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Sample records for quantitative structure-property relationship

  1. Quantitative structure-property relationships in pharmaceutical research - Part 2.

    PubMed

    Grover; Singh; Bakshi

    2000-02-01

    Part one of this two-part review described the advantages and limitations of quantitative structure-property relationships (QSPR), and offered an overview of the components involved in the development of correlations1. Part two provides a discussion of a few notable examples of relationships with organoleptic, physicochemical and pharmaceutical properties.

  2. Construction of coherent nano quantitative structure-properties relationships (nano-QSPR) models and catastrophe theory.

    PubMed

    Carbó-Dorca, R; Besalú, E

    2011-10-01

    The structure one can associate to coherent nano-quantitative structure-properties relationship (nano-QSPR) models is briefly discussed. Such nano-QSPR model functions are described as possessing three parts: a particle size polynomial; a typical QSPR function; and a special effects function. The expected behaviour of the particle size part is discussed from the point of view of catastrophe theory, in this way providing a plausible general picture about the emergence of new properties of nanoparticles and holographic location of information content.

  3. Quantitative structure-property relationship modeling of Grätzel solar cell dyes.

    PubMed

    Venkatraman, Vishwesh; Åstrand, Per-Olof; Alsberg, Bjørn Kåre

    2014-01-30

    With fossil fuel reserves on the decline, there is increasing focus on the design and development of low-cost organic photovoltaic devices, in particular, dye-sensitized solar cells (DSSCs). The power conversion efficiency (PCE) of a DSSC is heavily influenced by the chemical structure of the dye. However, as far as we know, no predictive quantitative structure-property relationship models for DSSCs with PCE as one of the response variables have been reported. Thus, we report for the first time the successful application of comparative molecular field analysis (CoMFA) and vibrational frequency-based eigenvalue (EVA) descriptors to model molecular structure-photovoltaic performance relationships for a set of 40 coumarin derivatives. The results show that the models obtained provide statistically robust predictions of important photovoltaic parameters such as PCE, the open-circuit voltage (V(OC)), short-circuit current (J(SC)) and the peak absorption wavelength λ(max). Some of our findings based on the analysis of the models are in accordance with those reported in the literature. These structure-property relationships can be applied to the rational structural design and evaluation of new photovoltaic materials.

  4. Quantitative structure property relationships for the adsorption of pharmaceuticals onto activated carbon.

    PubMed

    Dickenson, E R V; Drewes, J E

    2010-01-01

    Isotherms were determined for the adsorption of five pharmaceutical residues, primidone, carbamazepine, ibuprofen, naproxen and diclofenac, to Calgon Filtrasorb 300 powdered activated carbon (PAC). The sorption behavior was examined in ultra-pure and wastewater effluent organic matter (EfOM) matrices, where more sorption was observed in the ultra-pure water for PAC doses greater than 10 mg/L suggesting the presence of EfOM hinders the sorption of the pharmaceuticals to the PAC. Adsorption behaviors were described by the Freundlich isotherm model. Quantitative structure property relationships (QSPRs) in the form of polyparameter linear solvation energy relationships were developed for simulating the Freundlich adsorption capacity in both ultra-pure and EfOM matrices. The significant 3D-based descriptors for the QSPRs were the molar volume, polarizability and hydrogen-bond donor parameters.

  5. Application of quantitative structure-property relationship analysis to estimate the vapor pressure of pesticides.

    PubMed

    Goodarzi, Mohammad; Coelho, Leandro dos Santos; Honarparvar, Bahareh; Ortiz, Erlinda V; Duchowicz, Pablo R

    2016-06-01

    The application of molecular descriptors in describing Quantitative Structure Property Relationships (QSPR) for the estimation of vapor pressure (VP) of pesticides is of ongoing interest. In this study, QSPR models were developed using multiple linear regression (MLR) methods to predict the vapor pressure values of 162 pesticides. Several feature selection methods, namely the replacement method (RM), genetic algorithms (GA), stepwise regression (SR) and forward selection (FS), were used to select the most relevant molecular descriptors from a pool of variables. The optimum subset of molecular descriptors was used to build a QSPR model to estimate the vapor pressures of the selected pesticides. The Replacement Method improved the predictive ability of vapor pressures and was more reliable for the feature selection of these selected pesticides. The results provided satisfactory MLR models that had a satisfactory predictive ability, and will be important for predicting vapor pressure values for compounds with unknown values. This study may open new opportunities for designing and developing new pesticide.

  6. Boiling points of halogenated aliphatic compounds: a quantitative structure-property relationship for prediction and validation.

    PubMed

    Oberg, Tomas

    2004-01-01

    Halogenated aliphatic compounds have many technical uses, but substances within this group are also ubiquitous environmental pollutants that can affect the ozone layer and contribute to global warming. The establishment of quantitative structure-property relationships is of interest not only to fill in gaps in the available database but also to validate experimental data already acquired. The three-dimensional structures of 240 compounds were modeled with molecular mechanics prior to the generation of empirical descriptors. Two bilinear projection methods, principal component analysis (PCA) and partial-least-squares regression (PLSR), were used to identify outliers. PLSR was subsequently used to build a multivariate calibration model by extracting the latent variables that describe most of the covariation between the molecular structure and the boiling point. Boiling points were also estimated with an extension of the group contribution method of Stein and Brown.

  7. Quantitative structure-property relationships for prediction of boiling point, vapor pressure, and melting point.

    PubMed

    Dearden, John C

    2003-08-01

    Boiling point, vapor pressure, and melting point are important physicochemical properties in the modeling of the distribution and fate of chemicals in the environment. However, such data often are not available, and therefore must be estimated. Over the years, many attempts have been made to calculate boiling points, vapor pressures, and melting points by using quantitative structure-property relationships, and this review examines and discusses the work published in this area, and concentrates particularly on recent studies. A number of software programs are commercially available for the calculation of boiling point, vapor pressure, and melting point, and these have been tested for their predictive ability with a test set of 100 organic chemicals.

  8. Development of quantitative structure property relationships for predicting the melting point of energetic materials.

    PubMed

    Morrill, Jason A; Byrd, Edward F C

    2015-11-01

    The accurate prediction of the melting temperature of organic compounds is a significant problem that has eluded researchers for many years. The most common approach used to develop predictive models entails the derivation of quantitative structure-property relationships (QSPRs), which are multivariate linear relationships between calculated quantities that are descriptors of molecular or electronic features and a property of interest. In this report the derivation of QSPRs to predict melting temperatures of energetic materials based on descriptors calculated using the AM1 semiempirical quantum mechanical method are described. In total, the melting points and experimental crystal structures of 148 energetic materials were analyzed. Principal components analysis was performed in order to assess the relative importance and roles of the descriptors in our QSPR models. Also described are the results of k means cluster analysis, performed in order to identify natural groupings within our study set of structures. The QSPR models resulting from these analyses gave training set R(2) values of 0.6085 (RMSE = ± 15.7 °C) and 0.7468 (RMSE = ± 13.2 °C). The test sets for these clusters had R(2) values of 0.9428 (RMSE = ± 7.0 °C) and 0.8974 (RMSE = ± 8.8 °C), respectively. These models are among the best melting point QSPRs yet published for energetic materials.

  9. Interactions of Indole Derivatives with β-Cyclodextrin: A Quantitative Structure-Property Relationship Study

    PubMed Central

    Šoškić, Milan; Porobić, Ivana

    2016-01-01

    Retention factors for 31 indole derivatives, most of them with auxin activity, were determined by high-performance liquid chromatography, using bonded β-cyclodextrin as a stationary phase. A three-parameter QSPR (quantitative structure-property relationship) model, based on physico-chemical and structural descriptors was derived, which accounted for about 98% variations in the retention factors. The model suggests that the indole nucleus occupies the relatively apolar cavity of β-cyclodextrin while the carboxyl group of the indole -3-carboxylic acids makes hydrogen bonds with the hydroxyl groups of β-cyclodextrin. The length and flexibility of the side chain containing carboxyl group strongly affect the binding of these compounds to β-cyclodextrin. Non-acidic derivatives, unlike the indole-3-carboxylic acids, are poorly retained on the column. A reasonably well correlation was found between the retention factors of the indole-3-acetic acids and their relative binding affinities for human serum albumin, a carrier protein in the blood plasma. A less satisfactory correlation was obtained when the retention factors of the indole derivatives were compared with their affinities for auxin-binding protein 1, a plant auxin receptor. PMID:27124734

  10. Quantitative structure-property relationship modeling of remote liposome loading of drugs.

    PubMed

    Cern, Ahuva; Golbraikh, Alexander; Sedykh, Aleck; Tropsha, Alexander; Barenholz, Yechezkel; Goldblum, Amiram

    2012-06-10

    Remote loading of liposomes by trans-membrane gradients is used to achieve therapeutically efficacious intra-liposome concentrations of drugs. We have developed Quantitative Structure Property Relationship (QSPR) models of remote liposome loading for a data set including 60 drugs studied in 366 loading experiments internally or elsewhere. Both experimental conditions and computed chemical descriptors were employed as independent variables to predict the initial drug/lipid ratio (D/L) required to achieve high loading efficiency. Both binary (to distinguish high vs. low initial D/L) and continuous (to predict real D/L values) models were generated using advanced machine learning approaches and 5-fold external validation. The external prediction accuracy for binary models was as high as 91-96%; for continuous models the mean coefficient R(2) for regression between predicted versus observed values was 0.76-0.79. We conclude that QSPR models can be used to identify candidate drugs expected to have high remote loading capacity while simultaneously optimizing the design of formulation experiments.

  11. Predicting adsorption of aromatic compounds by carbon nanotubes based on quantitative structure property relationship principles

    NASA Astrophysics Data System (ADS)

    Rahimi-Nasrabadi, Mehdi; Akhoondi, Reza; Pourmortazavi, Seied Mahdi; Ahmadi, Farhad

    2015-11-01

    Quantitative structure property relationship (QSPR) models were developed to predict the adsorption of aromatic compounds by carbon nanotubes (CNTs). Five descriptors chosen by combining self-organizing map and stepwise multiple linear regression (MLR) techniques were used to connect the structure of the studied chemicals with their adsorption descriptor (K∞) using linear and nonlinear modeling techniques. Correlation coefficient (R2) of 0.99 and root-mean square error (RMSE) of 0.29 for multilayered perceptron neural network (MLP-NN) model are signs of the superiority of the developed nonlinear model over MLR model with R2 of 0.93 and RMSE of 0.36. The results of cross-validation test showed the reliability of MLP-NN to predict the K∞ values for the aromatic contaminants. Molar volume and hydrogen bond accepting ability were found to be the factors much influencing the adsorption of the compounds. The developed QSPR, as a neural network based model, could be used to predict the adsorption of organic compounds by CNTs.

  12. Quantitative structure-property relationships for octanol-water partition coefficients of polybrominated diphenyl ethers.

    PubMed

    Li, Linnan; Xie, Shaodong; Cai, Hao; Bai, Xuetao; Xue, Zhao

    2008-08-01

    Theoretical molecular descriptors were tested against logK(OW) values for polybrominated diphenyl ethers (PBDEs) using the Partial Least-Squares Regression method which can be used to analyze data with many variables and few observations. A quantitative structure-property relationship (QSPR) model was successfully developed with a high cross-validated value (Q(cum)(2)) of 0.961, indicating a good predictive ability and stability of the model. The predictive power of the QSPR model was further cross-validated. The values of logK(OW) for PBDEs are mainly governed by molecular surface area, energy of the lowest unoccupied molecular orbital and the net atomic charges on the oxygen atom. All these descriptors have been discussed to interpret the partitioning mechanism of PBDE chemicals. The bulk property of the molecules represented by molecular surface area is the leading factor, and K(OW) values increase with the increase of molecular surface area. Higher energy of the lowest unoccupied molecular orbital and higher net atomic charge on the oxygen atom of PBDEs result in smaller K(OW). The energy of the lowest unoccupied molecular orbital and the net atomic charge on PBDEs oxygen also play important roles in affecting the partition of PBDEs between octanol and water by influencing the interactions between PBDEs and solvent molecules.

  13. Predicting total organic halide formation from drinking water chlorination using quantitative structure-property relationships.

    PubMed

    Luilo, G B; Cabaniss, S E

    2011-10-01

    Chlorinating water which contains dissolved organic matter (DOM) produces disinfection byproducts, the majority of unknown structure. Hence, the total organic halide (TOX) measurement is used as a surrogate for toxic disinfection byproducts. This work derives a robust quantitative structure-property relationship (QSPR) for predicting the TOX formation potential of model compounds. Literature data for 49 compounds were used to train the QSPR in moles of chlorine per mole of compound (Cp) (mol-Cl/mol-Cp). The resulting QSPR has four descriptors, calibration [Formula: see text] of 0.72 and standard deviation of estimation of 0.43 mol-Cl/mol-Cp. Internal and external validation indicate that the QSPR has good predictive power and low bias (‰<‰1%). Applying this QSPR to predict TOX formation by DOM surrogates - tannic acid, two model fulvic acids and two agent-based model assemblages - gave a predicted TOX range of 136-184 µg-Cl/mg-C, consistent with experimental data for DOM, which ranged from 78 to 192 µg-Cl/mg-C. However, the limited structural variation in the training data may limit QSPR applicability; studies of more sulfur-containing compounds, heterocyclic compounds and high molecular weight compounds could lead to a more widely applicable QSPR.

  14. Prediction of photosensitivity of 1,4-dihydropyridine antihypertensives by quantitative structure-property relationship.

    PubMed

    Ioele, Giuseppina; De Luca, Michele; Oliverio, Filomena; Ragno, Gaetano

    2009-10-15

    A quantitative structure-property relationships (QSPR) model, correlating the light sensitivity against theoretical molecular descriptors, was developed for a set of 1,4-dihydropyridine calcium channel antagonist drugs. These compounds are characterized by a high tendency to degradation when exposed to light, furnishing in the most of cases a related oxidation product from aromatization of the dihydropyridinic ring. Photodegradation was forced by exposing the drugs to a Xenon lamp, in accordance with the ICH international rules, and degradation kinetics was monitored by spectrophotometry. The photodegradation rates combined with a series of descriptors related to the chemical structures were computed by Partial Least Squares (PLS) multivariate analysis. An accurate selection of the variables, fitting at the best the PLS model, was performed. Two descriptors related to the substituent information on both the dihydropyridinic and benzenic rings and four molecular descriptors, were selected. The QSPR model was fully cross validated and then optimized with an external set of novel 1,4-dihydropyridine drugs, obtaining very satisfactory statistical results. The good agreement between predicted and measured photodegradation rate (R(2)=0.8727) demonstrated the high accuracy of the QSPR model in predicting the photosensitivity of the drugs belonging to this class. The model was finally proposed as an effective tool to design new congeneric molecules characterized by high photostability.

  15. A quantum mechanical quantitative structure-property relationship study of the melting point of a variety of organosilicons.

    PubMed

    Liu, Yi; Holder, Andrew J

    2011-11-01

    We have developed quantitative structure-property relationship (QSPR) models that correlate the melting points of chain and cyclic silanes and siloxanes with their molecular structures. A comprehensive correlation was derived for a variety of molecules, but the quality of the comprehensive model was modest at best. This provided the impetus for the development of two additional models focused on silanes and siloxanes, respectively. Statistical analyses confirm the robustness of the refined models, and the chemical interpretation of the descriptors was consistent with effects expected for melting.

  16. Quantitative Structure-Property Relationship (QSPR) Modeling of Drug-Loaded Polymeric Micelles via Genetic Function Approximation

    PubMed Central

    Lin, Wenjing; Chen, Quan; Guo, Xindong; Qian, Yu; Zhang, Lijuan

    2015-01-01

    Self-assembled nano-micelles of amphiphilic polymers represent a novel anticancer drug delivery system. However, their full clinical utilization remains challenging because the quantitative structure-property relationship (QSPR) between the polymer structure and the efficacy of micelles as a drug carrier is poorly understood. Here, we developed a series of QSPR models to account for the drug loading capacity of polymeric micelles using the genetic function approximation (GFA) algorithm. These models were further evaluated by internal and external validation and a Y-randomization test in terms of stability and generalization, yielding an optimization model that is applicable to an expanded materials regime. As confirmed by experimental data, the relationship between microstructure and drug loading capacity can be well-simulated, suggesting that our models are readily applicable to the quantitative evaluation of the drug-loading capacity of polymeric micelles. Our work may offer a pathway to the design of formulation experiments. PMID:25780923

  17. Quantitative structure-property relationship of aromatic sulfur-containing carboxylates.

    PubMed

    Liu, Xin-hui; Yang, Zhi-feng; Wang, Lian-sheng

    2003-11-01

    Based on quantum chemical calculations, TLSER model (theoretical linear solvation energy relationships) and atomic charge approach were applied to model the partition properties(water solubility and octanol/water partition coefficient) of 96 aromatic sulfur-containing carboxylates, including phenylthio, phenylsulfinyl and phenylsulfonyl carboxylates. In comparison with TLSER models, the atomic charge models are more accurate and reliable to predict the partition properties of the kind of compounds. For the atomic charge models, the molecular descriptors are molecular surface area (S), molecular shape (O), weight( MW), net charges on carboxyl group (QOC), net charges of nitrogen atoms (QN), and the most negative atomic charge (q-) of the solute molecule. For water solubility (log SW) and octanol/water partition coefficient (log KOW), the correction coefficients r2adj (adjusted for degrees of freedom) are 0.936 and 0.938, and the standard deviations are 0.364 and 0.223, respectively.

  18. Quantitative structure--property relationships for enhancing predictions of synthetic organic chemical removal from drinking water by granular activated carbon.

    PubMed

    Magnuson, Matthew L; Speth, Thomas F

    2005-10-01

    Granular activated carbon is a frequently explored technology for removing synthetic organic contaminants from drinking water sources. The success of this technology relies on a number of factors based not only on the adsorptive properties of the contaminant but also on properties of the water itself, notably the presence of substances in the water which compete for adsorption sites. Because it is impractical to perform field-scale evaluations for all possible contaminants, the pore surface diffusion model (PSDM) has been developed and used to predict activated carbon column performance using single-solute isotherm data as inputs. Many assumptions are built into this model to account for kinetics of adsorption and competition for adsorption sites. This work further evaluates and expands this model, through the use of quantitative structure-property relationships (QSPRs) to predict the effect of natural organic matter fouling on activated carbon adsorption of specific contaminants. The QSPRs developed are based on a combination of calculated topographical indices and quantum chemical parameters. The QSPRs were evaluated in terms of their statistical predictive ability,the physical significance of the descriptors, and by comparison with field data. The QSPR-enhanced PSDM was judged to give results better than what could previously be obtained.

  19. Quantitative structure-property relationship analysis for the retention index of fragrance-like compounds on a polar stationary phase.

    PubMed

    Rojas, Cristian; Duchowicz, Pablo R; Tripaldi, Piercosimo; Pis Diez, Reinaldo

    2015-11-27

    A quantitative structure-property relationship (QSPR) was developed for modeling the retention index of 1184 flavor and fragrance compounds measured using a Carbowax 20M glass capillary gas chromatography column. The 4885 molecular descriptors were calculated using Dragon software, and then were simultaneously analyzed through multivariable linear regression analysis using the replacement method (RM) variable subset selection technique. We proceeded in three steps, the first one by considering all descriptor blocks, the second one by excluding conformational descriptor blocks, and the last one by analyzing only 3D-descriptor families. The models were validated through an external test set of compounds. Cross-validation methods such as leave-one-out and leave-many-out were applied, together with Y-randomization and applicability domain analysis. The developed model was used to estimate the I of a set of 22 molecules. The results clearly suggest that 3D-descriptors do not offer relevant information for modeling the retention index, while a topological index such as the Randić-like index from reciprocal squared distance matrix has a high relevance for this purpose.

  20. On the Development and Use of Large Chemical Similarity Networks, Informatics Best Practices and Novel Chemical Descriptors towards Materials Quantitative Structure Property Relationships

    ERIC Educational Resources Information Center

    Krein, Michael

    2011-01-01

    After decades of development and use in a variety of application areas, Quantitative Structure Property Relationships (QSPRs) and related descriptor-based statistical learning methods have achieved a level of infamy due to their misuse. The field is rife with past examples of overtrained models, overoptimistic performance assessment, and outright…

  1. Specific catalysis of asparaginyl deamidation by carboxylic acids: kinetic, thermodynamic, and quantitative structure-property relationship analyses.

    PubMed

    Connolly, Brian D; Tran, Benjamin; Moore, Jamie M R; Sharma, Vikas K; Kosky, Andrew

    2014-04-07

    Asparaginyl (Asn) deamidation could lead to altered potency, safety, and/or pharmacokinetics of therapeutic protein drugs. In this study, we investigated the effects of several different carboxylic acids on Asn deamidation rates using an IgG1 monoclonal antibody (mAb1*) and a model hexapeptide (peptide1) with the sequence YGKNGG. Thermodynamic analyses of the kinetics data revealed that higher deamidation rates are associated with predominantly more negative ΔS and, to a lesser extent, more positive ΔH. The observed differences in deamidation rates were attributed to the unique ability of each type of carboxylic acid to stabilize the energetically unfavorable transition-state conformations required for imide formation. Quantitative structure property relationship (QSPR) analysis using kinetic data demonstrated that molecular descriptors encoding for the geometric spatial distribution of atomic properties on various carboxylic acids are effective determinants for the deamidation reaction. Specifically, the number of O-O and O-H atom pairs on carboxyl and hydroxyl groups with interatomic distances of 4-5 Å on a carboxylic acid buffer appears to determine the rate of deamidation. Collectively, the results from structural and thermodynamic analyses indicate that carboxylic acids presumably form multiple hydrogen bonds and charge-charge interactions with the relevant deamidation site and provide alignment between the reactive atoms on the side chain and backbone. We propose that carboxylic acids catalyze deamidation by stabilizing a specific, energetically unfavorable transition-state conformation of l-asparaginyl intermediate II that readily facilitates bond formation between the γ-carbonyl carbon and the deprotonated backbone nitrogen for cyclic imide formation.

  2. A Quantitative Structure-Property Relationship (QSPR) Study of aliphatic alcohols by the method of dividing the molecular structure into substructure.

    PubMed

    Liu, Fengping; Cao, Chenzhong; Cheng, Bin

    2011-01-01

    A quantitative structure-property relationship (QSPR) analysis of aliphatic alcohols is presented. Four physicochemical properties were studied: boiling point (BP), n-octanol-water partition coefficient (lg P(OW)), water solubility (lg W) and the chromatographic retention indices (RI) on different polar stationary phases. In order to investigate the quantitative structure-property relationship of aliphatic alcohols, the molecular structure ROH is divided into two parts, R and OH to generate structural parameter. It was proposed that the property is affected by three main factors for aliphatic alcohols, alkyl group R, substituted group OH, and interaction between R and OH. On the basis of the polarizability effect index (PEI), previously developed by Cao, the novel molecular polarizability effect index (MPEI) combined with odd-even index (OEI), the sum eigenvalues of bond-connecting matrix (SX(1CH)) previously developed in our team, were used to predict the property of aliphatic alcohols. The sets of molecular descriptors were derived directly from the structure of the compounds based on graph theory. QSPR models were generated using only calculated descriptors and multiple linear regression techniques. These QSPR models showed high values of multiple correlation coefficient (R > 0.99) and Fisher-ratio statistics. The leave-one-out cross-validation demonstrated the final models to be statistically significant and reliable.

  3. Quantitative Relationships Between the Cytotoxicity of Flavonoids on the Human Breast Cancer Stem-Like Cells MCF7-SC and Their Structural Properties.

    PubMed

    Jung, Hyeryoung; Shin, Soon Young; Jung, Yearam; Tran, Thao Anh; Lee, Hye Ok; Jung, Kang-Yeoun; Koh, Dongsoo; Cho, Somi Kim; Lim, Yoongho

    2015-10-01

    As some breast cancer-related deaths can be attributed to the metastasis of cancer stem cells, chemotherapeutic agents targeting breast cancer stem cells are of interest as a potential treatment. Flavonoids that exhibit cytotoxicity on breast cancer stem cells have rarely been observed. Thus, the objective of this study was to measure potential cytotoxic effects of 42 different flavonoids on the human breast cancer stem-like cell line, MCF7-SC. The relationship between flavonoid structural properties and cytotoxicity has not been reported previously; therefore, we determined quantitative structure-activity relationships using both comparative molecular field analysis and comparative molecular similarity analysis. Further biological experiments including Western blot analysis, flow cytometry, and immunofluorescence microscopy were also conducted on the most cytotoxic 8-chloroflavanone.

  4. A quantitative structure-property relationship analysis of soot-water partition coefficients for persistent organic pollutants.

    PubMed

    Xu, Hui-Ying; Zou, Jian-Wei; Min, Jian-Qing; Wang, Wei

    2012-06-01

    Geometrical optimization and electrostatic potential calculations have been performed at the HF/6-31G level of theory for investigated persistent organic pollutants (POPs). A number of statistically based parameters have been obtained. Relationship between soot-water partition coefficients (logK(SC)) of POPs and the structural descriptors has been established by the multiple linear regression method. The result shows that the quantities derived from electrostatic potential V(s)(-)¯ and V(s,max), together with molecular surface area (A(S)) and the energy of the highest occupied molecular orbital (E(HOMO)) can be well used to express the quantitative relationship between structure and logK(SC) (QSPR) of POPs. Predictive capability of the model has been demonstrated by leave-one-out cross-validation with the cross-validated correlation coefficient of 0.9797. Furthermore, the predictive power of this model was further examined for the external test set with the correlation coefficient of 0.9811 between observed and predicted logK(SC), validating the robustness and good predictive ability of our model. Furthermore, in order to further investigate the applicability of these parameters derived from electrostatic potential in prediction of soot-water partition coefficient for organic pollutants, eleven polycyclic aromatic hydrocarbons (PAHs), eleven polychlorinated biphenyls (PCBs) and nine phenyl urea herbicides (PUHs) from other source have also been studied. The QSPR models established may provide a new powerful method for predicting soot-water partition coefficients (logK(SC)) of organic pollutants.

  5. Predicting equilibrium vapour pressure isotope effects by using artificial neural networks or multi-linear regression - A quantitative structure property relationship approach.

    PubMed

    Parinet, Julien; Julien, Maxime; Nun, Pierrick; Robins, Richard J; Remaud, Gerald; Höhener, Patrick

    2015-09-01

    We aim at predicting the effect of structure and isotopic substitutions on the equilibrium vapour pressure isotope effect of various organic compounds (alcohols, acids, alkanes, alkenes and aromatics) at intermediate temperatures. We attempt to explore quantitative structure property relationships by using artificial neural networks (ANN); the multi-layer perceptron (MLP) and compare the performances of it with multi-linear regression (MLR). These approaches are based on the relationship between the molecular structure (organic chain, polar functions, type of functions, type of isotope involved) of the organic compounds, and their equilibrium vapour pressure. A data set of 130 equilibrium vapour pressure isotope effects was used: 112 were used in the training set and the remaining 18 were used for the test/validation dataset. Two sets of descriptors were tested, a set with all the descriptors: number of(12)C, (13)C, (16)O, (18)O, (1)H, (2)H, OH functions, OD functions, CO functions, Connolly Solvent Accessible Surface Area (CSA) and temperature and a reduced set of descriptors. The dependent variable (the output) is the natural logarithm of the ratios of vapour pressures (ln R), expressed as light/heavy as in classical literature. Since the database is rather small, the leave-one-out procedure was used to validate both models. Considering higher determination coefficients and lower error values, it is concluded that the multi-layer perceptron provided better results compared to multi-linear regression. The stepwise regression procedure is a useful tool to reduce the number of descriptors. To our knowledge, a Quantitative Structure Property Relationship (QSPR) approach for isotopic studies is novel.

  6. Simple quantitative structure-property relationship (QSPR) modeling of 17O carbonyl chemical shifts in substituted benzaldehydes compared to DFT and empirical approaches.

    PubMed

    Kiralj, Rudolf; Ferreira, Márcia M C

    2008-07-10

    The geometry of 50 substituted benzaldehydes was optimized at the semiempirical PM3 level, and various electronic and steric descriptors accounting for properties of the benzene ring, aldehyde group, and their connecting carbon-carbon bond were calculated. Quantitative structure-property relationships (QSPR) between (17)O carbonyl chemical shifts and these descriptors were established using partial least-squares regression and principal component regression. These two parsimonious QSPR models were comparable with the literature empirical model and DFT (density functional theory) and capable of predicting (17)O chemical shifts for 10 benzaldehydes. Principal component analysis, hierarchical cluster analysis, and crystal structure data retrieved from the Cambridge Structural Database were additional methods for chemical verification of the regression models. The QSPR models are recommended as being more reliable than and superior to the empirical and DFT models due to the results of all validations, simplicity, and short time that regressions need for (17)O shift prediction.

  7. Predicting enthalpy of vaporization for Persistent Organic Pollutants with Quantitative Structure-Property Relationship (QSPR) incorporating the influence of temperature on volatility

    NASA Astrophysics Data System (ADS)

    Sosnowska, Anita; Barycki, Maciej; Jagiello, Karolina; Haranczyk, Maciej; Gajewicz, Agnieszka; Kawai, Toru; Suzuki, Noriyuki; Puzyn, Tomasz

    2014-04-01

    Enthalpy of vaporization (ΔHvap) is a thermodynamic property associated with the dispersal of Persistent Organic Pollutants (POPs) in the environment. Common problem in the environmental risk assessment studies is the lack of experimentally measured ΔHvap data. This problem can be solved by employing computational techniques, including QSPR (Quantitative Structure-Property Relationship) modelling to predict properties of interest. Majority of the published QSPR models can be applied to predict the enthalpy of vaporization of compounds from only one, particular group of POPs (i.e., polychlorinated biphenyls, PCBs). We have developed a more general QSPR model to estimate the ΔHvap values for 1436 polychlorinated and polybrominated benzenes, biphenyls, dibenzo-p-dioxins, dibenzofurans, diphenyl ethers, and naphthalenes. The QSPR model developed with Multiple Linear Regression analysis was characterized by satisfactory goodness-of-fit, robustness and the external predictive performance (R2 = 0.888, QCV2=0.878, QExt2=0.842, RMSEC = 5.11, RMSECV = 5.34, RMSEP = 5.74). Moreover, we quantified the temperature dependencies of vapour pressure for twelve groups of POPs based on the predictions at six different temperatures (logPL(T)). In addition, we found a simple arithmetic relationship between the logarithmic values of vapour pressure in pairs of chloro- and bromo-analogues. By employing this relationship it is possible to estimate logPL(T) for any brominated POP at any temperature utilizing only the logPL(T) value for its chlorinated analogues.

