of newly synthesized compounds well. Molecular docking studies revealed the availability of some hydrophobic interactions. In addition, the bioactivity of most potent compounds had good correlation with estimated free energy of binding (ΔGbinding) which was calculated according to docked best conformations.

Influence of Inorganic Ions and Organic Substances on the Degradation of Pharmaceutical Compound in Water Matrix

Directory of Open Access Journals (Sweden)

Edyta Kudlek

2016-11-01

Full Text Available The paper determined the influence of inorganic substances and high-molecular organic compounds on the decomposition of diclofenac, ibuprofen, and carbamazepine in the process of photocatalysis conducted with the presence of Titanium dioxide (TiO2. It was determined that the presence of such ions as CO 3 2 − , HCO 3 − , HPO 4 2 − as well as SO 4 2 − inhibited the decomposition of carbamazepine, whereas the efficiency of diclofenac degradation was decreased only by the presence of CO 3 2 − and HCO 3 − anions. In case of ibuprofen sodium salt (IBU, all investigated anions influenced the increase in its decomposition rate. The process of pharmaceutical photooxidation conducted in suspensions with Al3+ and Fe3+ cations was characterized by a significantly decreased efficiency when compared to the solution deprived of inorganic compounds. The addition of Ca2+, Mg2+ and NH4+ affected the increase of reaction rate constant value of diclofenac and ibuprofen decomposition. On the other hand, high molecular organic compounds present in the model effluent additionally catalysed the degradation process of pharmaceutical compounds and constituted an additional sorbent that enabled to decrease their concentration. Toxicological analysis conducted in deionized water with pharmaceutical compounds’ patterns proved the production of by-products from oxidation and/or reduction of micropollutants, which was not observed for model effluent irradiation.

Identification of fluorescent compounds with non-specific binding property via high throughput live cell microscopy.

Directory of Open Access Journals (Sweden)

Sangeeta Nath

Full Text Available INTRODUCTION: Compounds exhibiting low non-specific intracellular binding or non-stickiness are concomitant with rapid clearing and in high demand for live-cell imaging assays because they allow for intracellular receptor localization with a high signal/noise ratio. The non-stickiness property is particularly important for imaging intracellular receptors due to the equilibria involved. METHOD: Three mammalian cell lines with diverse genetic backgrounds were used to screen a combinatorial fluorescence library via high throughput live cell microscopy for potential ligands with high in- and out-flux properties. The binding properties of ligands identified from the first screen were subsequently validated on plant root hair. A correlative analysis was then performed between each ligand and its corresponding physiochemical and structural properties. RESULTS: The non-stickiness property of each ligand was quantified as a function of the temporal uptake and retention on a cell-by-cell basis. Our data shows that (i mammalian systems can serve as a pre-screening tool for complex plant species that are not amenable to high-throughput imaging; (ii retention and spatial localization of chemical compounds vary within and between each cell line; and (iii the structural similarities of compounds can infer their non-specific binding properties. CONCLUSION: We have validated a protocol for identifying chemical compounds with non-specific binding properties that is testable across diverse species. Further analysis reveals an overlap between the non-stickiness property and the structural similarity of compounds. The net result is a more robust screening assay for identifying desirable ligands that can be used to monitor intracellular localization. Several new applications of the screening protocol and results are also presented.

Screening for Antifibrotic Compounds Using High Throughput System Based on Fluorescence Polarization

Directory of Open Access Journals (Sweden)

Branko Stefanovic

2014-04-01

Full Text Available Fibroproliferative diseases are one of the leading causes of death worldwide. They are characterized by reactive fibrosis caused by uncontrolled synthesis of type I collagen. There is no cure for fibrosis and development of therapeutics that can inhibit collagen synthesis is urgently needed. Collagen α1(I mRNA and α2(I mRNA encode for type I collagen and they have a unique 5' stem-loop structure in their 5' untranslated regions (5'SL. Collagen 5'SL binds protein LARP6 with high affinity and specificity. The interaction between LARP6 and the 5'SL is critical for biosynthesis of type I collagen and development of fibrosis in vivo. Therefore, this interaction represents is an ideal target to develop antifibrotic drugs. A high throughput system to screen for chemical compounds that can dissociate LARP6 from 5'SL has been developed. It is based on fluorescence polarization and can be adapted to screen for inhibitors of other protein-RNA interactions. Screening of 50,000 chemical compounds yielded a lead compound that can inhibit type I collagen synthesis at nanomolar concentrations. The development, characteristics, and critical appraisal of this assay are presented.

Study on growth of highly pure uranium compounds

International Nuclear Information System (INIS)

Shikama, Tatsuo; Ochiai, Akira; Suzuki, Kenji.

1992-01-01

We developed the systems for growing highly pure uranium compounds to study their intrinsic physical properties. Uranium metal was zone refined under low contamination conditions as far as possible. Chemical analysis of the purified uranium was performed using the inductive coupled plasma emission spectrometry (ICP). The problem that emission spectra of the uranium conceal those of analyzed impurities was settled by extraction of the uranium using tri-n-butyl-phosphate (TBP). The result shows that some metallic impurities such as Pb, Mn, Cu etc. evaporated by the r.f. heating and other usual metallic impurities moved to the end of rod with molten zone. Therefore, we conclude that the zone refining technique is much effective to the removal of metallic impurities and we obtained highly purified uranium metal of 99.99 % up with regard to metallic impurities. Using the purified uranium, we attempted to grow a highly pure uranium-titanium single crystals. (author)

Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

Energy Technology Data Exchange (ETDEWEB)

Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.; Nico, Peter; Keiluweit, Marco; Ahmed, Musahid

2013-04-01

Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.

Application of Homochiral Alkylated Organic Cages as Chiral Stationary Phases for Molecular Separations by Capillary Gas Chromatography.

Science.gov (United States)

Xie, Shengming; Zhang, Junhui; Fu, Nan; Wang, Bangjin; Hu, Cong; Yuan, Liming

2016-11-08

Molecular organic cage compounds have attracted considerable attention due to their potential applications in gas storage, catalysis, chemical sensing, molecular separations, etc. In this study, a homochiral pentyl cage compound was synthesized from a condensation reaction of ( S , S )-1,2-pentyl-1,2-diaminoethane and 1,3,5-triformylbenzene. The imine-linked pentyl cage diluted with a polysiloxane (OV-1701) was explored as a novel stationary phase for high-resolution gas chromatographic separation of organic compounds. Some positional isomers were baseline separated on the pentyl cage-coated capillary column. In particular, various types of enantiomers including chiral alcohols, esters, ethers and epoxides can be resolved without derivatization on the pentyl cage-coated capillary column. The reproducibility of the pentyl cage-coated capillary column for separation was investigated using nitrochlorobenzene and styrene oxide as analytes. The results indicate that the column has good stability and separation reproducibility after being repeatedly used. This work demonstrates that molecular organic cage compounds could become a novel class of chiral separation media in the near future.

Application of Homochiral Alkylated Organic Cages as Chiral Stationary Phases for Molecular Separations by Capillary Gas Chromatography

Directory of Open Access Journals (Sweden)

Shengming Xie

2016-11-01

Full Text Available Molecular organic cage compounds have attracted considerable attention due to their potential applications in gas storage, catalysis, chemical sensing, molecular separations, etc. In this study, a homochiral pentyl cage compound was synthesized from a condensation reaction of (S,S-1,2-pentyl-1,2-diaminoethane and 1,3,5-triformylbenzene. The imine-linked pentyl cage diluted with a polysiloxane (OV-1701 was explored as a novel stationary phase for high-resolution gas chromatographic separation of organic compounds. Some positional isomers were baseline separated on the pentyl cage-coated capillary column. In particular, various types of enantiomers including chiral alcohols, esters, ethers and epoxides can be resolved without derivatization on the pentyl cage-coated capillary column. The reproducibility of the pentyl cage-coated capillary column for separation was investigated using nitrochlorobenzene and styrene oxide as analytes. The results indicate that the column has good stability and separation reproducibility after being repeatedly used. This work demonstrates that molecular organic cage compounds could become a novel class of chiral separation media in the near future.

Vapor Pressure Data and Analysis for Selected Organophosphorus Compounds, CMMP, DPMP, DMEP, and DEEP: Extrapolation of High-Temperature Data

Science.gov (United States)

2018-04-01

comparison. The correlation equations are presented using two common units systems , one with temperature given in kelvin (T) and pressure in pascal...This report documents vapor pressure data and correlations for four phosphonate ester compounds that have molecular structures similar to those of...Antoine equation Clausius–Clapeyron equation Enthalpy of vaporization Volatility Differential scanning calorimetry (DSC) Vapor saturation Normal boiling

High efficiency diffusion molecular retention tumor targeting.

Directory of Open Access Journals (Sweden)

Yanyan Guo

Full Text Available Here we introduce diffusion molecular retention (DMR tumor targeting, a technique that employs PEG-fluorochrome shielded probes that, after a peritumoral (PT injection, undergo slow vascular uptake and extensive interstitial diffusion, with tumor retention only through integrin molecular recognition. To demonstrate DMR, RGD (integrin binding and RAD (control probes were synthesized bearing DOTA (for (111 In(3+, a NIR fluorochrome, and 5 kDa PEG that endows probes with a protein-like volume of 25 kDa and decreases non-specific interactions. With a GFP-BT-20 breast carcinoma model, tumor targeting by the DMR or i.v. methods was assessed by surface fluorescence, biodistribution of [(111In] RGD and [(111In] RAD probes, and whole animal SPECT. After a PT injection, both probes rapidly diffused through the normal and tumor interstitium, with retention of the RGD probe due to integrin interactions. With PT injection and the [(111In] RGD probe, SPECT indicated a highly tumor specific uptake at 24 h post injection, with 352%ID/g tumor obtained by DMR (vs 4.14%ID/g by i.v.. The high efficiency molecular targeting of DMR employed low probe doses (e.g. 25 ng as RGD peptide, which minimizes toxicity risks and facilitates clinical translation. DMR applications include the delivery of fluorochromes for intraoperative tumor margin delineation, the delivery of radioisotopes (e.g. toxic, short range alpha emitters for radiotherapy, or the delivery of photosensitizers to tumors accessible to light.

TCP (truncated compound Poisson) process for multiplicity distributions in high energy collisions

International Nuclear Information System (INIS)

Srivastave, P.P.

1990-01-01

On using the Poisson distribution truncated at zero for intermediate cluster decay in a compound Poisson process, the authors obtain TCP distribution which describes quite well the multiplicity distributions in high energy collisions. A detailed comparison is made between TCP and NB for UA5 data. The reduced moments up to the fifth agree very well with the observed ones. The TCP curves are narrower than NB at high multiplicity tail, look narrower at very high energy and develop shoulders and oscillations which become increasingly pronounced as the energy grows. At lower energies the distributions, of the data for fixed intervals of rapidity for UA5 data and for the data (at low energy) for e + e - annihilation and pion-proton, proton-proton and muon-proton scattering. A discussion of compound Poisson distribution, expression of reduced moments and Poisson transforms are also given. The TCP curves and curves of the reduced moments for different values of the parameters are also presented

Intrinsically High Thermoelectric Performance in AgInSe2 n-Type Diamond-Like Compounds.

Science.gov (United States)

Qiu, Pengfei; Qin, Yuting; Zhang, Qihao; Li, Ruoxi; Yang, Jiong; Song, Qingfeng; Tang, Yunshan; Bai, Shengqiang; Shi, Xun; Chen, Lidong

2018-03-01

Diamond-like compounds are a promising class of thermoelectric materials, very suitable for real applications. However, almost all high-performance diamond-like thermoelectric materials are p-type semiconductors. The lack of high-performance n-type diamond-like thermoelectric materials greatly restricts the fabrication of diamond-like material-based modules and their real applications. In this work, it is revealed that n-type AgInSe 2 diamond-like compound has intrinsically high thermoelectric performance with a figure of merit ( zT ) of 1.1 at 900 K, comparable to the best p-type diamond-like thermoelectric materials reported before. Such high zT is mainly due to the ultralow lattice thermal conductivity, which is fundamentally limited by the low-frequency Ag-Se "cluster vibrations," as confirmed by ab initio lattice dynamic calculations. Doping Cd at Ag sites significantly improves the thermoelectric performance in the low and medium temperature ranges. By using such high-performance n-type AgInSe 2 -based compounds, the diamond-like thermoelectric module has been fabricated for the first time. An output power of 0.06 W under a temperature difference of 520 K between the two ends of the module is obtained. This work opens a new window for the applications using the diamond-like thermoelectric materials.

Sampling of high molecular weight hydrocarbons with adsorbent tubes

International Nuclear Information System (INIS)

Stroemberg, B.

1996-12-01

Adsorption tubes have been used to determine the content of hydrocarbons in gas samples from small scale combustion and gasification of biomass. Compounds from benzene (mw 78) to indeno (1,2,3-cd) pyrene (mw 276) have been examined. The results show that it is possible to analyze polyaromatic hydrocarbons (PAH) with 4 aromatic rings (mw 202). Detection limits for these compounds are 3 . PAH with higher molecule weight can be identified and quantified in samples with high amounts of PAH e.g. at gasification of biomass. Sampling on adsorption tubes is extremely quick and easy. The tube is inserted in the gas of interest and the sample is sucked through the tube with a pump. Sampling times of 2-10 minutes are often sufficient. High moisture content in the gas may result in losses of the most volatile compounds, when drying. Even very low concentrations of water in the tube may cause ice formation in the cold-trap and the sample will be destroyed. The analysis is unfortunately time-consuming because the desorption oven must be cooled between every analysis. This will reduce the number of samples which can be analyzed per day. The tubes can be stored for several weeks before analysis without deterioration. 4 refs, 5 figs, 3 tabs

A High-Content Live-Cell Viability Assay and Its Validation on a Diverse 12K Compound Screen.

Science.gov (United States)

Chiaravalli, Jeanne; Glickman, J Fraser

2017-08-01

We have developed a new high-content cytotoxicity assay using live cells, called "ImageTOX." We used a high-throughput fluorescence microscope system, image segmentation software, and the combination of Hoechst 33342 and SYTO 17 to simultaneously score the relative size and the intensity of the nuclei, the nuclear membrane permeability, and the cell number in a 384-well microplate format. We then performed a screen of 12,668 diverse compounds and compared the results to a standard cytotoxicity assay. The ImageTOX assay identified similar sets of compounds to the standard cytotoxicity assay, while identifying more compounds having adverse effects on cell structure, earlier in treatment time. The ImageTOX assay uses inexpensive commercially available reagents and facilitates the use of live cells in toxicity screens. Furthermore, we show that we can measure the kinetic profile of compound toxicity in a high-content, high-throughput format, following the same set of cells over an extended period of time.

A Structure-Activity Relationship (SAR Study of Neolignan Compounds with Anti-schistosomiasis Activity

Directory of Open Access Journals (Sweden)

Alves Claúdio N.

2002-01-01

Full Text Available A set of eighteen neolignan derivative compounds with anti-schistosomiasis activity was studied by using the quantum mechanical semi-empirical method PM3 and other theoretical methods in order to calculate selected molecular properties (variables or descriptors to be correlated to their biological activities. Exploratory data analysis (principal component analysis, PCA, and hierarchical cluster analysis, HCA, discriminant analysis (DA and the Kth nearest neighbor (KNN method were employed for obtaining possible relationships between the calculated descriptors and the biological activities studied and predicting the anti-schistosomiasis activity of new compounds from a test set. The molecular descriptors responsible for the separation between active and inactive compounds were: hydration energy (HE, molecular refractivity (MR and charge on the C19 carbon atom (Q19. These descriptors give information on the kind of interaction that can occur between the compounds and their respective biological receptor. The prediction study was done with a new set of ten derivative compounds by using the PCA, HCA, DA and KNN methods and only five of them were predicted as active against schistosomiasis.

PMG: online generation of high-quality molecular pictures and storyboarded animations

Science.gov (United States)

Autin, Ludovic; Tufféry, Pierre

2007-01-01

The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved using Dino coupled to POV-Ray. In order to produce highly informative images, the PMG includes capabilities of using different molecular representations at the same time to highlight particular molecular features. Moreover, sophisticated rendering concepts including scene definition, as well as modeling light and materials are available. The PMG accepts Protein Data Bank (PDB) files as input, which may include series of models or molecular dynamics trajectories and produces images or movies under various formats. PMG can be accessed at http://bioserv.rpbs.jussieu.fr/PMG.html. PMID:17478496

Atomic and molecular physics of plasma-based environmental technologies for abatement of volatile organic compounds

International Nuclear Information System (INIS)

Penetrante, B.M.; Hsiao, M.C.; Bardsley, J.N.; Merrit, B.T.; Vogtlin, G.E.; Kuthi, A.; Burkhart, C.P.; Bayless, J.R.