  8. A review of quantitative structure-property relationships for the fate of ionizable organic chemicals in water matrices and identification of knowledge gaps.

    PubMed

    Nolte, Tom M; Ragas, Ad M J

    2017-03-22

    Many organic chemicals are ionizable by nature. After use and release into the environment, various fate processes determine their concentrations, and hence exposure to aquatic organisms. In the absence of suitable data, such fate processes can be estimated using Quantitative Structure-Property Relationships (QSPRs). In this review we compiled available QSPRs from the open literature and assessed their applicability towards ionizable organic chemicals. Using quantitative and qualitative criteria we selected the 'best' QSPRs for sorption, (a)biotic degradation, and bioconcentration. The results indicate that many suitable QSPRs exist, but some critical knowledge gaps remain. Specifically, future focus should be directed towards the development of QSPR models for biodegradation in wastewater and sediment systems, direct photolysis and reaction with singlet oxygen, as well as additional reactive intermediates. Adequate QSPRs for bioconcentration in fish exist, but more accurate assessments can be achieved using pharmacologically based toxicokinetic (PBTK) models. No adequate QSPRs exist for bioconcentration in non-fish species. Due to the high variability of chemical and biological species as well as environmental conditions in QSPR datasets, accurate predictions for specific systems and inter-dataset conversions are problematic, for which standardization is needed. For all QSPR endpoints, additional data requirements involve supplementing the current chemical space covered and accurately characterizing the test systems used.

  9. Quantitative structure-property relationship modeling of water-to-wet butyl acetate partition coefficient of 76 organic solutes using multiple linear regression and artificial neural network.

    PubMed

    Dashtbozorgi, Zahra; Golmohammadi, Hassan

    2010-12-01

    The main aim of this study was the development of a quantitative structure-property relationship method using an artificial neural network (ANN) for predicting the water-to-wet butyl acetate partition coefficients of organic solutes. As a first step, a genetic algorithm-multiple linear regression model was developed; the descriptors appearing in this model were considered as inputs for the ANN. These descriptors are principal moment of inertia C (I(C)), area-weighted surface charge of hydrogen-bonding donor atoms (HACA-2), Kier and Hall index (order 2) ((2)χ), Balaban index (J), minimum bond order of a C atom (P(C)) and relative negative-charged SA (RNCS). Then a 6-4-1 neural network was generated for the prediction of water-to-wet butyl acetate partition coefficients of 76 organic solutes. By comparing the results obtained from multiple linear regression and ANN models, it can be seen that statistical parameters (Fisher ratio, correlation coefficient and standard error) of the ANN model are better than that regression model, which indicates that nonlinear model can simulate the relationship between the structural descriptors and the partition coefficients of the investigated molecules more accurately.

  10. Notes on quantitative structure-property relationships (QSPR), part 3: density functions origin shift as a source of quantum QSPR algorithms in molecular spaces.

    PubMed

    Carbó-Dorca, Ramon

    2013-04-05

    A general algorithm implementing a useful variant of quantum quantitative structure-property relationships (QQSPR) theory is described. Based on quantum similarity framework and previous theoretical developments on the subject, the present QQSPR procedure relies on the possibility to perform geometrical origin shifts over molecular density function sets. In this way, molecular collections attached to known properties can be easily used over other quantum mechanically well-described molecular structures for the estimation of their unknown property values. The proposed procedure takes quantum mechanical expectation value as provider of causal relation background and overcomes the dimensionality paradox, which haunts classical descriptor space QSPR. Also, contrarily to classical procedures, which are also attached to heavy statistical gear, the present QQSPR approach might use a geometrical assessment only or just some simple statistical outline or both. From an applied point of view, several easily reachable computational levels can be set up. A Fortran 95 program: QQSPR-n is described with two versions, which might be downloaded from a dedicated web site. Various practical examples are provided, yielding excellent results. Finally, it is also shown that an equivalent molecular space classical QSPR formalism can be easily developed.

  11. Quantitative structure-property relationship (QSPR) for the adsorption of organic compounds onto activated carbon cloth: Comparison between multiple linear regression and neural network

    SciTech Connect

    Brasquet, C.; Bourges, B.; Le Cloirec, P.

    1999-12-01

    The adsorption of 55 organic compounds is carried out onto a recently discovered adsorbent, activated carbon cloth. Isotherms are modeled using the Freundlich classical model, and the large database generated allows qualitative assumptions about the adsorption mechanism. However, to confirm these assumptions, a quantitative structure-property relationship methodology is used to assess the correlations between an adsorbability parameter (expressed using the Freundlich parameter K) and topological indices related to the compounds molecular structure (molecular connectivity indices, MCI). This correlation is set up by mean of two different statistical tools, multiple linear regression (MLR) and neural network (NN). A principal component analysis is carried out to generate new and uncorrelated variables. It enables the relations between the MCI to be analyzed, but the multiple linear regression assessed using the principal components (PCs) has a poor statistical quality and introduces high order PCs, too inaccurate for an explanation of the adsorption mechanism. The correlations are thus set up using the original variables (MCI), and both statistical tools, multiple linear regression and neutral network, are compared from a descriptive and predictive point of view. To compare the predictive ability of both methods, a test database of 10 organic compounds is used.

  12. Quantitative structure-property relationships of retention indices of some sulfur organic compounds using random forest technique as a variable selection and modeling method.

    PubMed

    Goudarzi, Nasser; Shahsavani, Davood; Emadi-Gandaghi, Fereshteh; Chamjangali, Mansour Arab

    2016-10-01

    In this work, a noble quantitative structure-property relationship technique is proposed on the basis of the random forest for prediction of the retention indices of some sulfur organic compounds. In order to calculate the retention indices of these compounds, the theoretical descriptors produced using their molecular structures are employed. The influence of the significant parameters affecting the capability of the developed random forest prediction power such as the number of randomly selected variables applied to split each node (m) and the number of trees (nt ) is studied to obtain the best model. After optimizing the nt and m parameters, the random forest model conducted for m = 70 and nt = 460 was found to yield the best results. The artificial neural network and multiple linear regression modeling techniques are also used to predict the retention index values for these compounds for comparison with the results of random forest model. The descriptors selected by the stepwise regression and random forest model are used to build the artificial neural network models. The results achieved showed the superiority of the random forest model over the other models for prediction of the retention indices of the studied compounds.

  13. On the Development and Use of Large Chemical Similarity Networks, Informatics Best Practices and Novel Chemical Descriptors Towards Materials Quantitative Structure Property Relationships

    NASA Astrophysics Data System (ADS)

    Krein, Michael

    After decades of development and use in a variety of application areas, Quantitative Structure Property Relationships (QSPRs) and related descriptor-based statistical learning methods have achieved a level of infamy due to their misuse. The field is rife with past examples of overtrained models, overoptimistic performance assessment, and outright cheating in the form of explicitly removing data to fit models. These actions do not serve the community well, nor are they beneficial to future predictions based on established models. In practice, in order to select combinations of descriptors and machine learning methods that might work best, one must consider the nature and size of the training and test datasets, be aware of existing hypotheses about the data, and resist the temptation to bias structure representation and modeling to explicitly fit the hypotheses. The definition and application of these best practices is important for obtaining actionable modeling outcomes, and for setting user expectations of modeling accuracy when predicting the endpoint values of unknowns. A wide variety of statistical learning approaches, descriptor types, and model validation strategies are explored herein, with the goals of helping end users understand the factors involved in creating and using QSPR models effectively, and to better understand relationships within the data, especially by looking at the problem space from multiple perspectives. Molecular relationships are commonly envisioned in a continuous high-dimensional space of numerical descriptors, referred to as chemistry space. Descriptor and similarity metric choice influence the partitioning of this space into regions corresponding to local structural similarity. These regions, known as domains of applicability, are most likely to be successfully modeled by a QSPR. In Chapter 2, the network topology and scaling relationships of several chemistry spaces are thoroughly investigated. Chemistry spaces studied include the

  14. Structure Property Relationships of Carboxylic Acid Isosteres.

    PubMed

    Lassalas, Pierrik; Gay, Bryant; Lasfargeas, Caroline; James, Michael J; Tran, Van; Vijayendran, Krishna G; Brunden, Kurt R; Kozlowski, Marisa C; Thomas, Craig J; Smith, Amos B; Huryn, Donna M; Ballatore, Carlo

    2016-04-14

    The replacement of a carboxylic acid with a surrogate structure, or (bio)-isostere, is a classical strategy in medicinal chemistry. The general underlying principle is that by maintaining the features of the carboxylic acid critical for biological activity, but appropriately modifying the physicochemical properties, improved analogs may result. In this context, a systematic assessment of the physicochemical properties of carboxylic acid isosteres would be desirable to enable more informed decisions of potential replacements to be used for analog design. Herein we report the structure-property relationships (SPR) of 35 phenylpropionic acid derivatives, in which the carboxylic acid moiety is replaced with a series of known isosteres. The data set generated provides an assessment of the relative impact on the physicochemical properties that these replacements may have compared to the carboxylic acid analog. As such, this study presents a framework for how to rationally apply isosteric replacements of the carboxylic acid functional group.

  15. Structure Property Relationships of Biobased Epoxy Resins

    NASA Astrophysics Data System (ADS)

    Maiorana, Anthony Surraht

    The thesis is about the synthesis, characterization, development, and application of epoxy resins derived from sustainable feedstocks such as lingo-cellulose, plant oils, and other non-food feedstocks. The thesis can be divided into two main topics 1) the synthesis and structure property relationship investigation of new biobased epoxy resin families and 2) mixing epoxy resins with reactive diluents, nanoparticles, toughening agents, and understanding co-curing reactions, filler/matrix interactions, and cured epoxy resin thermomechanical, viscoelastic, and dielectric properties. The thesis seeks to bridge the gap between new epoxy resin development, application for composites and advanced materials, processing and manufacturing, and end of life of thermoset polymers. The structures of uncured epoxy resins are characterized through traditional small molecule techniques such as nuclear magnetic resonance, high resolution mass spectrometry, and infrared spectroscopy. The structure of epoxy resin monomers are further understood through the process of curing the resins and cured resins' properties through rheology, chemorheology, dynamic mechanical analysis, tensile testing, fracture toughness, differential scanning calorimetry, scanning electron microscopy, thermogravimetric analysis, and notched izod impact testing. It was found that diphenolate esters are viable alternatives to bisphenol A and that the structure of the ester side chain can have signifi-cant effects on monomer viscosity. The structure of the cured diphenolate based epoxy resins also influence glass transition temperature and dielectric properties. Incorporation of reactive diluents and flexible resins can lower viscosity, extend gel time, and enable processing of high filler content composites and increase fracture toughness. Incorpora-tion of high elastic modulus nanoparticles such as graphene can provide increases in physical properties such as elastic modulus and fracture toughness. The synthesis

  16. Evaluation of a quantitative structure-property relationship (QSPR) for predicting mid-visible refractive index of secondary organic aerosol (SOA).

    PubMed

    Redmond, Haley; Thompson, Jonathan E

    2011-04-21

    In this work we describe and evaluate a simple scheme by which the refractive index (λ = 589 nm) of non-absorbing components common to secondary organic aerosols (SOA) may be predicted from molecular formula and density (g cm(-3)). The QSPR approach described is based on three parameters linked to refractive index-molecular polarizability, the ratio of mass density to molecular weight, and degree of unsaturation. After computing these quantities for a training set of 111 compounds common to atmospheric aerosols, multi-linear regression analysis was conducted to establish a quantitative relationship between the parameters and accepted value of refractive index. The resulting quantitative relationship can often estimate refractive index to ±0.01 when averaged across a variety of compound classes. A notable exception is for alcohols for which the model consistently underestimates refractive index. Homogenous internal mixtures can conceivably be addressed through use of either the volume or mole fraction mixing rules commonly used in the aerosol community. Predicted refractive indices reconstructed from chemical composition data presented in the literature generally agree with previous reports of SOA refractive index. Additionally, the predicted refractive indices lie near measured values we report for λ = 532 nm for SOA generated from vapors of α-pinene (R.I. 1.49-1.51) and toluene (R.I. 1.49-1.50). We envision the QSPR method may find use in reconstructing optical scattering of organic aerosols if mass composition data is known. Alternatively, the method described could be incorporated into in models of organic aerosol formation/phase partitioning to better constrain organic aerosol optical properties.

  17. Structure Property Relationships of Carboxylic Acid Isosteres

    PubMed Central

    2016-01-01

    The replacement of a carboxylic acid with a surrogate structure, or (bio)-isostere, is a classical strategy in medicinal chemistry. The general underlying principle is that by maintaining the features of the carboxylic acid critical for biological activity, but appropriately modifying the physicochemical properties, improved analogs may result. In this context, a systematic assessment of the physicochemical properties of carboxylic acid isosteres would be desirable to enable more informed decisions of potential replacements to be used for analog design. Herein we report the structure–property relationships (SPR) of 35 phenylpropionic acid derivatives, in which the carboxylic acid moiety is replaced with a series of known isosteres. The data set generated provides an assessment of the relative impact on the physicochemical properties that these replacements may have compared to the carboxylic acid analog. As such, this study presents a framework for how to rationally apply isosteric replacements of the carboxylic acid functional group. PMID:26967507

  18. Structure-Property Relationships of Bismaleimides

    NASA Technical Reports Server (NTRS)

    Tenteris-Noebe, Anita D.

    1997-01-01

    The purpose of this research was to control and systematically vary the network topology of bismaleimides through cure temperature and chemistry (addition of various coreactants) and subsequently attempt to determine structure-mechanical property relationships. Characterization of the bismaleimide structures by dielectric, rheological, and thermal analyses, and density measurements was subsequently correlated with mechanical properties such as modulus, yield strength, fracture energy, and stress relaxation. The model material used in this investigation was 4,4'-BismaleiMidodIphenyl methane (BMI). BMI was coreacted with either 4,4'-Methylene Dianiline (MDA), o,o'-diallyl bisphenol A (DABA) from Ciba Geigy, or Diamino Diphenyl Sulfone (DDS). Three cure paths were employed: a low- temperature cure of 140 C where chain extension should predominate, a high-temperature cure of 220 C where both chain extension and crosslinking should occur simultaneously, and a low-temperature (140 C) cure followed immediately by a high-temperature (220 C) cure where the chain extension reaction or amine addition precedes BMI homopolymerization or crosslinking. Samples of cured and postcured PMR-15 were also tested to determine the effects of postcuring on the mechanical properties. The low-temperature cure condition of BMI/MDA exhibited the highest modulus values for a given mole fraction of BMI with the modulus decreasing with decreasing concentration of BMI. The higher elastic modulus is the result of steric hindrance by unreacted BMI molecules in the glassy state. The moduli values for the high- and low/high-temperature cure conditions of BMI/MDA decreased as the amount of diamine increased. All the moduli values mimic the yield strength and density trends. For the high-temperature cure condition, the room- temperature modulus remained constant with decreasing mole fraction of BMT for the BMI/DABA and BMI/DDS systems. Postcuring PMR-15 increases the modulus over that of the cured

  19. Structure-property Relationships for Methyl-terminated Alkyl Self-assembled Monolayers

    SciTech Connect

    F DelRio; D Rampulla; C Jaye; G Stan; R Gates; D Fischer; R Cook

    2011-12-31

    Structure-property relationships for methyl-terminated alkyl self-assembled monolayers (SAMs) are developed using near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and atomic force microscopy (AFM). NEXAFS C K-edge spectra are used to compute the dichroic ratio, which provides a quantitative measure of the molecular structure. AFM data are analyzed with an elastic adhesive contact model, modified by a first-order elastic perturbation method to include substrate effects, to extract the monolayer mechanical properties. Using this approach, the measured mechanical properties are not influenced by the substrate, which allows universal structure-property relationships to be developed for methyl-terminated alkyl SAMs.

  20. Structure-Property Relationships of Solids in Pharmaceutical Processing

    NASA Astrophysics Data System (ADS)

    Chattoraj, Sayantan

    Pharmaceutical development and manufacturing of solid dosage forms is witnessing a seismic shift in the recent years. In contrast to the earlier days when drug development was empirical, now there is a significant emphasis on a more scientific and structured development process, primarily driven by the Quality-by-Design (QbD) initiatives of US Food and Drug Administration (US-FDA). Central to such an approach is the enhanced understanding of solid materials using the concept of Materials Science Tetrahedron (MST) that probes the interplay between four elements, viz., the structure, properties, processing, and performance of materials. In this thesis work, we have investigated the relationships between the structure and those properties of pharmaceutical solids that influence their processing behavior. In all cases, we have used material-sparing approaches to facilitate property assessment using very small sample size of materials, which is a pre-requisite in the early stages of drug development when the availability of materials, drugs in particular, is limited. The influence of solid structure, either at the molecular or bulk powder levels, on crystal plasticity and powder compaction, powder flow, and solid-state amorphization during milling, has been investigated in this study. Through such a systematic evaluation, we have captured the involvement of structure-property correlations within a wide spectrum of relevant processing behaviors of pharmaceutical solids. Such a holistic analysis will be beneficial for addressing both regulatory and scientific issues in drug development.

  1. Structure-Property Relationship in High Tg Thermosetting Polyimides

    NASA Technical Reports Server (NTRS)

    Chuang, Kathy C.; Meador, Mary Ann B.; HardyGreen, DeNise

    2000-01-01

    This viewgraph presentation gives an overview of the structure-property relationship in high glass transition temperatures (T(sub g)) thermosetting polyimides. The objectives of this work are to replace MDA in PMR-15 with 2,2-substituted benzidine and to evaluate the thermo-oxidative stability and mechanical properties of DMBZ-15 against PMR-15. Details are given on the T(sub g) of polyimide resins, the x-ray crystal structure of 2,2-Bis(trifluoro)benzidine (BFBZ), the isothermal aging of polyimide resins at 288 C under 1 atm of circulating air, the compressive strength of polyimide composites, and a gas evaluation profile of DMBZ-15 polyimide resins.

  2. Bio-related noble metal nanoparticle structure property relationships

    NASA Astrophysics Data System (ADS)

    Leonard, Donovan Nicholas

    Structure property relationships of noble metal nanoparticles (NPs) can be drastically different than bulk properties of the same metals. This research study used state-of-the-art analytical electron microscopy and scanned probe microscopy to determine material properties on the nanoscale of bio-related Au and Pd NPs. Recently, it has been demonstrated the self-assembly of Au NPs on functionalized silica surfaces creates a conductive surface. Determination of the aggregate morphology responsible for electron conduction was studied by atomic force microscopy (AFM) and scanning electron microscopy (SEM). In addition, changes in the electrical properties of the substrates after low temperature (<350°C) annealing was also studied. It was found that coalescence and densification of the Au NP aggregates disrupted the interconnected network which subsequently created a loss of conductivity. Investigation of bio-related Au/SiO2 core-shell NPs determined why published experimental results showed the sol-gel silica shell improved, by almost an order of magnitude, the detection efficiency of a DNA detection assay. Novel 360° rotation scanning TEM (STEM) imaging allowed study of individual NP surface morphology and internal structure. Electron energy loss spectroscopy (EELS) spectrum imaging determined optoelectronic properties and chemical composition of the silica shell used to encapsulate Au NPs. Results indicated the sol-gel deposited SiO2 had a band gap energy of ˜8.9eV, bulk plasmon-peak energy of ˜25.5eV and chemical composition of stoichiometric SiO2. Lastly, an attempt to elicit structure property relationships of novel RNA mediated Pd hexagon NPs was performed. Selected area electron diffraction (SAD), low voltage scanning transmission electron microscopy (LV-STEM), electron energy loss spectroscopy (EELS) and energy dispersive spectroscopy (EDS) were chosen for characterization of atomic ordering, chemical composition and optoelectronic properties of the novel

  3. Structure-property relationships in graphene/polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Iqbal, Muhammad Z.

    Graphene's unique combination of excellent electrical, thermal, and mechanical properties can provide multi-functional reinforcement for polymer nanocomposites. However, poor dispersion of graphene in non-polar polyolefins limits its applications as a universal filler. Thus, the overall goal of this thesis was to improve graphene's dispersion in graphene/polyolefin nanocomposites and develop processing-structure-property relationships. A new polymer matrix was synthesized by blending polyethylene (PE) with oxidized polyethylene (OPE). Inclusion of OPE in PE produced miscible blends, but the miscibility decreased with increasing OPE loading. Meanwhile, the Young's modulus of blends increased with increasing OPE concentration, attributed to decreased long period order in PE and increased crystallinity. In addition, the miscibility of OPE in PE substantially reduced the viscosity of blends. Using thermally reduced graphene (TRG) produced by simultaneous thermal exfoliation and reduction of graphite oxide, electrically conductive nanocomposites were manufactured by incorporating TRG in PE/OPE blends via solution blending. The rheological and electrical percolations decreased substantially to 0.3 and 0.13 vol% of TRG in PE/OPE/TRG nanocomposites compared to 1.0 and 0.3 vol% in PE/TRG nanocomposites. Improved dispersion of TRG in blends was attributed to increased TRG/polymer interactions, leading to high aspect ratio of the dispersed TRG. A universal Brownian dispersion mechanism for graphene was concluded similar to that of carbon nanotubes, following the Doi-Edwards theory. Furthermore, the improved dispersion of TRG correlated with the formation of surface fractals in PE/OPE/TRG nanocomposites, whereas the poor dispersion of TRG in PE led to the formation of only mass fractals. Moreover, graphene and carbon black (CB) were combined as a synergic filler for manufacturing electrically conductive PE nanocomposites. Smaller fractals were observed at lower CB

  4. Structure-property relationships in polymers for dielectric capacitors

    NASA Astrophysics Data System (ADS)

    Gupta, Sahil

    Effective energy storage is a key challenge of the 21st century that has fueled research in the area of energy storage devices. In this dissertation, structure-property relationships have been evaluated for polymers that might be suitable for storing energy in high-energy density, high-temperature capacitors. Firstly, hydroxyl-modified polypropylenes (PPOH) were synthesized by copolymerization of the propylene and undecenyloxytrimethylsilane monomers. The presence of H-bonding in PPOH copolymers increased their glass-transition temperature. Steric hindrance by the comonomer reduced the PP crystal growth rate and crystal size, resulting in a melting point depression. The comonomer was restricted outside the crystalline domains leaving the alpha-monoclinic crystal structure of PP unaffected, but increasing the fold-surface free energy. Crystallization was slower for PPOH copolymers than PP, but exhibited a skewed bell curve as a function of hydroxyl concentration. H-bonding persisted even at melt temperatures up to 250°C resulting in a higher elasticity and viscosity for PPOH copolymers. Secondly, sulfonated poly(ether ether ketone) (HSPEEK) was synthesized by sulfonating PEEK with sulfuric acid, and further neutralized with Zn to obtain ZnSPEEK. The thermal and dielectric properties of SPEEK were compared with PEEK. The glass-transition increased and melting point were high enough to enable the use of polymer at 180°C. The incorporation of sulfonic groups in PEEK increased the dielectric constant. HSPEEK had a higher dielectric constant than ZnSPEEK due to higher dipolar mobility, but the dielectric loss was also higher for HSPEEK due to electrode polarization and DC conduction. These results were consistent with our observations from sulfonated polystyrene (HSPS), which was used as a >model&lang' polymer. Lastly, commercial poly(4-methyl-1-pentene) (P4MP) was characterized to check its viability as a high-temperature polymer dielectric. Thermal stability up to

  5. Structure-property relationships of multiferroic materials: A nano perspective

    NASA Astrophysics Data System (ADS)

    Bai, Feiming

    The integration of sensors, actuators, and control systems is an ongoing process in a wide range of applications covering automotive, medical, military, and consumer electronic markets. Four major families of ceramic and metallic actuators are under development: piezoelectrics, electrostrictors, magnetostrictors, and shape-memory alloys. All of these materials undergo at least two phase transformations with coupled thermodynamic order parameters. These transformations lead to complex domain wall behaviors, which are driven by electric fields (ferroelectrics), magnetic fields (ferromagnetics), or mechanical stress (ferroelastics) as they transform from nonferroic to ferroic states, contributing to the sensing and actuating capabilities. This research focuses on two multiferroic crystals, Pb(Mg1/3Nb 2/3)O3-PbTiO3 and Fe-Ga, which are characterized by the co-existence and coupling of ferroelectric polarization and ferroelastic strain, or ferro-magnetization and ferroelastic strain. These materials break the conventional boundary between piezoelectric and electrostrictors, or magnetostrictors and shape-memory alloys. Upon applying field or in a poled condition, they yield not only a large strain but also a large strain over field ratio, which is desired and much benefits for advanced actuator and sensor applications. In this thesis, particular attention has been given to understand the structure-property relationships of these two types of materials from atomic to the nano/macro scale. X-ray and neutron diffraction were used to obtain the lattice structure and phase transformation characteristics. Piezoresponse and magnetic force microscopy were performed to establish the dependence of domain configurations on composition, thermal history and applied fields. It has been found that polar nano regions (PNRs) make significant contributions to the enhanced electromechanical properties of PMN-x%PT crystals via assisting intermediate phase transformation. With increasing PT

  6. Structure-property relationships in silica-siloxane nanocomposite materials

    SciTech Connect

    Ulibarri, T.A.; Derzon, D.K.; Wang, L.C.

    1997-03-01

    The simultaneous formation of a filler phase and a polymer matrix via in situ sol-gel techniques provides silica-siloxane nanocomposite materials of high strength. This study concentrates on the effects of temperature and relative humidity on a trimodal polymer system in an attempt to accelerate the reaction as well as evaluate subtle process- structure-property relations. It was found that successful process acceleration is only viable for high humidity systems when using the tin(IV) catalyst dibutyltin dilaurate. Processes involving low humidity were found to be very temperature and time dependent. Bimodal systems were investigated and demonstrated that the presence of a short-chain component led to enhanced material strength. This part of the study also revealed a link between the particle size and population density and the optimization of material properties.

  7. Structure-property relationships in major ampullate spider silk as deduced from polarized FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Papadopoulos, P.; Sölter, J.; Kremer, F.

    2007-10-01

    Polarized Fourier Transform Infrared (FTIR) spectroscopy is employed to study structure-property relationships in major ampullate spider silk being exposed to an external mechanical strain. From the measured infrared dichroism of aminoacid-residue - specific bands the molecular order parameter, the frequency width at half-maximum (FWHM) and the spectral position of the absorption maximum are determined in dependence on the external strain. For the highly ordered alanine-rich β sheets a change in the vibrational potential is found for macroscopic strains as low as a few percent. It can be quantitatively described by a quantum-mechanical approach in which the mechanical strain is treated as a weak external perturbation. The immediate microscopic response to the external field proves that β -sheeted crystals are tightly interconnected by pre-stretched chains as suggested recently (Y. Liu et al., Nat. Mater. 4, 901 (2005)).

  8. Structure-property relationships of flexible polyurethane foams

    NASA Astrophysics Data System (ADS)

    Aneja, Ashish

    This study examined several features of flexible polyurethane foams from a structure-property perspective. A major part of this dissertation addresses the issue of connectivity of the urea phase and its influence on mechanical and viscoelastic properties of flexible polyurethane foams and their plaque counterparts. Lithium salts (LiCl and LiBr) were used as additives to systematically alter the phase separation behavior, and hence the connectivity of the urea phase at different scale lengths. Macro connectivity, or the association of the large scale urea rich aggregates typically observed in flexible polyurethane foams was assessed using SAXS, TEM, and AFM. These techniques showed that including a lithium salt in the foam formulation suppressed the formation of the urea aggregates and thus led to a loss in the macro level connectivity of the urea phase. WAXS and FTIR were used to demonstrate that addition of LiCl or LiBr systematically disrupted the local ordering of the hard segments within the microdomains, i.e., it led to a reduction of micro level connectivity or the regularity in segmental packing of the urea phase. Based on these observations, the interaction of the lithium salt was thought to predominantly occur with the urea hard segments, and this hypothesis was confirmed using quantum mechanical calculations. Another feature of this research investigated model trisegmented polyurethanes based on monofunctional polyols, or "monos", with water-extended toluene diisocyanate (TDI) based hard segments. The formulations of the monol materials were maintained similar to those of flexible polyurethane foams with the exceptions that the conventional polyol was substituted by an oligomeric monofunctional polyether of ca. 1000 g/mol molecular weight. Plaques formed from these model systems were shown to be solid materials even at their relatively low molecular weights of 3000 g/mol and less, AFM phase images, for the first time, revealed the ability of the hard

  9. Structure-property relationships in semicrystalline copolymers and ionomers

    NASA Astrophysics Data System (ADS)

    Wakabayashi, Katsuyuki

    Many outstanding physical properties of ethylene/(meth)acrylic acid (E/(M)AA) copolymers and ionomers are associated with their nanometer-scale morphology, which consists of ethylene crystallites, amorphous segments, and acid/ionic functional groups. The goal of this dissertation is a fundamental understanding of the interplay between these structural motifs and the consequent effects on the material properties. We identify small-strain modulus as a key mechanical property and investigate its dependence upon material structure through X-ray scattering, calorimetry, and mechanical property measurements. We first treat E/(M)AA copolymers as composites of polyethylene crystallites and amorphous regions, and establish a quantitative combining rule to describe the copolymer modulus. At temperatures above the Tg of the copolymers, a monotonic increase in modulus with crystallinity is quantitatively described by the Davies equation for two-phase composites, which serves as the basis for separating the effects of amorphous and crystalline phases throughout this dissertation. The room-temperature modulus of E/(M)AA copolymers is concurrently affected by ethylene crystallinity and proximity to the amorphous phase Tg, which rises through room temperature with increasing comonomer content. In E/(M)AA ionomers, phase separation and aggregation of ionic groups provide additional stiffness and toughness. Ionomers are modeled as composites of crystallites and ionically crosslinked rubber, whose amorphous phase modulus far above the ionomer Tg is satisfactorily described by simple rubber elasticity theory. Thermomechanical analyses probe the multi-step relaxation behavior of E/(M)AA ionomers and lead to the development of a new semicrystalline ionomer morphological model, wherein secondary crystallites and ionic aggregates together form rigid percolated pathways throughout the amorphous phase. Metal soaps are oligomeric analogs of E/(M)AA ionomers, which can be blended into

  10. Incoloy 908 database report: On process -- structure -- property relationship

    SciTech Connect

    Toma, L.S.; Hwang, I.S.; Steeves, M.M.

    1993-05-01

    Incoloy 908 is a nickel-iron base superalloy with a coefficient of expansion (COE) and mechanical properties that have been optimized for use in Nb{sub 3}Sn superconducting magnets. It has been proposed for use as a conduit material for the International Thermonuclear Experimental Reactor (ITER) magnets. The relationship between manufacturing processes, microstructures and mechanical properties of Incoloy 908 are characterized in support of the magnet fabrication and quality control. This report presents microhardness, microstructure, and yield and ultimate tensile strengths as functions of thermomechanical process variables including heat treatment, annealing and cold work for laboratory prepared Incoloy 908 specimens. Empirical correlations have been developed for the microhardness at room temperature and tensile strength at room temperature and at 4K. These results may be used for manufacturing quality control or for design.

  11. An Investigation of College Chemistry Students' Understanding of Structure-Property Relationships

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Corley, Leah M.; Underwood, Sonia M.

    2013-01-01

    The connection between the molecular-level structure of a substance and its macroscopic properties is a fundamental concept in chemistry. Students in college-level general and organic chemistry courses were interviewed to investigate how they used structure-property relationships to predict properties such as melting and boiling points. Although…

  12. Processing-structure-property relationships of carbon nanotube and nanoplatelet enabled piezoresistive sensors

    NASA Astrophysics Data System (ADS)

    Luo, Sida

    Individual carbon nanotubes (CNTs) possess excellent piezoresistive performance, which is manifested by the significant electrical resistance change when subject to mechanical deformation. In comparison to individual CNTs, the CNT thin films, formed by a random assembly of individual tubes or bundles, show much lower piezoresistive sensitivity. Given the progress made to date in developing CNT ensemble based-piezoresistive sensors, the related piezoresistive mechanism(s) are still not well understood. The crucial step to obtain a better understanding of this issue is to study the effects of CNT structure in the dispersion on the piezoresistivity of CNT ensemble based-piezoresistive sensors. To reach this goal, my Ph.D. research first focuses on establishing the processing-structure-property relationship of SWCNT thin film piezoresistive sensors. The key accomplishment contains: 1) developing the combined preparative ultracentrifuge method (PUM) and dynamic light scattering (DLS) method to quantitatively characterized SWCNT particle size in dispersions under various sonication conditions; 2) designing combined ultrasonication and microfluidization processing protocol for high throughput and large-scale production of high quality SWCNT dispersions; 3) fabricating varied SWCNT thin film piezoresistive sensors through spray coating technique and immersion-drying post-treatment; and 4) investigating the effect of microstructures of SWCNTs on piezoresistivity of SWCNT thin film sensors. This experimental methodology for quantitative and systematic investigation of the processing-structure-property relationships provides a means for the performance optimization of CNT ensemble based piezoresistive sensors. As a start to understand the piezoresistive mechanism, the second focus of my Ph.D. research is studying charge transport behaviors in SWCNT thin films. It was found that the temperature-dependent sheet resistance of SWCNT thin films could be explained by a 3D variable

  13. Grain Boundary Plane Orientation Fundamental Zones and Structure-Property Relationships.

    PubMed

    Homer, Eric R; Patala, Srikanth; Priedeman, Jonathan L

    2015-10-26

    Grain boundary plane orientation is a profoundly important determinant of character in polycrystalline materials that is not well understood. This work demonstrates how boundary plane orientation fundamental zones, which capture the natural crystallographic symmetries of a grain boundary, can be used to establish structure-property relationships. Using the fundamental zone representation, trends in computed energy, excess volume at the grain boundary, and temperature-dependent mobility naturally emerge and show a strong dependence on the boundary plane orientation. Analysis of common misorientation axes even suggests broader trends of grain boundary energy as a function of misorientation angle and plane orientation. Due to the strong structure-property relationships that naturally emerge from this work, boundary plane fundamental zones are expected to simplify analysis of both computational and experimental data. This standardized representation has the potential to significantly accelerate research in the topologically complex and vast five-dimensional phase space of grain boundaries.

  14. Grain Boundary Plane Orientation Fundamental Zones and Structure-Property Relationships

    PubMed Central

    Homer, Eric R.; Patala, Srikanth; Priedeman, Jonathan L.

    2015-01-01

    Grain boundary plane orientation is a profoundly important determinant of character in polycrystalline materials that is not well understood. This work demonstrates how boundary plane orientation fundamental zones, which capture the natural crystallographic symmetries of a grain boundary, can be used to establish structure-property relationships. Using the fundamental zone representation, trends in computed energy, excess volume at the grain boundary, and temperature-dependent mobility naturally emerge and show a strong dependence on the boundary plane orientation. Analysis of common misorientation axes even suggests broader trends of grain boundary energy as a function of misorientation angle and plane orientation. Due to the strong structure-property relationships that naturally emerge from this work, boundary plane fundamental zones are expected to simplify analysis of both computational and experimental data. This standardized representation has the potential to significantly accelerate research in the topologically complex and vast five-dimensional phase space of grain boundaries. PMID:26498715

  15. Grain boundary plane orientation fundamental zones and structure-property relationships

    SciTech Connect

    Homer, Eric R.; Patala, Srikanth; Priedeman, Jonathan L.

    2015-10-26

    Grain boundary plane orientation is a profoundly important determinant of character in polycrystalline materials that is not well understood. This work demonstrates how boundary plane orientation fundamental zones, which capture the natural crystallographic symmetries of a grain boundary, can be used to establish structure-property relationships. Using the fundamental zone representation, trends in computed energy, excess volume at the grain boundary, and temperature-dependent mobility naturally emerge and show a strong dependence on the boundary plane orientation. Analysis of common misorientation axes even suggests broader trends of grain boundary energy as a function of misorientation angle and plane orientation. Due to the strong structure-property relationships that naturally emerge from this work, boundary plane fundamental zones are expected to simplify analysis of both computational and experimental data. This standardized representation has the potential to significantly accelerate research in the topologically complex and vast five-dimensional phase space of grain boundaries.

  16. Grain boundary plane orientation fundamental zones and structure-property relationships

    DOE PAGES

    Homer, Eric R.; Patala, Srikanth; Priedeman, Jonathan L.

    2015-10-26

    Grain boundary plane orientation is a profoundly important determinant of character in polycrystalline materials that is not well understood. This work demonstrates how boundary plane orientation fundamental zones, which capture the natural crystallographic symmetries of a grain boundary, can be used to establish structure-property relationships. Using the fundamental zone representation, trends in computed energy, excess volume at the grain boundary, and temperature-dependent mobility naturally emerge and show a strong dependence on the boundary plane orientation. Analysis of common misorientation axes even suggests broader trends of grain boundary energy as a function of misorientation angle and plane orientation. Due to themore » strong structure-property relationships that naturally emerge from this work, boundary plane fundamental zones are expected to simplify analysis of both computational and experimental data. This standardized representation has the potential to significantly accelerate research in the topologically complex and vast five-dimensional phase space of grain boundaries.« less

  17. A general structure-property relationship to predict the enthalpy of vaporisation at ambient temperatures.

    PubMed

    Oberg, T

    2007-01-01

    The vapour pressure is the most important property of an anthropogenic organic compound in determining its partitioning between the atmosphere and the other environmental media. The enthalpy of vaporisation quantifies the temperature dependence of the vapour pressure and its value around 298 K is needed for environmental modelling. The enthalpy of vaporisation can be determined by different experimental methods, but estimation methods are needed to extend the current database and several approaches are available from the literature. However, these methods have limitations, such as a need for other experimental results as input data, a limited applicability domain, a lack of domain definition, and a lack of predictive validation. Here we have attempted to develop a quantitative structure-property relationship (QSPR) that has general applicability and is thoroughly validated. Enthalpies of vaporisation at 298 K were collected from the literature for 1835 pure compounds. The three-dimensional (3D) structures were optimised and each compound was described by a set of computationally derived descriptors. The compounds were randomly assigned into a calibration set and a prediction set. Partial least squares regression (PLSR) was used to estimate a low-dimensional QSPR model with 12 latent variables. The predictive performance of this model, within the domain of application, was estimated at n=560, q2Ext=0.968 and s=0.028 (log transformed values). The QSPR model was subsequently applied to a database of 100,000+ structures, after a similar 3D optimisation and descriptor generation. Reliable predictions can be reported for compounds within the previously defined applicability domain.

  18. Modelling of the structure-property relationships in the α-quartz structures

    NASA Astrophysics Data System (ADS)

    Yao, Yongtao; Alderson, Kim; Alderson, Andrew; Leng, Jinsong

    2013-04-01

    The molecular mechanism has been employed to model the structure-property relationships of auxetic material with tetrahedral framework at the atomistic level. The germania α-quartz subject uniaxial stress loading in z direction will be investigated. The strain-dependent structure and mechanical properties will be predicted from the force field based simulations, including the transformation from positive-to-negative Poisson's ratio behaviour and vice versa.

  19. Structure-Property-Function Relationship in Humic Substances to Explain the Biological Activity in Plants

    PubMed Central

    García, Andrés Calderín; de Souza, Luiz Gilberto Ambrosio; Pereira, Marcos Gervasio; Castro, Rosane Nora; García-Mina, José María; Zonta, Everaldo; Lisboa, Francy Junior Gonçalves; Berbara, Ricardo Luis Louro

    2016-01-01

    Knowledge of the structure-property-function relationship of humic substances (HSs) is key for understanding their role in soil. Despite progress, studies on this topic are still under discussion. We analyzed 37 humic fractions with respect to their isotopic composition, structural characteristics, and properties responsible for stimulating plant root parameters. We showed that regardless of the source of origin of the carbon (C3 or C4), soil-extracted HSs and humic acids (HAs) are structurally similar to each other. The more labile and functionalized HS fraction is responsible for root emission, whereas the more recalcitrant and less functionalized HA fraction is related to root growth. Labile structures promote root stimulation at lower concentrations, while recalcitrant structures require higher concentrations to promote a similar stimulus. These findings show that lability and recalcitrance, which are derived properties of humic fractions, are related to the type and intensity of their bioactivity. In summary, the comparison of humic fractions allowed a better understanding of the relationship between the source of origin of plant carbon and the structure, properties, and type and intensity of the bioactivity of HSs in plants. In this study, scientific concepts are unified and the basis for the agronomic use of HSs is established. PMID:26862010

  20. Structure-property relationships in self-assembling peptide hydrogels, homopolypeptides and polysaccharides

    NASA Astrophysics Data System (ADS)

    Hule, Rohan A.

    The main objective of this dissertation is to investigate quantitative structure-property relationships in a variety of molecular systems including de novo designed peptides, peptide amphiphiles, polysaccharides and high molecular weight polypeptides. Peptide molecules consisting of 20 amino acids were designed to undergo thermally triggered intramolecular folding into asymmetric beta-hairpins and intermolecular self-assembly via a strand swapping mechanism into physically crosslinked fibrillar hydrogels. The self-assembly mechanism was confirmed by multiple characterization techniques such as circular dichroism and FITR spectroscopy, atomic force and transmission electron microscopy and small angle neutron scattering. Three distinct fibrillar nanostructures, i.e. non-twisted, twisted and laminated were produced, depending on the degree of strand asymmetry and peptide registry. Differences in the fibrillar morphology have a direct consequence on the mechanical properties of the hydrogels, with the laminated hydrogels exhibiting a significantly higher elastic modulus as compared to the twisted or non-twisted fibrillar hydrogels. SANS and cryo-TEM data reveal that the self-assembled fibrils form networks that are fractal in nature. Models employed to elucidate the fractal behavior can relate changes in the correlation lengths, low q (network), and high q (fibrillar) fractal exponents to the distinct fibrillar nanomorphology. The fractal dimension of the networks varies significantly, from a mass to a surface fractal and can be directly related to the local fibrillar morphology and changes in the peptide concentration. Transitions in the fractal behavior seen in the high q regime can be attributed to self-assembly kinetics. An identical model can be used to establish a direct correlation between the bulk properties and changes in both, the network density and underlying morphology, of a modified peptide-based hydrogel. As in the case of asymmetric peptides, changes in

  1. Polydopamine and eumelanin: from structure-property relationships to a unified tailoring strategy.

    PubMed

    d'Ischia, Marco; Napolitano, Alessandra; Ball, Vincent; Chen, Chun-Teh; Buehler, Markus J

    2014-12-16

    CONSPECTUS: Polydopamine (PDA), a black insoluble biopolymer produced by autoxidation of the catecholamine neurotransmitter dopamine (DA), and synthetic eumelanin polymers modeled to the black functional pigments of human skin, hair, and eyes have burst into the scene of materials science as versatile bioinspired functional systems for a very broad range of applications. PDA is characterized by extraordinary adhesion properties providing efficient and universal surface coating for diverse settings that include drug delivery, microfluidic systems, and water-treatment devices. Synthetic eumelanins from dopa or 5,6-dihydroxyindoles are the focus of increasing interest as UV-absorbing agents, antioxidants, free radical scavengers, and water-dependent hybrid electronic-ionic semiconductors. Because of their peculiar physicochemical properties, eumelanins and PDA hold considerable promise in nanomedicine and bioelectronics, as they are biocompatible, biodegradable, and exhibit suitable mechanical properties for integration with biological tissues. Despite considerable similarities, very few attempts have so far been made to provide an integrated unifying perspective of these two fields of technology-oriented chemical research, and progress toward application has been based more on empirical approaches than on a solid conceptual framework of structure-property relationships. The present Account is an attempt to fill this gap. Following a vis-à-vis of PDA and eumelanin chemistries, it provides an overall view of the various levels of chemical disorder in both systems and draws simple correlations with physicochemical properties based on experimental and computational approaches. The potential of large-scale simulations to capture the macroproperties of eumelanin-like materials and their hierarchical structures, to predict the physicochemical properties of new melanin-inspired materials, to understand the structure-property-function relationships of these materials from

  2. Structure-property relationships in the design, assembly and applications of polyelectrolyte multilayer thin films

    NASA Astrophysics Data System (ADS)

    Rmaile, Hassan H.

    Ultrathin films consisting of an alternating sequence of positively and negatively charged polyelectrolytes have been prepared by means of the electrostatic layer-by-layer sequential assembly technique. To augment their typical applications in the water treatment, personal care as well as the pulp and paper industry, the structure and the design of these polyelectrolytes were tailored synthetically to satisfy the requirements of different types of applications. Some were used for surface modifications, hydrophobic and hydrophilic coatings, corrosion protection, conducting and biocompatible surfaces. Others were found to be very efficient for membrane and chromatographic applications. The ease with which these multilayer coatings can be constructed, their robustness and stability make them very good candidates for industrial applications. The dissertation focuses mainly on the structure-property relationships of these polyelectrolytes and their corresponding thin films. Various polyelectrolytes were synthesized or modified in a strategic approach and gave novel and promising properties. Some of them exhibited permeabilities that were higher than any membranes reported in the literature. Also, some are potentially very useful for designing drug delivery systems such as tablets or encapsulations since they were shown to control the permeability of sample drugs and vitamins very efficiently based on their sensitivity to pH changes. Other synthesized polyelectrolytes proved to be very effective in preventing protein adsorption or promoting cell growth and differentiation. Some systems were very useful as robust stationary phases for simple chiral separations in capillary electrochromatography. Along with modifications and improvements, the approach might one day be applied commercially for chiral separations using high performance liquid chromatography and replace currently used stationary phases. Last but not least, the potential for these polyelectrolytes and their

  3. Investigating ionomer morphologies with STEM and SAXS: Toward rigorous processing-structure-property relationships

    NASA Astrophysics Data System (ADS)

    Benetatos, Nicholas M.

    Due to their extraordinary chemical and physical properties, ionomers have found wide-ranging applications including chemically resistant thermoplastics, robust coatings, and selectively permeable ion-transport membranes. The unique properties of ionomers result directly from the self-assembly/organization of ionic functional groups and counterions into nanoscale aggregates which act as transient physical crosslinks. For more than a half century, significant effort has been devoted toward understanding these structurally complex multi-component polymers, however, a complete description of their processing-structure-property relationships remains elusive. Quantifying these relationships will provide an important step toward the rational design, synthesis, and preparation of superior ionomeric materials. In order to rigorously advance the study of ionomer morphology, we combine traditional small angle X-ray scattering (SAXS) approaches with cutting-edge real space imaging via scanning transmission electron microscopy (STEM). This technique has provides high resolution imaging capability in which the image contrast is generated by differences in local average atomic number. Our work has shown that these characterization methods can be used to obtain complementary morphological information regarding the size, shape, and spatial distribution of the nanoscale ionic aggregates that control the physical properties of ionomers. With this information, we evaluate the validity of prevalent structural/morphological models and systematically explore how the nanoscale morphology is affected by changes in polymer backbone structure, materials chemistry, and processing.

  4. Localized surface plasmon resonance induced structure-property relationships of metal nanostructures

    NASA Astrophysics Data System (ADS)

    Vilayurganapathy, Subramanian

    The confluence of nanotechnology and plasmonics has led to new and interesting phenomena. The industrial need for fast, efficient and miniature devices which constantly push the boundaries on device performance tap into the happy marriage between these diverse fields. Designing devices for real life application that give superior performance when compared with existing ones are enabled by a better understanding of their structure-property relationships. Among all the design constraints, without doubt, the shape and size of the nanostructure along with the dielectric medium surrounding it has the maximum influence on the response and thereby the performance of the device. Hence a careful study of the above mentioned parameters is of utmost importance in designing efficient devices. In this dissertation, we synthesize and study the optical properties of nanostructures of different shapes and size. In particular, we estimated the plasmonic near field enhancement via surface-enhanced Raman scattering (SERS) and 2-photon Photoemission electron microscopy (2P-PEEM). We synthesized the nanostructures using four different techniques. One synthesis technique, the thermal growth method was employed to grow interesting Ag and Au nanostructures on Si. The absence of toxic chemicals during nanostructure synthesis via the thermal growth technique opens up myriad possibilities for applications in the fields of biomedical science, bioengineering, drug delivery among others along with the huge advantage of being environment friendly. The other three synthesis techniques (ion implantation, Electrodeposition and FIB lithography) were chosen with the specific goal of designing novel plasmonic metal, metal hybrid nanostructures as photocathode materials in next generation light sources. The synthesis techniques for these novel nanostructures were dictated by the requirement of high quantum efficiency, robustness under constant irradiation and coherent unidirectional electron emission

  5. Design, synthesis, and structure-property relationships of isoindigo-based conjugated polymers.

    PubMed

    Lei, Ting; Wang, Jie-Yu; Pei, Jian

    2014-04-15

    Conjugated polymers have developed rapidly due to their promising applications in low-cost, lightweight, and flexible electronics. The development of the third-generation donor-acceptor (D-A) polymers greatly improved the device performance in organic solar cells (OSCs) and field-effect transistors (FETs). However, for further improvement of device performance, scientists need to develop new building blocks, in particular electron-deficient aromatics, and gain an in-depth understanding of the structure-property relationships. Recently, isoindigo has been used as a new acceptor of D-A conjugated polymers. An isomer of indigo, isoindigo is a less well-known dye and can be isolated as a by-product from certain biological processes. It has two lactam rings and exhibits strong electron-withdrawing character. This electron deficiency gives isoindigo-based polymers intriguing properties, such as broad absorption and high open circuit voltage in OSCs, as well as high mobility and good ambient stability in FETs. In this Account, we review our recent progress on the design, synthesis, and structure-property relationship study of isoindigo-based polymers for FETs. Starting with some discussion on carrier transport in polymer films, we provide some basic strategies towards high-performance polymer FETs. We discuss the stability issue of devices, the impediment of the alkyl side chains, and the choice of the donor part of conjugated polymers. We demonstrate that introducing the isoindigo core effectively lowers the HOMO levels of polymers and provides FETs with long-time stability. In addition, we have found that when we use inappropriate alkyl side chains or non-centrosymmetric donors, the device performance of isoindigo polymers suffers. To further improve device performance and ambient stability, we propose several design strategies, such as using farther branched alkyl chains, modulating polymer energy levels, and extending π-conjugated backbones. We have found that using

  6. Structure/property relationships in polymer membranes for water purification and energy applications

    NASA Astrophysics Data System (ADS)

    Geise, Geoffrey

    Providing sustainable supplies of purified water and energy is a critical global challenge for the future, and polymer membranes will play a key role in addressing these clear and pressing global needs for water and energy. Polymer membrane-based processes dominate the desalination market, and polymer membranes are crucial components in several rapidly developing power generation and storage applications that rely on membranes to control rates of water and/or ion transport. Much remains unknown about the influence of polymer structure on intrinsic water and ion transport properties, and these relationships must be developed to design next generation polymer membrane materials. For desalination applications, polymers with simultaneously high water permeability and low salt permeability are desirable in order to prepare selective membranes that can efficiently desalinate water, and a tradeoff relationship between water/salt selectivity and water permeability suggests that attempts to prepare such materials should rely on approaches that do more than simply vary polymer free volume. One strategy is to functionalize hydrocarbon polymers with fixed charge groups that can ionize upon exposure to water, and the presence of charged groups in the polymer influences transport properties. Additionally, in many emerging energy applications, charged polymers are exposed to ions that are very different from sodium and chloride. Specific ion effects have been observed in charged polymers, and these effects must be understood to prepare charged polymers that will enable emerging energy technologies. This presentation discusses research aimed at further understanding fundamental structure/property relationships that govern water and ion transport in charged polymer films considered for desalination and electric potential field-driven applications that can help address global needs for clean water and energy.

  7. Probing Structure Property Relationships in Complex Engineering Silicones by 1H NMR

    SciTech Connect

    Chinn, S C; Gjersing, E L; Maxwell, R S; Eastwood, E; Bowen, D; Stephens, T

    2006-07-14

    It is generally accepted that the properties of polymeric materials are controlled by the network structure and the reactions by which they have been constructed. These properties include the bulk moduli at creation, but also the properties as a function of age during use. In order to interpret mechanical properties and predict the time dependent changes in these properties, detailed knowledge of the effect of structural changes must be obtained. The degree and type of crosslinking, the molecular weight between crosslinks, the number of elastically ineffective chains (loops, dangling chain ends, sol-fraction) must be characterized. A number of theoretical and experimental efforts have been reported in the last few years on model networks prepared by endlinking reactions and the relationships of those structures with the ultimate mechanical properties. A range of experimental methods have been used to investigate structure including rheometric, scattering, infrared, {sup 29}Si MAS and CPMAS, {sup 1}H relaxation measurements, and recently {sup 1}H multiple quantum methods. Characterization of the growth of multiple quantum coherences have recently been shown to provide detailed insight into silicone network structure by the ability to selective probe the individual components of the polymer network, such as the polymer-filler interface or network chains. We have employed recently developed MQ methods to investigate the structure-property relationships in a series of complex, endlinked filled-PDMS blends. Here, a systematic study of the relationship between the molecular formulation, as dictated by the amount and type of crosslinks present and by the remaining network chains, and the segmental dynamics as observed by MQ NMR was performed.

  8. Thermoelectric plastics: from design to synthesis, processing and structure-property relationships.

    PubMed

    Kroon, Renee; Mengistie, Desalegn Alemu; Kiefer, David; Hynynen, Jonna; Ryan, Jason D; Yu, Liyang; Müller, Christian

    2016-11-07

    Thermoelectric plastics are a class of polymer-based materials that combine the ability to directly convert heat to electricity, and vice versa, with ease of processing. Potential applications include waste heat recovery, spot cooling and miniature power sources for autonomous electronics. Recent progress has led to surging interest in organic thermoelectrics. This tutorial review discusses the current trends in the field with regard to the four main building blocks of thermoelectric plastics: (1) organic semiconductors and in particular conjugated polymers, (2) dopants and counterions, (3) insulating polymers, and (4) conductive fillers. The design and synthesis of conjugated polymers that promise to show good thermoelectric properties are explored, followed by an overview of relevant structure-property relationships. Doping of conjugated polymers is discussed and its interplay with processing as well as structure formation is elucidated. The use of insulating polymers as binders or matrices is proposed, which permit the adjustment of the rheological and mechanical properties of a thermoelectric plastic. Then, nanocomposites of conductive fillers such as carbon nanotubes, graphene and inorganic nanowires in a polymer matrix are introduced. A case study examines poly(3,4-ethylenedioxythiophene) (PEDOT) based materials, which up to now have shown the most promising thermoelectric performance. Finally, a discussion of the advantages provided by bulk architectures e.g. for wearable applications highlights the unique advantages that thermoelectric plastics promise to offer.

  9. Structure-property relationship in core-shell rubber toughened epoxy nanocomposites

    NASA Astrophysics Data System (ADS)

    Gam, Ki Tak

    The structure-property relationships of epoxy nanocomposites with inorganic layer-structure nanofillers have been studied to obtain the fundamental understanding of the role of nanofillers and the physics of polymer nanocomposites in this dissertation. Several polymer nanocomposite systems with modified montmorillonite (MMT) or alpha-zirconium phosphate (ZrP) nanofillers were prepared with epoxy matrices of different ductility and properties. The successful nanofiller's exfoliations were confirmed with X-ray diffraction and transmission electronic microscopy (TEM). Dynamic mechanical analysis (DMA) on the prepared epoxy nanocomposites revealed the significant increase in rubbery plateau moduli of the epoxy nanocomposite systems above Tg, as high as 4.5 times, and tensile test results showed improved modulus by the nanofiller addition, while the fracture toughness was not affected or slightly decreased by nanofillers. The brittle epoxy nanocomposite systems were toughened with core shell rubber (CSR) particles and showed remarkable increase in fracture toughness (KIC) value up to 270%. The CSR toughening is more effective at ductile matrices, and TEM observation indicates that major toughening mechanisms induced by the CSR addition involve a large scale CSR cavitation, followed by massive shear deformation of the matrix.

  10. Probing structure-property relationships in perpendicularly magnetized Fe/Cu(001) using MXLD and XPD

    SciTech Connect

    Cummins, T.R.; Waddill, G.D.; Goodman, K.W.

    1997-04-01

    Magnetic X-ray Linear Dichroism (MXLD) in Photoelectron Spectroscopy and X-Ray Photoelectron Diffraction (XPD) of the Fe 3p core level have been used to probe the magnetic structure-property relationships of perpendicularly magnetized Fe/Cu(001), in an element-specific fashion. A strong MEXLD effect was observed in the high resolution photoelectron spectroscopy of the Fe 3p at {open_quotes}normal{close_quotes} emission and was used to follow the loss of perpendicular ferromagnetic ordering as the temperature was raised toward room temperature. In parallel with this, {open_quotes}Forward Focussing{close_quotes} in XPD was used as a direct measure of geometric structure in the overlayer. These results and the implications of their correlation will be discussed. Additionally, an investigation of the effect of Mn doping of the Fe/Cu(001) will be described. These measurements were performed at the Spectromicroscopy Facility (Beamline 7.0.1) of the Advanced Light Source.

  11. Processable fluoropolymers with low dielectric constants: Preparation and structure-property relationships of polyacrylates and polymethacrylates

    SciTech Connect

    Hu, H. S.W.; Griffith, J.R.

    1993-12-31

    The preparation of a series of processable heavily fluorinated acrylic and methacrylic homo- and co-polymers with low dielectric constants is carried out to elucidate the structure-property relationships. The monomers were prepared through the condensation of the respective alcohols with acryloyl and methacryloyl chloride. Unlike tetrafluoroethylene, these monomers are easy to process into transparent polymers under normal conditions due to their liquid or semisolid nature. All polymers exhibit dielectric constants around 2.06-2.41 with variation within 0.03 over a frequency region of 500 MHz to 18.5 GHz. These values are very close to the minimum known dielectric constants of 2.0-2.08 for Teflon and 1.89-1.93 for Teflon AF. The factors which affect the dielectric constant include the fluorine content, the polymer type and molecular features. Lower dielectric constants are obtained as fluorine contents from polymer backbone or sidechain increase, when acrylate is replaced by methacrylate, when ether linkages are present in the fluorocarbon and when aromatic structure is symmetrically meta-substituted.

  12. Size-separation characterization of starch and glycogen for biosynthesis-structure-property relationships.

    PubMed

    Gilbert, Robert G

    2011-02-01

    Starch and glycogen are highly branched polymers of glucose of great importance to humans in managing and mitigating nutrition-related diseases, especially diabetes and obesity, and in industrial uses, for example in food and paper-making. Size-separation characterization using multiple-detection size-exclusion chromatography (SEC, also known as gel-permeation chromatography, GPC) is able to furnish substantial amounts of information on the relationships between the biosynthesis, processing, structure, and properties of these biopolymers, and achieves superior characterization for use in industrial product and process improvements. Multi-detector SEC is able to give much more information about structure than simple averages such as total molecular weight or size; the detailed information yielded by this technique has already given new information on important biosynthesis-structure-property reactions, and has considerable potential in this field in the future. However, it must be used with care to avoid artifacts arising from incomplete dissolution of the substrate and shear scission during separation. It is also essential in interpreting data to appreciate that this size-separation technique can only ever give size distributions, never true molecular weight distributions. Other size-separation techniques, particularly field-flow fractionation, require substantial technical development to be used on undegraded native starches.

  13. Quantitative criticism of literary relationships.

    PubMed

    Dexter, Joseph P; Katz, Theodore; Tripuraneni, Nilesh; Dasgupta, Tathagata; Kannan, Ajay; Brofos, James A; Bonilla Lopez, Jorge A; Schroeder, Lea A; Casarez, Adriana; Rabinovich, Maxim; Haimson Lushkov, Ayelet; Chaudhuri, Pramit

    2017-04-03

    Authors often convey meaning by referring to or imitating prior works of literature, a process that creates complex networks of literary relationships ("intertextuality") and contributes to cultural evolution. In this paper, we use techniques from stylometry and machine learning to address subjective literary critical questions about Latin literature, a corpus marked by an extraordinary concentration of intertextuality. Our work, which we term "quantitative criticism," focuses on case studies involving two influential Roman authors, the playwright Seneca and the historian Livy. We find that four plays related to but distinct from Seneca's main writings are differentiated from the rest of the corpus by subtle but important stylistic features. We offer literary interpretations of the significance of these anomalies, providing quantitative data in support of hypotheses about the use of unusual formal features and the interplay between sound and meaning. The second part of the paper describes a machine-learning approach to the identification and analysis of citational material that Livy loosely appropriated from earlier sources. We extend our approach to map the stylistic topography of Latin prose, identifying the writings of Caesar and his near-contemporary Livy as an inflection point in the development of Latin prose style. In total, our results reflect the integration of computational and humanistic methods to investigate a diverse range of literary questions.