1996-01-01

Non-thermal plasma techniques represent a new generation of air emission control technology that potentially could treat large-volume emissions containing dilute concentrations of volatile organic compounds (VOCs). In order to apply non-thermal in an industrial scale, it is important to establish the electrical power requirements and byproducts of the process. There is a need for reliable data concerning the primary decomposition mechanisms and subsequent chemical kinetics associated with non-thermal plasma processing of VOCs. There are many basic atomic and molecular physics issues that are essential in evaluating the economic performance of non-thermal plasma reactor. These studies are important in understanding how the input electrical power is dissipated in the plasma and how efficiency it is converted to the production of the plasma species (radicals, ions or electrons) responsible for the decomposition of the VOCs. This paper presents results from basic experimental and theoretical studied aimed at identifying the reaction mechanisms responsible for the primary decomposition of various types of VOCs. (Authors)

Antioxidant behavior of mearnsetin and myricetin flavonoid compounds — A DFT study

Science.gov (United States)

Sadasivam, K.; Kumaresan, R.

2011-06-01

The molecular characteristics of two naturally occurring flavonoid compounds mearnsetin and myricetin have been computed using density functional theory (DFT) approach with B3LYP/6-311G(d,p) level of theory. The computation and analysis of bond dissociation enthalpy magnitudes for all the OH sites for both the compounds clearly denotes the contribution of the B-ring for the antioxidant activity. The analysis has also indicated the higher values of BDE on the C5-OH radical species in both the compounds. The computed vibrational frequency analysis indicates the absence of imaginary frequency in the neutral as well as radical species of both the flavonoid compounds. The ionisation potential (IP) analysis was found to be within the range of the IP of synthetic food additives. In addition, various molecular descriptors such as electron affinity, hardness, softness, electronegativity, electrophilic index have also been calculated and the validity of Koopman's theorem is verified. The plot of frontier molecular orbital and spin density distribution analysis for neutral and the corresponding radical species for both the compounds have been computed and interpreted. The polar nature and their polarizing capacity are well established through the analysis of dipole moment and polarisability magnitudes.

Quantitative prediction of solvation free energy in octanol of organic compounds.

Science.gov (United States)

Delgado, Eduardo J; Jaña, Gonzalo A

2009-03-01

The free energy of solvation, DeltaGS0, in octanol of organic compounds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a DeltaGS0 range from about -50 to 0 kJ.mol(-1). The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ.mol(-1), just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set.

NATO Conference on Molecular Metals

CERN Document Server

1979-01-01

During the past few years there has been intense research activity in the design, synthesis, and characterization of materials which are formed from molecular precursors, and which have high or metal-like electrical conductivities, i.e. dcr/dT < O. It has been widely supposed that these new materials, which are commonly called molecular metals, would be pressed into service, for example as devices. Up to now, widespread, practical applications of these sub­ stances have not developed. The NATO Advanced Research Institute on Molecular Metals at Les Arcs, France, September 10-16, 1978 was organized to discuss the scientific and technological potential of research and development in this field. The proceedings of the Institute constitute this book. Several lectures were devoted to the assessment of the present status of research on systems which serve to define major components of the field. The systems which were discussed included TTF-TCNQ, platinum chain compounds, (SN)x, polyacetylene, polydiacetylene, g...

Ferroelectric and magnetic properties in high-pressure synthesized BiFeO3 compound

International Nuclear Information System (INIS)

Zhai, L.; Shi, Y.G.; Gao, J.L.; Tang, S.L.; Du, Y.W.

2011-01-01

Highlights: → A high-density polycrystalline BiFeO 3 compound was synthesized by high-pressure annealing method. → The sample showed weak ferromagnetic at room temperature, which could be attributed to the lattice distortion induced by the high-pressure annealing. → Irregular domains were observed on the surface of the sample by piezoresponse force microscopy, and a typical hysteresis loop was obtained. - Abstract: High-density polycrystalline BiFeO 3 compound was synthesized by high-pressure annealing. Measurements of crystal structure, magnetic, and ferroelectric properties were made on the sample. It was found that the sample was almost single phase with a distorted R3c structure. The results of the X-ray photoelectron spectra demonstrate that the oxidation state of Fe in the sample is Fe 3+ . The room-temperature field dependence of magnetization for BiFeO 3 exhibits a hysteretic behavior. The observed weak ferromagnetism could be ascribed to the lattice distortion induced by the high-pressure annealing. In addition, the local ferroelectric performance of the sample was studied by piezoresponse force microscopy.

pH-Dependent dissolving nano- and microparticles for improved peroral delivery of a highly lipophilic compound in dogs.

Science.gov (United States)

De Jaeghere, F; Allémann, E; Cerny, R; Galli, B; Steulet, A F; Müller, I; Schütz, H; Doelker, E; Gurny, R

2001-01-01

RR01, a new highly lipophilic drug showing extremely low water solubility and poor oral bioavailability, has been incorporated into pH-dependent dissolving particles made of a poly(methacrylic acid-co-ethylacrylate) copolymer. The physicochemical properties of the particles were determined using laser-light-scattering techniques, scanning electron microscopy, high-performance liquid chromatography, and x-ray powder diffraction. Suspension of the free drug in a solution of hydroxypropylcellulose (reference formulation) and aqueous dispersions of pH-sensitive RR01-loaded nanoparticles or microparticles were administered orally to Beagle dogs according to a 2-block Latin square design (n = 6). Plasma samples were obtained over the course of 48 hours and analyzed by gas chromatography/mass spectrometry. The administration of the reference formulation resulted in a particularly high interindividual variability of pharmacokinetic parameters, with low exposure to compound RR01 (AUC0-48h of 6.5 microg x h/mL and coefficient of variation (CV) of 116%) and much higher Tmax, as compared to both pH-sensitive formulations. With respect to exposure and interindividual variability, nanoparticles were superior to microparticles (AUC0-48h of 27.1 microg x h/mL versus 17.7 microg x h/mL with CV of 19% and 40%, respectively), indicating that the particle size may play an important role in the absorption of compound RR01. The performance of pH-sensitive particles is attributed to their ability to release the drug selectively in the upper part of the intestine in a molecular or amorphous form. In conclusion, pH-dependent dissolving particles have a great potential as oral delivery systems for drugs with low water solubility and acceptable permeation properties.

Fingerprinting analysis of non-crystalline pharmaceutical compounds using high energy X-rays and the total scattering pair distribution function

Science.gov (United States)

Davis, Timur D.

2011-12-01

In the development of new medicinal products, poor oral bioavailability, due to the low solubilities of many active pharmaceutical ingredients (APIs), is increasingly a barrier for treatments to be administered using tablet or capsule formulations and one of the main challenges facing the pharmaceutical industry. Non-crystalline phases such as the amorphous and nanostructured states can confer increased solubility to a drug, and therefore, have recently garnered a lot of interest from pharmaceutical researchers. However, little is known about local ordering in non-crystalline pharmaceuticals due to the lack of reliable experimental probes, hindering the clinical application of these compounds. The powerful tools of crystallography begin to lose their potency for structures on the nanoscale; conventional X-ray powder diffraction (XRPD) patterns become broad and featureless in these cases and are not useful for differentiating between different local molecular packing arrangements. In this thesis, we introduce the use of high energy X-rays coupled with total scattering pair distribution function (TSPDF) and fingerprinting analysis to investigate the local structures of non-crystalline pharmaceutical compounds. The high energy X-rays allow us to experimentally collect diffuse scattering intensities, which contain information about a sample's local ordering, in addition to the Bragg scattering available in conventional XRPD experiments, while the TSPDF allows us to view the intra- and inter-molecular correlations in real space. The goal of this study was to address some fundamental problems involving fingerprinting non-crystalline APIs using TSPDF in order to lay the groundwork for the proper use of the technique by the pharmaceutical community. We achieved this by developing the methodology as well as the exploring the scientific implications. On the methodology side, we introduced PDFGetX3, a new software program for calculating TSPDFs that simplifies the procedure

Computational Study on Spirocyclic Compounds as Energetic Materials (I)

Energy Technology Data Exchange (ETDEWEB)

Seok, Won K. [Dongguk Univ., Seoul (Korea, Republic of)

2014-04-15

The molecular structures of 2,6-diaza-1,3,5,7-tetraoxaspiro heptane and its dinitro derivative, 2,6-dinitro-2,6-diaza-1,3,5,7-tetraoxaspiro heptane, were fully optimized without symmetry constraints at HF/6-31G level of theory. A bisected conformation with respect to the ring is preferred with a C{sub 2} symmetric structure. The density of each molecule in the crystalline state was estimated to 1.12 and 2.36 g/cm{sup 3} using PM3/VSTO-3G calculations from the molecular volume. The heat of formation was calculated for two compounds at the CBS-4M level of theory. The detonation parameters were computed using the EXPLO5 software: D = 6282 m/s, P{sub C-J} = 127 kbar for compound, D = 7871 m/s, P{sub C-J} = 307 kbar for compound, and D = 6975 m/s, P{sub C-J} = 170 kbar for 60% compound with 40% TNT. Specific impulse of compound 1 in aluminized formulation when used as monopropellants was very similar to that of the conventional ammonium perchlorate in the same formulation of aluminum.

Contribution to high-temperature chromatography and high-temperature-gas-chromatography-mass spectrometry of lipids

International Nuclear Information System (INIS)

Aichholz, R.

1998-04-01

This thesis describes the use of high temperature gas chromatography for the investigation of unusual triacylglycerols, cyanolipids and bees waxes. The used glass capillary columns were pretreated and coated with tailor made synthesized high temperature stable polysiloxane phases. The selective separation properties of the individual columns were tested with a synthetic lipid mixture. Suitable derivatization procedures for the gaschromatographic analyses of neutral lipids, containing multiple bonds as well as hydroxy-, epoxy-, and carboxyl groups, were developed and optimized. Therefore conjugated olefinic-, conjugated olefinic-acetylenic-, hydroxy-, epoxy-, and conjugated olefinic keto triacylglycerols in miscellaneous plant seed oils as well as hydroxy monoesters, diesters and hydroxy diesters in bees waxes could be analysed directly with high temperature gas chromatography for the first time. In order to elucidate the structures of separated lipid compounds, high temperature gas chromatography was coupled to mass spectrometry and tandem mass spectrometry, respectively. Comparable analytical systems are hitherto not commercial available. Therefore instrumental prerequisites for a comprehensive and detailed analysis of seed oils and bees waxes were established. In GC/MS commonly two ionization methods are used, electron impact ionization and chemical ionization. For the analysis of lipids the first is of limited use only. Due to intensive fragmentation only weak molecular ions are observed. In contrast, the chemical ionization yields in better results. Dominant quasi molecular ions enable an unambiguous determination of the molecular weight. Moreover, characteristic fragment ions provide important indications of certain structural features of the examined compounds. Nevertheless, in some cases the chromatographic resolution was insufficient in order to separate all compounds present in natural lipid mixtures. Owing to the selected detection with mass spectrometry

Formation of highly oxygenated organic molecules from aromatic compounds

Science.gov (United States)

Molteni, Ugo; Bianchi, Federico; Klein, Felix; El Haddad, Imad; Frege, Carla; Rossi, Michel J.; Dommen, Josef; Baltensperger, Urs

2018-02-01

Anthropogenic volatile organic compounds (AVOCs) often dominate the urban atmosphere and consist to a large degree of aromatic hydrocarbons (ArHCs), such as benzene, toluene, xylenes, and trimethylbenzenes, e.g., from the handling and combustion of fuels. These compounds are important precursors for the formation of secondary organic aerosol. Here we show that the oxidation of aromatics with OH leads to a subsequent autoxidation chain reaction forming highly oxygenated molecules (HOMs) with an O : C ratio of up to 1.09. This is exemplified for five single-ring ArHCs (benzene, toluene, o-/m-/p-xylene, mesitylene (1,3,5-trimethylbenzene) and ethylbenzene), as well as two conjugated polycyclic ArHCs (naphthalene and biphenyl). We report the elemental composition of the HOMs and show the differences in the oxidation patterns of these ArHCs. A potential pathway for the formation of these HOMs from aromatics is presented and discussed. We hypothesize that AVOCs may contribute substantially to new particle formation events that have been detected in urban areas.

Formation of highly oxygenated organic molecules from aromatic compounds

Directory of Open Access Journals (Sweden)

U. Molteni

2018-02-01

Full Text Available Anthropogenic volatile organic compounds (AVOCs often dominate the urban atmosphere and consist to a large degree of aromatic hydrocarbons (ArHCs, such as benzene, toluene, xylenes, and trimethylbenzenes, e.g., from the handling and combustion of fuels. These compounds are important precursors for the formation of secondary organic aerosol. Here we show that the oxidation of aromatics with OH leads to a subsequent autoxidation chain reaction forming highly oxygenated molecules (HOMs with an O : C ratio of up to 1.09. This is exemplified for five single-ring ArHCs (benzene, toluene, o-/m-/p-xylene, mesitylene (1,3,5-trimethylbenzene and ethylbenzene, as well as two conjugated polycyclic ArHCs (naphthalene and biphenyl. We report the elemental composition of the HOMs and show the differences in the oxidation patterns of these ArHCs. A potential pathway for the formation of these HOMs from aromatics is presented and discussed. We hypothesize that AVOCs may contribute substantially to new particle formation events that have been detected in urban areas.

Impact of fuel molecular structure on auto-ignition behavior – Design rules for future high performance gasolines

KAUST Repository

Boot, Michael D.

2016-12-29

At a first glance, ethanol, toluene and methyl tert-butyl ether look nothing alike with respect to their molecular structures. Nevertheless, all share a similarly high octane number. A comprehensive review of the inner workings of such octane boosters has been long overdue, particularly at a time when feedstocks for transport fuels other than crude oil, such as natural gas and biomass, are enjoying a rapidly growing market share. As high octane fuels sell at a considerable premium over gasoline, diesel and jet fuel, new entrants into the refining business should take note and gear their processes towards knock resistant compounds if they are to maximize their respective bottom lines. Starting from crude oil, the route towards this goal is well established. Starting from biomass or natural gas, however, it is less clear what dots on the horizon to aim for. The goal of this paper is to offer insight into the chemistry behind octane boosters and to subsequently distill from this knowledge, taking into account recent advances in engine technology, multiple generic design rules that guarantee good anti-knock performance. Careful analysis of the literature suggests that highly unsaturated (cyclic) compounds are the preferred octane boosters for modern spark-ignition engines. Additional side chains of any variety will dilute this strong performance. Multi-branched paraffins come in distant second place, owing to their negligible sensitivity. Depending on the type and location of functional oxygen groups, oxygenates can have a beneficial, neutral or detrimental impact on anti-knock quality.

Molecular materials for organic field-effect transistors

International Nuclear Information System (INIS)

Mori, T

2008-01-01

Organic field-effect transistors are important applications of thin films of molecular materials. A variety of materials have been explored for improving the performance of organic transistors. The materials are conventionally classified as p-channel and n-channel, but not only the performance but also even the carrier polarity is greatly dependent on the combinations of organic semiconductors and electrode materials. In this review, particular emphasis is laid on multi-sulfur compounds such as tetrathiafulvalenes and metal dithiolates. These compounds are components of highly conducting materials such as organic superconductors, but are also used in organic transistors. The charge-transfer complexes are used in organic transistors as active layers as well as electrodes. (topical review)

Low molecular-weight phenols in Tannat wines made by alternative winemaking procedures.

Science.gov (United States)

Favre, Guzmán; Peña-Neira, Álvaro; Baldi, Cecilia; Hernández, Natalia; Traverso, Sofía; Gil, Graciela; González-Neves, Gustavo

2014-09-01

Low molecular weight phenols of Tannat red wines produced by Traditional Maceration (TM), Prefermentative Cold Maceration (PCM), Maceration Enzyme (ENZ) and grape-Seed Tannins additions (ST), were performed and discussed. Alternatives to TM increased wine phenolic contents but unequally, ST increased mainly smaller flavans-3-ol, PCM anthocyanins and ENZ proanthocyanidins (up to 2250 mg/L). However low molecular weight flavan-3-ols remained below 9 mg/L in all wines, showing that there is not necessarily a correspondence between wine richness in total tannins and flavan-3-ols contents at low molecular weight. PCM wines had particularly high concentrations of tyrosol and tryptophol, yeast metabolism derived compounds. The use of grape-seed enological tannins did not increase grape seed derived phenolic compounds such as gallic acid. Caftaric acid was found in concentrations much higher than those reported in other grape varieties. Wine phenolic content and composition was considerably affected by the winemaking procedures tested. Copyright © 2014 Elsevier Ltd. All rights reserved.

Extensive Evaluation of the Conductor-like Screening Model for Real Solvents Method in Predicting Liquid-Liquid Equilibria in Ternary Systems of Ionic Liquids with Molecular Compounds.

Science.gov (United States)

Paduszyński, Kamil

2018-04-12

A conductor-like screening model for real solvents (COSMO-RS) is nowadays one of the most popular and commonly applied tools for the estimation of thermodynamic properties of complex fluids. The goal of this work is to provide a comprehensive review and analysis of the performance of this approach in calculating liquid-liquid equilibrium (LLE) phase diagrams in ternary systems composed of ionic liquid and two molecular compounds belonging to diverse families of chemicals (alkanes, aromatics, S/N-compounds, alcohols, ketones, ethers, carboxylic acid, esters, and water). The predictions are presented for extensive experimental database, including 930 LLE data sets and more than 9000 data points (LLE tie lines) reported for 779 unique ternary mixtures. An impact of the type of molecular binary subsystem on the accuracy of predictions is demonstrated and discussed on the basis of representative examples. The model's capability of capturing qualitative trends in the LLE distribution ratio and selectivity is also checked for a number of structural effects. Comparative analysis of two levels of quantum chemical theory (BP-TZVP-COSMO vs BP-TZVPD-FINE) for the input molecular data for COSMO-RS is presented. Finally, some general recommendations for the applicability of the model are indicated based on the analysis of the global performance as well as on the results obtained for systems relevant from the point of view of important separation problems.