  14. Structure property relationships of nitride superlattice hard coatings prepared by pulsed laser deposition

    NASA Astrophysics Data System (ADS)

    Patel, Nitin

    Today, more than 40% of all cutting tools used in machining applications are covered with coatings. Coatings improve wear resistance, increase tool life, enable use at higher speed, and broaden the application range. Superlattices, where thin layers (typically <10 nm) of two different materials (e.g. TiN and AlN) are deposited in an alternating fashion, are widely used commercially. Importantly, the hardness value of a superlattice (e.g. TiN/AlN) can significantly exceed the rule of mixture value. Superlattice coatings built from crystallographically dissimilar materials are not widely studied but hold promise for improvements in performance by allowing for both hardness and toughness to be simultaneously optimized. This is what this thesis is concerned with: a structure-property comparison of isostructural superlattices with corresponding non-isostructural superlattices. In order to grow both isostructural and non-isostructural superlattices from the same set of materials, it is necessary to grow monolithic films in different phases. Towards this end, the synthesis of different phases of AlN, (Ti,Al)N, TaN, and TiN was investigated. Films were grown by pulsed laser deposition in two different chambers that had different base pressures to study the effect of background gases on the phases and orientations of the films. Growth of AlN and (Ti,Al)N films is strongly affected in a chamber that had a base pressure of 10-6 Torr, but the films adopt their stable nitride structures in a chamber with the lower base pressure of 10-8 Torr. TaN adopts either the cubic rock salt structure or its stable hexagonal structure, depending on the growth temperature, while TiN grows as rock salt in all conditions. Single crystal epitaxial superlattices were then grown with different compositions, periodicities, and crystallographic orientations to compare the effect of chemistry, nanostructure, and crystallographic texture on hardness. Finally, the structure-property relationships of

  15. Development of structure-property relationships for intrinsically microporous polymers through molecular simulations

    NASA Astrophysics Data System (ADS)

    Hart, Kyle E.

    Creating a safe and effective means to store and/or capture small molecules is of paramount importance, as these processes are some of the highest energy consumers today. New materials will have profound impacts on various environmentally conscious applications, such as alternative fuel storage, hydrogen recovery, natural gas purification, and carbon dioxide capture and storage. Designing a material that meets the demanding performance criteria of real-world use has proven a challenging endeavor, but microporous polymers are a promising alternative. This is primarily due to the material's pore sizes being on the order of molecular dimensions, while simultaneously retaining the ability for the polymer-gas physicochemical interactions to be tailored for specific gas separation applications. Both experimental and computational investigations have shown that seemingly minor changes in the chemical structure can have a profound effect on the gas adsorption and separation properties of a polymeric material; however, the vast number of possible functionalities makes the evaluation of potential structures a daunting challenge. This dissertation focuses on developing and utilizing computationally efficient means to analyze candidate polymeric materials for use in carbon dioxide adsorption and separation applications. After validating the simulation models for structural and adsorptive performance, several important structure-property relationships are described. In particular, this work proposes and analyzes multiple families of functionalized polymers of intrinsic microporosity, from which we obtain important design principles of gas separation performance. It is shown that the explicit modeling of a polymer's micropore structure facilitates a fundamental understanding of the nature of the polymer-gas interactions, which was used as a means to reveal the most influential pore characteristics for each application. The molecular simulation results discussed here will aid

  16. Structure-property relationship of quinuclidinium surfactants--Towards multifunctional biologically active molecules.

    PubMed

    Skočibušić, Mirjana; Odžak, Renata; Štefanić, Zoran; Križić, Ivana; Krišto, Lucija; Jović, Ozren; Hrenar, Tomica; Primožič, Ines; Jurašin, Darija

    2016-04-01

    Motivated by diverse biological and pharmacological activity of quinuclidine and oxime compounds we have synthesized and characterized novel class of surfactants, 3-hydroxyimino quinuclidinium bromides with different alkyl chains lengths (CnQNOH; n=12, 14 and 16). The incorporation of non conventional hydroxyimino quinuclidinium headgroup and variation in alkyl chain length affects hydrophilic-hydrophobic balance of surfactant molecule and thereby physicochemical properties important for its application. Therefore, newly synthesized surfactants were characterized by the combination of different experimental techniques: X-ray analysis, potentiometry, electrical conductivity, surface tension and dynamic light scattering measurements, as well as antimicrobial susceptibility tests. Comprehensive investigation of CnQNOH surfactants enabled insight into structure-property relationship i.e., way in which the arrangement of surfactant molecules in the crystal phase correlates with their solution behavior and biologically activity. The synthesized CnQNOH surfactants exhibited high adsorption efficiency and relatively low critical micelle concentrations. In addition, all investigated compounds showed very potent and promising activity against Gram-positive and clinically relevant Gram-negative bacterial strains compared to conventional antimicrobial agents: tetracycline and gentamicin. The overall results indicate that bicyclic headgroup with oxime moiety, which affects both hydrophilicity and hydrophobicity of CnQNOH molecule in addition to enabling hydrogen bonding, has dominant effect on crystal packing and physicochemical properties. The unique structural features of cationic surfactants with hydroxyimino quinuclidine headgroup along with diverse biological activity have made them promising structures in novel drug discovery. Obtained fundamental understanding how combination of different functionalities in a single surfactant molecule affects its physicochemical

  17. Unraveling Structure-Property Relationships in Polymer Blends for Intelligent Materials Design

    NASA Astrophysics Data System (ADS)

    Irwin, Matthew Tyler

    Block polymers provide an accessible route to structured, composite materials by combining two or more components with disparate mechanical, chemical, and electrical properties into a single bulk material with nanoscale domains. However, the characteristic lengthscale of these systems is limited, and the choice of components is restricted to those that are able to undergo microstructural ordering at accessible temperatures. This thesis details routes to overcoming these limitations through the addition of a lithium salt, a blend of homopolymers, or both. Chapter 2 describes a study wherein complex sphere phases such as the Frank-Kasper sigma phase can be observed in otherwise disordered asymmetric block polymers through the addition of a lithium salt. Chapter 3 discusses the development and characterization of a ternary polymer blend of an AB diblock copolymer and A and B homopolymers doped with a lithium salt. Detailed characterization showed that doping blends that are otherwise disordered with lithium salt induced microstructural ordering and largely recovers the phase behavior of traditional ternary polymer blends. A systematic study of the ionic conductivity of the blends at a fixed salt concentration demonstrates that, at a given composition, disordered, yet highly structured blends consistently exhibit better conductivity than polycrystalline morphologies with long range order. Chapter 4 extends the methodology of Chapter 3 and details a systematic study of the effects of cross-linker concentration on the performance of polymer electrolyte membranes produced via polymerization-induced microphase separation that exhibit a highly structured, globally disordered microstructure. Finally, Chapter 5 details efforts to develop a water filtration membrane using a polyethylene template derived from a polymeric bicontinuous microemulsion. Throughout all of this work, the goal is to better understand structure-property relationships at the molecular level in order to

  18. Hybrid Mixed Media Nonwovens: An Investigation of Structure-Property Relationships

    NASA Astrophysics Data System (ADS)

    Hollowell, Kendall Birckhead

    There have been myriad studies on utilizing bicomponent splittables produced through spunbond/spunlace processes. These production methods have proven to yield microfibers which increase the surface area of the nonwoven structures. There has been recent focus on studying the microfibers within these nonwoven structures as well as using a multiplicity of deniers of fibers within the nonwoven. There have also been studies on producing nonwovens with fibers of differing cross-sectional shapes and diameters. The purpose of this study is to examine the properties of a nonwoven structure, marrying the concepts of multi-denier fibers with multi-shaped fibers in two configurations: three-layer and alternating. The basis for this study will be US Patent 6,964,931 B2 "Method of making Continuous Filament Web with Statistical Filament Distribution" as well as US Patent 7,981,336 B2 "Process of Making Mixed Fibers and Nonwoven Fabrics". This study addresses the melt-spinning and hydroentanglement of nonwoven webs made from bicomponent fibers in three-layer and alternating configurations. The bicomponent cross-sections that will be used include 16-segmented pie and 7-islands-in-the-sea. In this study the establishment of the utility of mixed media nonwovens will take place through property and structure analysis in order to determine the inherent properties of the mixed media structures as well as the structure-property relationships of the nonwoven fabric. Property and structure analysis will also take place on mixed media structures containing poly(lactic acid) as a sacrificial component in the bicomponent fiber after optimizing the removal conditions of the poly(lactic acid) in a sodium hydroxide (NaOH) bath.

  19. Hierarchical multiscale structure-property relationships of the red-bellied woodpecker (Melanerpes carolinus) beak.

    PubMed

    Lee, Nayeon; Horstemeyer, M F; Rhee, Hongjoo; Nabors, Ben; Liao, Jun; Williams, Lakiesha N

    2014-07-06

    We experimentally studied beaks of the red-bellied woodpecker to elucidate the hierarchical multiscale structure-property relationships. At the macroscale, the beak comprises three structural layers: an outer rhamphotheca layer (keratin sheath), a middle foam layer and an inner bony layer. The area fraction of each layer changes along the length of the beak giving rise to a varying constitutive behaviour similar to functionally graded materials. At the microscale, the rhamphotheca comprises keratin scales that are placed in an overlapping pattern; the middle foam layer has a porous structure; and the bony layer has a big centre cavity. At the nanoscale, a wavy gap between the keratin scales similar to a suture line was evidenced in the rhamphotheca; the middle foam layer joins two dissimilar materials; and mineralized collagen fibres were revealed in the inner bony layer. The nano- and micro-indentation tests revealed that the hardness (associated with the strength, modulus and stiffness) of the rhamphotheca layer (approx. 470 MPa for nano and approx. 320 MPa for micro) was two to three times less than that of the bony layer (approx. 1200 MPa for nano and approx. 630 MPa for micro). When compared to other birds (chicken, finch and toucan), the woodpecker's beak has more elongated keratin scales that can slide over each other thus admitting dissipation via shearing; has much less porosity in the bony layer thus strengthening the beak and focusing the stress wave; and has a wavy suture that admits local shearing at the nanoscale. The analysis of the woodpeckers' beaks provides some understanding of biological structural materials' mechanisms for energy absorption.

  20. Relationship between enhanced dewaterability and structural properties of hydrothermal sludge after hydrothermal treatment of excess sludge.

    PubMed

    Wang, Liping; Li, Aimin; Chang, Yuzhi

    2017-04-01

    Hydrothermal treatment is an effective method to enhance the deep dewaterability of excess sludge with low energy consumption. In this study, an insight into the relationship between enhanced dewaterability and structural properties of the produced hydrothermal sludge was presented, aiming at better understanding the effect of hydrothermal process on excess sludge dewatering performance. The results indicated that hydrothermal effect induced the transformation of surface water to interstitial and free water by lowering the binding strength between adjacent water and solid particles and that free water became the main form for moisture existence in hydrothermal sludge as temperature was higher than 180 °C. Increase in temperature of hydrothermal treatment generated a significant size reduction of sludge flocs but treated sludge with a higher rigidity, which not only strengthened the network of hydrothermal sludge but also destroyed the binding of EPS with water. Hydrothermal process caused crevice and pore structures of excess sludge to disappear gradually, which was a main driving force of water removal as temperature was below 150 °C. With the temperature of hydrothermal treatment exceeding 180 °C, the morphology of hydrothermal sludge became rough which linked closely to the solid precipitation of condensation polymerization, and further became smooth at higher temperature (210 °C) due to the coal-like structures with higher aromaticities, indicating that hydrothermal reaction pathways began to play a main role in enhanced dewaterability. Hydrothermal treatment led to more alkyl and aromatic carbon, but lower O-alkyl, carboxyl and carbonyl carbon.

  1. Quantitative relationships in delphinid neocortex

    PubMed Central

    Mortensen, Heidi S.; Pakkenberg, Bente; Dam, Maria; Dietz, Rune; Sonne, Christian; Mikkelsen, Bjarni; Eriksen, Nina

    2014-01-01

    Possessing large brains and complex behavioral patterns, cetaceans are believed to be highly intelligent. Their brains, which are the largest in the Animal Kingdom and have enormous gyrification compared with terrestrial mammals, have long been of scientific interest. Few studies, however, report total number of brain cells in cetaceans, and even fewer have used unbiased counting methods. In this study, using stereological methods, we estimated the total number of cells in the neocortex of the long-finned pilot whale (Globicephala melas) brain. For the first time, we show that a species of dolphin has more neocortical neurons than any mammal studied to date including humans. These cell numbers are compared across various mammals with different brain sizes, and the function of possessing many neurons is discussed. We found that the long-finned pilot whale neocortex has approximately 37.2 × 109 neurons, which is almost twice as many as humans, and 127 × 109 glial cells. Thus, the absolute number of neurons in the human neocortex is not correlated with the superior cognitive abilities of humans (at least compared to cetaceans) as has previously been hypothesized. However, as neuron density in long-finned pilot whales is lower than that in humans, their higher cell number appears to be due to their larger brain. Accordingly, our findings make an important contribution to the ongoing debate over quantitative relationships in the mammalian brain. PMID:25505387

  2. Solid solution directionally solidified eutectics: Model systems for structure-property relationships in interfacial fracture

    NASA Astrophysics Data System (ADS)

    Brewer, Luke Nathaniel

    The next generation of high temperature materials for application in aerospace and power generation systems will be required to withstand temperatures well in excess of 1200°C, often in oxidizing atmospheres. Oxide-oxide directionally solidified eutectics (DSE's) have shown promise as high temperature ceramic materials, only to be limited by their lack of fracture toughness at room temperature. In the case of DSE oxide materials, the interfacial fracture behavior has been blamed for the poor performance in the past and is the subject of interest in this work. In this thesis, the solid solution, directionally solidified quaternary eutectic (SS-DSE), Co1-xNixO/ZrO2(CaO), is developed as a model system for the study of interfacial fracture in oxide-oxide DSE's. A variety of structural and mechanical characterization techniques are applied to investigate structure-property relationships for interfacial fracture behavior. The optical floating zone technique was employed for growing both the eutectic crystals and their single crystal counterparts, Co1-x NixO. Co1-xNixO/ZrO2(CaO) was shown to possess the necessary structural elements to serve as a model system for interfacial fracture. Lamellar microstructures were observed for all compositions. The crystallographic relationships between phases evolved as a model solid solution. Interdiffusion of chemical species was minimal, allowing the layers to treated independently. The core of this thesis is dedicated to studying the nature of interfacial fracture behavior in oxide eutectics. This study is motivated by the novel observation of extensive interfacial delamination for the system CoO/ZrO 2(CaO). A transition from interfacial delamination to interfacial penetration is observed for compositions of Co1-xNixO/ZrO 2(CaO) with x > 0.2. The residual stress state in these materials was investigated using X-ray and neutron diffraction-based techniques. The role of plasticity in interfacial fracture was explored using a

  3. Understanding Structure-Property Relationships for Palladium-Gold Nanoparticles as Colloidal Catalysts

    NASA Astrophysics Data System (ADS)

    Fang, Yu-Lun

    Bimetallic palladium-gold (PdAu) nanoparticle (NP) catalysts have been demonstrated for the better catalytic performance than monometallic Pd catalysts in various reactions; however, the enhancement mechanism is not completely clear for most reactions. This thesis addresses the investigation of PdAu NP catalysts with emphasis on the structure-property relationships in water-phase reactions, using hydrodechlorination (HDC) of trichloroethene (TCE) as the model reaction. Catalyzed TCE HDC is a potential approach for water pollution control, in which colloidal Pd-decorated Au NPs (Pd/Au NPs) are known to be significantly better catalysts than monometallic Pd ones. X-ray absorption spectroscopy (XAS) of carbon-supported Pd/Au NPs with different surface Pd coverages verified their core-shell structure (Au-rich core and Pd-rich shell). Structure evolution was observed upon heat treatment, in which Pd was in the form of surface Pd ensembles at room temperature. The metals formed a surface PdAu alloy or a bulk PdAu alloy above 200°C, as determined from the average coordination environment. Results suggested a new way to promote Pd catalysis, namely, by impregnating supported Pd catalysts with gold salt followed by thermal annealing; such post-impregnation with different heat treatments could lead to >15-fold increase in TCE HDC activity. Pd ensembles on the Au NP surface were demonstrated to be major active sites for TCE HDC as the reaction rates correlated strongly with the size of Pd ensembles determined from XAS. The geometric effect, in which atomic ensembles act as active sites, appeared to dominate over the mixed metal site effect and the electronic effect. Au NPs could stabilize surface Pd atoms in the metallic form, possibly leading to a set of highly active sites that is not present in monometallic Pd NPs. The TCE HDC reaction with Pd/Au NPs and Pd NPs was conducted as a closed batch system. Mass transfer effects in this three-phase reaction were assessed and

  4. The Structure-property Relationships of D-π-A BODIPY Dyes for Dye-sensitized Solar Cells.

    PubMed

    Mao, Mao; Song, Qin-Hua

    2016-04-01

    BODIPY dyes have attracted considerable attention as potential photosensitizers in dye-sensitized solar cells (DSSCs) owing to their excellent optical properties and facile structural modification. This account focuses on recent advances in the molecular design of D-π-A BODIPY dyes for applications in DSSCs. Special attention has been paid to the structure-property relationships of D-π-A BODIPY dyes for DSSCs. The developmental process in the modified position at the BODIPY core with a donor/acceptor is described. The devices based on 2,6-modified BODIPY dyes exhibit better photovoltaic performance over other modified BODIPY dyes. Meanwhile, the research reveals the correlation of molecular structures (various donor chromophores, extended units, molecular frameworks, and long alkyl groups) with their photophysical and electrochemical properties and relates it to their performance in DSSCs. The structure-property relationships give valuable information and guidelines for designing new D-π-A BODIPY dyes for DSSCs.

  5. Land-use and land-management change: relationships with earthworm and fungi communities and soil structural properties

    PubMed Central

    2013-01-01

    Background Change in land use and management can impact massively on soil ecosystems. Ecosystem engineers and other functional biodiversity in soils can be influenced directly by such change and this in turn can affect key soil functions. Here, we employ meta-analysis to provide a quantitative assessment of the effects of changes in land use and land management across a range of successional/extensification transitions (conventional arable → no or reduced tillage → grassland → wooded land) on community metrics for two functionally important soil taxa, earthworms and fungi. An analysis of the relationships between community change and soil structural properties was also included. Results Meta-analysis highlighted a consistent trend of increased earthworm and fungal community abundances and complexity following transitions to lower intensity and later successional land uses. The greatest changes were seen for early stage transitions, such as introduction of reduced tillage regimes and conversion to grassland from arable land. Not all changes, however, result in positive effects on the assessed community metrics. For example, whether woodland conversion positively or negatively affects community size and complexity depends on woodland type and, potentially, the changes in soil properties, such as pH, that may occur during conversion. Alterations in soil communities tended to facilitate subsequent changes in soil structure and hydrology. For example, increasing earthworm abundances and functional group composition were shown to be positively correlated with water infiltration rate (dependent on tillage regime and habitat characteristics); while positive changes in fungal biomass measures were positively associated with soil microaggregate stability. Conclusions These findings raise the potential to manage landscapes to increase ecosystem service provision from soil biota in relation to regulation of soil structure and water flow. PMID:24289220

  6. Chemical Modification and Structure-property Relationships of Acrylic and Ionomeric Thermoplastic Elastomer Gels

    NASA Astrophysics Data System (ADS)

    Vargantwar, Pruthesh Hariharrao

    Block copolymers (BCs) have remained at the forefront of materials research due to their versatility in applications ranging from hot-melt/pressure-sensitive adhesives and impact modifiers to compatibilizing agents and vibration-dampening/nanotemplating media. Of particular interest are macromolecules composed of two or more chemically dissimilar blocks covalently linked together to form triblock or pentablock copolymers. If the blocks are sufficiently incompatible and the copolymer behaves as a thermoplastic elastomer, the molecules can spontaneously self-assemble to form nanostructured materials that exhibit shape memory due to the formation of a supramolecular network. The BCs of these types are termed as conventional. When BCs contain blocks having ionic moieties such as sulfonic acid groups, they are termed as block ionomers. Designing new systems based on either conventional or ionic BCs, characterizing their structure-property relationships and later using them as electroacive polymers form the essential objectives of this work. Electroactive polymers (EAPs) exhibit electromechanical actuation when stimulated by an external electric field. In the first part of this work, it is shown that BCs resolve some of the outstanding problems presently encountered in the design of two different classes of EAP actuators: dielectric elastomers (DEs) and ionic polymer metal composites (IPMCs). All-acrylic triblock copolymer gels used as DEs actuate with high efficacy without any requirement of mechanical prestrain and, thus, eliminate the need for bulky and heavy hardware essential with prestrained dielectric actuators, as well as material problems associated with stress relaxation. The dependence of actuation behavior on gel morphology as evaluated from mechanical and microstructure studies is observed. In the case of IPMCs, ionic BCs employed in this study greatly facilitate processing compared to other contenders such as NafionRTM, which is commonly used in this class

  7. Structure-property-performance relationships of new high temperature relaxors for capacitor applications

    NASA Astrophysics Data System (ADS)

    Stringer, Craig J.

    temperature (Tf) of ˜150°C. Static and in-situ transmission electron microscopy investigations of the BS-PMN-PT compositions demonstrated a frustrated microstructure of nanometer scale regions and were used to establish structure-property relationships with different electric field and thermal histories. A comparative study of the key relaxor parameters, EA, T f, and TD was tabulated with previously investigated relaxor ferroelectrics. These parameters were found to scale relative to other lead-based perovskite relaxor ferroelectric compounds and solid solutions, with the BS-PMN-PT ternary system exhibiting the highest temperature behavior. Finally, to demonstrate one possible application area for these materials, multilayer ceramic capacitor devices were designed for operation at 300°C and up to 10 kHz. The voltage saturation was found to be extremely encouraging at 300°C with observed changes in capacitance (˜3%) on the application of 10 kV/cm. The insulation resistivity followed an Arrhenius behavior and at 300°C was ˜1010 O-cm. Weibull statistics were used to estimate a characteristic breakdown field at 300°C for the BS-PMN-PT multilayer capacitors of ˜40 kV/cm. Current-voltage measurements were performed to voltages up to breakdown and exhibited Ohmic behavior, indicating intrinsically controlled conduction. Highly accelerated life time tests were performed on BS-PMN-PT capacitors. It was observed that silver migration from termination electrodes caused premature failure at elevated temperature.

  8. Structure-Property Relationships of Polymer Brushes in Restricted Geometries and their Utilization as Ultra-Low Lubricants

    SciTech Connect

    Kuhl, Tonya Lynn; Faller, Roland

    2015-09-28

    Though polymer films are widely used to modify or tailor the physical, chemical and mechanical properties of interfaces in both solid and liquid systems, the rational design of interface- or surface-active polymer modifiers has been hampered by a lack of information about the behavior and structure-property relationships of this class of molecules. This is especially true for systems in which the role of the polymer is to modify the interaction between two solid surfaces in intimate contact and under load, to cause them to be mechanically coupled (e.g. to promote adhesion and wetting) or to minimize their interaction (e.g. lubrication, colloidal stabilization, etc.). Detailed structural information on these systems has largely been precluded by the many difficulties and challenges associated with direct experimental measurements of polymer structure in these geometries. As a result, many practitioners have been forced to employ indirect measurements or rely wholly on theoretical modeling. This has resulted in an incomplete understanding of the structure-property relationships, which are relied upon for the rational design of improved polymer modifiers. Over the course of this current research program, we made direct measurements of the structure of polymers at the interface between two solid surfaces under confinement and elucidated the fundamental physics behind these phenomena using atomistic and coarse grained simulations. The research has potential to lead to new lubricants and wear reducing agents to improve efficiency.

  9. Quantitative structure-hydrophobicity relationships of molecular fragments and beyond.

    PubMed

    Zou, Jian-Wei; Huang, Meilan; Huang, Jian-Xiang; Hu, Gui-Xiang; Jiang, Yong-Jun

    2016-03-01

    Quantitative structure-property relationship (QSPR) models were firstly established for the hydrophobic substituent constant (πX) using the theoretical descriptors derived solely from electrostatic potentials (EPSs) at the substituent atoms. The descriptors introduced are found to be related to hydrogen-bond basicity, hydrogen-bond acidity, cavity, or dipolarity/polarizability terms in linear solvation energy relationship, which endows the models good interpretability. The predictive capabilities of the models constructed were also verified by rigorous Monte Carlo cross-validation. Then, eight groups of meta- or para-disubstituted benzenes and one group of substituted pyridines were investigated. QSPR models for individual systems were achieved with the ESP-derived descriptors. Additionally, two QSPR models were also established for Rekker's fragment constants (foct), which is a secondary-treatment quantity and reflects average contribution of the fragment to logP. It has been demonstrated that the descriptors derived from ESPs at the fragments, can be well used to quantitatively express the relationship between fragment structures and their hydrophobic properties, regardless of the attached parent structure or the valence state. Finally, the relations of Hammett σ constant and ESP quantities were explored. It implies that σ and π, which are essential in classic QSAR and represent different type of contributions to biological activities, are also complementary in interaction site.

  10. Uniaxial Extensional Behavior of A--B--A Thermoplastic Elastomers: Structure-Properties Relationship and Modeling

    NASA Astrophysics Data System (ADS)

    Martinetti, Luca

    examined at temperatures where the A domains are glassy. Characteristic length scales and tube model parameters were determined, and the role of the glassy A domains on the entangled rubbery B network was assessed. Thermo-rheological complexity, observed near and below Tg,A, was attributed to augmented motional freedom of the B block ends at the corresponding A/B interfaces, in harmony with the theoretical treatment of thermo-rheological complexity for two-phase materials developed by Fesko and Tschoegl. When the magnitude of the steepness index was taken into account, the shift behavior was analogous to the response measured for pure B melts. Building upon the procedure proposed by Ferry and co-workers for entangled and unfilled polymer melts, a new method was developed to extract the matrix monomeric friction coefficient zeta0 from the linear response behavior of a filled system in the rubber-glass transition region, and to estimate the size of Gaussian submolecules. Stress relaxation beyond the path equilibration time was found qualitatively and quantitatively compatible with dynamically undiluted arm retraction dynamics of entangled dangling structures (originating either from a fraction of triblock chains having one end residing outside A domains or from diblock impurities). By employing tube models and rubber elasticity theories, suitably modified to account for microphase-segregation, the linear elastic behavior across the rubbery plateau and up to the entanglement time was modeled, and a simple analytical expression relating the Langley trapping factor with the fraction of entangled and unentangled dangling structures of the material was obtained. The critical-gel-like behavior typical of A--B--A TPEs at service temperatures approaching Tg,A was analyzed in terms of a power-law distribution of relaxation times derived from the wedge distribution, shown to be equivalent to Chambon--Winter's critical gel model and to the mechanical behavior of a fractional element. A

  11. Structure-property relationships in multilayered polymeric system and olefinic block copolymers

    NASA Astrophysics Data System (ADS)

    Khariwala, Devang

    Chapter 1. The effect of tie-layer thickness on delamination behavior of polypropylene/tie-layer/Nylon-6 multilayers is examined in this study. Various maleated polypropylene resins were compared for their effectiveness as tie-layers. Delamination failure occurred cohesively in all the multilayer systems. Two adhesion regimes were defined based on the change in slope of the linear relationship between the delamination toughness and the tie-layer thickness. The measured delamination toughness of the various tie-layers was quantitatively correlated to the damage zone length formed at the crack tip. In addition, the effect of tie-layer thickness on the multilayer tensile properties was correlated with the delamination behavior. The fracture strain of the multilayers decreased with decreasing tie-layer thickness. Examination of the prefracture damage mechanism of stretched multilayers revealed good correlation with the delamination toughness of the tie-layers. In thick tie-layers (>2microm) the delamination toughness of the tie-layers was large enough to prevent delamination of multilayers when they were stretched. In the thin tie-layers (<2microm) the delamination toughness of all the tie-layers is low and consequently delamination led to premature fracture in stretched multilayers. Chapter 2. The kinetics of interdiffusion in the layer multiplying coextrusion process was studied between the miscible Nylon-6 and EVOH pair. The interdiffusion was followed by studying multilayer films of alternating Nylon-6 and EVOH layers that were coextruded with increasing number of layers. The AFM confirmed that the layers interdiffused with increasing number of layers and were forced to a homogeneous blend after several multiplications. The oxygen permeability of Nylon-6/EVOH multilayers was strongly affected by the amount of interdiffusion. The symmetry of the multilayers made it possible to model the composition profile through the layer thickness by application of Fick's law of

  12. Redox properties of structural Fe in clay minerals: 3. Relationships between smectite redox and structural properties.

    PubMed

    Gorski, Christopher A; Klüpfel, Laura E; Voegelin, Andreas; Sander, Michael; Hofstetter, Thomas B

    2013-01-01

    Structural Fe in clay minerals is an important redox-active species in many pristine and contaminated environments as well as in engineered systems. Understanding the extent and kinetics of redox reactions involving Fe-bearing clay minerals has been challenging due to the inability to relate structural Fe(2+)/Fe(total) fractions to fundamental redox properties, such as reduction potentials (EH). Here, we overcame this challenge by using mediated electrochemical reduction (MER) and oxidation (MEO) to characterize the fraction of redox-active structural Fe (Fe(2+)/Fe(total)) in smectites over a wide range of applied EH-values (-0.6 V to +0.6 V). We examined Fe(2+)/Fe(total )- EH relationships of four natural Fe-bearing smectites (SWy-2, SWa-1, NAu-1, NAu-2) in their native, reduced, and reoxidized states and compared our measurements with spectroscopic observations and a suite of mineralogical properties. All smectites exhibited unique Fe(2+)/Fe(total) - EH relationships, were redox active over wide EH ranges, and underwent irreversible electron transfer induced structural changes that were observable with X-ray absorption spectroscopy. Variations among the smectite Fe(2+)/Fe(total) - EH relationships correlated well with both bulk and molecular-scale properties, including Fe(total) content, layer charge, and quadrupole splitting values, suggesting that multiple structural parameters determined the redox properties of smectites. The Fe(2+)/Fe(total) - EH relationships developed for these four commonly studied clay minerals may be applied to future studies interested in relating the extent of structural Fe reduction or oxidation to EH-values.