Molecular size evolution of oligomers in organic aerosols collected in urban atmospheres and generated in a smog chamber.

Science.gov (United States)

Kalberer, Markus; Sax, Mirjam; Samburova, Vera

2006-10-01

Only a minor fraction of the total organic aerosol mass can be resolved on a molecular level. High molecular weight compounds in organic aerosols have recently gained much attention because this class of compound potentially explains a major fraction of the unexplained organic aerosol mass. These compounds have been identified with different mass spectrometric methods, and compounds with molecular masses up to 1000 Da are found in secondary organic aerosols (SOA) generated from aromatic and terpene precursors in smog chamber experiments. Here, we apply matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to SOA particles from two biogenic precursors, alpha-pinene and isoprene. Similar oligomer patterns are found in these two SOA systems, but also in SOA from trimethylbenzene, an anthropogenic SOA precursor. However, different maxima molecular sizes were measured for these three SOA systems. While oligomers in alpha-pinene and isoprene have sizes mostly below 600-700 Da, they grow up to about 1000 Da in trimethylbenzene-SOA. The final molecular size of the oligomers is reached early during the particle aging process, whereas other particle properties related to aging, such as the overall acid concentration or the oligomer concentration, increase continuously over a much longer time scale. This kinetic behavior of the oligomer molecular size growth can be explained by a chain growth kinetic regime. Similar oligomer mass patterns were measured in aqueous extracts of ambient aerosol samples (measured with the same technique). Distinct differences between summer and winter were observed. In summer a few single mass peaks were measured with much higher intensity than in winter, pointing to a possible difference in the formation processes of these compounds in winter and summer.

In silico identification of anti-cancer compounds and plants from traditional Chinese medicine database

Science.gov (United States)

Dai, Shao-Xing; Li, Wen-Xing; Han, Fei-Fei; Guo, Yi-Cheng; Zheng, Jun-Juan; Liu, Jia-Qian; Wang, Qian; Gao, Yue-Dong; Li, Gong-Hua; Huang, Jing-Fei

2016-05-01

There is a constant demand to develop new, effective, and affordable anti-cancer drugs. The traditional Chinese medicine (TCM) is a valuable and alternative resource for identifying novel anti-cancer agents. In this study, we aim to identify the anti-cancer compounds and plants from the TCM database by using cheminformatics. We first predicted 5278 anti-cancer compounds from TCM database. The top 346 compounds were highly potent active in the 60 cell lines test. Similarity analysis revealed that 75% of the 5278 compounds are highly similar to the approved anti-cancer drugs. Based on the predicted anti-cancer compounds, we identified 57 anti-cancer plants by activity enrichment. The identified plants are widely distributed in 46 genera and 28 families, which broadens the scope of the anti-cancer drug screening. Finally, we constructed a network of predicted anti-cancer plants and approved drugs based on the above results. The network highlighted the supportive role of the predicted plant in the development of anti-cancer drug and suggested different molecular anti-cancer mechanisms of the plants. Our study suggests that the predicted compounds and plants from TCM database offer an attractive starting point and a broader scope to mine for potential anti-cancer agents.

Organic-based molecular switches for molecular electronics.

Science.gov (United States)

Fuentes, Noelia; Martín-Lasanta, Ana; Alvarez de Cienfuegos, Luis; Ribagorda, Maria; Parra, Andres; Cuerva, Juan M

2011-10-05

In a general sense, molecular electronics (ME) is the branch of nanotechnology which studies the application of molecular building blocks for the fabrication of electronic components. Among the different types of molecules, organic compounds have been revealed as promising candidates for ME, due to the easy access, great structural diversity and suitable electronic and mechanical properties. Thanks to these useful capabilities, organic molecules have been used to emulate electronic devices at the nanoscopic scale. In this feature article, we present the diverse strategies used to develop organic switches towards ME with special attention to non-volatile systems.

Multivariate characterisation and quantitative structure-property relationship modelling of nitroaromatic compounds

Energy Technology Data Exchange (ETDEWEB)

Joensson, S. [Man-Technology-Environment Research Centre, Department of Natural Sciences, Orebro University, 701 82 Orebro (Sweden)], E-mail: sofie.jonsson@nat.oru.se; Eriksson, L.A. [Department of Natural Sciences and Orebro Life Science Center, Orebro University, 701 82 Orebro (Sweden); Bavel, B. van [Man-Technology-Environment Research Centre, Department of Natural Sciences, Orebro University, 701 82 Orebro (Sweden)

2008-07-28

A multivariate model to characterise nitroaromatics and related compounds based on molecular descriptors was calculated. Descriptors were collected from literature and through empirical, semi-empirical and density functional theory-based calculations. Principal components were used to describe the distribution of the compounds in a multidimensional space. Four components described 76% of the variation in the dataset. PC1 separated the compounds due to molecular weight, PC2 separated the different isomers, PC3 arranged the compounds according to different functional groups such as nitrobenzoic acids, nitrobenzenes, nitrotoluenes and nitroesters and PC4 differentiated the compounds containing chlorine from other compounds. Quantitative structure-property relationship models were calculated using partial least squares (PLS) projection to latent structures to predict gas chromatographic (GC) retention times and the distribution between the water phase and air using solid-phase microextraction (SPME). GC retention time was found to be dependent on the presence of polar amine groups, electronic descriptors including highest occupied molecular orbital, dipole moments and the melting point. The model of GC retention time was good, but the precision was not precise enough for practical use. An important environmental parameter was measured using SPME, the distribution between headspace (air) and the water phase. This parameter was mainly dependent on Henry's law constant, vapour pressure, log P, content of hydroxyl groups and atmospheric OH rate constant. The predictive capacity of the model substantially improved when recalculating a model using these five descriptors only.

Non-volatile memory devices with redox-active diruthenium molecular compound

International Nuclear Information System (INIS)

Pookpanratana, S; Zhu, H; Bittle, E G; Richter, C A; Li, Q; Hacker, C A; Natoli, S N; Ren, T

2016-01-01

Reduction-oxidation (redox) active molecules hold potential for memory devices due to their many unique properties. We report the use of a novel diruthenium-based redox molecule incorporated into a non-volatile Flash-based memory device architecture. The memory capacitor device structure consists of a Pd/Al 2 O 3 /molecule/SiO 2 /Si structure. The bulky ruthenium redox molecule is attached to the surface by using a ‘click’ reaction and the monolayer structure is characterized by x-ray photoelectron spectroscopy to verify the Ru attachment and molecular density. The ‘click’ reaction is particularly advantageous for memory applications because of (1) ease of chemical design and synthesis, and (2) provides an additional spatial barrier between the oxide/silicon to the diruthenium molecule. Ultraviolet photoelectron spectroscopy data identified the energy of the electronic levels of the surface before and after surface modification. The molecular memory devices display an unsaturated charge storage window attributed to the intrinsic properties of the redox-active molecule. Our findings demonstrate the strengths and challenges with integrating molecular layers within solid-state devices, which will influence the future design of molecular memory devices. (paper)

Amorphization of Molecular Liquids of Pharmaceutical Drugs by Acoustic Levitation

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C. J. Benmore

2011-08-01

Full Text Available It is demonstrated that acoustic levitation is able to produce amorphous forms from a variety of organic molecular compounds with different glass forming abilities. This can lead to enhanced solubility for pharmaceutical applications. High-energy x-ray experiments show that several viscous gels form from saturated pharmaceutical drug solutions after 10–20 min of levitation at room temperature, most of which can be frozen in solid form. Laser heating of ultrasonically levitated drugs can also result in the vitrification of molecular liquids, which is not attainable using conventional amorphization methods.

High-Flux Carbon Molecular Sieve Membranes for Gas Separation.

Science.gov (United States)

Richter, Hannes; Voss, Hartwig; Kaltenborn, Nadine; Kämnitz, Susanne; Wollbrink, Alexander; Feldhoff, Armin; Caro, Jürgen; Roitsch, Stefan; Voigt, Ingolf

2017-06-26

Carbon membranes have great potential for highly selective and cost-efficient gas separation. Carbon is chemically stable and it is relative cheap. The controlled carbonization of a polymer coating on a porous ceramic support provides a 3D carbon material with molecular sieving permeation performance. The carbonization of the polymer blend gives turbostratic carbon domains of randomly stacked together sp 2 hybridized carbon sheets as well as sp 3 hybridized amorphous carbon. In the evaluation of the carbon molecular sieve membrane, hydrogen could be separated from propane with a selectivity of 10 000 with a hydrogen permeance of 5 m 3 (STP)/(m 2 hbar). Furthermore, by a post-synthesis oxidative treatment, the permeation fluxes are increased by widening the pores, and the molecular sieve carbon membrane is transformed from a molecular sieve carbon into a selective surface flow carbon membrane with adsorption controlled performance and becomes selective for carbon dioxide. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical intermediate detection following corona discharge on volatile organic compounds: general method using molecular beam techniques

International Nuclear Information System (INIS)

He Luning; Sulkes, Mark

2011-01-01

Nonthermal plasma (NTP)-based treatments of volatile organic compounds (VOCs) have potential for effective environmental remediation. Theory and experiment that consider the basic science pertaining to discharge events have helped improve NTP remediation outcomes. If direct information on early post-discharge chemical intermediates were also available, it would likely lead to additional improvement in NTP remediation outcomes. To this point, however, experiments yielding direct information on post-NTP VOC intermediates have been limited. An approach using supersonic expansion molecular beam methods offers general promise for detection of post-discharge VOC intermediates. To illustrate the potential utility of these methods, we present mass spectra showing the growth of early products formed when pulsed corona discharges were carried out on toluene in He and then in He with added O 2 . Good general detection of neutral post-discharge species was obtained using 800 nm 150 fs photoionization pulses.

The comparison of naturally weathered oil and artificially photo-degraded oil at the molecular level by a combination of SARA fractionation and FT-ICR MS

International Nuclear Information System (INIS)

Islam, Ananna; Cho, Yunju; Yim, Un Hyuk; Shim, Won Joon; Kim, Young Hwan; Kim, Sunghwan

2013-01-01

Highlights: • Weathered oils from the Hebei Spirit oil spill and photo degraded oils are compared. • We investigate changes of polar species at the molecular level by 15T FT-ICR MS. • Significant reduction of sulfur class compounds in saturates fraction is observed. • The relative abundance of protonated compounds (presumably basic nitrogen compounds) increase after degradation. • Changes of polar compounds occurred by natural and photo degradation are similar. -- Abstract: Two sets of oil samples, one obtained from different weathering stages of the M/V Hebei Spirit oil spill site and the other prepared by an in vitro photo-degradation experiment, were analyzed and compared at the molecular level by atmospheric pressure photo-ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). For a more detailed comparison at the molecular level, the oil samples were separated into saturate, aromatic, resin, and asphaltene (SARA) fractions before MS analysis. Gravimetric analysis of the SARA fractions revealed a decreased weight percentage of the aromatic fraction and an increased resin fraction in both sets of samples. Molecular-level investigations of the SARA fractions showed a significant reduction in the S 1 class in the saturate fraction and increase of S 1 O 1 class compounds with high DBE values in resin fraction. Levels of N 1 and N 1 O 1 class compounds resulting in protonated ions (presumably basic nitrogen compounds) increased after degradation compared to compounds generating molecular ions (presumably non-basic nitrogen compounds). This study revealed changes occurring in heteroatom polar species of crude oils such as sulfur and nitrogen containing compounds that have not been easily detected with conventional GC based techniques

Correlation effects in high-Tc superconductors and heavy fermion compounds

International Nuclear Information System (INIS)

Kuzemsky, A.L.

1993-10-01

This paper describes certain aspects of Highly Correlated Systems (HCS) such as high Tc superconductors (HTSC) and some new class of Heavy Fermion (HF) systems which have been studied recently. The problem is discussed on how the charge and spin degrees of freedom participate in the specific character of superconductivity in the copper oxides and competition of the magnetism and Kondo screening in heavy fermions. The electronic structure and possible superconducting mechanisms of HTSC compounds are discussed. The similarity and dissimilarity with HF compounds is pointed out. It is shown that the spins and carriers in the copper oxides are coupled in a very nontrivial way in order to introduce the discussion and the comparison of the Emery model, the t - J-model and the Kondo-Heisenberg model. It concerns attempts to derive from fundamental multi-band Hamiltonian the reduced effective Hamiltonians to extract and separate the relevant low-energy physics. A short review of the arguments which seem to support the spin-polaron pairing mechanism in HTSC are presented. Many other topics like the idea of mixed valence states in oxides, the role of charge transfer (CT) excitations, phase separation, self-consistent nonperturbative technique, etc. are also discussed. (author). 161 refs

EDITORIAL: New materials with high spin polarization: half-metallic Heusler compounds

Science.gov (United States)

Felser, Claudia; Hillebrands, Burkard

2007-03-01

The development of magnetic Heusler compounds, specifically designed as materials for spintronic applications, has made tremendous progress in the very recent past [1-21]. Heusler compounds can be made as half-metals, showing a high spin polarization of the conduction electrons of up to 100% [1]. These materials are exceptionally well suited for applications in magnetic tunnel junctions acting, for example, as sensors for magnetic fields. The tunnelling magneto-resistance (TMR) effect is the relative change in the electrical resistance upon application of a small magnetic field. Tunnel junctions with a TMR effect of 580% at 4 K were reported by the group of Miyazaki and Ando [1], consisting of two Co2MnSi Heusler electrodes. High Curie temperatures were found in Co2 Heusler compounds with values up to 1120 K in Co2FeSi [2]. The latest results are for a TMR device made from the Co2FeAl0.5Si0.5 Heusler compound and working at room temperature with a TMR effect of 174% [3]. The first significant magneto-resistance effect was discovered in Co2Cr0.6Fe0.4Al (CCFA) in Mainz [4]. With the classical Heusler compound CCFA as one electrode, the record TMR effect at 4 K is 240% [5]. Positive and negative TMR values at room temperature utilizing magnetic tunnel junctions with one Heusler compound electrode render magnetic logic possible [6]. Research efforts exist, in particular, in Japan and in Germany. The status of research as of winter 2005 was compiled in a recent special volume of Journal of Physics D: Applied Physics [7-20]. Since then specific progress has been made on the issues of (i) new advanced Heusler materials, (ii) advanced characterization, and (iii) advanced devices using the new materials. In Germany, the Mainz and Kaiserslautern based Research Unit 559 `New Materials with High Spin Polarization', funded since 2004 by the Deutsche Forschungsgemeinschaft, is a basic science approach to Heusler compounds, and it addresses the first two topics in particular

First-principles calculations of a high-pressure synthesized compound PtC

International Nuclear Information System (INIS)

Li Linyan; Yu Wen; Jin Changqing

2005-01-01

The first-principles density-functional method is used to study the recently high-pressure synthesized compound PtC. It is confirmed by our calculations that platinum carbide has a zinc-blende ground-state phase at zero pressure and that the rock-salt structure is a high-pressure phase. The theoretical transition pressure from zinc-blende to rock-salt structure is determined to be 52 GPa. Furthermore, our calculation shows the possibility that the PtC experimentally synthesized under high pressure conditions might undergo a transition from rock-salt to zinc-blende structure after a pressure quench to ambient conditions

High-speed vibrational imaging and spectral analysis of lipid bodies by compound Raman microscopy.

Science.gov (United States)

Slipchenko, Mikhail N; Le, Thuc T; Chen, Hongtao; Cheng, Ji-Xin

2009-05-28

Cells store excess energy in the form of cytoplasmic lipid droplets. At present, it is unclear how different types of fatty acids contribute to the formation of lipid droplets. We describe a compound Raman microscope capable of both high-speed chemical imaging and quantitative spectral analysis on the same platform. We used a picosecond laser source to perform coherent Raman scattering imaging of a biological sample and confocal Raman spectral analysis at points of interest. The potential of the compound Raman microscope was evaluated on lipid bodies of cultured cells and live animals. Our data indicate that the in vivo fat contains much more unsaturated fatty acids (FAs) than the fat formed via de novo synthesis in 3T3-L1 cells. Furthermore, in vivo analysis of subcutaneous adipocytes and glands revealed a dramatic difference not only in the unsaturation level but also in the thermodynamic state of FAs inside their lipid bodies. Additionally, the compound Raman microscope allows tracking of the cellular uptake of a specific fatty acid and its abundance in nascent cytoplasmic lipid droplets. The high-speed vibrational imaging and spectral analysis capability renders compound Raman microscopy an indispensible analytical tool for the study of lipid-droplet biology.

Biochemical studies on certain biologically active nitrogenous compounds

International Nuclear Information System (INIS)

Abdel kader, S.M.; El Sayed, M.M.; El Malt, E.A.; Shaker, E.S.; Abdel Aziz, H.G.