  13. Understanding nanocellulose chirality and structure-properties relationship at the single fibril level

    NASA Astrophysics Data System (ADS)

    Usov, Ivan; Nyström, Gustav; Adamcik, Jozef; Handschin, Stephan; Schütz, Christina; Fall, Andreas; Bergström, Lennart; Mezzenga, Raffaele

    2015-06-01

    Nanocellulose fibrils are ubiquitous in nature and nanotechnologies but their mesoscopic structural assembly is not yet fully understood. Here we study the structural features of rod-like cellulose nanoparticles on a single particle level, by applying statistical polymer physics concepts on electron and atomic force microscopy images, and we assess their physical properties via quantitative nanomechanical mapping. We show evidence of right-handed chirality, observed on both bundles and on single fibrils. Statistical analysis of contours from microscopy images shows a non-Gaussian kink angle distribution. This is inconsistent with a structure consisting of alternating amorphous and crystalline domains along the contour and supports process-induced kink formation. The intrinsic mechanical properties of nanocellulose are extracted from nanoindentation and persistence length method for transversal and longitudinal directions, respectively. The structural analysis is pushed to the level of single cellulose polymer chains, and their smallest associated unit with a proposed 2 × 2 chain-packing arrangement.

  14. Synthesis and Structure-Property Relationships of Phosphole-Based π Systems and Their Applications in Organic Solar Cells.

    PubMed

    Matano, Yoshihiro

    2015-06-01

    Phosphole is a chemically tunable heterole, and its π-conjugated derivatives are potential candidates for optoelectronic materials. This account describes recent developments in the synthesis and structure-property relationships of π-conjugated phosphole derivatives made by my research group. Thiophene-phosphole-styrene, phosphole-acetylene-arene, oligophosphole, polyphosphole, areno[c]phosphole, and phosphole-heterole π systems are synthesized using titanacycle-mediated metathesis and palladium-catalyzed cross-coupling reactions. The structural, optical, and electrochemical properties of selected compounds are discussed. Initial results on some applications of thiophene-phosphole copolymers, acenaphtho[c]phospholes, and amine-terthiophene-phosphole donor-π-acceptor dyes in organic solar cells are described. These results give valuable information and guidelines for designing new phosphorus-containing organic materials for molecular electronics.

  15. Study of Chemistry and Structure-Property Relationship on Tunable Plasmonic Nanostructures

    NASA Astrophysics Data System (ADS)

    Jing, Hao

    In this dissertation, the rational design and controllable fabrication of an array of novel plasmonic nanostructures with geometrically tunable optical properties are demonstrated, including metal-semiconductor hybrid hetero-nanoparticles, bimetallic noble metal nanoparticles and hollow nanostructures (nanobox and nanocage). Firstly, I have developed a robust wet chemistry approach to the geometry control of Ag-Cu2O core-shell nanoparticles through epitaxial growth of Cu2O nanoshells on the surfaces of various Ag nanostructures, such as quasi-spherical nanoparticles, nanocubes, and nanocuboids. Precise control over the core and the shell geometries enables me to develop detailed, quantitative understanding of how the Cu2O nanoshells introduce interesting modifications to the resonance frequencies and the extinction spectral line shapes of multiple plasmon modes of the Ag cores. Secondly, I present a detailed and systematic study of the controlled overgrowth of Pd on Au nanorods. The overgrowth of Pd nanoshells with fine-controlled dimensions and architectures on single-crystalline Au nanorods through seed-mediated growth protocol in the presence of various surfactants is investigated. Thirdly, I have demonstrated that creation of high-index facets on subwavelength metallic nanoparticles provides a unique approach to the integration of desired plasmonic and catalytic properties on the same nanoparticle. Through site-selective surface etching of metallic nanocuboids whose surfaces are dominated by low-index facets, I have controllably fabricated nanorice and nanodumbbell particles, which exhibit drastically enhanced catalytic activities arising from the catalytically active high index facets abundant on the particle surfaces. And the nanorice and nanodumbbell particles also possess appealing tunable plasmonic properties that allow us to gain quantitative insights into nanoparticle-catalyzed reactions with unprecedented sensitivity and detail through time

  16. Processing, structure, property and performance relationships for the thermal spray of the internal surface of aluminum cylinders

    NASA Astrophysics Data System (ADS)

    Cook, David James

    The increased need for automotive weight reduction has necessitated the use of aluminum for engine blocks. Conventional aluminum alloys cannot survive the constant wear from a piston ring reciprocating on the surface. However, a wear resistant thermal spray coating can be applied on the internal surface of the cylinder bore, which has significant advantages over other available options. Thermal spray is a well-established process for depositing molten, semi-molten, or solid particles onto a substrate to form a protective coating. For this application, the two main challenges were obtaining good wear resistance, and achieving good adhesion. To design a system capable of producing a well-adhered, wear resistant coating for this high volume application it is necessary to identify the overall processing, structure, properties, and performance relationships. The results will demonstrate that very important relationships exist among particle characteristics, substrate conditions, and the properties of the final coating. However, it is the scientific studies to understand some of the process physics in these relationships that allow recognition of the critical processing conditions that need to be controlled to ensure a consistent, reliable thermal spray coating. In this investigation, it will be shown that the critical microstructural aspect of the coating that produced the required tribological properties was the presence of wuestite (FeO). It was found that by using a low carbon steel material with compressed air atomizing gas, it was possible to create an Fe/FeO structure that exhibited excellent tribological properties. This study will also show that traditional thermal spray surface preparation techniques were not ideal for this application, therefore a novel alternative approach was developed. The application of a flux to the aluminum surface prior to thermal spray promotes excellent bond strengths to non-roughened aluminum. Analysis will show that this flux strips

  17. Processing-structure-property relationships in electron beam physical vapor deposited yttria stabilized zirconia coatings

    SciTech Connect

    Rao, D. Srinivasa; Valleti, Krishna; Joshi, S. V.; Janardhan, G. Ranga

    2011-05-15

    The physical and mechanical properties of yttria stabilized zirconia (YSZ) coatings deposited by the electron beam physical vapor deposition technique have been investigated by varying the key process variables such as vapor incidence angle and sample rotation speed. The tetragonal zirconia coatings formed under varying process conditions employed were found to have widely different surface and cross-sectional morphologies. The porosity, phase composition, planar orientation, hardness, adhesion, and surface residual stresses in the coated specimens were comprehensively evaluated to develop a correlation with the process variables. Under transverse scratch test conditions, the YSZ coatings exhibited two different crack formation modes, depending on the magnitude of residual stress. The influence of processing conditions on the coating deposition rate, column orientation angle, and adhesion strength has been established. Key relationships between porosity, hardness, and adhesion are also presented.

  18. Chlorophenol sorption on multi-walled carbon nanotubes: DFT modeling and structure-property relationship analysis.

    PubMed

    Watkins, Marquita; Sizochenko, Natalia; Moore, Quentarius; Golebiowski, Marek; Leszczynska, Danuta; Leszczynski, Jerzy

    2017-02-01

    The presence of chlorophenols in drinking water can be hazardous to human health. Understanding the mechanisms of adsorption under specific experimental conditions would be beneficial when developing methods to remove toxic substances from drinking water during water treatment in order to limit human exposure to these contaminants. In this study, we investigated the sorption of chlorophenols on multi-walled carbon nanotubes using a density functional theory (DFT) approach. This was applied to study selected interactions between six solvents, five types of nanotubes, and six chlorophenols. Experimental data were used to construct structure-adsorption relationship (SAR) models that describe the recovery process. Specific interactions between solvents and chlorophenols were taken into account in the calculations by using novel specific mixture descriptors.

  19. Structure-property relationship in cytotoxicity and cell uptake of poly(2-oxazoline) amphiphiles

    PubMed Central

    Luxenhofer, Robert; Sahay, Gaurav; Schulz, Anita; Alakhova, Daria; Bronich, Tatiana K.; Jordan, Rainer; Kabanov, Alexander V.

    2011-01-01

    The family of poly(2-oxazoline)s (POx) is being increasingly investigated in the context of biomedical applications. We tested the relative cytotoxicity of POx and were able to confirm that these polymers are typically not cytotoxic even at high concentrations. Furthermore, we report structure-uptake relationships of a series of amphiphilic POx block copolymers that have different architectures, molar mass and chain termini. The rate of endocytosis can be fine-tuned over a broad range by changing the polymer structure. The cellular uptake increases with the hydrophobic character of the polymers and is observed even at nanomolar concentrations. Considering the structural versatility of this class of polymers, the relative ease of preparation and their stability underlines the potential of POx as a promising platform candidate for the preparation of next-generation polymer therapeutics. PMID:21513750

  20. S09 Symposium KK, Structure-Property Relationships in Biomineralized and Biomimetic Composites

    SciTech Connect

    David Kisailus; Lara Estroff; Himadri S. Gupta; William J. Landis; Pablo D. Zavattieri

    2010-06-07

    The technical presentations and discussions at this symposium disseminated and assessed current research and defined future directions in biomaterials research, with a focus on structure-function relationships in biological and biomimetic composites. The invited and contributed talks covered a diverse range of topics from fundamental biology, physics, chemistry, and materials science to potential applications in developing areas such as light-weight composites, multifunctional and smart materials, biomedical engineering, and nanoscaled sensors. The invited speakers were chosen to create a stimulating program with a mixture of established and junior faculty, industrial and academic researchers, and American and international experts in the field. This symposium served as an excellent introduction to the area for younger scientists (graduate students and post-doctoral researchers). Direct interactions between participants also helped to promote potential future collaborations involving multiple disciplines and institutions.

  1. Structure-Property Relationships in Atomic-Scale Junctions: Histograms and Beyond.

    PubMed

    Hybertsen, Mark S; Venkataraman, Latha

    2016-03-15

    Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure-function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, the scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics. Such link groups (amines, methylsuflides, pyridines, etc.) maintain a stable lone pair configuration that selectively bonds to specific, undercoordinated transition metal atoms available following rupture of a metal point contact in the STM-BJ experiments. This basic chemical principle rationalizes the observation of highly reproducible conductance signatures. Subsequently, the method has been extended to probe a variety of physical phenomena ranging from basic I-V characteristics to more complex properties such as thermopower and electrochemical response. By adapting the technique to a conducting cantilever atomic force microscope (AFM-BJ), simultaneous measurement of the mechanical characteristics of nanoscale junctions as they

  2. Experimental and theoretical study on the structure-property relationship of novel 1-aryl-3-methylsuccinimides

    NASA Astrophysics Data System (ADS)

    Banjac, Nebojša R.; Božić, Bojan Đ.; Mirković, Jelena M.; Vitnik, Vesna D.; Vitnik, Željko J.; Valentić, Nataša V.; Ušćumlić, Gordana S.

    2017-02-01

    A series of ten 1-aryl-3-methylsuccinimides was synthesized and their solvatochromic properties were studied in a set of fifteen binary solvent mixtures. The solute-solvent interactions were analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The electronic effect of the substituents on the UV-Vis absorption and NMR spectra was analyzed using the simple Hammett equation. Moreover, the B3LYP, CAM-B3LYP, and M06-2X functionals using the 6-311G(d,p) basic set have been assessed in light of the position of experimental absorption maxima obtained for these compounds. The integration grid effects have also been evaluated. An interpretation of the substituent-effect transmission through the molecular skeleton and the nature of the HOMO and LUMO orbitals based on quantum-chemical calculations is given. The values of partial atomic charges from the atomic polar tenzors (APT), natural population analysis (NBO), and charges fit to the electrostatic potential using the B3LYP, CAM-B3LYP, and M06-2X methods are produced and correlated with different experimental properties. In order to estimate the chemical activity of the molecule, the molecular electrostatic potential (MEP) surface map is calculated for the optimized geometry of 1-phenyl-3-methylsuccinimide.

  3. Structure - Property Relationships of Furanyl Thermosetting Polymer Materials Derived from Biobased Feedstocks

    NASA Astrophysics Data System (ADS)

    Hu, Fengshuo

    Biobased thermosetting polymers have drawn significant attention due to their potential positive economic and ecological impacts. New materials should mimic the rigid, phenylic structures of incumbent petroleum-based thermosetting monomers and possess superior thermal and mechanical properties. Furans and triglycerides derived from cellulose, hemicellulose and plant oils are promising candidates for preparing such thermosetting materials. In this work, furanyl diepoxies, diamines and di-vinyl esters were synthesized using biobased furanyl materials, and their thermal and mechanical properties were investigated using multiple techniques. The structure versus property relationship showed that, compared with the prepared phenylic analogues, biobased furanyl thermosetting materials possess improved glassy storage modulus (E '), advanced fracture toughness, superior high-temperature char yield and comparable glass transition temperature (Tg) properties. An additive molar function analysis of the furanyl building block to the physical properties, such as Tg and density, of thermosetting polymers was performed. The molar glass transition function value (Yg) and molar volume increment value (Va,i) of the furanyl building block were obtained. Biobased epoxidized soybean oil (ESO) was modified using different fatty acids at varying molar ratios, and these prepared materials dramatically improved the critical strain energy release rate (G1c) and the critical stress intensity factor (K1c) values of commercial phenylic epoxy resins, without impairing their Tg and E ' properties. Overall, it was demonstrated that biobased furans and triglycerides possess promising potential for use in preparing high-performance thermosetting materials, and the established methodologies in this work can be utilized to direct the preparation of thermosetting materials with thermal and mechanical properties desired for practical applications.

  4. Structure-Property Relationships in Lithium, Silver, and Cesium Uranyl Borates

    SciTech Connect

    Wang, Shuao; Alekseev, Evgeny V.; Stritzinger, Jared T.; Liu, Guokui; Depmeier, Wulf; Albrecht-Schmitt, Thomas E.

    2010-11-09

    Four new uranyl borates, Li[UO{sub 2}B{sub 5}O{sub 9}]·H{sub 2}O (LiUBO-1), Ag[(UO{sub 2})B{sub 5}O{sub 8}(OH){sub 2}] (AgUBO-1), α-Cs[(UO{sub 2}){sub 2}B{sub 11}O{sub 16}(OH){sub 6}] (CsUBO-1), and β-Cs[(UO{sub 2}){sub 2}B{sub 11}O{sub 16}(OH){sub 6}] (CsUBO-2) were synthesized via the reaction of uranyl nitrate with a large excess of molten boric acid in the presence of lithium, silver, or cesium nitrate. These compounds share a common structural motif consisting of a linear uranyl, UO{sub 2}{sup 2+}, cation surrounded by BO{sub 3} triangles and BO{sub 4} tetrahedra to create an UO{sub 8} hexagonal bipyramidal environment around uranium. The borate anions bridge between uranyl units to create sheets. Additional BO{sub 3} triangles extend from the polyborate layers, and are directed approximately perpendicular to the sheets. In Li[(UO{sub 2})B{sub 5}O{sub 9}]·H{sub 2}O, the additional BO{sub 3} triangles connect these sheets together to form a three-dimensional framework structure. Li[UO{sub 2})B{sub 5}O{sub 9}]·H{sub 2}O and β-Cs[(UO{sub 2}){sub 2}B{sub 11}O{sub 16}(OH){sub 6}] adopt noncentrosymmetric structures, while Ag[(UO{sub 2})B{sub 5}O{sub 8}(OH){sub 2}] and α-Cs[(UO{sub 2}){sub 2}B{sub 11}O{sub 16}(OH){sub 6}] are centrosymmetric. Li[(UO{sub 2})B{sub 5}O{sub 9}]·H{sub 2}O, which can be obtained as pure phase, displays second-harmonic generation of 532 nm light from 1064 nm light. Topological relationships of all actinyl borates are developed.

  5. Structure-property relationships: Synthesis and characterization of Perovskite-related transition metal oxides

    NASA Astrophysics Data System (ADS)

    Whaley, Louis

    The fundamental structural component of perovskite-related phases is the octahedrally coordinated transition metal ion, symbolized as BO6 . Corner-sharing networks of BO6 octahedra are present in perovskites and related Ruddlesden-Popper Phases, ABO3 and AO(ABO 3)n, respectively. Face-sharing octahedra arranged into columns are characteristic of hexagonal, perovskite-related phases, and the relationship will be described in detail in Chapter 1. Edge sharing octahedra are characteristic of Keggin- and Lindquist-type polyoxometallates, which at first glance, seem unconnected from perovskites. However, Chapter 1 will show the deep connections among all of the phases mentioned above, by starting with perovskite phases. Temperature- and field-dependent, magnetic and electronic transitions are linked to the structure by overlap of metal d-orbitals with oxygen 2p orbitals, and (in special cases) direct d-d overlap. A mixed-transition metal oxide with two or more type of B ions provides an environment in which dissimilar B-ion orbitals can interact via exchange of charge carriers (hole or electron transport). The general goal in choosing two B ions is to provide an opportunity for the large combined magnetic moment and a low barrier to hopping of charge carriers, achieved by pairing a 3d-ion having 3 to 5 unpaired d-electrons, with a 4d or 5d transition metal ion, having 1 or 2 unpaired electrons, such as Fe(III) and Mo(V), which have compatible reduction potentials (i.e., they can co-exist in the same oxide, and exchange takes place with a low barrier). This research includes the following systems: an n = 2 Ruddlesden-Popper (RP) phase, Sr3Fe5/4Mo3/4O6.9, containing 3-7% Sr2FeMoO6, as intergrowths (not separate crystal grains, by high-resolution transmission electron microscopy), and G-type antiferromagnetism below 150°K and a "partial spin-reorientation transition" by powder neutron diffraction (PND), not previously reported for n = 2 RP phases in the Sr-Fe-Mo-O system

  6. Composition-structure-property relationships for non-classical ionomer cements formulated with zinc-boron germanium-based glasses.

    PubMed

    Zhang, Xiaofang; Werner-Zwanziger, Ulrike; Boyd, Daniel

    2015-04-01

    Non-classical ionomer glasses like those based on zinc-boron-germanium glasses are of special interest in a variety of medical applications owning to their unique combination of properties and potential therapeutic efficacy. These features may be of particular benefit with respect to the utilization of glass ionomer cements for minimally invasive dental applications such as the atruamatic restorative treatment, but also for expanded clinical applications in orthopedics and oral-maxillofacial surgery. A unique system of zinc-boron-germanium-based glasses (10 compositions in total) has been designed using a Design of Mixtures methodology. In the first instance, ionomer glasses were examined via differential thermal analysis, X-ray diffraction, and (11)B MAS NMR spectroscopy to establish fundamental composition - structure-property relationships for the unique system. Secondly, cements were synthesized based on each glass and handling characteristics (working time, Wt, and setting time, St) and compression strength were quantified to facilitate the development of both experimental and mathematical composition-structure-property relationships for the new ionomer cements. The novel glass ionomer cements were found to provide Wt, St, and compression strength in the range of 48-132 s, 206-602 s, and 16-36 MPa, respectively, depending on the ZnO/GeO2 mol fraction of the glass phase. A lower ZnO mol fraction in the glass phase provides higher glass transition temperature, higher N4 rate, and in combination with careful modulation of GeO2 mol fraction in the glass phase provides a unique approach to extending the Wt and St of glass ionomer cement without compromising (in fact enhancing) compression strength. The data presented in this work provide valuable information for the formulation of alternative glass ionomer cements for applications within and beyond the dental clinic, especially where conventional approaches to modulating working time and strength exhibit co

  7. Quantitative structure-property relationships for chemical functional use and weight fractions in consumer articles

    EPA Science Inventory

    Chemical functional use -- the functional role a chemical plays in processes or products -- may be a useful heuristic for predicting human exposure potential in that it comprises information about the compound's likely physical properties and the product formulations or articles ...

  8. Quantitative structure-property relationships for predicting Henry's law constant from molecular structure.

    PubMed

    Dearden, John C; Schüürmann, Gerrit

    2003-08-01

    Various models are available for the prediction of Henry's law constant (H) or the air-water partition coefficient (Kaw), its dimensionless counterpart. Incremental methods are based on structural features such as atom types, bond types, and local structural environments; other regression models employ physicochemical properties, structural descriptors such as connectivity indices, and descriptors reflecting the electronic structure. There are also methods to calculate H from the ratio of vapor pressure (p(v)) and water solubility (S(w)) that in turn can be estimated from molecular structure, and quantum chemical continuum-solvation models to predict H via the solvation-free energy (deltaG(s)). This review is confined to methods that calculate H from molecular structure without experimental information and covers more than 40 methods published in the last 26 years. For a subset of eight incremental methods and four continuum-solvation models, a comparative analysis of their prediction performance is made using a test set of 700 compounds that includes a significant number of more complex and drug-like chemical structures. The results reveal substantial differences in the application range as well as in the prediction capability, a general decrease in prediction performance with decreasing H, and surprisingly large individual prediction errors, which are particularly striking for some quantum chemical schemes. The overall best-performing method appears to be the bond contribution method as implemented in the HENRYWIN software package, yielding a predictive squared correlation coefficient (q2) of 0.87 and a standard error of 1.03 log units for the test set.

  9. Quantitative Structure-Property Relationships for Melting Points and Densities of Ionic Liquids

    DTIC Science & Technology

    2004-07-01

    316. (27) Fukui, K. Theory of Orientation and Stereoselection , Springer-Verlag, Berlin. 1975. (28)Trohalaki, S.; Pachter, R. SAR and QSAR in...UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Air Force Research Laboratory (AFMC),AFRL/PRSP,10 E. Saturn Blvd.,Edwards AFB,CA,93524...7680 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) 11. SPONSOR

  10. Process-Structure-Property Relationships for 316L Stainless Steel Fabricated by Additive Manufacturing and Its Implication for Component Engineering

    NASA Astrophysics Data System (ADS)

    Yang, Nancy; Yee, J.; Zheng, B.; Gaiser, K.; Reynolds, T.; Clemon, L.; Lu, W. Y.; Schoenung, J. M.; Lavernia, E. J.

    2016-12-01

    We investigate the process-structure-property relationships for 316L stainless steel prototyping utilizing 3-D laser engineered net shaping (LENS), a commercial direct energy deposition additive manufacturing process. The study concluded that the resultant physical metallurgy of 3-D LENS 316L prototypes is dictated by the interactive metallurgical reactions, during instantaneous powder feeding/melting, molten metal flow and liquid metal solidification. The study also showed 3-D LENS manufacturing is capable of building high strength and ductile 316L prototypes due to its fine cellular spacing from fast solidification cooling, and the well-fused epitaxial interfaces at metal flow trails and interpass boundaries. However, without further LENS process control and optimization, the deposits are vulnerable to localized hardness variation attributed to heterogeneous microstructure, i.e., the interpass heat-affected zone (HAZ) from repetitive thermal heating during successive layer depositions. Most significantly, the current deposits exhibit anisotropic tensile behavior, i.e., lower strain and/or premature interpass delamination parallel to build direction (axial). This anisotropic behavior is attributed to the presence of interpass HAZ, which coexists with flying feedstock inclusions and porosity from incomplete molten metal fusion. The current observations and findings contribute to the scientific basis for future process control and optimization necessary for material property control and defect mitigation.

  11. Nanoporous-Gold-Based Electrode Morphology Libraries for Investigating Structure-Property Relationships in Nucleic Acid Based Electrochemical Biosensors.

    PubMed

    Matharu, Zimple; Daggumati, Pallavi; Wang, Ling; Dorofeeva, Tatiana S; Li, Zidong; Seker, Erkin

    2017-01-31

    Nanoporous gold (np-Au) electrode coatings significantly enhance the performance of electrochemical nucleic acid biosensors because of their three-dimensional nanoscale network, high electrical conductivity, facile surface functionalization, and biocompatibility. Contrary to planar electrodes, the np-Au electrodes also exhibit sensitive detection in the presence of common biofouling media due to their porous structure. However, the pore size of the nanomatrix plays a critical role in dictating the extent of biomolecular capture and transport. Small pores perform better in the case of target detection in complex samples by filtering out the large nonspecific proteins. On the other hand, larger pores increase the accessibility of target nucleic acids in the nanoporous structure, enhancing the detection limits of the sensor at the expense of more interference from biofouling molecules. Here, we report a microfabricated np-Au multiple electrode array that displays a range of electrode morphologies on the same chip for identifying feature sizes that reduce the nonspecific adsorption of proteins but facilitate the permeation of target DNA molecules into the pores. We demonstrate the utility of the electrode morphology library in studying DNA functionalization and target detection in complex biological media with a special emphasis on revealing ranges of electrode morphologies that mutually enhance the limit of detection and biofouling resilience. We expect this technique to assist in the development of high-performance biosensors for point-of-care diagnostics and facilitate studies on the electrode structure-property relationships in potential applications ranging from neural electrodes to catalysts.

  12. Conformationally dynamic π-conjugation: probing structure-property relationships of fluorescent tris(N-salicylideneaniline)s.

    PubMed

    Vieweger, Mario; Jiang, Xuan; Lim, Young-Kwan; Jo, Junyong; Lee, Dongwhan; Dragnea, Bogdan

    2011-11-24

    We recently reported the design and synthesis of a series of conformationally dynamic chromophores that are built on the C(3)-symmetric tris(N-salicylideneaniline) platform. This system utilizes cooperative structural folding-unfolding motions for fluorescence switching, which is driven by the assembly and disassembly of hydrogen bonds between the rigid core and rotatable peripheral part of the molecule. Here, we report detailed time-resolved spectroscopic studies to investigate the structure-property relationships of a series of functionalized tris(N-salicylideneaniline)s. Time-resolved fluorescence decay spectroscopy was applied to determine the main relaxation mechanisms of these π-extended fluorophores, and to address the effects of hydrogen bonding, steric constraints, and extension of the π-conjugation on their relaxation dynamics. Our results agree well with the conformational switching model that was previously suggested from steady-state experiments. Notably, extension of the π-conjugation from peripheral aryl groups resulted in the stabilization of the excited states, as evidenced by longer lifetimes and lower nonradiative decay constants. As a consequence, an increase in the fluorescence quantum yields was observed, which could be explained by the suppression of the torsional motions about the C-N bonds from an overall increase in the quinoid character of the excited states. A combination of time-resolved and steady-state techniques also revealed intermolecular interactions through π-π stacking at higher concentrations, which provide additional de-excitation pathways that become more pronounced in solid samples.

  13. Two-photon polarity probes built from octupolar fluorophores: synthesis, structure-properties relationships, and use in cellular imaging.

    PubMed

    Le Droumaguet, Céline; Sourdon, Aude; Genin, Emilie; Mongin, Olivier; Blanchard-Desce, Mireille

    2013-12-01

    A series of octupolar fluorophores built from a triphenylamine (TPA) core connected to electron-withdrawing (EW) peripheral groups through conjugated spacers has been synthesized. Their photoluminescence, solvatochromism, and two-photon absorption (2PA) properties were systematically investigated to derive structure-property relationships. All derivatives exhibit two 2PA bands in the 700-1000 nm region: a first band at low energy correlated with a core-to-periphery intramolecular charge transfer that leads to an intense 1PA in the blue-visible range, and a second more intense band at higher energy due to an efficient coupling of the branches through the TPA core. Increasing the strength of the EW end groups or the length of the conjugated spacers and replacing triple-bond linkers with double bonds induces both enhancement and broadening of the 2PA responses, thereby leading to cross-sections up to 2100 GM at peak and higher than 1000 GM over the whole 700-900 nm range. All derivatives exhibit intense photoluminescence (PL) in low- to medium-polarity environments (with quantum yields in the 0.5-0.9 range) and display a strong positive solvatochromic behavior (with Lippert-Mataga specific shifts ranging from 15,000 to 27,500 cm(-1)), triple bonds, and phenyl moieties in the conjugated spacers, thereby leading to larger sensitivities than those of double bonds and thienyl moieties. More hydrophilic derivatives were also shown to be biocompatible, to retain their 2PA and PL properties in biological conditions, and finally to be suitable as polarity sensors for multiphoton cell imaging.

  14. Multi-scale effects of poling on structure-property relationships in lead magnesium niobate-lead titanate single crystals

    NASA Astrophysics Data System (ADS)

    Sehirlioglu, Alp

    Ferroelectric Pb(Mg1/3Nb2/3)O 3-PbTiO3 (PMN-PT) single crystals are the most promising candidates for the next generation of ultrasonic devices. These materials have superior properties (d33= 3000 PC/N, d31= -1800 pC/N, d15= 5000 pC/N, k33 >0.90) when compared with conventional PZT ceramics. The outstanding properties of ferroelectric piezoelectrics depend in large part on the domain reorientation process known as poling. In this thesis, the multi-scale effects of poling on structure-property relationships are investigated, as a function of crystallographic orientation and temperature, for compositions in the morphotropic phase boundary (MPB) region. Thermal softening and expansion coefficients were determined by dilatometry, and a unique direction was discovered along one of the crystallographic equivalent <001> directions, even for unpoled melt-grown crystals. Values of dielectric constant (K33) tripled along the unique direction for compositions near the MPB, compared with the other orthogonal directions. Poling along <001> doubled K33 at room temperature (from K33≈2000 to ≈5000) for compositions near the critical point, and increased over ten-fold (from K33≈1200 to ≈14000) for compositions near the MPB. Room temperature poling also affected the domain structure, and the phase transformation characteristics. Onsets in non-linearity for thermal strain and Curie-Weiss behavior were found to correlate with the Burns temperature. Diffuse dielectric phase anomalies for compositions close to the critical point were attributed to a convergence of three phases rather than classic relaxor behavior. In addition, hyper-Raman measurements revealed softening of a new composition-independent non-polar mode at the Burns temperature. A never-before-seen superlattice in the MPB region was revealed by XRD in the transmission mode. Poling increased the average significance of the superlattice, signifying a structural contribution to the super-structure. The effects of

  15. A novel approach to study the structure-property relationships and applications in living systems of modular Cu2+ fluorescent probes

    NASA Astrophysics Data System (ADS)

    She, Mengyao; Yang, Zheng; Hao, Likai; Wang, Zhaohui; Luo, Tianyou; Obst, Martin; Liu, Ping; Shen, Yehua; Zhang, Shengyong; Li, Jianli

    2016-08-01

    A series of Cu2+ probe which contains 9 probes have been synthesized and established. All the probes were synthesized using Rhodamine B as the fluorophore, conjugated to various differently substituted cinnamyl aldehyde with C=N Schiff base structural motif as their core moiety. The structure-property relationships of these probes have been investigated. The change of optical properties, caused by different electronic effect and steric effect of the recognition group, has been analyzed systematically. DFT calculation simulation of the Ring-Close and Ring-Open form of all the probes have been employed to illuminate, summarize and confirm these correlations between optical properties and molecular structures. In addition, biological experiment demonstrated that all the probes have a high potential for both sensitive and selective detection, mapping of adsorbed Cu2+ both in vivo and environmental microbial systems. This approach provides a significant strategy for studying structure-property relationships and guiding the synthesis of probes with various optical properties.

  16. Elucidation of the structure-property relationship of p-type organic semiconductors through rapid library construction via a one-pot, Suzuki-Miyaura coupling reaction.

    PubMed

    Fuse, Shinichiro; Matsumura, Keisuke; Wakamiya, Atsushi; Masui, Hisashi; Tanaka, Hiroshi; Yoshikawa, Susumu; Takahashi, Takashi

    2014-09-08

    The elucidation of the structure-property relationship is an important issue in the development of organic electronics. Combinatorial synthesis and the evaluation of systematically modified compounds is a powerful tool in the work of elucidating structure-property relationships. In this manuscript, D-π-A structure, 32 p-type organic semiconductors were rapidly synthesized via a one-pot, Suzuki-Miyaura coupling with subsequent Knoevenagel condensation. Evaluation of the solubility and photovoltaic properties of the prepared compounds revealed that the measured solubility was strongly correlated with the solubility parameter (SP), as reported by Fedors. In addition, the SPs were correlated with the Jsc of thin-film organic solar cells prepared using synthesized compounds. Among the evaluated photovoltaic properties of the solar cells, Jsc and Voc had strong correlations with the photoconversion efficiency (PCE).

  17. Retrospective hit-deconvolution of mixed metal oxides: spotting structure-property-relationships in gas phase oxidation catalysis through high throughput experimentation.

    PubMed

    Schunk, Stephan Andreas; Sundermann, Andreas; Hibst, Hartmut

    2007-01-01

    Complex multi-element lead structures of mixed metal oxides that may be identified as hits during high throughput experimentation (HTE) campaigns, can be deconvoluted retrospectively on the basis of simple binary and ternary oxides as illustrated in the current example of a hit found in an ammoxidation reaction. On the basis of the performance of the simple binary and ternary mixed metal oxides structure property relationships can be established, that give insight into the roles of the different components of the complex mixed metal oxides and may also help in establishing a reaction mechanism and converting the hit into a development candidate.

  18. Structure-Property Relationships in W Doped (Ba,Sr)TiO(3) Thin Films Deposited by Pulsed Laser Deposition on (001) MgO

    DTIC Science & Technology

    2003-04-03

    UNCLASSIFIED Defense Technical Information Center Compilation Part Notice ADP013347 TITLE: Structure-Property Relationships in W Doped [Ba,Sr]TiO[3... Doped (Ba,Sr)TiO 3 Thin Films Deposited by Pulsed Laser Deposition on (001) MgO N. Navi1’*, J.S. Horwitz, H.-D. Wu2 and S.B. Qadri, Naval Research...oscillators, delay lines and phase shifters [1]. These devices will reduce the size and the operating power of the current semiconducting and ferrite based

  19. Energetic N-Nitramino/N-Oxyl-Functionalized Pyrazoles with Versatile π-π Stacking: Structure-Property Relationships of High-Performance Energetic Materials.

    PubMed

    Yin, Ping; Mitchell, Lauren A; Parrish, Damon A; Shreeve, Jean'ne M

    2016-11-07

    N-Nitramino/N-oxyl functionalization strategies were employed to investigate structure-property relationships of energetic materials. Based on single-crystal diffraction data, π-π stacking of pyrazole backbones can be tailored effectively by energetic functionalities, thereby resulting in diversified energetic compounds. Among them, hydroxylammonium 4-amino-3,5-dinitro-1H-pyrazol-1-olate and dipotassium N,N'-(3,5-dinitro-1H-pyrazol-1,4-diyl)dinitramidate, with unique face-to-face π-π stacking, can be potentially used as a high-performance explosive and an energetic oxidizer, respectively.

  20. The relationship between star formation activity and galaxy structural properties in CANDELS and a semi-analytic model

    NASA Astrophysics Data System (ADS)

    Brennan, Ryan; Pandya, Viraj; Somerville, Rachel S.; Barro, Guillermo; Bluck, Asa F. L.; Taylor, Edward N.; Wuyts, Stijn; Bell, Eric F.; Dekel, Avishai; Faber, Sandra; Ferguson, Henry C.; Koekemoer, Anton M.; Kurczynski, Peter; McIntosh, Daniel H.; Newman, Jeffrey A.; Primack, Joel

    2017-02-01

    We study the correlation of galaxy structural properties with their location relative to the SFR-M* correlation, also known as the star formation `star-forming main sequence' (SFMS), in the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey and Galaxy and Mass Assembly Survey and in a semi-analytic model (SAM) of galaxy formation. We first study the distribution of median Sérsic index, effective radius, star formation rate (SFR) density and stellar mass density in the SFR-M* plane. We then define a redshift-dependent main sequence and examine the medians of these quantities as a function of distance from this main sequence, both above (higher SFRs) and below (lower SFRs). Finally, we examine the distributions of distance from the main sequence in bins of these quantities. We find strong correlations between all of these galaxy structural properties and the distance from the SFMS, such that as we move from galaxies above the SFMS to those below it, we see a nearly monotonic trend towards higher median Sérsic index, smaller radius, lower SFR density, and higher stellar density. In the SAM, bulge growth is driven by mergers and disc instabilities, and is accompanied by the growth of a supermassive black hole which can regulate or quench star formation via active galactic nucleus feedback. We find that our model qualitatively reproduces the trends described above, supporting a picture in which black holes and bulges co-evolve, and active galactic nucleus feedback plays a critical role in moving galaxies off of the SFMS.

  1. A novel approach to study the structure-property relationships and applications in living systems of modular Cu2+ fluorescent probes

    PubMed Central

    She, Mengyao; Yang, Zheng; Hao, Likai; Wang, Zhaohui; Luo, Tianyou; Obst, Martin; Liu, Ping; Shen, Yehua; Zhang, Shengyong; Li, Jianli

    2016-01-01

    A series of Cu2+ probe which contains 9 probes have been synthesized and established. All the probes were synthesized using Rhodamine B as the fluorophore, conjugated to various differently substituted cinnamyl aldehyde with C=N Schiff base structural motif as their core moiety. The structure-property relationships of these probes have been investigated. The change of optical properties, caused by different electronic effect and steric effect of the recognition group, has been analyzed systematically. DFT calculation simulation of the Ring-Close and Ring-Open form of all the probes have been employed to illuminate, summarize and confirm these correlations between optical properties and molecular structures. In addition, biological experiment demonstrated that all the probes have a high potential for both sensitive and selective detection, mapping of adsorbed Cu2+ both in vivo and environmental microbial systems. This approach provides a significant strategy for studying structure-property relationships and guiding the synthesis of probes with various optical properties. PMID:27485974

  2. Effect of Fe(3)O(4) on the sedimentation and structure-property relationship of starch under different pHs.

    PubMed

    Palanikumar, S; Siva, P; Meenarathi, B; Kannammal, L; Anbarasan, R

    2014-06-01

    The nanosized ferrite (Fe3O4) was synthesized and characterized by analytical techniques such as Fourier transform infrared (FTIR) spectroscopy, UV-visible spectroscopy, fluorescence spectroscopy and transmission electron microscopy (TEM). The structure-property relationship of starch was studied under three different pHs namely 3.8, 7.1 and 12.5. The starch treated under acidic condition was degraded. In a similar manner, the structure-property relationship of starch in the presence of ferrite nanoparticles at three different pHs, as mentioned above was studied. The starch/ferrite nanocomposite prepared under acidic condition showed a degraded structure. Further, the polymer/nanocomposite systems were characterized by analytical techniques such as FTIR, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), vibrating sample measurement (VSM), TEM and scanning electron microscopy (SEM). Finally, the settling velocity of starch under three different pHs both in the presence and absence of Fe3O4 was carried out to ensure the role of pH and effect of Fe3O4 on the settling velocity of starch.

  3. Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design.

    PubMed

    Matta, Chérif F; Arabi, Alya A

    2011-06-01

    The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

  4. Structure-Property-Performance Relationships for Organic Photovoltaics and the Utilization of Photoconducting Atomic Force Microscopy for Characterizing Organic Thin Films

    NASA Astrophysics Data System (ADS)

    Guide, Michele Elyse

    Progress in the development of organic photovoltaics (OPVs) depends on a continually growing understanding of the effects of chemical composition or processing method on the optoelectronic and structural properties and, in turn, how those properties influence device performance. Unfortunately, no single characterization method can provide all of the necessary information to develop these structure-property-performance relationships. This thesis details examples of structure-property-performance studies in which multiple characterization methods are used to identify the root cause of limited device performance for a particular photovoltaic system. As a large part of this work, the refinement and utilization of a nanoscale characterization technique, namely photoconducting atomic force microscopy (pc-AFM) is presented, not as an alternative to other characterization methods, but as a unique approach to characterizing the nanoscale morphology and local optoelectronic properties of an organic thin film simultaneously. The goal of this work was to make pc-AFM as robust and reliable a characterization tool and as close an analog to bulk OPV performance testing as possible. The first sections of this thesis focus on the development of pc-AFM for the characterization of OPVs. The capabilities of pc-AFM at the time this research commenced are illustrated in a study of a multilayered p/i/n architecture OPV system comprising a thermoset small molecule donor, tetrabenzoporphyrin (BP) and one of two structurally similar soluble fullerene derivative acceptors. By investigating the nanoscale topography, dark current, and photocurrent in each layer of these multilayer devices, the differences in bulk device performance can be rationalized and the composition of specific morphological features can be identified. At the same time, this study demonstrates how interpretation of pc-AFM measurements was not straightforward and required knowledge of the bulk performance. This issue

  5. Research on the relationship between the structural properties of bedding layer in spring mattress and sleep quality.

    PubMed

    Shen, Liming; Chen, Yu-xia; Guo, Yong; Zhong, ShiLu; Fang, Fei; Zhao, Jing; Hu, Tian-Yi

    2012-01-01

    Mattress, as a sleep platform, its types and physical properties has an important effect on sleep quality and rest efficiency. In this paper, by subjective evaluations, analysis of sleeping behaviors and tests of depth of sleep, the relationship between characteristics of the bedding materials, the structure of mattress, sleep quality and sleep behaviors were studied. The results showed that: (1) Characteristics of the bedding materials and structure of spring mattress had a remarkable effect on sleep behaviors and sleep quality. An optimum combination of the bedding materials, the structure of mattress and its core could improve the overall comfort of mattress, thereby improving the depth of sleep and sleep quality. (2) Sleep behaviors had a close relationship with sleeping postures and sleep habits. The characteristics of sleep behaviors vary from person to person.

  6. Structure-property relationships: Model studies on melt-extruded uniaxially-oriented high density polyethylene films having well defined morphologies

    NASA Astrophysics Data System (ADS)

    Zhou, Hongyi

    High density polyethylene (HDPE) films having simple and well-defined stacked lamellar morphology, either with or without a distinct presence of row-nucleated fibril structures, have been utilized as model materials to carry out investigations on solid state structure-property relationships. Mechanical tests, including tensile (INSTRON), creep (TMA), and dynamic mechanical (DMTA) tests, were performed at different angles with respect to the original machine direction (MD) of the melt extruded films; morphological changes as a result of these mechanical tests were detected by WAXS, SAXS, and TEM. Crystalline lamellar thickness and its distribution were determined by DSC, SAXS, TEM and AFM experiments. In the large strain deformation study (chapter 4.0), samples were stretched at 00sp°, 45sp° and 90sp° angles with respect to the original MD. A distinct orientation dependence of the tensile behavior was observed and correlated to the corresponding deformation modes and morphological changes, namely (1) lamellar separation and fragmentation by chain slip for the 00sp° stretch, (2) lamellar break-up via chain pull-out for the 90sp° stretch, and (3) lamellar shear, rotation and break-up through chain slip and/or tilt for the 45sp° stretch. A strong strengthening effect was observed for samples with row-nucleated fibril structures at the 00sp° stretch; whereas for the 90sp° stretch, the presence of such structures significantly limited deformability of the samples. In the dynamic strain mechanical alpha relaxation study (chapter 5.0), samples were tested at nine different angles with respect to the original MD, and the morphologies of samples before and after the dynamic tests were also investigated. The mechanical dispersions for the 00sp° and 90sp° tests were believed to arise essentially from the crystalline phase, and they contain contributions from two earlier recognized sub-relaxations of alphasbI and alphasbII. While for the 45sp° test, in addition to a

  7. Chemical Modification of Graphene Oxide through Diazonium Chemistry and Its Influence on the Structure-Property Relationships of Graphene Oxide-Iron Oxide Nanocomposites.

    PubMed

    Rebuttini, Valentina; Fazio, Enza; Santangelo, Saveria; Neri, Fortunato; Caputo, Gianvito; Martin, Cédric; Brousse, Thierry; Favier, Frédéric; Pinna, Nicola

    2015-08-24

    4-Carboxyphenyl groups are covalently grafted onto graphene oxide via diazonium chemistry for studying their role on the adsorption of iron oxide nanoparticles. The nanoparticles are deposited via a novel phase-transfer approach involving specific interactions at the interface between two immiscible solvents. The increased density and the homogeneous distribution of surface carboxyl moieties enable the preparation of a nanocomposite with improved iron oxide distribution and loading. Structure-properties relationships are investigated by analysing the electrochemical properties of the nanocomposites, which are regarded as promising active materials for application in supercapacitors. It is demonstrated that the nature of the interactions between the components similarly affects the overall electrochemical performances of the nanocomposites and the structure of the materials.

  8. Revealing the structure-property relationship of covalent organic frameworks for CO₂ capture from postcombustion gas: a multi-scale computational study.

    PubMed

    Tong, Minman; Yang, Qingyuan; Xiao, Yuanlong; Zhong, Chongli

    2014-08-07

    With the aid of multi-scale computational methods, a diverse set of 46 covalent organic frameworks (COFs), covering the most typical COFs synthesized to date, were collected to study the structure-property relationship of COFs for CO2 capture. For this purpose, CO2 capture from postcombustion gas (CO2-N2 mixture) under industrial vacuum swing adsorption (VSA) conditions was considered as an example. This work shows that adsorption selectivity, CO2 working capacity and the sorbent selection parameter of COFs all exhibit strong correlation with the difference in the adsorbility of adsorbates (ΔAD), highlighting that realization of large ΔAD can be regarded as an important starting point for designing COFs with improved separation performance. Furthermore, it was revealed that the separation performance of 2D-layered COFs can be greatly enhanced by generating "splint effects", which can be achieved through structural realignment to form slit-like pores with suitable size in the structures. Such "splint effects" in 2D-COFs can find their similar counterpart of "catenation effects" in 3D-COFs or MOFs. On the basis of these observations, a new design strategy was proposed to strengthen the separation performance of COFs. It could be expected that the information obtained in this work not only will enrich the knowledge of the structure-property relationship of COFs for separation, but also will largely facilitate their future applications to the fields related to energy and environmental science, such as natural gas purification, CO2, NO(x) and SO(x) capture, etc.

  9. Processing-Structure-Property Relationships for Lignin-Based Carbonaceous Materials Used in Energy-Storage Applications

    DOE PAGES

    García-Negrón, Valerie; Phillip, Nathan D.; Li, Jianlin; ...

    2016-11-18

    Lignin, an abundant organic polymer and a byproduct of pulp and biofuel production, has potential applications owing to its high carbon content and aromatic structure. Processing structure relationships are difficult to predict because of the heterogeneity of lignin. Here, this work discusses the roles of unit operations in the carbonization process of softwood lignin, and their resulting impacts on the material structure and electrochemical properties in application as the anode in lithium-ion cells. The processing variables include the lignin source, temperature, and duration of thermal stabilization, pyrolysis, and reduction. Materials are characterized at the atomic and microscales. High-temperature carbonization, atmore » 2000 °C, produces larger graphitic domains than at 1050 °C, but results in a reduced capacity. Coulombic efficiencies over 98 % are achieved for extended galvanostatic cycling. Consequently, a properly designed carbonization process for lignin is well suited for the generation of low-cost, high-efficiency electrodes.« less

  10. Processing-Structure-Property Relationships for Lignin-Based Carbonaceous Materials Used in Energy-Storage Applications

    SciTech Connect

    García-Negrón, Valerie; Phillip, Nathan D.; Li, Jianlin; Daniel, Claus; Wood, David; Keffer, David J.; Rios, Orlando; Harper, David P.

    2016-11-18

    Lignin, an abundant organic polymer and a byproduct of pulp and biofuel production, has potential applications owing to its high carbon content and aromatic structure. Processing structure relationships are difficult to predict because of the heterogeneity of lignin. Here, this work discusses the roles of unit operations in the carbonization process of softwood lignin, and their resulting impacts on the material structure and electrochemical properties in application as the anode in lithium-ion cells. The processing variables include the lignin source, temperature, and duration of thermal stabilization, pyrolysis, and reduction. Materials are characterized at the atomic and microscales. High-temperature carbonization, at 2000 °C, produces larger graphitic domains than at 1050 °C, but results in a reduced capacity. Coulombic efficiencies over 98 % are achieved for extended galvanostatic cycling. Consequently, a properly designed carbonization process for lignin is well suited for the generation of low-cost, high-efficiency electrodes.

  11. Analyis of structure/property relationships in silkworm (Bombyx mori) and spider dragline (Nephila edulis) silks using Raman spectroscopy.

    PubMed

    Sirichaisit, Jutarat; Brookes, Victoria L; Young, Robert J; Vollrath, Fritz

    2003-01-01

    The molecular deformation of both silkworm (Bombyx mori) and spider dragline (Nephila edulis) silks has been studied using a combination of mechanical deformation and Raman spectroscopy. The stress/strain curves for both kinds of silk showed elastic behavior followed by plastic deformation. It was found that both materials have well-defined Raman spectra and that some of the bands in the spectra shift to lower frequency under the action of tensile stress or strain. The band shift was linearly dependent upon stress for both types of silk fiber. This observation provides a unique insight into the effect of tensile deformation upon molecular structure and the relationship between structure and mechanical properties. Two similar bands in the Raman spectra of both types of silk in the region of 1000-1300 cm(-1) had significant identical rates of Raman band shift of about 7 cm(-1)/GPa and 14 cm(-1)/GPa demonstrating the similarity between the silk fibers from two different animals.

  12. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

  13. QSAR in Chromatography: Quantitative Structure-Retention Relationships (QSRRs)

    NASA Astrophysics Data System (ADS)

    Kaliszan, Roman; Bączek, Tomasz

    To predict a given physicochemical or biological property, the relationships can be identified between the chemical structure and the desired property. Ideally these relationships should be described in reliable quantitative terms. To obtain statistically significant relationships, one needs relatively large series of property parameters. Chromatography is a unique method which can provide a great amount of quantitatively precise, reproducible, and comparable retention data for large sets of structurally diversified compounds (analytes). On the other hand, chemometrics is recognized as a valuable tool for accomplishing a variety of tasks in a chromatography laboratory. Chemometrics facilitates the interpretation of large sets of complex chromatographic and structural data. Among various chemometric methods, multiple regression analysis is most often performed to process retention data and to extract chemical information on analytes. And the methodology of quantitative structure-(chromatographic) retention relationships (QSRRs) is mainly based on multiple regression analysis. QSRR can be a valuable source of knowledge on both the nature of analytes and of the macromolecules forming the stationary phases. Therefore, quantitative structure-retention relationships have been considered as a model approach to establish strategy and methods of property predictions.

  14. Processing-structure-property relationships of thermal barrier coatings deposited using the solution precursor plasma spray process

    NASA Astrophysics Data System (ADS)

    Xie, Liangde

    This research is intended to develop a novel process, solution-precursor plasma-spray (SPPS), for the deposition of highly durable thermal barrier coatings (TBCs). In the SPPS process a solution precursor feedstock, that results in ZrO2-7 wt% Y2O3 ceramic, is injected into the plasma jet and the coating is deposited on a metal substrate. The formed coating has the following novel microstructural features: (i) ultra-fine splats, (ii) through-thickness cracks, (iii) micrometer and nanometer porosity, and (iv) interpass boundaries. The deposition mechanisms of the solution precursor droplets injected into the different regions of the plasma jet were found to be different due to large temperature variation across the plasma jet. The solution precursor droplets injected into the core of the plasma jet are deposited on the substrate as ultra-fine splats that account for around 65 volume% of the coating. The other 35 volume% of the coating includes porosity and deposits formed from the solution precursor droplets injected into other regions of the plasma jet. The optimum processing condition for highly durable TBCs was determined using Taguchi design of experiments. Meanwhile, the relationship of the microstructural features and processing parameters was revealed. During thermal cycling, the unmelted particles in the coating were observed to pyloyze and/or sinter, while no sign of sintering was observed for the ultra-fine splats. The spacing of through-thickness cracks remains in the range of 160 to 190 mum throughout the thermal cycling test. Three stages of oxidation of the bond coat were observed. Failure of the SPPS TBC starts with the crack nucleation along the unmelted particles in the top coat and the Ni, Cr, Co-rich oxides of large thickness. These cracks propagate and coalesce with thermal cycling. The extensive cracking of the rapidly formed Ni, Cr, Co-rich oxides resulting from the depletion of aluminum in the bond coat leads to the development of large

  15. Endochin optimization: structure-activity and structure-property relationship studies of 3-substituted 2-methyl-4(1H)-quinolones with antimalarial activity.

    PubMed

    Cross, R Matthew; Monastyrskyi, Andrii; Mutka, Tina S; Burrows, Jeremy N; Kyle, Dennis E; Manetsch, Roman

    2010-10-14

    Since the 1940s endochin and analogues thereof were known to be causal prophylactic and potent erythrocytic stage agents in avian models. Preliminary screening in a current in vitro assay identified several 4(1H)-quinolones with nanomolar EC(50) against erythrocytic stages of multidrug resistant W2 and TM90-C2B isolates of Plasmodium falciparum. Follow-up structure-activity relationship (SAR) studies on 4(1H)-quinolone analogues identified several key features for biological activity. Nevertheless, structure-property relationship (SPR) studies conducted in parallel revealed that 4(1H)-quinolone analogues are limited by poor solubilities and rapid microsomal degradations. To improve the overall efficacy, multiple 4(1H)-quinolone series with varying substituents on the benzenoid quinolone ring and/or the 3-position were synthesized and tested for in vitro antimalarial activity. Several structurally diverse 6-chloro-2-methyl-7-methoxy-4(1H)-quinolones with EC(50) in the low nanomolar range against the clinically relevant isolates W2 and TM90-C2B were identified with improved physicochemical properties while maintaining little to no cross-resistance with atovaquone.

  16. Quantitative structure-activity relationships for fluoroelastomer/chlorofluorocarbon systems

    SciTech Connect

    Paciorek, K.J.L.; Masuda, S.R.; Nakahara, J.H. ); Snyder, C.E. Jr.; Warner, W.M. )

    1991-12-01

    This paper reports on swell, tensile, and modulus data that were determined for a fluoroelastomer after exposure to a series of chlorofluorocarbon model fluids. Quantitative structure-activity relationships (QSAR) were developed for the swell as a function of the number of carbons and chlorines and for tensile strength as a function of carbon number and chlorine positions in the chlorofluorocarbons.

  17. Partitioning and lipophilicity in quantitative structure-activity relationships.

    PubMed Central

    Dearden, J C

    1985-01-01

    The history of the relationship of biological activity to partition coefficient and related properties is briefly reviewed. The dominance of partition coefficient in quantitation of structure-activity relationships is emphasized, although the importance of other factors is also demonstrated. Various mathematical models of in vivo transport and binding are discussed; most of these involve partitioning as the primary mechanism of transport. The models describe observed quantitative structure-activity relationships (QSARs) well on the whole, confirming that partitioning is of key importance in in vivo behavior of a xenobiotic. The partition coefficient is shown to correlate with numerous other parameters representing bulk, such as molecular weight, volume and surface area, parachor and calculated indices such as molecular connectivity; this is especially so for apolar molecules, because for polar molecules lipophilicity factors into both bulk and polar or hydrogen bonding components. The relationship of partition coefficient to chromatographic parameters is discussed, and it is shown that such parameters, which are often readily obtainable experimentally, can successfully supplant partition coefficient in QSARs. The relationship of aqueous solubility with partition coefficient is examined in detail. Correlations are observed, even with solid compounds, and these can be used to predict solubility. The additive/constitutive nature of partition coefficient is discussed extensively, as are the available schemes for the calculation of partition coefficient. Finally the use of partition coefficient to provide structural information is considered. It is shown that partition coefficient can be a valuable structural tool, especially if the enthalpy and entropy of partitioning are available. PMID:3905374

  18. Learning Quantitative Sequence-Function Relationships from Massively Parallel Experiments

    NASA Astrophysics Data System (ADS)

    Atwal, Gurinder S.; Kinney, Justin B.

    2016-03-01

    A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships—functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques for effectively measuring these relationships been developed. The advent of such "massively parallel" experiments presents an exciting opportunity for the concepts and methods of statistical physics to inform the study of biological systems. After reviewing these recent experimental advances, we focus on the problem of how to infer parametric models of sequence-function relationships from the data produced by these experiments. Specifically, we retrace and extend recent theoretical work showing that inference based on mutual information, not the standard likelihood-based approach, is often necessary for accurately learning the parameters of these models. Closely connected with this result is the emergence of "diffeomorphic modes"—directions in parameter space that are far less constrained by data than likelihood-based inference would suggest. Analogous to Goldstone modes in physics, diffeomorphic modes arise from an arbitrarily broken symmetry of the inference problem. An analytically tractable model of a massively parallel experiment is then described, providing an explicit demonstration of these fundamental aspects of statistical inference. This paper concludes with an outlook on the theoretical and computational challenges currently facing studies of quantitative sequence-function relationships.

  19. Structure-property relationships in an Al matrix Ca nanofilamentary composite conductor with potential application in high-voltage power transmission

    NASA Astrophysics Data System (ADS)

    Tian, Liang

    This study investigated the processing-structure-properties relationships in an Al/Ca composites using both experiments and modeling/simulation. A particular focus of the project was understanding how the strength and electrical conductivity of the composite are related to its microstructure in the hope that a conducting material with light weight, high strength, and high electrical conductivity can be developed to produce overhead high-voltage power transmission cables. The current power transmission cables (e.g., Aluminum Conductor Steel Reinforced (ACSR)) have acceptable performance for high-voltage AC transmission, but are less well suited for high-voltage DC transmission due to the poorly conducting core materials that support the cable weight. This Al/Ca composite was produced by powder metallurgy and severe plastic deformation by extrusion and swaging. The fine Ca metal powders have been produced by centrifugal atomization with rotating liquid oil quench bath, and a detailed study about the atomization process and powder characteristics has been conducted. The microstructure of Al/Ca composite was characterized by electron microscopy. Microstructure changes at elevated temperature were characterized by thermal analysis and indirect resistivity tests. The strength and electrical conductivity were measured by tensile tests and four-point probe resistivity tests. Predicting the strength and electrical conductivity of the composite was done by micro-mechanics-based analytical modeling. Microstructure evolution was studied by mesoscale-thermodynamics-based phase field modeling and a preliminary atomistic molecular dynamics simulation. The application prospects of this composite was studied by an economic analysis. This study suggests that the Al/Ca (20 vol. %) composite shows promise for use as overhead power transmission cables. Further studies are needed to measure the corrosion resistance, fatigue properties and energized field performance of this composite.

  20. The synthesis, characterization, and structure-property relationships of regioregular 4,4'-dialkyl-2,2'-bithiazole oligomers and polymers

    NASA Astrophysics Data System (ADS)

    Nanos, John I.

    2005-12-01

    The 4,4'-dialkyl-2,2'-bithiazole moiety can be efficiently coupled to produce well-defined oligomers or block co-oligomers via Stille reactions of mono-bromo and tin substituted precursors. Dehalogenative polycondensations produce high molecular weight homo-polymers and Stille coupling of dibromo and di-tin monomers yields alternating copolymers. The symmetry of the bithiazole monomeric unit produces regioregular oligomers and polymers with the HH-TT dyad sequence. Model compound oligomers were synthesized and studied to explore the progression of structure property relationships with main chain extension. DSC measurements indicate the potential presence of at least three phases in solution cast thin films---the disordered isotropic melt, a stable low temperature morphology designated the alpha-phase, and a high temperature meta-stable morphology designated the beta-phase. Melt transition temperatures are inversely proportional to side alkyl chain length and directly proportional to main chain length and the interplay between the two effects greatly influences the observed thermochromism. Temperature dependent IR studies show an increase in the gauche conformations of the side chains at the low temperature alpha-beta phase transition and main chain twisting at the beta-isotropic transition. The onset of side chain and main chain motion at these phase transition temperatures was confirmed with variable temperature solid state NMR. Temperature dependent XRD results indicate the presence of a solid-to-solid crystal phase change at the low temperature transition followed by formation of preferred orientations of the beta and alpha ordered phases upon cooling from the isotropic melt. The solid-to-solid crystal phase transition is triggered by the increased motion of the side chains, and the magnitude of the intermolecular side chain packing forces dictate if the transitions occur cooperatively (observed isosbestic point) or as isolated events. Comparison with the 3

  1. Quantitative Structure – Property Relationship Modeling of Remote Liposome Loading Of Drugs

    PubMed Central

    Cern, Ahuva; Golbraikh, Alexander; Sedykh, Aleck; Tropsha, Alexander; Barenholz, Yechezkel; Goldblum, Amiram

    2012-01-01

    Remote loading of liposomes by trans-membrane gradients is used to achieve therapeutically efficacious intra-liposome concentrations of drugs. We have developed Quantitative Structure Property Relationship (QSPR) models of remote liposome loading for a dataset including 60 drugs studied in 366 loading experiments internally or elsewhere. Both experimental conditions and computed chemical descriptors were employed as independent variables to predict the initial drug/lipid ratio (D/L) required to achieve high loading efficiency. Both binary (to distinguish high vs. low initial D/L) and continuous (to predict real D/L values) models were generated using advanced machine learning approaches and five-fold external validation. The external prediction accuracy for binary models was as high as 91–96%; for continuous models the mean coefficient R2 for regression between predicted versus observed values was 0.76–0.79. We conclude that QSPR models can be used to identify candidate drugs expected to have high remote loading capacity while simultaneously optimizing the design of formulation experiments. PMID:22154932

  2. Quantitative structure-activity relationships for the toxicity of chlorophenols to mammalian submitochondrial particles.