2010-01-01

Certain biologically active nitrogenous compounds such as alkaloids are widely distributed in many wild and medicinal plants such as peganum harmala L. (Phycophyllaceae). However, less literature cited on the natural compounds was extracted from the aerial parts of this plant; therefore this study was conducted on harmal leaves using several solvents. Data indicated that methanol extract was the inhibitoriest effect against some pathogenic bacteria, particularly Streptococcus pyogenus. Chromatographic separation illustrated that presence of four compounds; the most active one was the third compound (3). Elementary analysis (C, H, N) revealed that the primary chemical structure of the active antibacterial compound (C3) was: C17 H21 N3 O7 S with molecular weight 411. Spectroscopic analysis proved that coninical structure was = 1- thioformyl, 8?- D glucoperanoside- Bis- 2, 3 dihydroisopyridino pyrrol. This new compound is represented as a noval ?- carboline alkaloid compound

Urea and deuterium mixtures at high pressures

Energy Technology Data Exchange (ETDEWEB)

Donnelly, M., E-mail: m.donnelly-2@sms.ed.ac.uk; Husband, R. J.; Frantzana, A. D.; Loveday, J. S. [Centre for Science at Extreme Conditions and School of Physics and Astronomy, The University of Edinburgh, Erskine Williamson Building, Peter Guthrie Tait Road, The King’s Buildings, Edinburgh EH9 3FD (United Kingdom); Bull, C. L. [ISIS, Rutherford Appleton Laboratory, Oxford Harwell, Didcot OX11 0QX (United Kingdom); Klotz, S. [IMPMC, CNRS UMR 7590, Université P and M Curie, 4 Place Jussieu, 75252 Paris (France)

2015-03-28

Urea, like many network forming compounds, has long been known to form inclusion (guest-host) compounds. Unlike other network formers like water, urea is not known to form such inclusion compounds with simple molecules like hydrogen. Such compounds if they existed would be of interest both for the fundamental insight they provide into molecular bonding and as potential gas storage systems. Urea has been proposed as a potential hydrogen storage material [T. A. Strobel et al., Chem. Phys. Lett. 478, 97 (2009)]. Here, we report the results of high-pressure neutron diffraction studies of urea and D{sub 2} mixtures that indicate no inclusion compound forms up to 3.7 GPa.

A Pan-GTPase Inhibitor as a Molecular Probe.

Directory of Open Access Journals (Sweden)

Lin Hong

Full Text Available Overactive GTPases have often been linked to human diseases. The available inhibitors are limited and have not progressed far in clinical trials. We report here a first-in-class small molecule pan-GTPase inhibitor discovered from a high throughput screening campaign. The compound CID1067700 inhibits multiple GTPases in biochemical, cellular protein and protein interaction, as well as cellular functional assays. In the biochemical and protein interaction assays, representative GTPases from Rho, Ras, and Rab, the three most generic subfamilies of the GTPases, were probed, while in the functional assays, physiological processes regulated by each of the three subfamilies of the GTPases were examined. The chemical functionalities essential for the activity of the compound were identified through structural derivatization. The compound is validated as a useful molecular probe upon which GTPase-targeting inhibitors with drug potentials might be developed.

Magnetostriction of some cubic rare earth-Co2 compounds in high magnetic fields

International Nuclear Information System (INIS)

Moral, A. del; Melville, D.

1975-01-01

Magnetostriction measurements have been carried out in the cubic Laves phase compounds DyCo 2 , HoCo 2 and ErCo 2 from 10 K to well above their respective Neel temperatures Tsub(N). Pulsed magnetic fields up to 15 T (150kOe) were applied. The observed magnetostrictions are very large (approximately 10 -3 ) being similar to those found in the RFe 2 compounds. The measurements confirm the extremely high anisotropy of these materials. At the highest fields the polycrystalline samples are still undergoing rotational magnetization processes. The expected values of the saturation magnetostriction at O K are similar in sign and magnitude to those found in the corresponding rare earth metals. This fact and the scaling of magnetostriction with rare earth sublattice magnetization indicates that the rare earth ion is the main source of the magnetostriction. The metamagnetic transition above Tsub(N) has been studied, the relation between critical field and temperature being nonlinear for HoCo 2 and ErCo 2 . The compounds are highly anisotropic above Tsub(N) and all the features indicate that the field-induced phases are likely to be ferrimagnetic. (author)

Catalytic Reforming of Lignin-Derived Bio-Oil Over a Nanoporous Molecular Sieve Silicoaluminophosphate-11.

Science.gov (United States)

Park, Y K; Kang, Hyeon Koo; Jang, Hansaem; Suh, Dong Jin; Park, Sung Hoon

2016-05-01

Catalytic pyrolysis of lignin, a major constituent of biomass, was performed. A nanoporous molecular sieve silicoaluminophosphate-11 (SAPO-11) was selected as catalyst. Thermogravimetric analysis showed that 500 degrees C was the optimal pyrolysis temperature. Pyrolyzer-gas chromatography/mass spectroscopy was used to investigate the pyrolysis product distribution. Production of phenolics, the dominant product from the pyrolysis of lignin, was promoted by the increase in the catalyst dose. In particular, low-molecular-mass phenolics were produced more over SAPO-11, while high-molecular-mass phenolics and double-bond-containing phenolics were produced less. The fraction of aromatic compounds, including benzene, toluene, xylene, and ethylbenzene, was also increased by catalytic reforming. The catalytic effects were more pronounced when the catalyst/biomass ratio was increased. The enhanced production of aromatic compounds by an acidic catalyst obtained in this study is in good agreement with the results of previous studies.

Removal of the metal ions from aqueous solutions by nanoscaled low molecular pectin isolated from seagrass Phyllospadix iwatensis

International Nuclear Information System (INIS)

Khozhaenko, Elena; Kovalev, Valeri; Podkorytova, Elena; Khotimchenko, Maksim

2016-01-01

Pectins from sea grasses are considered as promising substances with pronounced metal-binding activity. Due to the high molecular weight and heterogeneous structure, the use of pectins for removal of metal ions is difficult. Technology of directed pectin degradation was developed and homogenous degraded nanoscaled pectin polymers were synthesized. Experimental samples of degraded pectin isolated from Phyllospadix iwatensis were tested for their metal binding activity in comparison with native pectin from this seagrass and commercial citrus pectin. The metal uptake of all pectin compounds was highest within the pH range from 4.0 to 6.0. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants. Results showed that depolymerized pectin exerts highest lead and cadmium binding activity with pronounced affinity. All pectin compounds were suggested to be favorable sorbents. Therefore, it can be concluded that degraded pectin is a prospective material for creation of metal-removing water treatment systems. - Highlights: • Low molecular nanoscaled pectin was obtained using original hydrolysis method • Metal binding activity of pectin compounds was studied in a batch sorption system • Pectins exert highest metal binding activity at pH 6.0 • Metal binding isotherms of all pectins are best described by the Langmuir equation • Low molecular pectin from seagrasses is more effective than high-molecular pectins

Removal of the metal ions from aqueous solutions by nanoscaled low molecular pectin isolated from seagrass Phyllospadix iwatensis

Energy Technology Data Exchange (ETDEWEB)

Khozhaenko, Elena [Far Eastern Federal University, School of Biomedicine, 8, Sukhanova str., Vladivostok 690091 (Russian Federation); A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation); Kovalev, Valeri; Podkorytova, Elena [A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation); Khotimchenko, Maksim, E-mail: maxkhot@yandex.ru [Far Eastern Federal University, School of Biomedicine, 8, Sukhanova str., Vladivostok 690091 (Russian Federation); A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation)

2016-09-15

Pectins from sea grasses are considered as promising substances with pronounced metal-binding activity. Due to the high molecular weight and heterogeneous structure, the use of pectins for removal of metal ions is difficult. Technology of directed pectin degradation was developed and homogenous degraded nanoscaled pectin polymers were synthesized. Experimental samples of degraded pectin isolated from Phyllospadix iwatensis were tested for their metal binding activity in comparison with native pectin from this seagrass and commercial citrus pectin. The metal uptake of all pectin compounds was highest within the pH range from 4.0 to 6.0. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants. Results showed that depolymerized pectin exerts highest lead and cadmium binding activity with pronounced affinity. All pectin compounds were suggested to be favorable sorbents. Therefore, it can be concluded that degraded pectin is a prospective material for creation of metal-removing water treatment systems. - Highlights: • Low molecular nanoscaled pectin was obtained using original hydrolysis method • Metal binding activity of pectin compounds was studied in a batch sorption system • Pectins exert highest metal binding activity at pH 6.0 • Metal binding isotherms of all pectins are best described by the Langmuir equation • Low molecular pectin from seagrasses is more effective than high-molecular pectins.

Molecular events leading to HPV-induced high grade neoplasia

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Saskia M. Wilting

2016-12-01

Full Text Available Cervical cancer is initiated by high-risk types of the human papillomavirus (hrHPV and develops via precursor stages, called cervical intraepithelial neoplasia (CIN. High-grade CIN lesions are considered true precancerous lesions when the viral oncogenes E6 and E7 are aberrantly expressed in the dividing cells. This results in abolishment of normal cell cycle control via p53 and pRb degradation. However, it has become clear that these viral oncogenes possess additional oncogenic properties, including interference with the DNA methylation machinery and mitotic checkpoints. Identification of the resulting molecular events leading to high-grade neoplasia will 1 increase our understanding of cervical carcinogenesis, 2 yield biomarkers for early diagnosis, and 3 identify therapeutic targets for HPV-induced (pre cancerous lesions.This review will briefly summarise current advances in our understanding of the molecular alterations in the host cell genome that occur during HPV-induced carcinogenesis.

Optimization of on-line hydrogen stable isotope ratio measurements of halogen- and sulfur-bearing organic compounds using elemental analyzer–chromium/high-temperature conversion isotope ratio mass spectrometry (EA-Cr/HTC-IRMS)

Science.gov (United States)

Gehre, Matthias; Renpenning, Julian; Geilmann, Heike; Qi, Haiping; Coplen, Tyler B.; Kümmel, Steffen; Ivdra, Natalija; Brand, Willi A.; Schimmelmann, Arndt

2017-01-01

Rationale: Accurate hydrogen isotopic analysis of halogen- and sulfur-bearing organics has not been possible with traditional high-temperature conversion (HTC) because the formation of hydrogen-bearing reaction products other than molecular hydrogen (H2) is responsible for non-quantitative H2 yields and possible hydrogen isotopic fractionation. Our previously introduced, new chromium-based EA-Cr/HTC-IRMS (Elemental Analyzer–Chromium/High-Temperature Conversion Isotope Ratio Mass Spectrometry) technique focused primarily on nitrogen-bearing compounds. Several technical and analytical issues concerning halogen- and sulfur-bearing samples, however, remained unresolved and required further refinement of the reactor systems.

Simulations of charge transport in organic compounds

Energy Technology Data Exchange (ETDEWEB)

Vehoff, Thorsten

2010-05-05

We study the charge transport properties of organic liquid crystals, i.e. hexabenzocoronene and carbazole macrocycle, and single crystals, i.e. rubrene, indolocarbazole and benzothiophene derivatives (BTBT, BBBT). The aim is to find structure-property relationships linking the chemical structure as well as the morphology with the bulk charge carrier mobility of the compounds. To this end, molecular dynamics (MD) simulations are performed yielding realistic equilibrated morphologies. Partial charges and molecular orbitals are calculated based on single molecules in vacuum using quantum chemical methods. The molecular orbitals are then mapped onto the molecular positions and orientations, which allows calculation of the transfer integrals between nearest neighbors using the molecular orbital overlap method. Thus we obtain realistic transfer integral distributions and their autocorrelations. In case of organic crystals the differences between two descriptions of charge transport, namely semi-classical dynamics (SCD) in the small polaron limit and kinetic Monte Carlo (KMC) based on Marcus rates, are studied. The liquid crystals are investigated solely in the hopping limit. To simulate the charge dynamics using KMC, the centers of mass of the molecules are mapped onto lattice sites and the transfer integrals are used to compute the hopping rates. In the small polaron limit, where the electronic wave function is spread over a limited number of neighboring molecules, the Schroedinger equation is solved numerically using a semi-classical approach. The carbazole macrocycles form columnar structures arranged on a hexagonal lattice with side chains facing inwards, so columns can closely approach each other allowing inter-columnar and thus three-dimensional transport. We are able to show that, on the time-scales of charge transport, static disorder due to slow side chain motions is the main factor determining the mobility. The high mobility of rubrene is explained by two main

Molecular modeling reveals the novel inhibition mechanism and binding mode of three natural compounds to staphylococcal α-hemolysin.

Directory of Open Access Journals (Sweden)

Jiazhang Qiu

Full Text Available α-Hemolysin (α-HL is a self-assembling, channel-forming toxin that is produced as a soluble monomer by Staphylococcus aureus strains. Until now, α-HL has been a significant virulence target for the treatment of S. aureus infection. In our previous report, we demonstrated that some natural compounds could bind to α-HL. Due to the binding of those compounds, the conformational transition of α-HL from the monomer to the oligomer was blocked, which resulted in inhibition of the hemolytic activity of α-HL. However, these results have not indicated how the binding of the α-HL inhibitors influence the conformational transition of the whole protein during the oligomerization process. In this study, we found that three natural compounds, Oroxylin A 7-O-glucuronide (OLG, Oroxin A (ORA, and Oroxin B (ORB, when inhibiting the hemolytic activity of α-HL, could bind to the "stem" region of α-HL. This was completed using conventional Molecular Dynamics (MD simulations. By interacting with the novel binding sites of α-HL, the ligands could form strong interactions with both sides of the binding cavity. The results of the principal component analysis (PCA indicated that because of the inhibitors that bind to the "stem" region of α-HL, the conformational transition of α-HL from the monomer to the oligomer was restricted. This caused the inhibition of the hemolytic activity of α-HL. This novel inhibition mechanism has been confirmed by both the steered MD simulations and the experimental data obtained from a deoxycholate-induced oligomerization assay. This study can facilitate the design of new antibacterial drugs against S. aureus.

Assessment of mural invasion depth of gastric carcinoma with high-resolution compound sonographic imaging in vitro

Energy Technology Data Exchange (ETDEWEB)

Park, Seong Hoon; Kim, Eun A; Yoon, Kwon Ha; Yun, Ki Jung; Kim, Jeong Ho; Won, Jong Jin [Wonkwang University School of Medicine, Iksan (Korea, Republic of)

2002-11-01

To evaluate whether the accuracy of invasion depth assessment in gastric carcinoma in vitro can be improved with high-resolution spatial compound sonographic imaging. In sixteen fresh gastric specimens obtained from patients with preoperatively biopsy proven gastric carcinoma, normal and lesional areas were scanned using conventional and compound imaging technique with a 15-MHz linear transducer. Two radiologists independently compared the sharpness and the contrast of images obtained with two different modes and determined the layers invaded by cancer with consensus. The invasion depths by images were compared with histopathologic results. The sharpness and the contrast in normal and lesional areas were significantly higher in compound imaging (p<0.01) than those in conventional imaging and interobserver agreement was over moderate, with k-value of 0.41 to 0.86. But the accuracy in invasion depth assessment was 68.8% (11/16) on conventional imaging and 75% (12/16) on compound imaging and non different significantly between two modes (p>0305). High-resolution spatial compound sonographic imaging has improved image quality, compared with conventional imaging, but the accuracy of invasion depth assessment in gastric carcinoma was not significantly different.

Endocannabinoids, Related Compounds and Their Metabolic Routes

Directory of Open Access Journals (Sweden)

Filomena Fezza

2014-10-01

Full Text Available Endocannabinoids are lipid mediators able to bind to and activate cannabinoid receptors, the primary molecular targets responsible for the pharmacological effects of the Δ9-tetrahydrocannabinol. These bioactive lipids belong mainly to two classes of compounds: N-acylethanolamines and acylesters, being N-arachidonoylethanolamine (AEA and 2-arachidonoylglycerol (2-AG, respectively, their main representatives. During the last twenty years, an ever growing number of fatty acid derivatives (endocannabinoids and endocannabinoid-like compounds have been discovered and their activities biological is the subject of intense investigations. Here, the most recent advances, from a therapeutic point of view, on endocannabinoids, related compounds, and their metabolic routes will be reviewed.

High Molecular Weight Polymers in the New Chemicals Program

Science.gov (United States)

There are three categories or types of High Molecular Weight (HMW, 10,000 daltons) polymers typically reviewed by the New Chemicals Program: Soluble, insoluble, and water absorbing. Each of the three types are treated differently.

Wall-slip of highly filled powder injection molding compounds: Effect of flow channel geometry and roughness

Science.gov (United States)

Hausnerova, Berenika; Sanetrnik, Daniel; Paravanova, Gordana

2014-05-01

The paper deals with the rheological behavior of highly filled compounds proceeded via powder injection molding (PIM) and applied in many sectors of industry (automotive, medicine, electronic or military). Online rheometer equipped with slit dies varying in surface roughness and dimensions was applied to investigate the wall-slip as a rheological phenomenon, which can be considered as a parameter indicating the separation of compound components (polymer binder and metallic powder) during high shear rates when injection molded.