    PubMed

    Argese, E; Bettiol, C; Giurin, G; Miana, P

    1999-04-01

    The toxicity of a series of chlorophenols, determined by a short-term in vitro assay utilizing mammalian submitochondrial particles, was related to the physicochemical and structural properties of these compounds. Quantitative Structure-Activity Relationships were defined by correlating EC50 values with six molecular descriptors, chosen to represent lipophilic, electronic and steric effects: the n-octanol/water partition coefficient (log Kow), the constant of Hammett (sigma sigma), the acid dissociation constant (pKa), the first order valence molecular connectivity index (1 chi v), the perimeter of the efficacious section (sigma D) and the melting point (m.p.). The results of regression analysis showed that log Kow is the most successful descriptor, indicating that the ability of chlorophenols to partition into the lipid bilayer of the mitochondrial membrane has an important role in determining their toxic effects. These results are consistent with a molecular mechanism of uncoupling action based on the chemiosmotic theory and on the protonophoric properties of chlorophenols. The quality of the QSAR models confirms the suitability of the SMP assay as a short-term prediction tool for aquatic toxicity of environmental pollutants acting on respiratory functions.

  3. Investigation and prediction of protein precipitation by polyethylene glycol using quantitative structure-activity relationship models.

    PubMed

    Hämmerling, Frank; Ladd Effio, Christopher; Andris, Sebastian; Kittelmann, Jörg; Hubbuch, Jürgen

    2017-01-10

    Precipitation of proteins is considered to be an effective purification method for proteins and has proven its potential to replace costly chromatography processes. Besides salts and polyelectrolytes, polymers, such as polyethylene glycol (PEG), are commonly used for precipitation applications under mild conditions. Process development, however, for protein precipitation steps still is based mainly on heuristic approaches and high-throughput experimentation due to a lack of understanding of the underlying mechanisms. In this work we apply quantitative structure-activity relationships (QSARs) to model two parameters, the discontinuity point m* and the β-value, that describe the complete precipitation curve of a protein under defined conditions. The generated QSAR models are sensitive to the protein type, pH, and ionic strength. It was found that the discontinuity point m* is mainly dependent on protein molecular structure properties and electrostatic surface properties, whereas the β-value is influenced by the variance in electrostatics and hydrophobicity on the protein surface. The models for m* and the β-value exhibit a good correlation between observed and predicted data with a coefficient of determination of R(2)≥0.90 and, hence, are able to accurately predict precipitation curves for proteins. The predictive capabilities were demonstrated for a set of combinations of protein type, pH, and ionic strength not included in the generation of the models and good agreement between predicted and experimental data was achieved.

  4. Quantitative Structure-Antifungal Activity Relationships for cinnamate derivatives.

    PubMed

    Saavedra, Laura M; Ruiz, Diego; Romanelli, Gustavo P; Duchowicz, Pablo R

    2015-12-01

    Quantitative Structure-Activity Relationships (QSAR) are established with the aim of analyzing the fungicidal activities of a set of 27 active cinnamate derivatives. The exploration of more than a thousand of constitutional, topological, geometrical and electronic molecular descriptors, which are calculated with Dragon software, leads to predictions of the growth inhibition on Pythium sp and Corticium rolfsii fungi species, in close agreement to the experimental values extracted from the literature. A set containing 21 new structurally related cinnamate compounds is prepared. The developed QSAR models are applied to predict the unknown fungicidal activity of this set, showing that cinnamates like 38, 28 and 42 are expected to be highly active for Pythium sp, while this is also predicted for 28 and 34 in C. rolfsii.

  5. Investigation of the structure/property relationship of spray-formed 7XXX series high-strength aluminum alloys and their metal matrix composites

    NASA Astrophysics Data System (ADS)

    Sharma-Judd, Malavika M.

    2000-12-01

    The purpose of this investigation was to identify the structure/property relationship of spray formed 7XXX series alloys. High solute, ultra-high strength 7XXX series aluminum alloys with solute contents close to equilibrium solid solubility limits of the Al-Zn-Mg-Cu system have been produced by rapid solidification using spray deposition. The process yields massive preforms directly from the liquid state. Various elements, including chromium, manganese, silver, zirconium and scandium, were incorporated to produce a variety of microstructures and mechanical properties. SiC particulate was added to these same alloy compositions to produce metal matrix composites (MMCs). The resulting extruded products in the T6 and T7 conditions were evaluated and compared. Under peak-aged conditions in the unreinforced materials, strengths in excess of 860 MPa were achieved, with one alloy exceeding 900 MPa. Apart from the elongation to failure, the mechanical properties of the composite materials were equal to or superior to those of their unreinforced counterparts. The superior strength properties of the spray formed alloys were attributed to two major substructures with different scale; nanometer sized eta ' metastable precipitates and slightly larger, but finely distributed dispersoids. The large volume fraction of plate-like eta' precipitates (average size 58A, ranging up to 73 A in diameter) were identified as having a hexagonal structure with lattice parameters a = 0.488 nm and c = 1.376. The remarkable strengthening is predominantly attributed to precipitation hardening. The enhanced mechanical properties of the MMC materials are attributed to the increased dislocation density, and thus, a higher concentration of structural particles compared to the unreinforced materials. Higher gas-to-metal ratios of 4.45, as opposed to lower gas-to-metal ratios of 1.95 produced a refined grain structure with an evenly distributed second phase. In both unreinforced and MMC materials

  6. A Quantitative review of relationships between Ecosystem services

    NASA Astrophysics Data System (ADS)

    Lee, H.; Lautenbach, S.

    2014-12-01

    Each decision in natural resources management can generate trade-offs with respect to the provisioning of ecosystem services (ES). If the increase of one ES happens directly or indirectly at the cost of another ES, an attempt to maximize the provision of a single ES will lead to suboptimal results. However, decisions in natural resources management are often made without considering such trade-offs, despite their crucial role toward supporting better decision-making. The research on trade-offs between ES has gained some attention in the scientific community. However, a synthesis on existing knowledge and knowledge gaps is missing so far. We aim at closing that gap by a quantitative review of recent literature on trade-offs of ES. We looked at the pairs of ES that have been studied in ~100 case studies that report on trade-offs between ES. If a case study analyzed more than one ES pair, we looked at all pairwise combinations. We categorized relationships between these pairs of ES into the categories "trade-off", "synergy" or "no-effect". Most pairs of ES had a clear association with one category: the majority of case studies that studied a specific pair of ES identified the same category of relationship between the two ES. Pairs of regulating services were typically synergetic in relationship, whereas provisioning services and regulating services typically showed a trade-off. However, for several pairs of ES we were not able to identify a dominate category of relationship. Our hypothesis is that this relates to either the scale of the analysis, the land system where the analysis took place or the method used to quantify the relationship. The number of case studies for each pair of ES was spread unevenly. This hinders the support for a conclusive statement drawn for the pairs. Our results showed further that the method used to identify the relationship between services had a strong effect on the direction of the effect. This suggests that researchers should consider

  7. Quantitative structure activity relationship studies of mushroom tyrosinase inhibitors

    NASA Astrophysics Data System (ADS)

    Xue, Chao-Bin; Luo, Wan-Chun; Ding, Qi; Liu, Shou-Zhu; Gao, Xing-Xiang

    2008-05-01

    Here, we report our results from quantitative structure-activity relationship studies on tyrosinase inhibitors. Interactions between benzoic acid derivatives and tyrosinase active sites were also studied using a molecular docking method. These studies indicated that one possible mechanism for the interaction between benzoic acid derivatives and the tyrosinase active site is the formation of a hydrogen-bond between the hydroxyl (aOH) and carbonyl oxygen atoms of Tyr98, which stabilized the position of Tyr98 and prevented Tyr98 from participating in the interaction between tyrosinase and ORF378. Tyrosinase, also known as phenoloxidase, is a key enzyme in animals, plants and insects that is responsible for catalyzing the hydroxylation of tyrosine into o-diphenols and the oxidation of o-diphenols into o-quinones. In the present study, the bioactivities of 48 derivatives of benzaldehyde, benzoic acid, and cinnamic acid compounds were used to construct three-dimensional quantitative structure-activity relationship (3D-QSAR) models using comparative molecular field (CoMFA) and comparative molecular similarity indices (CoMSIA) analyses. After superimposition using common substructure-based alignments, robust and predictive 3D-QSAR models were obtained from CoMFA ( q 2 = 0.855, r 2 = 0.978) and CoMSIA ( q 2 = 0.841, r 2 = 0.946), with 6 optimum components. Chemical descriptors, including electronic (Hammett σ), hydrophobic (π), and steric (MR) parameters, hydrogen bond acceptor (H-acc), and indicator variable ( I), were used to construct a 2D-QSAR model. The results of this QSAR indicated that π, MR, and H-acc account for 34.9, 31.6, and 26.7% of the calculated biological variance, respectively. The molecular interactions between ligand and target were studied using a flexible docking method (FlexX). The best scored candidates were docked flexibly, and the interaction between the benzoic acid derivatives and the tyrosinase active site was elucidated in detail. We believe

  8. Quantitative structure-activity relationship studies on nitrofuranyl antitubercular agents

    PubMed Central

    Hevener, Kirk E.; Ball, David M.; Buolamwini, John K.

    2008-01-01

    A series of nitrofuranylamide and related aromatic compounds displaying potent activity against M. tuberculosis has been investigated utilizing 3-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) techniques. Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods were used to produce 3D-QSAR models that correlated the Minimum Inhibitory Concentration (MIC) values against M. tuberculosis with the molecular structures of the active compounds. A training set of 95 active compounds was used to develop the models, which were then evaluated by a series of internal and external cross-validation techniques. A test set of 15 compounds was used for the external validation. Different alignment and ionization rules were investigated as well as the effect of global molecular descriptors including lipophilicity (cLogP, LogD), Polar Surface Area (PSA), and steric bulk (CMR), on model predictivity. Models with greater than 70% predictive ability, as determined by external validation, and high internal validity (cross validated r2 > .5) have been developed. Incorporation of lipophilicity descriptors into the models had negligible effects on model predictivity. The models developed will be used to predict the activity of proposed new structures and advance the development of next generation nitrofuranyl and related nitroaromatic anti-tuberculosis agents. PMID:18701298

  9. Relationship between electrical admittivity and quantitative histopathology in human prostate

    NASA Astrophysics Data System (ADS)

    Halter, Ryan; Milone, Michael; Schned, Alan; Heaney, John

    2010-04-01

    Passive bioelectrical properties have been demonstrated to provide sufficient contrast for use in differentiating benign from malignant tissue in a number of different organs including breast, prostate, cervix, bladder, and skin. The underlying microscopic anatomy responsible for these measured differences has been primarily speculative in the past. In this study we recorded electrical conductivity and permittivity spectra (100 Hz - 100 kHz) from 464 three mm diameter circular prostate samples. Each of these tissue specimens were stained with hematoxylin and eosin, processed onto microscopy slides, and digitized using optical microscopy. We used digital imaging processing tools to extract quantitative morphological features including total number of glands, average and total glandular lumen size, shape characteristics of the luminal spaces, and average and total glandular perimeter lengths. Correlative analysis was performed to assess the relationships between the tissue architectural features and the precisely co-registered electrical properties. We report on the findings from this analysis. This statistical assessment aims to provide a valuable piece of new information to help formulate a better understanding of the precise influence morphological architecture has on the flow of current through tissue.

  10. [Quantitative relationships of intra- and interspecific competition in Cryptocarya concinna].

    PubMed

    Zhang, Chi; Huang, Zhongliang; Li, Jiong; Shi, Junhui; Li, Lin

    2006-01-01

    The monsoon evergreen broad-leaved forest (MEBF) in Dinghushan Nature Reserve (DNR) has been considered as a zonal vegetation in lower subtropical China, with a history of more than 400 years. In this paper, the intra- and interspecific competition intensity in Cryptocarya concinna, one of the constructive species in MEBF in DNR was quantitatively analyzed by Hegyi single-tree competition index model. The results showed that the intraspecific competition intensity in C. concinna decreased gradually with increasing tree diameter. For C. concinna, its intraspecific competition was weaker than its interspecific competition with Aporosa yunnanensis. The competition intensity of interspecific competition with C. concinna followed the order of A. yunnanensis > Schima superba > Gironniera subaequalis > Acmena acuminatissima > Castanopsis chinensis > Syzygium rehderianum > Pygeum topengii > Blastus cochinchinensis > Sarcosperma laurinum > Pterospermum lanceaefolium > Cryptocarya chinensis. The relationship of the DBH of objective tree and the competition intensity between competitive tree and objective tree in the whole forest and C. concinna population nearly conformed to power function, while that between other competitive tree and the objective C. concinna tree conformed to logarithm function. There was a significantly negative correlation between the competition intensity and the DBH of objective tree.

  11. Designing a Quantitative Structure-Activity Relationship for the ...

    EPA Pesticide Factsheets

    Toxicokinetic models serve a vital role in risk assessment by bridging the gap between chemical exposure and potentially toxic endpoints. While intrinsic metabolic clearance rates have a strong impact on toxicokinetics, limited data is available for environmentally relevant chemicals including nearly 8000 chemicals tested for in vitro bioactivity in the Tox21 program. To address this gap, a quantitative structure-activity relationship (QSAR) for intrinsic metabolic clearance rate was developed to offer reliable in silico predictions for a diverse array of chemicals. Models were constructed with curated in vitro assay data for both pharmaceutical-like chemicals (ChEMBL database) and environmentally relevant chemicals (ToxCast screening) from human liver microsomes (2176 from ChEMBL) and human hepatocytes (757 from ChEMBL and 332 from ToxCast). Due to variability in the experimental data, a binned approach was utilized to classify metabolic rates. Machine learning algorithms, such as random forest and k-nearest neighbor, were coupled with open source molecular descriptors and fingerprints to provide reasonable estimates of intrinsic metabolic clearance rates. Applicability domains defined the optimal chemical space for predictions, which covered environmental chemicals well. A reduced set of informative descriptors (including relative charge and lipophilicity) and a mixed training set of pharmaceuticals and environmentally relevant chemicals provided the best intr

  12. Plant-derived flavones as inhibitors of aurora B kinase and their quantitative structure-activity relationships.

    PubMed

    Jung, Yearam; Shin, Soon Young; Yong, Yeonjoong; Jung, Hyeryoung; Ahn, Seunghyun; Lee, Young Han; Lim, Yoongho

    2015-05-01

    Although several plant-derived flavones inhibit aurora B kinase (aurB), quantitative relationships between the structural properties of plant-derived flavones and their inhibitory effects on aurB remain unclear. In this report, these quantitative structure-activity relationships were obtained. For quercetagetin, found in the Eriocaulon species, showing the best IC50 value among the flavone derivatives tested in this report, further biological tests were performed using cell-based assays, including Western blot analysis, flow cytometry, and immunofluorescence microscopy. In vitro cellular experiments demonstrated that quercetagetin inhibits aurB. The molecular-binding mode between quercetagetin and aurB was elucidated using in silico docking. Quercetagetin binds to aurB, aurA, and aurC and prevents the active phosphorylation of all three aurora kinases. In addition, quercetagetin triggers mitotic arrest and caspase-mediated apoptosis. These observations suggest that quercetagetin is an aurora kinase inhibitor. Induction of mitosis-associated tumor cell death by quercetagetin is a promising strategy for developing novel chemotherapeutic anticancer agents.

  13. Quantitative structure-activity relationships for organophosphates binding to acetylcholinesterase.

    PubMed

    Ruark, Christopher D; Hack, C Eric; Robinson, Peter J; Anderson, Paul E; Gearhart, Jeffery M

    2013-02-01

    Organophosphates are a group of pesticides and chemical warfare nerve agents that inhibit acetylcholinesterase, the enzyme responsible for hydrolysis of the excitatory neurotransmitter acetylcholine. Numerous structural variants exist for this chemical class, and data regarding their toxicity can be difficult to obtain in a timely fashion. At the same time, their use as pesticides and military weapons is widespread, which presents a major concern and challenge in evaluating human toxicity. To address this concern, a quantitative structure-activity relationship (QSAR) was developed to predict pentavalent organophosphate oxon human acetylcholinesterase bimolecular rate constants. A database of 278 three-dimensional structures and their bimolecular rates was developed from 15 peer-reviewed publications. A database of simplified molecular input line entry notations and their respective acetylcholinesterase bimolecular rate constants are listed in Supplementary Material, Table I. The database was quite diverse, spanning 7 log units of activity. In order to describe their structure, 675 molecular descriptors were calculated using AMPAC 8.0 and CODESSA 2.7.10. Orthogonal projection to latent structures regression, bootstrap leave-random-many-out cross-validation and y-randomization were used to develop an externally validated consensus QSAR model. The domain of applicability was assessed by the William's plot. Six external compounds were outside the warning leverage indicating potential model extrapolation. A number of compounds had residuals >2 or <-2, indicating potential outliers or activity cliffs. The results show that the HOMO-LUMO energy gap contributed most significantly to the binding affinity. A mean training R (2) of 0.80, a mean test set R (2) of 0.76 and a consensus external test set R (2) of 0.66 were achieved using the QSAR. The training and external test set RMSE values were found to be 0.76 and 0.88. The results suggest that this QSAR model can be used in

  14. Structure property relationships in polymer blends and composites. Part I. Polymer/POSS composites. Part II. Poly(ethylene terephthalate) ionomer/polyamide 6 blends. Part III. Elastomer/boron nitride composites

    NASA Astrophysics Data System (ADS)

    Iyer, Subramanian

    Multiphase polymer systems are an increasingly important technical area of polymer science. By definition, a multiphase system is one that has two or more distinct phases. From the standpoint of commercial applications and developments, polymer blending represents one of the easiest ways to achieve properties not available in individual materials. This work discusses the structure property relationships in polymer certain blends and composites. Polymer/polyhedral oligomeric silsesquioxanes (POSSRTM) blends and copolymers have gained significant attention in the last decade due the unique properties of the inorganic-organic hybrid structure of POSS. The majority of the research in polymer/POSS has been in the form of copolymers and thermosets. The criteria for the reinforcement of polymers using POSS as a filler material is not been discussed in literature. Part I of the thesis will highlight the effect of blending POSS with different polymers and discuss the rules for reinforcement of polymers when using POSS as a filler material. Part II of the thesis will discuss the structure property relationships in poly(ethylene terephthalate) ionomer/polyamide 6 blends. Part III will discuss the control of coefficient of thermal expansion of elastomers using boron nitride as a filler material.

  15. Misconceived Relationships between Logical Positivism and Quantitative Research: An Analysis in the Framework of Ian Hacking.

    ERIC Educational Resources Information Center

    Yu, Chong Ho

    Although quantitative research methodology is widely applied by psychological researchers, there is a common misconception that quantitative research is based on logical positivism. This paper examines the relationship between quantitative research and eight major notions of logical positivism: (1) verification; (2) pro-observation; (3)…

  16. Structure-Property Relationships in CO2-philic (Co)polymers: Phase Behavior, Self-Assembly, and Stabilization of Water/CO2 Emulsions.

    PubMed

    Girard, Etienne; Tassaing, Thierry; Marty, Jean-Daniel; Destarac, Mathias

    2016-04-13

    This Review provides comprehensive guidelines for the design of CO2-philic copolymers through an exhaustive and precise coverage of factors governing the solubility of different classes of polymers. Starting from computational calculations describing the interactions of CO2 with various functionalities, we describe the phase behavior in sc-CO2 of the main families of polymers reported in literature. The self-assembly of amphiphilic copolymers of controlled architecture in supercritical carbon dioxide and their use as stabilizers for water/carbon dioxide emulsions then are covered. The relationships between the structure of such materials and their behavior in solutions and at interfaces are systematically underlined throughout these sections.

  17. PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

  18. Quantitative Structure--Activity Relationship Modeling of Rat Acute Toxicity by Oral Exposure

    EPA Science Inventory

    Background: Few Quantitative Structure-Activity Relationship (QSAR) studies have successfully modeled large, diverse rodent toxicity endpoints. Objective: In this study, a combinatorial QSAR approach has been employed for the creation of robust and predictive models of acute toxi...

  19. Optimization of 1,2,3,4-tetrahydroacridin-9(10H)-ones as antimalarials utilizing structure-activity and structure-property relationships.

    PubMed

    Cross, R Matthew; Maignan, Jordany R; Mutka, Tina S; Luong, Lisa; Sargent, Justin; Kyle, Dennis E; Manetsch, Roman

    2011-07-14

    Antimalarial activity of 1,2,3,4-tetrahydroacridin-9(10H)-ones (THAs) has been known since the 1940s and has garnered more attention with the development of the acridinedione floxacrine (1) in the 1970s and analogues thereof such as WR 243251 (2a) in the 1990s. These compounds failed just prior to clinical development because of suboptimal activity, poor solubility, and rapid induction of parasite resistance. Moreover, detailed structure-activity relationship (SAR) studies of the THA core scaffold were lacking and SPR studies were nonexistent. To improve upon initial findings, several series of 1,2,3,4-tetrahydroacridin-9(10H)-ones were synthesized and tested in a systematic fashion, examining each compound for antimalarial activity, solubility, and permeability. Furthermore, a select set of compounds was chosen for microsomal stability testing to identify physicochemical liabilities of the THA scaffold. Several potent compounds (EC(50) < 100 nM) were identified to be active against the clinically relevant isolates W2 and TM90-C2B while possessing good physicochemical properties and little to no cross-resistance.

  20. Structure-property relationship for in vitro siRNA delivery performance of cationic 2-hydroxypropyl-β-cyclodextrin: PEG-PPG-PEG polyrotaxane vectors.

    PubMed

    Badwaik, Vivek D; Aicart, Emilio; Mondjinou, Yawo A; Johnson, Merrell A; Bowman, Valorie D; Thompson, David H

    2016-04-01

    Nanoparticle-mediated siRNA delivery is a promising therapeutic approach, however, the processes required for transport of these materials across the numerous extracellular and intracellular barriers are poorly understood. Efficient delivery of siRNA-containing nanoparticles would ultimately benefit from an improved understanding of how parameters associated with these barriers relate to the physicochemical properties of the nanoparticle vectors. We report the synthesis of three Pluronic(®)-based, cholesterol end-capped cationic polyrotaxanes (PR(+)) threaded with 2-hydroxypropyl-β-cyclodextrin (HPβCD) for siRNA delivery. The biological data showed that PR(+):siRNA complexes were well tolerated (∼90% cell viability) and produced efficient silencing (>80%) in HeLa-GFP and NIH 3T3-GFP cell lines. We further used a multi-parametric approach to identify relationships between the PR(+) structure, PR(+):siRNA complex physical properties, and biological activity. Small angle X-ray scattering and cryoelectron microscopy studies reveal periodicity and lamellar architectures for PR(+):siRNA complexes, whereas the biological assays, ζ potential measurements, and imaging studies suggest that silencing efficiency is influenced by the effective charge ratio (ρeff), polypropylene oxide (PO) block length, and central PO block coverage (i.e., rigidity) of the PR(+) core. We infer from our findings that more compact PR(+):siRNA nanostructures arising from lower molecular weight, rigid rod-like PR(+) polymer cores produce improved silencing efficiency relative to higher molecular weight, more flexible PR(+) vectors of similar effective charge. This study demonstrates that PR(+):siRNA complex formulations can be produced having higher performance than Lipofectamine(®) 2000, while maintaining good cell viability and siRNA sequence protection in cell culture.

  1. Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts.

    PubMed

    Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

    2015-05-07

    observed enhancement of the catalytic activity of PtxRu100-x alloy NPs at x ∼ 50. Implications of so-established relationships between the atomic structure and catalytic activity of Pt-Ru alloy NPs on efforts aimed at improving further the latter by tuning-up the former are discussed and the usefulness of detailed NP structure studies to advancing science and technology of metallic NPs - exemplified.

  2. Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts

    NASA Astrophysics Data System (ADS)

    Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

    2015-04-01

    observed enhancement of the catalytic activity of PtxRu100-x alloy NPs at x ~ 50. Implications of so-established relationships between the atomic structure and catalytic activity of Pt-Ru alloy NPs on efforts aimed at improving further the latter by tuning-up the former are discussed and the usefulness of detailed NP structure studies to advancing science and technology of metallic NPs - exemplified.An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic

  3. Quantitative relationship of sick building syndrome symptoms with ventilation rates

    SciTech Connect

    Fisk, William J.; Mirer, Anna G.; Mendell, Mark J.

    2009-01-01

    Data from published studies were combined and analyzed to develop best-fit equations and curves quantifying the change in sick building syndrome (SBS) symptom prevalence in office workers with ventilation rate. For each study, slopes were calculated, representing the fractional change in SBS symptom prevalence per unit change in ventilation rate per person. Values of ventilation rate, associated with each value of slope, were also calculated. Linear regression equations were fitted to the resulting data points, after weighting by study size. Integration of the slope-ventilation rate equations yielded curves of relative SBS symptom prevalence versus ventilation rate. Based on these analyses, as the ventilation rate drops from 10 to 5 L/s-person, relative SBS symptom prevalence increases approximately 23percent (12percent to 32percent), and as ventilation rate increases from 10 to 25 L/s-person, relative prevalence decreases approximately 29percent (15percent to 42percent). Variations in SBS symptom types, building features, and outdoor air quality may cause the relationship ofSBS symptom prevalence with ventilation rate in specific situations to differ from the average relationship predicted in this paper.

  4. Development of Quantitative Structure-Activity Relationship Models for Predicting Chronic Toxicity of Substituted Benzenes to Daphnia Magna.

    PubMed

    Fan, Deling; Liu, Jining; Wang, Lei; Yang, Xianhai; Zhang, Shenghu; Zhang, Yan; Shi, Lili

    2016-05-01

    The chronic toxicity of anthropogenic molecules such as substituted benzenes to Daphnia magna is a basic eco-toxicity parameter employed to assess their environmental risk. As the experimental methods are laborious, costly, and time-consuming, development in silico models for predicting the chronic toxicity is vitally important. In this study, on the basis of five molecular descriptors and 48 compounds, a quantitative structure-property relationship model that can predict the chronic toxicity of substituted benzenes were developed by employing multiple linear regressions. The correlation coefficient (R (2)) and root-mean square error (RMSE) for the training set were 0.836 and 0.390, respectively. The developed model was validated by employing 10 compounds tested in our lab. The R EXT (2) and RMSE EXT for the validation set were 0.736 and 0.490, respectively. To further characterizing the toxicity mechanism of anthropogenic molecules to Daphnia, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were developed.

  5. Heterogeneous fenton degradation of azo dyes catalyzed by modified polyacrylonitrile fiber fe complexes: QSPR (quantitative structure peorperty relationship) study.

    PubMed

    Li, Bing; Dong, Yongchun; Ding, Zhizhong

    2013-07-01

    The amidoximated polyacrylonitrile (PAN) fiber Fe complexes were prepared and used as the heterogeneous Fenton catalysts for the degradation of 28 anionic water soluble azo dyes in water under visible irradiation. The multiple linear regression (MLR) method was employed to develop the quantitative structure property relationship (QSPR) model equations for the decoloration and mineralization of azo dyes. Moreover, the predictive ability of the QSPR model equations was assessed using Leave-one-out (LOO) and cross-validation (CV) methods. Additionally, the effect of Fe content of catalyst and the sodium chloride in water on QSPR model equations were also investigated. The results indicated that the heterogeneous photo-Fenton degradation of the azo dyes with different structures was conducted in the presence of the amidoximated PAN fiber Fe complex. The QSPR model equations for the dye decoloration and mineralization were successfully developed using MLR technique. MW/S (molecular weight divided by the number of sulphonate groups) and NN=N (the number of azo linkage) are considered as the most important determining factor for the dye degradation and mineralization, and there is a significant negative correlation between MW/S or NN=N and degradation percentage or total organic carbon (TOC) removal. Moreover, LOO and CV analysis suggested that the obtained QSPR model equations have the better prediction ability. The variation in Fe content of catalyst and the addition of sodium chloride did not alter the nature of the QSPR model equations.

  6. Using three-dimensional quantitative structure-activity relationships to examine estrogen receptor binding affinities of polychlorinated hydroxybiphenyls

    SciTech Connect

    Waller, C.L.; Minor, D.L.; McKinney, J.D.

    1995-07-01

    Certain phenyl-substituted hydrocarbons of environmental concern have the potential to disrupt the endocrine system of animals, apparently in association with their estrogenic properties. Competition with natural estrogens for the estrogen receptor is a possible mechanism by which such effects could occur. We used comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (QSAR) paradigm, to examine the underlying structural properties of ortho-chlorinated hydroxybiphenyl analogs known to bind to the estrogen receptor. The cross-validated and conventional statistical results indicate a high degree of internal predictability for the molecules included in the training data set. In addition to the phenolic (A) ring system, conformational restriction of the overall structure appears to play an important role in estrogen receptor binding affinity. Hydrophobic character as assessed using hydropathic interaction fields also contributes in a positive way to binding affinity. The CoMFA-derived QSARs may be useful in examining the estrogenic activity of a wider range of phenyl-substituted hydrocarbons of environmental concern. 37 refs., 2 figs., 2 tabs.

  7. Improving quantitative structure-activity relationships through multiobjective optimization.

    PubMed

    Nicolotti, Orazio; Giangreco, Ilenia; Miscioscia, Teresa Fabiola; Carotti, Angelo

    2009-10-01

    A multiobjective optimization algorithm was proposed for the automated integration of structure- and ligand-based molecular design. Driven by a genetic algorithm, the herein proposed approach enabled the detection of a number of trade-off QSAR models accounting simultaneously for two independent objectives. The first was biased toward best regressions among docking scores and biological affinities; the second minimized the atom displacements from a properly established crystal-based binding topology. Based on the concept of dominance, 3D QSAR equivalent models profiled the Pareto frontier and were, thus, designated as nondominated solutions of the search space. K-means clustering was, then, operated to select a representative subset of the available trade-off models. These were effectively subjected to GRID/GOLPE analyses for quantitatively featuring molecular determinants of ligand binding affinity. More specifically, it was demonstrated that a) diverse binding conformations occurred on the basis of the ligand ability to profitably contact different part of protein binding site; b) enzyme selectivity was better approached and interpreted by combining diverse equivalent models; and c) trade-off models were successful and even better than docking virtual screening, in retrieving at high sensitivity active hits from a large pool of chemically similar decoys. The approach was tested on a large series, very well-known to QSAR practitioners, of 3-amidinophenylalanine inhibitors of thrombin and trypsin, two serine proteases having rather different biological actions despite a high sequence similarity.

  8. Structure-property relationships in block copolymers

    NASA Technical Reports Server (NTRS)

    Mcgrath, J. E.

    1976-01-01

    Block copolymers are a class of relatively new materials which contain long sequences of two (or more) chemically different repeat units. Unlike random copolymers, each segment may retain some properties which are characteristic of its homopolymer. It is well known that most physical blends of two different homopolymers are incompatible on a macro-scale. By contrast most block copolymers display only a microphase (eg. 100-200 A domains) separation. Complete separation is restricted because of a loss in configurational entropy. The latter is due to presence of chemical bond(s) between the segments. Novel physical properties can be obtained because it is possible to prepare any desired combination of rubber-like, glassy, or crystalline blocks. The architecture and sequential arrangement of the segments can strongly influence mechanical behavior.