High field magnetization process of (Sm, Nd)2Fe17Ny compounds

International Nuclear Information System (INIS)

Yu, M.J.; Tang, N.; Liu, Y.L.; Tegus, O.; Lu, Y.; Kuang, J.P.; Yang, F.M.; Li, X.; Zhou, G.F.; Boer, F.R. de

1992-01-01

The crystal structure and high-field magnetization process of (Sm 1-x Nd x ) 2 Fe 17 N y compounds (x = 0.0, 0.1, ..., 1.0, 2 1-x Nd x ) 2 Fe 17 N y compounds were found to crystallize in the rhombohedral Th 2 Zn 17 structure. As x increases, the Curie temperature decreases. The anisotropy fields and easy magnetization direction were investigated from 1.5 K to room temperature by means of high-field magnetization measurements and AC-susceptibility measurements, combined with X-ray diffraction on random and magnetically aligned powder samples. The anisotropy field decreases with increasing x and approaches a minimum value at about x = 0.6, then increases again. A tentative spin phase diagram for the (Sm 1-x Nd x ) 2 Fe 17 N y series is presented. At room temperature, the easy magnetization direction remains along the c-axis up to x = 0.6. (orig.)

Multiple-heteroatom-containing sulfur compounds in a high sulfur coal

International Nuclear Information System (INIS)

Winans, R.E.; Neill, P.H.

1990-01-01

Flash vacuum pyrolysis of a high sulfur coal has been combined with high resolution mass spectrometry yielding information on aromatic sulfur compounds containing an additional heteroatom. Sulfur emission from coal utilization is a critical problem and in order to devise efficient methods for removing organic sulfur, it is important to know what types of molecules contain sulfur. A high sulfur Illinois No. 6 bituminous coal (Argonne Premium Coal Sample No. 3) was pyrolyzed on a platinum grid using a quartz probe inserted into a modified all glass heated inlet system and the products characterized by high resolution mass spectrometry (HRMS). A significant number of products were observed which contained both sulfur and an additional heteroatom. In some cases two additional heteroatoms were observed. These results are compared to those found in coal extracts and liquefaction products

Anaerobic catabolism of aromatic compounds: a genetic and genomic view.

Science.gov (United States)

Carmona, Manuel; Zamarro, María Teresa; Blázquez, Blas; Durante-Rodríguez, Gonzalo; Juárez, Javier F; Valderrama, J Andrés; Barragán, María J L; García, José Luis; Díaz, Eduardo

2009-03-01

Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach.

Facile Syntheses and Molecular-Docking of Novel Substituted 3,4-Dimethyl-1H-pyrrole-2-carboxamide/carbohydrazide Analogues with Antimicrobial and Antifungal Properties

Directory of Open Access Journals (Sweden)

Jitendra D. Bhosale

2018-04-01

Full Text Available The article describes the use of facile one-pot, high-yielding reactions to synthesize substituted 3,4-dimethyl-1H-pyrrole-2-carboxamides 3a–m and carbohydrazide analogues 5a–l as potential antifungal and antimicrobial agents. The structural identity and purity of the synthesized compounds were assigned based on appropriate spectroscopic techniques. Synthesized compounds were assessed in vitro for antifungal and antibacterial activity. The compounds 5h, 5i and 5j were found to be the most potent against Aspergillus fumigatus, with MIC values of 0.039 mg/mL. The compound 5f bearing a 2, 6-dichloro group on the phenyl ring was found to be the most active broad spectrum antibacterial agent with a MIC value of 0.039 mg/mL. The mode of action of the most promising antifungal compounds (one representative from each series; 3j and 5h was established by their molecular docking with the active site of sterol 14α-demethylase. Molecular docking studies revealed a highly spontaneous binding ability of the tested compounds in the access channel away from catalytic heme iron of the enzyme, which suggested that the tested compounds inhibit this enzyme and would avoid heme iron-related deleterious side effects observed with many existing antifungal compounds.

Large reversible magnetostrictive effect of MnCoSi-based compounds prepared by high-magnetic-field solidification

Science.gov (United States)

Hu, Q. B.; Hu, Y.; Zhang, S.; Tang, W.; He, X. J.; Li, Z.; Cao, Q. Q.; Wang, D. H.; Du, Y. W.

2018-01-01

The MnCoSi compound is a potential magnetostriction material since the magnetic field can drive a metamagnetic transition from an antiferromagnetic phase to a high magnetization phase in it, which accompanies a large lattice distortion. However, a large driving magnetic field, magnetic hysteresis, and poor mechanical properties seriously hinder its application for magnetostriction. By substituting Fe for Mn and introducing vacancies of the Mn element, textured and dense Mn0.97Fe0.03CoSi and Mn0.88CoSi compounds are prepared through a high-magnetic-field solidification approach. As a result, large room-temperature and reversible magnetostriction effects are observed in these compounds at a low magnetic field. The origin of this large magnetostriction effect and potential applications are discussed.

A small-molecule compound inhibits a collagen-specific molecular chaperone and could represent a potential remedy for fibrosis.

Science.gov (United States)

Ito, Shinya; Ogawa, Koji; Takeuchi, Koh; Takagi, Motoki; Yoshida, Masahito; Hirokawa, Takatsugu; Hirayama, Shoshiro; Shin-Ya, Kazuo; Shimada, Ichio; Doi, Takayuki; Goshima, Naoki; Natsume, Tohru; Nagata, Kazuhiro

2017-12-08

Fibrosis can disrupt tissue structure and integrity and impair organ function. Fibrosis is characterized by abnormal collagen accumulation in the extracellular matrix. Pharmacological inhibition of collagen secretion therefore represents a promising strategy for the management of fibrotic disorders, such as liver and lung fibrosis. Hsp47 is an endoplasmic reticulum (ER)-resident collagen-specific molecular chaperone essential for correct folding of procollagen in the ER. Genetic deletion of Hsp47 or inhibition of its interaction with procollagen interferes with procollagen triple helix production, which vastly reduces procollagen secretion from fibroblasts. Thus, Hsp47 could be a potential and promising target for the management of fibrosis. In this study, we screened small-molecule compounds that inhibit the interaction of Hsp47 with collagen from chemical libraries using surface plasmon resonance (BIAcore), and we found a molecule AK778 and its cleavage product Col003 competitively inhibited the interaction and caused the inhibition of collagen secretion by destabilizing the collagen triple helix. Structural information obtained with NMR analysis revealed that Col003 competitively binds to the collagen-binding site on Hsp47. We propose that these structural insights could provide a basis for designing more effective therapeutic drugs for managing fibrosis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

STATUS REPORT ON DEVELOPMENT OF A HIGH-SPEED HIGH-INTENSITY MOLECULAR BEAM

Energy Technology Data Exchange (ETDEWEB)

Knuth, Eldon L.

1963-07-15

Status of a high-speed high-intensity molecular beam under development is described. Bases for designs of the several components are presented. Using an arc-heated source and a hypersonic jet, molecular energies exceeding 1 ev and beam intensities of the order of 10/sup 16/ molecules/ cm/sup 2/ sec are anticipated. A two-disk beam chopper and speed selector provides a means for analyzing the speed distribution in the generated beam, for chopping the beam into bursts of nearly monoenergetic molecules suitable for scattering studies using the time-of-flight technique, and for modulating the beam in order to facilitate detection. A through-flow ionization detector possesses the versatility required for scattering studies using the time-of-flight technique. A sorption pump and a turbo pump serve as central components of alternative pumping systems for the collimating chamber. Using the arc-heated source, the converging nozzle, the conduction-radiation-cooled skimmer, the turbo pump (turning at 3400 rpm), the chopperselector (acting only as a chopper), and the detector, an arc-heated beam is generated and detected. (auth)

Specific Electrostatic Molecular Recognition in Water

DEFF Research Database (Denmark)

Li, Ming; Hoeck, Casper; Schoffelen, Sanne

2016-01-01

The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure-biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide......-bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen-bond complementarities. From MD...

The electrochemical reduction processes of solid compounds in high temperature molten salts.

Science.gov (United States)

Xiao, Wei; Wang, Dihua

2014-05-21

Solid electrode processes fall in the central focus of electrochemistry due to their broad-based applications in electrochemical energy storage/conversion devices, sensors and electrochemical preparation. The electrolytic production of metals, alloys, semiconductors and oxides via the electrochemical reduction of solid compounds (especially solid oxides) in high temperature molten salts has been well demonstrated to be an effective and environmentally friendly process for refractory metal extraction, functional materials preparation as well as spent fuel reprocessing. The (electro)chemical reduction of solid compounds under cathodic polarizations generally accompanies a variety of changes at the cathode/melt electrochemical interface which result in diverse electrolytic products with different compositions, morphologies and microstructures. This report summarizes various (electro)chemical reactions taking place at the compound cathode/melt interface during the electrochemical reduction of solid compounds in molten salts, which mainly include: (1) the direct electro-deoxidation of solid oxides; (2) the deposition of the active metal together with the electrochemical reduction of solid oxides; (3) the electro-inclusion of cations from molten salts; (4) the dissolution-electrodeposition process, and (5) the electron hopping process and carbon deposition with the utilization of carbon-based anodes. The implications of the forenamed cathodic reactions on the energy efficiency, chemical compositions and microstructures of the electrolytic products are also discussed. We hope that a comprehensive understanding of the cathodic processes during the electrochemical reduction of solid compounds in molten salts could form a basis for developing a clean, energy efficient and affordable production process for advanced/engineering materials.

Molecular catalytic coal liquid conversion

Energy Technology Data Exchange (ETDEWEB)

Stock, L.M.; Yang, Shiyong [Univ. of Chicago, IL (United States)

1995-12-31

This research, which is relevant to the development of new catalytic systems for the improvement of the quality of coal liquids by the addition of dihydrogen, is divided into two tasks. Task 1 centers on the activation of dihydrogen by molecular basic reagents such as hydroxide ion to convert it into a reactive adduct (OH{center_dot}H{sub 2}){sup {minus}} that can reduce organic molecules. Such species should be robust withstanding severe conditions and chemical poisons. Task 2 is focused on an entirely different approach that exploits molecular catalysts, derived from organometallic compounds that are capable of reducing monocyclic aromatic compounds under very mild conditions. Accomplishments and conclusions are discussed.

Tunable catalytic properties of bi-functional mixed oxides in ethanol conversion to high value compounds

Energy Technology Data Exchange (ETDEWEB)

Ramasamy, Karthikeyan K.; Gray, Michel J.; Job, Heather M.; Smith, Colin D.; Wang, Yong

2016-04-10

tA highly versatile ethanol conversion process to selectively generate high value compounds is pre-sented here. By changing the reaction temperature, ethanol can be selectively converted to >C2alcohols/oxygenates or phenolic compounds over hydrotalcite derived bi-functional MgO–Al2O3cata-lyst via complex cascade mechanism. Reaction temperature plays a role in whether aldol condensationor the acetone formation is the path taken in changing the product composition. This article containsthe catalytic activity comparison between the mono-functional and physical mixture counterpart to thehydrotalcite derived mixed oxides and the detailed discussion on the reaction mechanisms.

High-performance liquid chromatography of quinoidal imminium compounds derived from triphenylmethanes

Science.gov (United States)

Abidi, S.L.

1983-01-01

A series of eleven p-aminotriphenylmethane dyes have been studied by high-performance liquid chromatography (HPLC). The combined use of HPLC and spectrophotometry permits specific detection of these compounds in the visible range around 600 nm. As the high affinity of the imminium cations for the active sites of the hydrocarbonaceous stationary phase has presented difficulties for reversed-phase HPLC with pure solvents, organic electrolytes were added to the mobile phase to facilitate the elution of the components with improved selectivity, sensitivity (minimum detection limit, 0.1 μg/ml), and peak symmetry. The effects of chromatographic variables on the component retentivity were investigated. Retention times of the dye analytes decreased with increasing concentration of the added ionic reagent and with decreasing number of the hydrophobic alkyl substituents on the nitrogen atom. The influence of pH on the retention parameters appears to parallel that observed previously for cationic quaternary ammonium compounds. Among the acidic reagents employed, naphthalenesulfonic acid yielded the most satisfactory results. The use of binary electrolyte systems invariably improved the chromatographic behavior of the imminium solutes analyzed. Results obtained with two different octadecylsilica columns have been compared.

The relative importance of competing pathways for the formation of high-molecular-weight peroxides in the ozonolysis of organic aerosol particles

Directory of Open Access Journals (Sweden)

M. Mochida

2006-01-01

Full Text Available High-molecular-weight (HMW organic compounds are an important component of atmospheric particles, although their origins, possibly including in situ formation pathways, remain incompletely understood. This study investigates the formation of HMW organic peroxides through reactions involving stabilized Criegee intermediates (SCI's. The model system is methyl oleate (MO mixed with dioctyl adipate (DOA and myristic acid (MA in submicron aerosol particles, and Criegee intermediates are formed by the ozonolysis of the double bond in methyl oleate. An aerosol flow tube coupled to a quadrupole aerosol mass spectrometer (AMS is employed to determine the relative importance of different HMW organic peroxides following the ozonolysis of different mixing mole fractions of MO in DOA and MA. Possible peroxide products include secondary ozonides (SOZ's, α-acyloxyalkyl hydroperoxides and α-acyloxyalkyl alkyl peroxides (αAAHP-type compounds, diperoxides, and monoperoxide oligomers. Of these, the AMS data identify two SOZ's as major HMW products in the ozonolysis of pure methyl oleate as well as in an inert matrix of DOA to as low as 0.04 mole fraction MO. In comparison, in mixed particles of MO and MA, αAAHP-type compounds form in high yields for MO mole fractions of 0.5 or less, suggesting that SCI's efficiently attack the carboxylic acid group of myristic acid. The reactions of SCI's with carboxylic acid groups to form αAAHP-type compounds therefore compete with those of SCI's with aldehydes to form SOZ's, provided that both types of functionalities are present at significant concentrations. The results therefore suggest that SCI's in atmospheric particles contribute to the transformation of carboxylic acids and other protic groups into HMW organic peroxides.

High-temperature thermopower of some REIn3 compounds

International Nuclear Information System (INIS)

Kletowski, Z.; Resel, R.

1995-01-01

The temperature dependences of the thermopower of six REIn 3 compounds (RE=La, Pr, Gd, Dy, Er and Lu) were measured in the temperature range up to 1000 K. The observed changes in the slopes of the temperature versus thermopower curves for all the investigated compounds are interpreted as originating from a special shape of the density of states (DOS) near the Fermi energy, E F . ((orig.))

Mechanistic and quantitative insight into cell surface targeted molecular imaging agent design.

Science.gov (United States)

Zhang, Liang; Bhatnagar, Sumit; Deschenes, Emily; Thurber, Greg M

2016-05-05

Molecular imaging agent design involves simultaneously optimizing multiple probe properties. While several desired characteristics are straightforward, including high affinity and low non-specific background signal, in practice there are quantitative trade-offs between these properties. These include plasma clearance, where fast clearance lowers background signal but can reduce target uptake, and binding, where high affinity compounds sometimes suffer from lower stability or increased non-specific interactions. Further complicating probe development, many of the optimal parameters vary depending on both target tissue and imaging agent properties, making empirical approaches or previous experience difficult to translate. Here, we focus on low molecular weight compounds targeting extracellular receptors, which have some of the highest contrast values for imaging agents. We use a mechanistic approach to provide a quantitative framework for weighing trade-offs between molecules. Our results show that specific target uptake is well-described by quantitative simulations for a variety of targeting agents, whereas non-specific background signal is more difficult to predict. Two in vitro experimental methods for estimating background signal in vivo are compared - non-specific cellular uptake and plasma protein binding. Together, these data provide a quantitative method to guide probe design and focus animal work for more cost-effective and time-efficient development of molecular imaging agents.

Electronic structures of melatonin and related compounds studied by photoelectron spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Kubota, Mari. E-mail: marik@hc.cc.keio.ac.jp; Kobayashi, Tsunetoshi

2003-02-01

Melatonin is a hormone structurally regarded as being composed of a 5-methoxyindole group and an N-ethylacetamide group; its various physiological activities have attracted a great deal of attention recently. The gas phase He(I) photoelectron spectra of melatonin (M) and its related compounds including N-acetylserotonin have been studied with the aid of molecular orbital calculations. The first photoelectron spectral band group of compound M is ascribed to ionizations from the two {pi} orbitals localized on the methoxyindole group. The second band group is quite complicated and is regarded as being composed of several bands. The lower energy part of the second band group is ascribed to the three orbitals relevant to the third highest occupied {pi} orbital of 5-methoxyindole and the highest occupied {pi} and the n{sub C=0} orbitals of N-ethylacetamide. The interactions among the three orbitals have been found to operate on the basis of the molecular orbital calculations; these interactions depend strongly on the conformations. The high energy end of the second band group is relevant to the {pi} orbital mainly localized on the 5-methoxyindole group and is ascribed to the fourth highest occupied {pi} orbital of 5-methoxyindole.

Electronic structures of melatonin and related compounds studied by photoelectron spectroscopy

International Nuclear Information System (INIS)

Kubota, Mari.; Kobayashi, Tsunetoshi

2003-01-01

Melatonin is a hormone structurally regarded as being composed of a 5-methoxyindole group and an N-ethylacetamide group; its various physiological activities have attracted a great deal of attention recently. The gas phase He(I) photoelectron spectra of melatonin (M) and its related compounds including N-acetylserotonin have been studied with the aid of molecular orbital calculations. The first photoelectron spectral band group of compound M is ascribed to ionizations from the two π orbitals localized on the methoxyindole group. The second band group is quite complicated and is regarded as being composed of several bands. The lower energy part of the second band group is ascribed to the three orbitals relevant to the third highest occupied π orbital of 5-methoxyindole and the highest occupied π and the n C=0 orbitals of N-ethylacetamide. The interactions among the three orbitals have been found to operate on the basis of the molecular orbital calculations; these interactions depend strongly on the conformations. The high energy end of the second band group is relevant to the π orbital mainly localized on the 5-methoxyindole group and is ascribed to the fourth highest occupied π orbital of 5-methoxyindole

Nasal Delivery of High Molecular Weight Drugs

Directory of Open Access Journals (Sweden)

Erdal Cevher

2009-09-01

Full Text Available Nasal drug delivery may be used for either local or systemic effects. Low molecular weight drugs with are rapidly absorbed through nasal mucosa. The main reasons for this are the high permeability, fairly wide absorption area, porous and thin endothelial basement membrane of the nasal epithelium. Despite the many advantages of the nasal route, limitations such as the high molecular weight (HMW of drugs may impede drug absorption through the nasal mucosa. Recent studies have focused particularly on the nasal application of HMW therapeutic agents such as peptide-protein drugs and vaccines intended for systemic effects. Due to their hydrophilic structure, the nasal bioavailability of peptide and protein drugs is normally less than 1%. Besides their weak mucosal membrane permeability and enzymatic degradation in nasal mucosa, these drugs are rapidly cleared from the nasal cavity after administration because of mucociliary clearance. There are many approaches for increasing the residence time of drug formulations in the nasal cavity resulting in enhanced drug absorption. In this review article, nasal route and transport mechanisms across the nasal mucosa will be briefly presented. In the second part, current studies regarding the nasal application of macromolecular drugs and vaccines with nanoand micro-particulate carrier systems will be summarised.

Radiocarbon content of synthetic and natural semi-volatile halogenated organic compounds

International Nuclear Information System (INIS)

Reddy, C.M.; Xu Li; Eglinton, T.I.; Boon, J.P.; Faulkner, D.J.

2002-01-01

New developments in molecular-level 14 C analysis techniques enable clues about natural versus commercial synthesis of trace organic contaminants. - Some halogenated organic compounds, such as polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs) and polybrominated diphenyl ethers (PBDEs), have been suggested to have natural sources but separating these compounds from their commercially synthesized counterparts is difficult. Molecular-level 14 C analysis may be beneficial since most synthetic compounds are manufactured from petrochemicals ( 14 C-free) and natural compounds should have 'modern' or 'contemporary' 14 C levels. As a baseline study, we measured, for the first time, the 14 C abundance in commercial PCB and PBDE mixtures, a number of organochlorine pesticides, as well as one natural product 2-(3', 5'-dibromo-2'-methoxyphenoxy)-3,5-dibromoanisole. The latter compound was isolated from a marine sponge and is similar in structure to a PBDE. All of the synthetic compounds were 14 C-free except for the pesticide toxaphene, which had a modern 14 C abundance, as did the brominated natural compound. The result for toxaphene was not surprising since it was commercially synthesized by the chlorination of camphene derived from pine trees. These results suggest that measuring the 14 C content of halogenated organic compounds may be quite useful in establishing whether organic compounds encountered in the environment have natural or synthetic origins (or both) provided that any synthetic counterparts derive from petrochemical feedstock

Modification of -Adenosyl--Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation

Directory of Open Access Journals (Sweden)

Usman Sumo Friend Tambunan

2017-04-01

Full Text Available Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world’s population in tropical and subtropical countries. Nonstructural protein 5 (NS5 methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S -adenosyl- l -methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2′OH, resulting in S -adenosyl- l -homocysteine (SAH. The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity test. The 2 simulations were performed using Molecular Operating Environment (MOE 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356 based on ΔG binding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.

Organic compounds as corrosion inhibitors for mild steel in acidic media: correlation between inhibition efficiency and chemical structure

Energy Technology Data Exchange (ETDEWEB)

Elias, Elizandra C.S.; Chrisman, Erika C.A.N. [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Escola de Quimica

2009-12-19

The use of inhibitors for mild steels corrosion control which are in contact with aggressive environment is an accepted practice in acid treatment of oil-wells. Organic compounds have been studied to evaluate their corrosion inhibition potential. Film-forming corrosion inhibitors, commonly used to protect oil-field equipment, can be absorbed on the steel surface to give structurally ordered layers. Therefore, the electrons should act as an important role for this adsorption. Studies reveal that organic compounds show significant inhibition efficiency. For this purpose, their molecules should contain N, O and S heteroatoms in various functional groups, long hydrocarbon linear or branched radical and anion and cation active components. However, most of these compounds are not only expensive but also toxic to living beings. According to the 'Green Chemistry' rules, corrosion inhibitors based on organic compounds should be cheap, with low toxicity and have high inhibition efficiency. In this study, the effects of some organic compounds with different groups such as amide, ether, phenyldiamine, anime and aminophenol on the corrosion behavior of mild steel in acidic media have been investigated. The experimental data were obtained by gravimetric measurements. The results show that these compounds reveal a promising corrosion inhibition where phenyldiamine is the most efficient. The effect of molecular structure on the corrosion inhibition efficiency was investigated by semi-empirical quantum chemical calculations. The electronic properties such as highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO) energy levels, and LUMO-HOMO energy gap orbital density were calculated. The relations between the inhibition efficiency and some quantum parameters are discussed and correlations are proposed. The highest values for the HOMO densities were found in the vicinity nitrogen atom, indicating that it is the most probable adsorption center

Discovery of novel inhibitors of Mycobacterium tuberculosis MurG: homology modelling, structure based pharmacophore, molecular docking, and molecular dynamics simulations.

Science.gov (United States)

Saxena, Shalini; Abdullah, Maaged; Sriram, Dharmarajan; Guruprasad, Lalitha

2017-10-17

MurG (Rv2153c) is a key player in the biosynthesis of the peptidoglycan layer in Mycobacterium tuberculosis (Mtb). This work is an attempt to highlight the structural and functional relationship of Mtb MurG, the three-dimensional (3D) structure of protein was constructed by homology modelling using Discovery Studio 3.5 software. The quality and consistency of generated model was assessed by PROCHECK, ProSA and ERRAT. Later, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with substrate Uridine-diphosphate-N-acetylglucosamine (UD1) facilitated us to employ structure-based virtual screening approach to obtain new hits from Asinex database using energy-optimized pharmacophore modelling (e-pharmacophore). The pharmacophore model was validated using enrichment calculations, and finally, validated model was employed for high-throughput virtual screening and molecular docking to identify novel Mtb MurG inhibitors. This study led to the identification of 10 potential compounds with good fitness, docking score, which make important interactions with the protein active site. The 25 ns MD simulations of three potential lead compounds with protein confirmed that the structure was stable and make several non-bonding interactions with amino acids, such as Leu290, Met310 and Asn167. Hence, we concluded that the identified compounds may act as new leads for the design of Mtb MurG inhibitors.

Biodesulfurization of refractory organic sulfur compounds in fossil fuels.

Science.gov (United States)

Soleimani, Mehran; Bassi, Amarjeet; Margaritis, Argyrios

2007-01-01

The stringent new regulations to lower sulfur content in fossil fuels require new economic and efficient methods for desulfurization of recalcitrant organic sulfur. Hydrodesulfurization of such compounds is very costly and requires high operating temperature and pressure. Biodesulfurization is a non-invasive approach that can specifically remove sulfur from refractory hydrocarbons under mild conditions and it can be potentially used in industrial desulfurization. Intensive research has been conducted in microbiology and molecular biology of the competent strains to increase their desulfurization activity; however, even the highest activity obtained is still insufficient to fulfill the industrial requirements. To improve the biodesulfurization efficiency, more work is needed in areas such as increasing specific desulfurization activity, hydrocarbon phase tolerance, sulfur removal at higher temperature, and isolating new strains for desulfurizing a broader range of sulfur compounds. This article comprehensively reviews and discusses key issues, advances and challenges for a competitive biodesulfurization process.

High-pressure microscopy for tracking dynamic properties of molecular machines.

Science.gov (United States)

Nishiyama, Masayoshi

2017-12-01

High-pressure microscopy is one of the powerful techniques to visualize the effects of hydrostatic pressures on research targets. It could be used for monitoring the pressure-induced changes in the structure and function of molecular machines in vitro and in vivo. This review focuses on the dynamic properties of the assemblies and machines, analyzed by means of high-pressure microscopy measurement. We developed a high-pressure microscope that is optimized both for the best image formation and for the stability to hydrostatic pressure up to 150 MPa. Application of pressure could change polymerization and depolymerization processes of the microtubule cytoskeleton, suggesting a modulation of the intermolecular interaction between tubulin molecules. A novel motility assay demonstrated that high hydrostatic pressure induces counterclockwise (CCW) to clockwise (CW) reversals of the Escherichia coli flagellar motor. The present techniques could be extended to study how molecular machines in complicated systems respond to mechanical stimuli. Copyright © 2017 Elsevier B.V. All rights reserved.

Proton NMR relaxivity of blood samples in the presence of some gadolinium and dysprosium compounds

International Nuclear Information System (INIS)

Coroiu, I.; Darabont, Al.; Bogdan, M.

1999-01-01

The use of some new compounds in MRI tissue and blood characterisation based on nuclear spin relaxation time measurements cannot be sustained until the molecular sources of these variations are understood. Tissues and blood are complex molecular systems with complex NMR properties. A better comprehension of the molecular basis of relaxation offers the possibility to predict the changes expected for a given pathology. The purpose of this contribution is to evidence the different relaxation characteristics of some gadolinium and dysprosium compounds in the presence and absence of the blood and to give a possible explanation about the molecular processes that cause occurrence of changes. Some gadolinium and dysprosium compounds such as: Gd-CIT (gadolinium citrate), Dy-DTPA (DTPA-diethylenetriamine pentaacetic acid), iron oxide - gadolinium oxide (or dysprosium oxide)- dextran complexes were prepared. The longitudinal T 1 -1 and transverse T 2 -1 'relaxation rates' measurements have been carried out as a function of molar concentrations. All measurements have been made at room temperature (about 25 deg.C) and the proton Larmor frequency ν o = 90 MHz. The pulsed NMR spectrometer utilised was a commercial Bruker SXP4/100 spectrometer. Transverse relaxation rate measurements have been made using the Carr-Purcell method, while longitudinal relaxation rate measurements using the inversion recovery pulse sequence, 180 angle-τ-90 angle. The accuracy was about 2-3% for the longitudinal relaxation rates and about 5-7% for the transverse relaxation rates. R 1 and R 2 relaxivities, in mM -1 s -1 were determined from the least square determination of the slopes of plots 1/T 1,2 versus compound molar concentration, using at least five independent measurements at several concentrations between 0 and 2 mM. Increased R 2 relaxivity observed for dysprosium compounds in the blood presence can be explained by PRE effect. The largest gain in R 2 relaxivity seems to imply a noncovalent

The importance of atomic and molecular correlation on the bonding in transition metal compounds

Science.gov (United States)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Walch, Stephen P.

1986-01-01

The determination of accurate spectroscopic parameters for molecular systems containing transition metal atoms is shown to require extensive data sets and a high level correlation treatment, and techniques and their limitations are considered. Extensive results reported on the transition metal atoms, hydrides, oxides, and dimers makes possible the design of a calculation to correctly describe the mixing of different atomic asymptotes, and to give a correct balance between molecular bonding and exchange interactions. Examples considered include the dipole moment of the 2Delta state of NiH, which can help determine the mixture of 3d(8)4s(2) and 3d(9)4s(1) in the NiH wavefunction, and the bonding in CrO, where an equivalent description of the relative energies associated with the Cr 3d-3d atomic exchange and the Cr-O bond is important.

High Molecular Weight Forms of Mammalian Respiratory Chain Complex II

Czech Academy of Sciences Publication Activity Database

Kovářová, Nikola; Mráček, Tomáš; Nůsková, Hana; Holzerová, Eliška; Vrbacký, Marek; Pecina, Petr; Hejzlarová, Kateřina; Klučková, Katarína; Rohlena, Jakub; Neužil, Jiří; Houštěk, Josef

2013-01-01

Roč. 8, č. 8 (2013), e71869 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GPP303/10/P227; GA MŠk(CZ) LL1204; GA MZd(CZ) NT12370; GA ČR(CZ) GAP301/10/1937 Institutional research plan: CEZ:AV0Z50520701 Institutional support: RVO:67985823 Keywords : supercomplexes * high molecular weihgt forms of complex II * native electrophoretic systems Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.534, year: 2013

Molecular determinants of subtype-selective efficacies of cytisine and the novel compound NS3861 at heteromeric nicotinic acetylcholine receptors

DEFF Research Database (Denmark)

Harpsøe, Kasper; Hald, Helle; Timmermann, Daniel B

2013-01-01

Deciphering which specific agonist-receptor interactions affect efficacy levels is of high importance, because this will ultimately aid in designing selective drugs. The novel compound NS3861 and cytisine are agonists of nicotinic acetylcholine receptors (nAChRs) and both bind with high affinity...

High-efficiency THz modulator based on phthalocyanine-compound organic films

International Nuclear Information System (INIS)

He, Ting; Zhang, Bo; Shen, Jingling; Zang, Mengdi; Chen, Tianji; Hu, Yufeng; Hou, Yanbing

2015-01-01

We report a high efficiency, broadband terahertz (THz) modulator following a study of phthalocyanine-compound organic films irradiated with an external excitation laser. Both transmission and reflection modulations of each organic/silicon bilayers were measured using THz time-domain and continuous-wave systems. For very low intensities, the experimental results show that AlClPc/Si can achieve a high modulation factor for transmission and reflection, indicating that AlClPc/Si has a superior modulation efficiency compared with the other films (CuPc and SnCl 2 Pc). In contrast, the strong attenuation of the transmitted and reflected THz waves revealed that a nonlinear absorption process takes place at the organic/silicon interface

Quinolinic Carboxylic Acid Derivatives as Potential Multi-target Compounds for Neurodegeneration: Monoamine Oxidase and Cholinesterase Inhibition.

Science.gov (United States)

Khan, Nehal A; Khan, Imtiaz; Abid, Syed M A; Zaib, Sumera; Ibrar, Aliya; Andleeb, Hina; Hameed, Shahid; Iqbal, Jamshed

2018-01-01

Parkinson's disease (PD), a debilitating and progressive disorder, is among the most challenging and devastating neurodegenerative diseases predominantly affecting the people over 60 years of age. To confront PD, an advanced and operational strategy is to design single chemical functionality able to control more than one target instantaneously. In this endeavor, for the exploration of new and efficient inhibitors of Parkinson's disease, we synthesized a series of quinoline carboxylic acids (3a-j) and evaluated their in vitro monoamine oxidase and cholinesterase inhibitory activities. The molecular docking and in silico studies of the most potent inhibitors were performed to identify the probable binding modes in the active site of the monoamine oxidase enzymes. Moreover, molecular properties were calculated to evaluate the druglikeness of the compounds. The biological evaluation results revealed that the tested compounds were highly potent against monoamine oxidase (A & B), 3c targeted both the isoforms of MAO with IC50 values of 0.51 ± 0.12 and 0.51 ± 0.03 µM, respectively. The tested compounds also demonstrated high and completely selective inhibitory action against acetylcholinesterase (AChE) with IC50 values ranging from 4.36 to 89.24 µM. Among the examined derivatives, 3i was recognized as the most potent inhibitor of AChE with an IC50 value of 4.36 ± 0.12 ±µM. The compounds appear to be promising inhibitors and could be used for the future development of drugs targeting neurodegenerative disorders. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

High-Throughput and Rapid Screening of Low-Mass Hazardous Compounds in Complex Samples.

Science.gov (United States)

Wang, Jing; Liu, Qian; Gao, Yan; Wang, Yawei; Guo, Liangqia; Jiang, Guibin

2015-07-07

Rapid screening and identification of hazardous chemicals in complex samples is of extreme importance for public safety and environmental health studies. In this work, we report a new method for high-throughput, sensitive, and rapid screening of low-mass hazardous compounds in complex media without complicated sample preparation procedures. This method is achieved based on size-selective enrichment on ordered mesoporous carbon followed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry analysis with graphene as a matrix. The ordered mesoporous carbon CMK-8 can exclude interferences from large molecules in complex samples (e.g., human serum, urine, and environmental water samples) and efficiently enrich a wide variety of low-mass hazardous compounds. The method can work at very low concentrations down to part per trillion (ppt) levels, and it is much faster and more facile than conventional methods. It was successfully applied to rapidly screen and identify unknown toxic substances such as perfluorochemicals in human serum samples from athletes and workers. Therefore, this method not only can sensitively detect target compounds but also can identify unknown hazardous compounds in complex media.

Role of Dehalogenases in Aerobic Bacterial Degradation of Chlorinated Aromatic Compounds

Directory of Open Access Journals (Sweden)

Pankaj Kumar Arora

2014-01-01

Full Text Available This review was conducted to provide an overview of dehalogenases involved in aerobic biodegradation of chlorinated aromatic compounds. Additionally, biochemical and molecular characterization of hydrolytic, reductive, and oxygenolytic dehalogenases was reviewed. This review will increase our understanding of the process of dehalogenation of chlorinated aromatic compounds.

Phenolic compounds and bioactive properties of wild German and Roman chamomiles

OpenAIRE

Guimarães, Rafaela; Barros, Lillian; Dueñas, Montserrat; Calhelha, Ricardo C.; Carvalho, Ana Maria; Santos-Buelga, Celestino; Queiroz, Maria João R.P.; Ferreira, Isabel C.F.R.

2012-01-01

Natural products represent a rich source of biologically active compounds and are an example of molecular diversity, with recognized potential in drug discovery. In the present work, methanolic extracts of Matricaria recutita L. (German chamomile) and Chamaemelum nobile L. (Roman chamomile) and their decoction and infusion (the most consumed preparations of these herbs) were submitted to an analysis of phenolic compounds and bioactivity evaluation. Phenolic compounds were characterized by HPL...

Molecular modeling

Directory of Open Access Journals (Sweden)

Aarti Sharma

2009-01-01

Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.

Highly solvatochromic emission of electron donor-acceptor compounds containing propanedioato boron electron acceptors

NARCIS (Netherlands)

Brouwer, A.M.; Bakker, N.A.C.; Wiering, P.G.; Verhoeven, J.W.

1991-01-01

Light-induced electron transfer occurs in bifunctional compounds consisting of 1,3-diphenylpropanedioato boron oxalate or fluoride electron acceptors and simple aromatic electron-donor groups, linked by a methylene bridge; fluorescence from the highly polar charge-transfer excited state is

Development of PNTDs synthesized from monomers with different molecular length and analysis of molecular damages by heavy ion

International Nuclear Information System (INIS)

Kawashima, Hajime; Kodaira, Satoshi; Ihara, Daisuke; Yasuda, Nakahiro; Kusumoto, Tamon; Mori, Yutaka; Yamauchi, Tomoya; Kobayashi, Keiichi; Benton, Eric

2017-01-01

Our interests for years lay to investigate the reason why CR-39 polymer has such high sensitivity as plastic nuclear track detector (PNTD) on chemical structural aspects. We developed three PNTDs from three diacrylate compounds as monomers bearing different molecular length as well as different numbers of internal ether bonds. The polymer products obtained were colorless and transparent with 3-D molecular structures as CR-39 and different lattice structures each other. Our purpose of the current study was to investigate structural damages caused in newly prepared PNTDs and CR-39 by irradiation of Nitrogen ion (6 MeV/n, fluence of 5 x 10 11 cm -2 ). The structural damage by irradiation was analyzed by the magnitude of the relative absorbance of specific functional groups such as ester, C=O, ether and C-H bonds by means of FT-IR (ATR) method. The correlation between the relative absorbance and the molecular length of the monomers were discussed. (author)

Chirality-dependent friction of bulk molecular solids.

Science.gov (United States)

Yang, Dian; Cohen, Adam E

2014-08-26

We show that the solid-solid friction between bulk chiral molecular solids can depend on the relative chirality of the two materials. In menthol and 1-phenyl-1-butanol, heterochiral friction is smaller than homochiral friction, while in ibuprofen, heterochiral friction is larger. Chiral asymmetries in the coefficient of sliding friction vary with temperature and can be as large as 30%. In the three compounds tested, the sign of the difference between heterochiral and homochiral friction correlated with the sign of the difference in melting point between racemate (compound or conglomerate) and pure enantiomer. Menthol and ibuprofen each form a stable racemic compound, while 1-phenyl-1-butanol forms a racemic conglomerate. Thus, a difference between heterochiral and homochiral friction does not require the formation of a stable interfacial racemic compound. Measurements of chirality-dependent friction provide a unique means to distinguish the role of short-range intermolecular forces from all other sources of dissipation in the friction of bulk molecular solids.

Evolution of interstellar organic compounds under asteroidal hydrothermal conditions

Science.gov (United States)

Vinogradoff, V.; Bernard, S.; Le Guillou, C.; Remusat, L.

2018-05-01

Carbonaceous chondrites (CC) contain a diversity of organic compounds. No definitive evidence for a genetic relationship between these complex organic molecules and the simple organic molecules detected in the interstellar medium (ISM) has yet been reported. One of the many difficulties arises from the transformations of organic compounds during accretion and hydrothermal alteration on asteroids. Here, we report results of hydrothermal alteration experiments conducted on a common constituent of interstellar ice analogs, Hexamethylenetetramine (HMT - C6H12N4). We submitted HMT to asteroidal hydrothermal conditions at 150 °C, for various durations (up to 31 days) and under alkaline pH. Organic products were characterized by gas chromatography mass spectrometry, infrared spectroscopy and synchrotron-based X-ray absorption near edge structure spectroscopy. Results show that, within a few days, HMT has evolved into (1) a very diverse suite of soluble compounds dominated by N-bearing aromatic compounds (> 150 species after 31 days), including for instance formamide, pyridine, pyrrole and their polymers (2) an aromatic and N-rich insoluble material that forms after only 7 days of experiment and then remains stable through time. The reaction pathways leading to the soluble compounds likely include HMT dissociation, formose and Maillard-type reactions, e.g. reactions of sugar derivatives with amines. The present study demonstrates that, if interstellar organic compounds such as HMT had been accreted by chondrite parent bodies, they would have undergone chemical transformations during hydrothermal alteration, potentially leading to the formation of high molecular weight insoluble organic molecules. Some of the diversity of soluble and insoluble organic compounds found in CC may thus result from asteroidal hydrothermal alteration.

High pressure 129I Moessbauer studies of GeI4 molecular crystals

International Nuclear Information System (INIS)

Pasternak, M.P.; Taylor, R.D.

1989-01-01

The Moessbauer effect in 129 I in conjunction with Diamond-Anvil-Cell high pressure techniques was applied to investigate the high pressure phase(s) of the molecular crystal GeI 4 . The 129 I Quadrupole Interaction was the main probe for characterizing the intermolecular structural transformation with pressure. With increasing pressure, at about 15 GPAa, the onset of a partial molecular-association phase (HP1) is first observed. In HP1 two out of the four iodines strongly overlap to form linear chains of GeI 4 . The HP1 phase coexists with the low pressure (LP) molecular phase, but its population increases with increasing pressure. At P ∼20 GPa a second high pressure phase (HP2) is identified where all four iodines strongly overlap to form a three dimensional, fully molecular-associated structure. With increasing pressure and at P > 20 GPa, HP2 is the only phase up to P = 34 GPa, the highest pressure used. A significant hysteresis of the relative abundances with pressure is observed. The isomer shift of the HP2 and HP1 structures is considerably larger than that of the LP one. 11 refs., 3 figs

High pressure 129I Moessbauer studies of GeI4 molecular crystals

International Nuclear Information System (INIS)

Pasternak, M.P.; Los Alamos National Lab.; Taylor, R.D.

1990-01-01

The Moessbauer effect in 129 I in cunjunction with Diamond-Anvil-Cell high pressure techniques was applied to investigate the high pressure phase(s) of the molecular crystal GeI 4 . The 129 I Quadrupole Interaction was the main probe for characterizing the intermolecular structural transformation with pressure. With increasing pressure, at about 15 GPa, the onset of a partial molecular-association phase (HP1) is first observed. In HP1 two out of the four iodines strongly overlap to form linear chains of GeI 4 . The HP1 phase coexists with the low pressure (LP) molecular phase, but its population increases with increasing pressure. At P≅20 GPa a second high pressure phase (HP2) is identified where all four iodines strongly overlap to form a three dimensional, fully molecular-associated structure. With increasing pressure and at P>20 GPa, HP2 is the only phase up to P=34 GPa, the highest pressure used. A significant hysteresis of the relative abundances with pressure is observed. The isomer shift of the HP2 and HP1 structures is considerably larger than that of the LP one. (orig.)

Competing orbital ordering in RVO3 compounds: High-resolution x-ray diffraction and thermal expansion

International Nuclear Information System (INIS)

Sage, M. H.; Blake, G. R.; Palstra, T. T. M.; Marquina, C.

2007-01-01

We report evidence for the phase coexistence of orbital orderings of different symmetry in RVO 3 compounds with intermediate-size rare earths. Through a study by high-resolution x-ray powder diffraction and thermal expansion, we show that the competing orbital orderings are associated with the magnitude of the VO 6 octahedral tilting and magnetic exchange striction in these compounds and that the phase-separated state is stabilized by lattice strains

Blue emitting organic semiconductors under high pressure

DEFF Research Database (Denmark)

Knaapila, Matti; Guha, Suchismita

2016-01-01

This review describes essential optical and emerging structural experiments that use high GPa range hydrostatic pressure to probe physical phenomena in blue-emitting organic semiconductors including π-conjugated polyfluorene and related compounds. The work emphasizes molecular structure and inter......This review describes essential optical and emerging structural experiments that use high GPa range hydrostatic pressure to probe physical phenomena in blue-emitting organic semiconductors including π-conjugated polyfluorene and related compounds. The work emphasizes molecular structure...... and intermolecular self-organization that typically determine transport and optical emission in π-conjugated oligomers and polymers. In this context, hydrostatic pressure through diamond anvil cells has proven to be an elegant tool to control structure and interactions without chemical intervention. This has been...... and intermolecular interactions on optical excitations, electron–phonon interaction, and changes in backbone conformations. This picture is connected to the optical high pressure studies of other π-conjugated systems and emerging x-ray scattering experiments from polyfluorenes which provides a structure-property map...

Carbon transfer in soil - plant system. Molecular labelling utilization for determining rhizosphere compounds

International Nuclear Information System (INIS)

Leguay, J.J.

2000-01-01

The growing up of the bacteria developing in the rhizosphere of plants is dependent on the compounds exudation by plant roots. Even the bacterial genetics use has permitted to identify diverse functions involved in the process of the rhizosphere colonisation ( mobility, heterotrophic bacteria, growing rate, antibiotics production), there is a big delay in vegetal partners. To decrease this delay we tried to characterize the interactions between a plant model, Arabidopsis thaliana and the rhizosphere bacteria. An experimental device has been conceived for measuring the transfer of carbon issued from the photosynthesis to roots and soil. The exudation by roots has been studied. The analysis of rhizospheric compounds in situ pose some methodological problems, especially, the rhizospheric compounds must be extracted from the soil matrix. we suggest an analysis method of rhizospheric compound and of their dynamics. (F.M.)

Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

Energy Technology Data Exchange (ETDEWEB)

Zeng, Ying-Xu [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); Mjøs, Svein Are, E-mail: svein.mjos@kj.uib.no [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); David, Fabrice P.A. [Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne (Switzerland); Schmid, Adrien W. [Proteomics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland)

2016-03-31

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

International Nuclear Information System (INIS)

Zeng, Ying-Xu; Mjøs, Svein Are; David, Fabrice P.A.; Schmid, Adrien W.

2016-01-01

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

Antifungal chemical compounds identified using a C. elegans pathogenicity assay.

Directory of Open Access Journals (Sweden)

Julia Breger

2007-02-01

Full Text Available There is an urgent need for the development of new antifungal agents. A facile in vivo model that evaluates libraries of chemical compounds could solve some of the main obstacles in current antifungal discovery. We show that Candida albicans, as well as other Candida species, are ingested by Caenorhabditis elegans and establish a persistent lethal infection in the C. elegans intestinal track. Importantly, key components of Candida pathogenesis in mammals, such as filament formation, are also involved in nematode killing. We devised a Candida-mediated C. elegans assay that allows high-throughput in vivo screening of chemical libraries for antifungal activities, while synchronously screening against toxic compounds. The assay is performed in liquid media using standard 96-well plate technology and allows the study of C. albicans in non-planktonic form. A screen of 1,266 compounds with known pharmaceutical activities identified 15 (approximately 1.2% that prolonged survival of C. albicans-infected nematodes and inhibited in vivo filamentation of C. albicans. Two compounds identified in the screen, caffeic acid phenethyl ester, a major active component of honeybee propolis, and the fluoroquinolone agent enoxacin exhibited antifungal activity in a murine model of candidiasis. The whole-animal C. elegans assay may help to study the molecular basis of C. albicans pathogenesis and identify antifungal compounds that most likely would not be identified by in vitro screens that target fungal growth. Compounds identified in the screen that affect the virulence of Candida in vivo can potentially be used as "probe compounds" and may have antifungal activity against other fungi.

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

Directory of Open Access Journals (Sweden)

Fiehn Oliver

2007-03-01

seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65–81%. Corresponding software and supplemental data are available for downloads from the authors' website.

Triorganotin as a compound with potential reproductive toxicity in mammals

Directory of Open Access Journals (Sweden)

V.S. Delgado Filho

2011-09-01

Full Text Available Organotin compounds are typical environmental contaminants and suspected endocrine-disrupting substances, which cause irreversible sexual abnormality in female mollusks, called "imposex". However, little is known about the capability of triorganotin compounds, such as tributyltin and triphenyltin, to cause disorders in the sexual development and reproductive functions of mammals, including humans and rodents. Moreover, these compounds can act as potential competitive inhibitors of aromatase enzyme and other steroidogenic enzymes, affecting the reproductive capacity of male and female mammals. In this review, we discuss the cellular, biochemical, and molecular mechanisms by which triorganotin compounds induce adverse effects in the mammalian reproductive function.

Magnetic high throughput screening system for the development of nano-sized molecularly imprinted polymers for controlled delivery of curcumin.

Science.gov (United States)

Piletska, Elena V; Abd, Bashar H; Krakowiak, Agata S; Parmar, Anitha; Pink, Demi L; Wall, Katie S; Wharton, Luke; Moczko, Ewa; Whitcombe, Michael J; Karim, Kal; Piletsky, Sergey A

2015-05-07

Curcumin is a versatile anti-inflammatory and anti-cancer agent known for its low bioavailability, which could be improved by developing materials capable of binding and releasing drug in a controlled fashion. The present study describes the preparation of magnetic nano-sized Molecularly Imprinted Polymers (nanoMIPs) for the controlled delivery of curcumin and their high throughput characterisation using microtitre plates modified with magnetic inserts. NanoMIPs were synthesised using functional monomers chosen with the aid of molecular modelling. The rate of release of curcumin from five polymers was studied under aqueous conditions and was found to correlate well with the binding energies obtained computationally. The presence of specific monomers was shown to be significant in ensuring effective binding of curcumin and to the rate of release obtained. Characterisation of the polymer particles was carried out using dynamic light scattering (DLS) technique and scanning electron microscopy (SEM) in order to establish the relationship between irradiation time and particle size. The protocols optimised during this study could be used as a blueprint for the development of nanoMIPs capable of the controlled release of potentially any compound of interest.

Hydrodistillation-adsorption method for the isolation of water-soluble, non-soluble and high volatile compounds from plant materials.

Science.gov (United States)

Mastelić, J; Jerković, I; Blazević, I; Radonić, A; Krstulović, L

2008-08-15

Proposed method of hydrodistillation-adsorption (HDA) on activated carbon and hydrodistillation (HD) with solvent trap were compared for the isolation of water-soluble, non-soluble and high volatile compounds, such as acids, monoterpenes, isothiocyanates and others from carob (Certonia siliqua L.), rosemary (Rosmarinus officinalis L.) and rocket (Eruca sativa L.). Isolated volatiles were analyzed by GC and GC/MS. The main advantages of HDA method over ubiquitous HD method were higher yields of volatile compounds and their simultaneous separation in three fractions that enabled more detail analyses. This method is particularly suitable for the isolation and analysis of the plant volatiles with high amounts of water-soluble compounds. In distinction from previously published adsorption of remaining volatile compounds from distillation water on activated carbon, this method offers simultaneous hydrodistillation and adsorption in the same apparatus.

Analysis of multiple quaternary ammonium compounds in the brain using tandem capillary column separation and high resolution mass spectrometric detection.

Science.gov (United States)

Falasca, Sara; Petruzziello, Filomena; Kretz, Robert; Rainer, Gregor; Zhang, Xiaozhe

2012-06-08

Endogenous quaternary ammonium compounds are involved in various physiological processes in the central nervous system. In the present study, eleven quaternary ammonium compounds, including acetylcholine, choline, carnitine, acetylcarnitine and seven other acylcarnitines of low polarity, were analyzed from brain extracts using a two dimension capillary liquid chromatography-Fourier transform mass spectrometry method. To deal with their large difference in hydrophobicities, tandem coupling between reversed phase and hydrophilic interaction chromatography columns was used to separate all the targeted quaternary ammonium compounds. Using high accuracy mass spectrometry in selected ion monitoring mode, all the compounds could be detected from each brain sample with high selectivity. The developed method was applied for the relative quantification of these quaternary ammonium compounds in three different brain regions of tree shrews: prefrontal cortex, striatum, and hippocampus. The comparative analysis showed that quaternary ammonium compounds were differentially distributed across the three brain areas. The analytical method proved to be highly sensitive and reliable for simultaneous determination of all the targeted analytes from brain samples. Copyright © 2012 Elsevier B.V. All rights reserved.

A QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP AND MOLECULAR DOCKING STUDY ON A SERIES OF PYRIMIDINES ACTING AS ANTI-HEPATITIS C VIRUS AGENTS

Directory of Open Access Journals (Sweden)

Sakshi Gupta

2013-12-01

Full Text Available A QSAR and molecular modeling study was performed on a series of pyrimidines acting as hepatitis C virus inhibitors. In this case, anti-HCV potency of the compounds was found to be significantly correlated with the hydrophobic property of the molecule, Kier’s first-order valence molecular connectivity index for a particular substituent, total structure connectivity index of the molecule, and an indicator parameter used for the presence of benzothiazole ring. The validity of the correlation was judged by leave-one-out jackknife procedure and predicting the activity of some test compounds. Using the correlation obtained, some new compounds of high potency have been predicted in the series. A docking study using Molegro Virtual Docker was performed on these predicted compounds to decipher their interactions with the receptor. It was observed that all the predicted compounds had better interaction energy and docking score than the ligand complexed with the protein.

Steroid-like compounds in Chinese medicines promote blood circulation via inhibition of Na+/K+ -ATPase.

Science.gov (United States)

Chen, Ronald J Y; Chung, Tse-yu; Li, Feng-yin; Yang, Wei-hung; Jinn, Tzyy-rong; Tzen, Jason T C

2010-06-01

To examine if steroid-like compounds found in many Chinese medicinal products conventionally used for the promotion of blood circulation may act as active components via the same molecular mechanism triggered by cardiac glycosides, such as ouabain. The inhibitory potency of ouabain and the identified steroid-like compounds on Na(+)/K(+)-ATPase activity was examined and compared. Molecular modeling was exhibited for the docking of these compounds to Na(+)/K(+)-ATPase. All the examined steroid-like compounds displayed more or less inhibition on Na(+)/K(+)-ATPase, with bufalin (structurally almost equivalent to ouabain) exhibiting significantly higher inhibitory potency than the others. In the pentacyclic triterpenoids examined, ursolic acid and oleanolic acid were moderate inhibitors of Na(+)/K(+)-ATPase, and their inhibitory potency was comparable to that of ginsenoside Rh2. The relatively high inhibitory potency of ursolic acid or oleanolic acid was due to the formation of a hydrogen bond between its carboxyl group and the Ile322 residue in the deep cavity close to two K(+) binding sites of Na(+)/K(+)-ATPase. Moreover, the drastic difference observed in the inhibitory potency of ouabain, bufalin, ginsenoside Rh2, and pentacyclic triterpenoids is ascribed mainly to the number of hydrogen bonds and partially to the strength of hydrophobic interaction between the compounds and residues around the deep cavity of Na(+)/K(+)-ATPase. Steroid-like compounds seem to contribute to therapeutic effects of many cardioactive Chinese medicinal products. Chinese herbs, such as Prunella vulgaris L, rich in ursolic acid, oleanolic acid and their glycoside derivatives may be adequate sources for cardiac therapy via effective inhibition on Na(+)/K(+)-ATPase.

Molecular simulation studies on thermophysical properties with application to working fluids

CERN Document Server

Raabe, Gabriele

2017-01-01

This book discusses the fundamentals of molecular simulation, starting with the basics of statistical mechanics and providing introductions to Monte Carlo and molecular dynamics simulation techniques. It also offers an overview of force-field models for molecular simulations and their parameterization, with a discussion of specific aspects. The book then summarizes the available know-how for analyzing molecular simulation outputs to derive information on thermophysical and structural properties. Both the force-field modeling and the analysis of simulation outputs are illustrated by various examples. Simulation studies on recently introduced HFO compounds as working fluids for different technical applications demonstrate the value of molecular simulations in providing predictions for poorly understood compounds and gaining a molecular-level understanding of their properties. This book will prove a valuable resource to researchers and students alike.

A novel high resolution, high sensitivity SPECT detector for molecular imaging of cardiovascular diseases

Science.gov (United States)

Cusanno, F.; Argentieri, A.; Baiocchi, M.; Colilli, S.; Cisbani, E.; De Vincentis, G.; Fratoni, R.; Garibaldi, F.; Giuliani, F.; Gricia, M.; Lucentini, M.; Magliozzi, M. L.; Majewski, S.; Marano, G.; Musico, P.; Musumeci, M.; Santavenere, F.; Torrioli, S.; Tsui, B. M. W.; Vitelli, L.; Wang, Y.

2010-05-01

Cardiovascular diseases are the most common cause of death in western countries. Understanding the rupture of vulnerable atherosclerotic plaques and monitoring the effect of innovative therapies of heart failure is of fundamental importance. A flexible, high resolution, high sensitivity detector system for molecular imaging with radionuclides on small animal models has been designed for this aim. A prototype has been built using tungsten pinhole and LaBr3(Ce) scintillator coupled to Hamamatsu Flat Panel PMTs. Compact individual-channel readout has been designed, built and tested. Measurements with phantoms as well as pilot studies on mice have been performed, the results show that the myocardial perfusion in mice can be determined with sufficient precision. The detector will be improved replacing the Hamamatsu Flat Panel with Silicon Photomultipliers (SiPMs) to allow integration of the system with MRI scanners. Application of LaBr3(Ce) scintillator coupled to photosensor with high photon detection efficiency and excellent energy resolution will allow dual-label imaging to monitor simultaneously the cardiac perfusion and the molecular targets under investigation during the heart therapy.

Just Working with the Cellular Machine: A High School Game for Teaching Molecular Biology

Science.gov (United States)

Cardoso, Fernanda Serpa; Dumpel, Renata; Gomes da Silva, Luisa B.; Rodrigues, Carlos R.; Santos, Dilvani O.; Cabral, Lucio Mendes; Castro, Helena C.

2008-01-01

Molecular biology is a difficult comprehension subject due to its high complexity, thus requiring new teaching approaches. Herein, we developed an interdisciplinary board game involving the human immune system response against a bacterial infection for teaching molecular biology at high school. Initially, we created a database with several…

Molecular Selectivity of Brown Carbon Chromophores

Energy Technology Data Exchange (ETDEWEB)

Laskin, Julia; Laskin, Alexander; Nizkorodov, Sergey; Roach, Patrick J.; Eckert, Peter A.; Gilles, Mary K.; Wang, Bingbing; Lee, Hyun Ji; Hu, Qichi

2014-10-21

Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (SOA) generated from ozonolysis of two structural monoterpene isomers: D-limonene (LSOA) and a-pinene (PSOA). Laboratory simulated aging of LSOA and PSOA, through conversion of carbonyls into imines mediated by NH3 vapors in humid air, resulted in selective browning of the LSOA sample, while the PSOA sample remained white. Comparative analysis of the reaction products in the aged LSOA and PSOA samples provided insights into chemistry relevant to formation of brown carbon chromophores. A significant fraction of carbonyl-imine conversion products with identical molecular formulas were detected in both samples. This reflects the high level of similarity in the molecular composition of these two closely related SOA materials. Several highly conjugated products were detected exclusively in the brown LSOA sample and were identified as potential chromophores responsible for the observed color change. The majority of the unique products in the aged LSOA sample with the highest number of double bonds contain two nitrogen atoms. We conclude that chromophores characteristic of the carbonyl- imine chemistry in LSOA are highly conjugated oligomers of secondary imines (Schiff bases) present at relatively low concentrations. Formation of this type of conjugated compounds in PSOA is hindered by the structural rigidity of the a-pinene oxidation products. Our results suggest that the overall light-absorbing properties of SOA may be determined by trace amounts of strong brown carbon chromophores.

High-performance liquid chromatography separation of unsaturated organic compounds by a monolithic silica column embedded with silver nanoparticles.

Science.gov (United States)

Zhu, Yang; Morisato, Kei; Hasegawa, George; Moitra, Nirmalya; Kiyomura, Tsutomu; Kurata, Hiroki; Kanamori, Kazuyoshi; Nakanishi, Kazuki

2015-08-01

The optimization of a porous structure to ensure good separation performances is always a significant issue in high-performance liquid chromatography column design. Recently we reported the homogeneous embedment of Ag nanoparticles in periodic mesoporous silica monolith and the application of such Ag nanoparticles embedded silica monolith for the high-performance liquid chromatography separation of polyaromatic hydrocarbons. However, the separation performance remains to be improved and the retention mechanism as compared with the Ag ion high-performance liquid chromatography technique still needs to be clarified. In this research, Ag nanoparticles were introduced into a macro/mesoporous silica monolith with optimized pore parameters for high-performance liquid chromatography separations. Baseline separation of benzene, naphthalene, anthracene, and pyrene was achieved with the theoretical plate number for analyte naphthalene as 36,000 m(-1). Its separation function was further extended to cis/trans isomers of aromatic compounds where cis/trans stilbenes were chosen as a benchmark. Good separation of cis/trans-stilbene with separation factor as 7 and theoretical plate number as 76,000 m(-1) for cis-stilbene was obtained. The trans isomer, however, is retained more strongly, which contradicts the long- established retention rule of Ag ion chromatography. Such behavior of Ag nanoparticles embedded in a silica column can be attributed to the differences in the molecular geometric configuration of cis/trans stilbenes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal and molecular simulation of high-performance polymers.

Science.gov (United States)

Colquhoun, H M; Williams, D J

2000-03-01

Single-crystal X-ray analyses of oligomeric models for high-performance aromatic polymers, interfaced to computer-based molecular modeling and diffraction simulation, have enabled the determination of a range of previously unknown polymer crystal structures from X-ray powder data. Materials which have been successfully analyzed using this approach include aromatic polyesters, polyetherketones, polythioetherketones, polyphenylenes, and polycarboranes. Pure macrocyclic homologues of noncrystalline polyethersulfones afford high-quality single crystals-even at very large ring sizes-and have provided the first examples of a "protein crystallographic" approach to the structures of conventionally amorphous synthetic polymers.

Elevated levels of high-molecular-weight adiponectin in type 1 diabetes

DEFF Research Database (Denmark)

Leth, H.; Andersen, K.K.; Frystyk, J.

2008-01-01

BACKGROUND: Several studies have shown that type 1 diabetic patients have elevated total levels of the adipocyte-derived adipocytokine adiponectin. However, adiponectin circulates in three different subforms, and the high-molecular-weight (HMW) subform is believed to be the primary biologically...... active form. The effects of the medium-molecular-weight (MMW) subform and the low-molecular-weight (LMW) subform are still unresolved. PURPOSE: The objective of the study was to investigate the distribution of the three molecular subforms of adiponectin in well-characterized groups of type 1 diabetics...... with varying degrees of nephropathy as well as in healthy control subjects. STUDY POPULATION: Two hundred seven individuals were included: 58 type 1 diabetics with normoalbuminuria, 46 with microalbuminuria, 46 with macroalbuminuria, and 57 matched controls. METHODS: The HMW, MMW, and LMW subforms were...

Black molecular adsorber coatings for spaceflight applications

Science.gov (United States)

Abraham, Nithin S.; Hasegawa, Mark M.; Straka, Sharon A.

2014-09-01

The molecular adsorber coating is a new technology that was developed to mitigate the risk of on-orbit molecular contamination on spaceflight missions. The application of this coating would be ideal near highly sensitive, interior surfaces and instruments that are negatively impacted by outgassed molecules from materials, such as plastics, adhesives, lubricants, epoxies, and other similar compounds. This current, sprayable paint technology is comprised of inorganic white materials made from highly porous zeolite. In addition to good adhesion performance, thermal stability, and adsorptive capability, the molecular adsorber coating offers favorable thermal control characteristics. However, low reflectivity properties, which are typically offered by black thermal control coatings, are desired for some spaceflight applications. For example, black coatings are used on interior surfaces, in particular, on instrument baffles for optical stray light control. Similarly, they are also used within light paths between optical systems, such as telescopes, to absorb light. Recent efforts have been made to transform the white molecular adsorber coating into a black coating with similar adsorptive properties. This result is achieved by optimizing the current formulation with black pigments, while still maintaining its adsorption capability for outgassing control. Different binder to pigment ratios, coating thicknesses, and spray application techniques were explored to develop a black version of the molecular adsorber coating. During the development process, coating performance and adsorption characteristics were studied. The preliminary work performed on black molecular adsorber coatings thus far is very promising. Continued development and testing is necessary for its use on future contamination sensitive spaceflight missions.

New architectures for molecular materials

International Nuclear Information System (INIS)

Arico, Fabio

2002-01-01

The work described in this thesis is concerned mainly with the synthesis of novel macrocyclic and macropolycyclic oligomers by nucleophilic aromatic substitution under pseudo-high dilution conditions. The cyclic nature of the compounds obtained has been investigated by a range of different analytical techniques, including in some cases single crystal X-ray diffraction. Ring-opening polymerisation of selected macrocycles, in the melt or in solution, was studied as a route to high molecular weight aromatic polymers. In one case the reverse reaction, ring-closing depolymerisation has also been explored for application in the recovery and recycling of a high-value condensation polymer. A potential application of cyclic systems in sub-micron polymer fabrication has been demonstrated using microporous alumina membranes as template for the production of nanoscale polymeric fibrils and tubules. In the present work it is also shown that the previously studied relationship between macrocycles and polymer chains can be extended to a third dimension. Thus, polycondensations involving trifunctional monomers, which would normally afford highly branched or even fully crosslinked polymers, are here shown also to give, under pseudo-high dilution conditions, a series of very large aromatic cage-type molecules. Chemical modification of these macropolycycles was investigated by reducing the carbonyl groups within the cage structures to methylene linkages. The reduced cages so obtained were more tractable and soluble due to the less polar and less rigid methylene groups and the crystals obtained for the latter compounds proved suitable for X-ray crystallographic analysis in order to confirm their macropolycyclic structures. Exploratory studies have shown that a cage-type ether-ketone may be used as a crosslinking agent macrocyclic ring-opening polymerisation. Finally a project, carried out at the University of Strasbourg, under the EU 'Socrates' exchange programme, resulted in the

Plant-Derived Polyphenols in Human Health: Biological Activity, Metabolites and Putative Molecular Targets.

Science.gov (United States)

Olivares-Vicente, Marilo; Barrajon-Catalan, Enrique; Herranz-Lopez, Maria; Segura-Carretero, Antonio; Joven, Jorge; Encinar, Jose Antonio; Micol, Vicente

2018-01-01

Hibiscus sabdariffa, Lippia citriodora, Rosmarinus officinalis and Olea europaea, are rich in bioactive compounds that represent most of the phenolic compounds' families and have exhibited potential benefits in human health. These plants have been used in folk medicine for their potential therapeutic properties in human chronic diseases. Recent evidence leads to postulate that polyphenols may account for such effects. Nevertheless, the compounds or metabolites that are responsible for reaching the molecular targets are unknown. data based on studies directly using complex extracts on cellular models, without considering metabolic aspects, have limited applicability. In contrast, studies exploring the absorption process, metabolites in the blood circulation and tissues have become essential to identify the intracellular final effectors that are responsible for extracts bioactivity. Once the cellular metabolites are identified using high-resolution mass spectrometry, docking techniques suppose a unique tool for virtually screening a large number of compounds on selected targets in order to elucidate their potential mechanisms. we provide an updated overview of the in vitro and in vivo studies on the toxicity, absorption, permeability, pharmacokinetics and cellular metabolism of bioactive compounds derived from the abovementioned plants to identify the potential compounds that are responsible for the observed health effects. we propose the use of targeted metabolomics followed by in silico studies to virtually screen identified metabolites on selected protein targets, in combination with the use of the candidate metabolites in cellular models, as the methods of choice for elucidating the molecular mechanisms of these compounds. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Steroidogenic activity of high molecular weight forms of ACTH

International Nuclear Information System (INIS)

Gasson, J.C.

1979-01-01

The relative steroidogenic potencies of high molecular weight forms of adrenocorticotropic hormone (ACTH) were investigated using in vitro bioassays. In order to prepare pools of separated pro-ACTH/endorphin, ACTH biosynthetic intermediate and glycosylated ACTH (1-39), the protein present in serum-free tissue culture medium obtained from cultured AtT-20/D-16v mouse pituitary tumor cells was concentrated and fractionated by gel filtration. Based on sodium dodecyl sulfate polyacrylamide gel electrophoresis, over 97% of the immunoactive ACTH in each pool had the appropriate molecular weight. Suspensions of isolated rat and guinea pig adrenal cortical cells were prepared by enzymatic dissociation and mechanical dispersion. Cells were incubated in complete tissue culture medium overnight then used in a 2 hour steroid production assay. Synthetic hACTH(1-39) was used as a bioassay and immunoassay standard. The amounts of pro-ACTH/endorphin, ACTH biosynthetic intermediate and glycosylated ACTH(1-39) bioassayed were estimated by ACTH(17-24) radioimmunoassay. All three high molecular weight forms of ACTH were capable of stimulating the same maximal level of steroidogenesis, by both isolated rat and guinea pig adrenal cells, as hACTH(1-39). Glycosylated ACTH(1-39) was equipotent with hACTH(1-39); pro-ACTH/endorphin and ACTH biosynthetic intermediate were two orders of magnitude less potent than hACTH(1-39) in both bioassay systems