  9. Structure-Property Relationships in Intercalated Graphite.

    DTIC Science & Technology

    1985-07-10

    McNeil, J. Steinbeck, L. Salamanca- Riba and G. Dresselhaus, Bull. APS 29, 253 (1984). 4. "The Effect of Impurities on the Electronic Phase Transition In...12. "Raman Microprobe Observation of Intercalate Contraction In Graphite Inter- calation Compounds", L.E. McNeil, J. Steinbeck, L. Salamanca- Riba and...17. "High Resolution Electron Microscopy and X-Ray Diffraction Studies on SbCl5 - GI0", G. Roth, L. Salamanca- Riba , A.R. Kortan, G. Dresselhaus, R.J

  10. Structure Property Relationships in Liquid Crystalline Thermosets

    DTIC Science & Technology

    2003-04-25

    Adhesion Science and Technology , 2002, 16, 15-32 Jianxun Feng and Elliot P. Douglas, “Permeability of a liquid crystalline epoxy”, Materials Research...Arthur J. Gavrin and Elliot P. Douglas, “Cure behavior of liquid crystalline thermosets”, poster presentation at POLY Millenial 2000, Waikoloa, HI...December, 2000 Elliot P. Douglas, "Liquid crystalline thermosets", Massachusetts Institute of Technology , Cambridge, MA, April, 2000 Arthur J. Gavrin

  11. THREE-DIMENSIONAL QUANTITATIVE STRUCTURE-PROPERTY RELATIONSHIP (3D-QSPR) MODELS FOR PREDICTION OF THERMODYNAMIC PROPERTIES OF POLYCHLORINATED BIPHENYLS (PCBS): ENTHALPY OF VAPORIZATION. (R826133)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  12. THREE-DIMENSIONAL QUANTITATIVE STRUCTURE-PROPERTY RELATIONSHIP (3D-QSPR) MODELS FOR PREDICTION OF THERMODYNAMIC PROPERTIES OF POLYCHLORINATED BIPHENYLS (PCBS): ENTHALPY OF SUBLIMATION. (R826133)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  13. Prediction of the Formulation Dependence of the Glass Transition Temperature for Amine-Epoxy Copolymers Using a Quantitative Structure-Property Relationship Based on the AM1 Method

    DTIC Science & Technology

    2004-02-01

    theory . Despite this difficulty, attempts have been made by researchers to model the effect of the extent of crosslinking on Tg. Galy used a group...1969, C3, 69–103. 37. Fukui, K. Theory of Orientation and Stereoselection ; Springer-Verlag: Berlin, 1975. NO. OF NO. OF COPIES...6. AUTHOR(S) Jason A. Morrill,* Robert E. Jensen, Phillip H. Madison,† and Cary F. Chabalowski 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION

  14. Structure-property relationships in self-assembled metalorganic chemical vapor deposition-grown CoFe{sub 2}O{sub 4-}-PbTiO{sub 3} multiferroic nanocomposites using three-dimensional characterization.

    SciTech Connect

    Pan, M.; Liu, Y.; Bai, G.; Hong, S.; Dravid, V. P.; Petford-Long, A. K.

    2011-01-01

    Multiferroic nanocomposites, consisting of branched, ferrimagnetic CoFe{sub 2}O{sub 4} filaments and large protruding PbTiO{sub 3} particles embedded in a piezoelectric PbTiO{sub 3} matrix, have been fabricated by co-deposition using metalorganic chemical vapor deposition. Branched CoFe{sub 2}O{sub 4} filaments reduce the CoFe{sub 2}O{sub 4}/PbTiO{sub 3} interfacial strain and induce a perpendicular magnetic anisotropy. Three-dimensional characterizations reveal that in addition to the c-domain, grains with a second orientation in PbTiO{sub 3} particles contribute to an additional four apparent variants of polarization. In contrast, the PbTiO{sub 3} matrix exhibits only c-domain polarization with a smaller magnitude. The smaller piezoresponse results from the constraints imposed by the branched CoFe{sub 2}O{sub 4} filaments. Three-dimensional microstructure and property analysis provide a comprehensive insight on the structure-property relationship of multiferroic nanocomposites grown by metalorganic chemical vapor deposition.

  15. Elucidating the structure-property relationships of donor-π-acceptor dyes for dye-sensitized solar cells (DSSCs) through rapid library synthesis by a one-pot procedure.

    PubMed

    Fuse, Shinichiro; Sugiyama, Sakae; Maitani, Masato M; Wada, Yuji; Ogomi, Yuhei; Hayase, Shuzi; Katoh, Ryuzi; Kaiho, Tatsuo; Takahashi, Takashi

    2014-08-18

    The creation of organic dyes with excellent high power conversion efficiency (PCE) is important for the further improvement of dye-sensitized solar cells. We wish to describe the rapid synthesis of a 112-membered donor-π-acceptor dye library by a one-pot procedure, evaluation of PCEs, and elucidation of structure-property relationships. No obvious correlations between ε, and the η were observed, whereas the HOMO and LUMO levels of the dyes were critical for η. The dyes with a more positive E(HOMO), and with an E(LUMO)<-0.80 V, exerted higher PCEs. The proper driving forces were crucial for a high J(sc), and it was the most important parameter for a high η. The above criteria of E(HOMO) and E(LUMO) should be useful for creating high PCE dyes; nevertheless, that was not sufficient for identifying the best combination of donor, π, and acceptor blocks. Combinatorial synthesis and evaluation was important for identifying the best dye.

  16. An investigation of the structure-property relationships in ionic polymer polymer composites (IP2Cs) manufactured by polymerization in situ of PEDOT/PSS on Nafion®117

    NASA Astrophysics Data System (ADS)

    Di Pasquale, G.; Graziani, S.; Messina, F. G.; Pollicino, A.; Puglisi, R.; Umana, E.

    2014-03-01

    Ionic polymer polymer composites (IP2Cs) are all-organic electroactive polymers (EAPs) that show sensing and actuation capabilities when a deformation or a voltage is applied, respectively. They are fabricated starting from an ionic polymer coated on both sides with a conducting polymer as electrode element. In this work, poly(3,4-ethylendioxytiophene)-poly-(styrenesulfonate) (PEDOT/PSS) has been polymerized directly on Nafion®117 membrane and devices have been manufactured varying the polymerization time. Water and ethylene glycol (EG) have been used as solvents. The obtained IP2Cs have been characterized using thermal and mechanical analyses and electromechanically tested. The results have shown that in IP2Cs manufactured by polymerization in situ the PEDOT/PSS layer adheres very strongly on the Nafion®117 film, improving the possibility of rehydrating the devices after use. Moreover, taking into account that the different polymerization times influence the uniformity of the surface of the organic electrode and, consequently, both device stiffness and electrode conductivity, the structure-property relationships of the obtained devices have been investigated. The influence of the different solvents inside the devices has also been studied when IP2Cs have been used as actuators or sensors. Reported results show that it is possible to modulate the performances of IP2Cs by varying some manufacture parameters and the solvent.

  17. Quantitative structure-sorption relationships of pesticides used in the sugarcane industry in the northern coastal area of Paraíba State, Brazil.

    PubMed

    da S Soares, Gabriela C; de M e Silva, Luana; de A Farias, Carlos H; Scotti, Luciana; Scotti, Marcus T

    2014-03-01

    Sorption coefficients (K(oc)) are useful in the prediction of whether a pesticide will remain dissolved in solution or will become adsorbed onto soil particles after its application. Measuring this process experimentally is difficult, expensive and time-consuming. Hence, much effort has been directed toward estimating K(oc) through statistical modelling. In this study, we investigated the physicochemical properties of pesticides employed by a local sugarcane company, in the northern coastal plain of Paraíba state in Brazil, by using several molecular descriptors, among them, GRid INdependent Descriptors (GRIND). Quantitative assessment of the structure-property relationship (QSPR) model indicated that size, shape, octanol-water coefficient, solubility and the balance between hydrophilic and lipophilic regions, are all relevant to K(oc) values.

  18. Structure-property relationship of 3-(4-substituted benzyl)-1,3-diazaspiro[4.4]nonane-2,4-diones as new potentional anticonvulsant agents. An experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Lazić, Anita M.; Božić, Bojan Đ.; Vitnik, Vesna D.; Vitnik, Željko J.; Rogan, Jelena R.; Radovanović, Lidija D.; Valentić, Nataša V.; Ušćumlić, Gordana S.

    2017-01-01

    The structure-property relationship of newly synthesized 3-(4-substituted benzyl)-1,3-diazaspiro [4.4]nonane-2,4-diones was studied by experimental and calculated methods. The prepared compounds were characterized by UV-Vis, FT-IR, 1H NMR and 13C NMR spectroscopy and elemental analysis. The crystal structure was elucidated by single-crystal X-ray diffraction. The 3-benzyl-1,3-diazaspiro[4.4]nonane-2,4-dione crystallizes in triclinic P-1 space group, with two crystallographically independent molecules in the asymmetric unit. Cyclopentane ring adopts an envelope conformation. A three-dimensional crystal packing is governed by hydrogen N-H⋯O bonds, numerous C-H⋯O/N and C-H … π interactions between neighboring molecules. Density functional theory (DFT) calculations with B3LYP and M06-2X methods using 6-311++G(d,p) basis set were performed to provide structural and spectroscopic information. Comparisons between experimental and calculated UV-Vis spectral properties suggest that the monomeric form of the investigated spirohydantoins is dominant in all used solvents. The effects of substituents on the absorption spectra of spirohydantoins are interpreted by correlation of absorption frequencies with Hammett equation. The lipophilicities of the investigated molecules were estimated by calculation of their log P values. Some of the spirohydantoins synthesized in this work, exhibit the lipophilicities comparable to the standard medicine anticonvulsant drug Phenytoin. The results obtained in this investigation afford guidelines for the preparation of new derivatives of spirohydantoin as potential anticonvulsant agents and for better understanding the structure-activity relationship.

  19. Semiconductor alloys - Structural property engineering

    NASA Technical Reports Server (NTRS)

    Sher, A.; Van Schilfgaarde, M.; Berding, M.; Chen, A.-B.

    1987-01-01

    Semiconductor alloys have been used for years to tune band gaps and average bond lengths to specific applications. Other selection criteria for alloy composition, and a growth technique designed to modify their structural properties, are presently considered. The alloys Zn(1-y)Cd(y)Te and CdSe(y)Te(1-y) are treated as examples.

  20. Quantitative structure activity relationships of some pyridine derivatives as corrosion inhibitors of steel in acidic medium.

    PubMed

    El Ashry, El Sayed H; El Nemr, Ahmed; Ragab, Safaa

    2012-03-01

    Quantum chemical calculations using the density functional theory (B3LYP/6-31G DFT) and semi-empirical AM1 methods were performed on ten pyridine derivatives used as corrosion inhibitors for mild steel in acidic medium to determine the relationship between molecular structure and their inhibition efficiencies. Quantum chemical parameters such as total negative charge (TNC) on the molecule, energy of highest occupied molecular orbital (E (HOMO)), energy of lowest unoccupied molecular orbital (E (LUMO)) and dipole moment (μ) as well as linear solvation energy terms, molecular volume (Vi) and dipolar-polarization (π) were correlated to corrosion inhibition efficiency of ten pyridine derivatives. A possible correlation between corrosion inhibition efficiencies and structural properties was searched to reduce the number of compounds to be selected for testing from a library of compounds. It was found that theoretical data support the experimental results. The results were used to predict the corrosion inhibition of 24 related pyridine derivatives.

  1. A Quantitative Study of the Relationship between Leadership Practice and Strategic Intentions to Use Cloud Computing

    ERIC Educational Resources Information Center

    Castillo, Alan F.

    2014-01-01

    The purpose of this quantitative correlational cross-sectional research study was to examine a theoretical model consisting of leadership practice, attitudes of business process outsourcing, and strategic intentions of leaders to use cloud computing and to examine the relationships between each of the variables respectively. This study…

  2. Quantitative Causal-Comparative Relationship between Interactive Whiteboard Instruction and Student Science Proficiency

    ERIC Educational Resources Information Center

    Danelczyk, Ewa Krystyna

    2013-01-01

    The purpose of this quantitative causal-comparative study was to investigate the relationship between the instructional effects of the interactive whiteboard and students' proficiency levels in eighth-grade science as evidenced by the state FCAT scores. A total of 46 eighth-grade science teachers in a South Florida public school district completed…

  3. Quantitative structure-activity relationships and docking studies of calcitonin gene-related peptide antagonists.

    PubMed

    Kyani, Anahita; Mehrabian, Mohadeseh; Jenssen, Håvard

    2012-02-01

    Defining the role of calcitonin gene-related peptide in migraine pathogenesis could lead to the application of calcitonin gene-related peptide antagonists as novel migraine therapeutics. In this work, quantitative structure-activity relationship modeling of biological activities of a large range of calcitonin gene-related peptide antagonists was performed using a panel of physicochemical descriptors. The computational studies evaluated different variable selection techniques and demonstrated shuffling stepwise multiple linear regression to be superior over genetic algorithm-multiple linear regression. The linear quantitative structure-activity relationship model revealed better statistical parameters of cross-validation in comparison with the non-linear support vector regression technique. Implementing only five peptide descriptors into this linear quantitative structure-activity relationship model resulted in an extremely robust and highly predictive model with calibration, leave-one-out and leave-20-out validation R(2) of 0.9194, 0.9103, and 0.9214, respectively. We performed docking of the most potent calcitonin gene-related peptide antagonists with the calcitonin gene-related peptide receptor and demonstrated that peptide antagonists act by blocking access to the peptide-binding cleft. We also demonstrated the direct contact of residues 28-37 of the calcitonin gene-related peptide antagonists with the receptor. These results are in agreement with the conclusions drawn from the quantitative structure-activity relationship model, indicating that both electrostatic and steric factors should be taken into account when designing novel calcitonin gene-related peptide antagonists.

  4. A Quantitative Exploration of the Relationship between Patient Health and Electronic Personal Health Records

    ERIC Educational Resources Information Center

    Hines, Denise Williams

    2009-01-01

    The use of electronic personal health records is becoming increasingly more popular as healthcare providers, healthcare and government leaders, and patients are seeking ways to improve healthcare quality and to decrease costs (Abrahamsen, 2007). This quantitative, descriptive correlational study examined the relationship between the degree of…

  5. QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS FOR CHEMICAL REDUCTIONS OF ORGANIC CONTAMINANTS

    EPA Science Inventory

    Sufficient kinetic data on abiotic reduction reactions involving organic contaminants are now available that quantitative structure-activity relationships (QSARs) for these reactions can be developed. Over 50 QSARs have been reported, most in just the last few years, and they ar...

  6. Research on the quantitative structure-carcinogenic activity relationship of N-nitroso compounds.

    PubMed

    Li-Jiao, Zhao; Ru-Gang, Zhong; Yan, Zhen; Qian-Huan, Dai

    2005-01-01

    According to the results of quantitative pattern recognition for 153 N-nitroso compounds (NNCs) based on Di-region theory, it is put forward that the esters formed from the metabolism of NNCs on ..- or ..-position could be alkylating agents of DNA bases with the anchimeric assistance of the N-nitroso group. This viewpoint, combined with the conception of ..-metabolism activation, can explain the structurecarcinogenic activity relationship reasonably. Quantum chemistry ab initio calculations are carried out to study the activity of different metabolites of NNCs in direct alkylation and the anchimeric assistant processes. By ONIOM method, a QM/MM calculation is carried out to study the crosslink of DNA base pair by methylalkylnitrosamines. Based on the computational results, the quantitative structure and carcinogenic activity relationship of 58 N-nitrosoureas that have got animal carcinogenicity tests reported are studied.

  7. Mixture designs to assess composition-structure-property relationships in SiO₂-CaO-ZnO-La₂O₃-TiO₂-MgO-SrO-Na₂O glasses: potential materials for embolization.

    PubMed

    Kehoe, Sharon; Langman, Maxine; Werner-Zwanziger, Ulli; Abraham, Robert J; Boyd, Daniel

    2013-09-01

    Embolization with micron-sized particulates is widely applied to treat uterine fibroids. The objective of this work was to develop mixture designs to predict materials composition-structure-property relationships for the SiO₂-CaO-ZnO-La₂O₃-TiO₂-MgO-SrO-Na₂O glass system and compare its fundamental materials properties (density and cytocompatibility), against a state-of-the-art embolic agent (contour polyvinyl alcohol) to assess the potential of these materials for embolization therapies. The glass structures were evaluated using ²⁹Si MAS NMR to identify chemical shift and line width; the particulate densities were determined using helium pycnometry and the cell viabilities were assessed via MTT assay. ²⁹Si MAS NMR results indicated peak maxima for each glass in the range of -82.3 ppm to -89.9 ppm; associated with Q² to Q³ units in silicate glasses. All experimental embolic compositions showed enhanced in vitro compatibility in comparison to Contour PVA with the exceptions of ORP9 and ORP11 (containing no TiO₂). In this study, optimal compositions for cell viability were obtained for the following compositional ranges: 0.095-0.188 mole fraction ZnO; 0.068-0.159 mole fraction La₂O₃; 0.545-0.562 mole fraction SiO₂ and 0.042-0.050 mole fraction TiO₂. To ensure ease of producibility in obtaining good melts, a maximum loading of 0.068 mole fraction La₂O₃ is required. This is confirmed by the desirability approach, for which the only experimental composition (ORP5) of the materials evaluated was presented as an optimum composition; combining high cell viability with ease of production (0.188 mole fraction ZnO; 0.068 mole fraction La₂O₃; 0.562 mole fraction SiO₂ and 0.042 mole fraction TiO₂).

  8. Anticancer Activity of Estradiol Derivatives: A Quantitative Structure--Activity Relationship Approach

    NASA Astrophysics Data System (ADS)

    Muranaka, Ken

    2001-10-01

    Commercial packages to implement modern QSAR (quantitative structure-activity relationship) techniques are highly priced; however, the essence of QSAR can be taught without them. Microsoft Excel was used to analyze published data on anticancer activities of estradiol analogs by a QSAR approach. The resulting QSAR equations highly correlate the structural features and physicochemical properties of the analogs with the observed biological activities by multiple linear regression.

  9. Quantitative structure-activity relationships for the in vitro antimycobacterial activity of pyrazinoic acid esters.

    PubMed

    Bergmann, K E; Cynamon, M H; Welch, J T

    1996-08-16

    Substituted pyrazinoic acid esters have previously been reported to have in vitro activity against Mycobacterium avium and Mycobacterium kansasii as well as Mycobacterium tuberculosis. Modification of both the pyrazine nucleus and the ester functionality was successful in expanding the antimycobacterial activity associated with pyrazinamide to include M. avium and M. kansasii, organisms usually not susceptible to pyrazinamide. In an attempt to understand the relationship between the activity of the esters with the needed biostability, a quantitative structure-activity relationship has been developed. This derived relationship is consistent with the observation that tert-butyl 5-chloropyrazinoate (13) and 2'-(2'-methyldecyl) 5-chloropyrazinoate (25), compounds which are both 100-fold more active than pyrazinamide against M. tuberculosis and possess a serum stability 900-1000 times greater than the lead compounds in the series.

  10. Quantitative structure-antifungal activity relationships of some benzohydrazides against Botrytis cinerea.

    PubMed

    Reino, José L; Saiz-Urra, Liane; Hernandez-Galan, Rosario; Aran, Vicente J; Hitchcock, Peter B; Hanson, James R; Gonzalez, Maykel Perez; Collado, Isidro G

    2007-06-27

    Fourteen benzohydrazides have been synthesized and evaluated for their in vitro antifungal activity against the phytopathogenic fungus Botrytis cinerea. The best antifungal activity was observed for the N',N'-dibenzylbenzohydrazides 3b-d and for the N-aminoisoindoline-derived benzohydrazide 5. A quantitative structure-activity relationship (QSAR) study has been developed using a topological substructural molecular design (TOPS-MODE) approach to interpret the antifungal activity of these synthetic compounds. The model described 98.3% of the experimental variance, with a standard deviation of 4.02. The influence of an ortho substituent on the conformation of the benzohydrazides was investigated by X-ray crystallography and supported by QSAR study. Several aspects of the structure-activity relationships are discussed in terms of the contribution of different bonds to the antifungal activity, thereby making the relationships between structure and biological activity more transparent.

  11. Trophic relationships in an estuarine environment: A quantitative fatty acid analysis signature approach

    NASA Astrophysics Data System (ADS)

    Magnone, Larisa; Bessonart, Martin; Gadea, Juan; Salhi, María

    2015-12-01

    In order to better understand the functioning of aquatic environments, it is necessary to obtain accurate diet estimations in food webs. Their description should incorporate information about energy flow and the relative importance of trophic pathways. Fatty acids have been extensively used in qualitative studies on trophic relationships in food webs. Recently a new method to estimate quantitatively single predator diet has been developed. In this study, a model of aquatic food web through quantitative fatty acid signature analysis was generated to identify the trophic interactions among the species in the Rocha Lagoon. The biological sampling over two consecutive annual periods was comprehensive enough to identify all functional groups in the aquatic food web (except birds and mammals). Heleobia australis seemed to play a central role in this estuarine ecosystem. As both, a grazer and a prey to several other species, probably H. australis is transferring a great amount of energy to upper trophic levels. Most of the species at Rocha Lagoon have a wide range of prey items in their diet reflecting a complex food web, which is characteristic of extremely dynamic environment as estuarine ecosystems. QFASA is a model in tracing and quantitative estimate trophic pathways among species in an estuarine food web. The results obtained in the present work are a valuable contribution in the understanding of trophic relationships in Rocha Lagoon.

  12. The quantitative relationship of urinary peptide hydroxyproline excretion to collagen degradation

    PubMed Central

    Weiss, Phillip H.; Klein, LeRoy

    1969-01-01

    To determine the quantitative relationship of urinary hydroxyproline peptide excretion to collagen breakdown, known quantities of radioactive hydroxyproline peptides were administered to unlabeled animals and excertion of radioactivity in respiratory carbon dioxide, urine, and feces was measured. The major routes of excretion of collagen peptide metabolites were respiratory carbon dioxide (75%) and urine, as hydroxyproline-containing peptides (25%). Since the predominant urine hydroxyproline peptide linkage is proly-hydroxyproline, L-prolyl-L-hydroxyproline-3H was administered to unlabeled animals. Greater than 80% of the administered dipeptide was excreted in urine, suggesting that this peptide linkage is not hydrolyzed to a significant extent in vivo. These data suggest that urinary hydroxyproline excretion is a “fairly” sensitive indicator of collagen breakdown and can be used at the clinical level to quantitate changes in collagen breakdown. PMID:5765022

  13. Quantitative analysis of saltwater-freshwater relationships in groundwater systems-A historical perspective

    USGS Publications Warehouse

    Reilly, T.E.; Goodman, A.S.

    1985-01-01

    Although much progress has been made toward the mathematical description of saltwater-freshwater relationships in groundwater systems since the late 19th century, the advective and dispersive mechanisms involved are still incompletely understood. This article documents the major historical advances in this subject and summarizes the major direction of current studies. From the time of Badon Ghyben and Herzberg, it has been recognized that density is important in mathematically describing saltwater-freshwater systems. Other mechanisms, such as hydrodynamic dispersion, were identified later and are still not fully understood. Quantitative analysis of a saltwater-freshwater system attempts to mathematically describe the physical system and the important mechanisms using reasonable simplifications and assumptions. This paper, in developing the history of quantitative analysis discusses many of these simplifications and assumptions and their effect on describing and understanding the phenomenon. ?? 1985.

  14. Quantitative relationship between contact stress and magnetic signal strength in perpendicular recording media

    NASA Astrophysics Data System (ADS)

    Liu, Yuliang; Xiong, Shaomin; Lou, Jia; Bogy, David B.; Zhang, Guangyu

    2014-05-01

    A series of nanoscratch experiments is conducted using constant loading scratch profiles to apply mechanical contact stress on perpendicular magnetic recording (PMR) media to cause its magnetic signal strength decay, which is characterized by the magnetic force microscope. The dependence of the magnetic signal strength on the applied normal load is quantitatively investigated. The results indicate that an increase of the applied normal load leads to a decrease of the magnetic signal strength. In addition, in order to obtain a more complete understanding of the results, a 3D finite element model is created to calculate the stress under different normal loads. Finally, the quantitative relationship between residual shear stress and magnetic signal strength is identified.

  15. Modeling the nucleophilic reactivity of small organochlorine electrophiles: A mechanistically based quantitative structure-activity relationship

    SciTech Connect

    Verhaar, H.J.M.; Seinen, W.; Hermens, J.L.M.; Rorije, E.; Borkent, H.

    1996-06-01

    Environmental pollutants can be divided into four broad categories, narcosis-type chemicals, less inert (polar narcosis) chemicals, reactive chemicals, and specifically acting chemicals. For narcosis-type, or baseline, chemicals and for less inert chemicals, adequate quantitative structure-activity relationships (QSARs) are available for estimation of toxicity to aquatic species. This is not the case for reactive chemicals and specifically acting chemicals. A possible approach to develop aquatic toxicity QSARs for reactive chemicals based on simple considerations regarding their reactivity is given. It is shown that quantum chemical calculations on reaction transition states can be used to quantitatively predict the reactivity of sets of reactive chemicals. These predictions can then be used to develop aquatic toxicity QSARs.

  16. Quantitative Analysis of the Relationship Between Microstructures and Thermal Conductivity for YSZ Coatings

    NASA Astrophysics Data System (ADS)

    Chen, Ning; Song, Xuemei; Liu, Ziwei; Lin, Chucheng; Zeng, Yi; Huang, Liping; Zheng, Xuebing

    2017-03-01

    The thermal conductivities of as-sprayed yttria-stabilized zirconia thermal barrier coating prepared by atmospheric plasma spraying at different temperatures are investigated based on quantitative microstructural analysis. Multiple linear regression is used to develop quantitative models which describe the relationship between multiple elements such as porosity, grain boundary density, monoclinic phase content, temperature and thermal conductivity. Results reveal that the thermal conductivity of the coating is mainly determined by the porosity and grain boundary density below 300 °C and by the monoclinic phase content above 800 °C. Furthermore, based on the significance testing analysis, the confidence interval under a confidence level of 95% at different temperatures enables researchers to predict the thermal conductivity based on microstructural information.

  17. Quantitative genetics model as the unifying model for defining genomic relationship and inbreeding coefficient.

    PubMed

    Wang, Chunkao; Da, Yang

    2014-01-01

    The traditional quantitative genetics model was used as the unifying approach to derive six existing and new definitions of genomic additive and dominance relationships. The theoretical differences of these definitions were in the assumptions of equal SNP effects (equivalent to across-SNP standardization), equal SNP variances (equivalent to within-SNP standardization), and expected or sample SNP additive and dominance variances. The six definitions of genomic additive and dominance relationships on average were consistent with the pedigree relationships, but had individual genomic specificity and large variations not observed from pedigree relationships. These large variations may allow finding least related genomes even within the same family for minimizing genomic relatedness among breeding individuals. The six definitions of genomic relationships generally had similar numerical results in genomic best linear unbiased predictions of additive effects (GBLUP) and similar genomic REML (GREML) estimates of additive heritability. Predicted SNP dominance effects and GREML estimates of dominance heritability were similar within definitions assuming equal SNP effects or within definitions assuming equal SNP variance, but had differences between these two groups of definitions. We proposed a new measure of genomic inbreeding coefficient based on parental genomic co-ancestry coefficient and genomic additive correlation as a genomic approach for predicting offspring inbreeding level. This genomic inbreeding coefficient had the highest correlation with pedigree inbreeding coefficient among the four methods evaluated for calculating genomic inbreeding coefficient in a Holstein sample and a swine sample.

  18. A computational quantitative structure-activity relationship study of carbamate anticonvulsants using quantum pharmacological methods.

    PubMed

    Knight, J L; Weaver, D F

    1998-10-01

    A pattern recognition quantitative structure-activity relationship (QSAR) study has been performed to determine the molecular features of carbamate anticonvulsants which influence biological activity. Although carbamates, such as felbamate, have been used to treat epilepsy, their mechanisms of efficacy and toxicity are not completely understood. Quantum and classical mechanics calculations have been exploited to describe 46 carbamate drugs. Employing a principal component analysis and multiple linear regression calculations, five crucial structural descriptors were identified which directly relate to the bioactivity of the carbamate family. With the resulting mathematical model, the biological activity of carbamate analogues can be predicted with 85-90% accuracy.

  19. Quantitative MRI in refractory temporal lobe epilepsy: relationship with surgical outcomes

    PubMed Central

    Bonilha, Leonardo

    2015-01-01

    Medically intractable temporal lobe epilepsy (TLE) remains a serious health problem. Across treatment centers, up to 40% of patients with TLE will continue to experience persistent postoperative seizures at 2-year follow-up. It is unknown why such a large number of patients continue to experience seizures despite being suitable candidates for resective surgery. Preoperative quantitative MRI techniques may provide useful information on why some patients continue to experience disabling seizures, and may have the potential to develop prognostic markers of surgical outcome. In this article, we provide an overview of how quantitative MRI morphometric and diffusion tensor imaging (DTI) data have improved the understanding of brain structural alterations in patients with refractory TLE. We subsequently review the studies that have applied quantitative structural imaging techniques to identify the neuroanatomical factors that are most strongly related to a poor postoperative prognosis. In summary, quantitative imaging studies strongly suggest that TLE is a disorder affecting a network of neurobiological systems, characterized by multiple and inter-related limbic and extra-limbic network abnormalities. The relationship between brain alterations and postoperative outcome are less consistent, but there is emerging evidence suggesting that seizures are less likely to remit with surgery when presurgical abnormalities are observed in the connectivity supporting brain regions serving as network nodes located outside the resected temporal lobe. Future work, possibly harnessing the potential from multimodal imaging approaches, may further elucidate the etiology of persistent postoperative seizures in patients with refractory TLE. Furthermore, quantitative imaging techniques may be explored to provide individualized measures of postoperative seizure freedom outcome. PMID:25853080

  20. Toxicity challenges in environmental chemicals: Prediction of human plasma protein binding through quantitative structure-activity relationship (QSAR) models

    EPA Science Inventory

    The present study explores the merit of utilizing available pharmaceutical data to construct a quantitative structure-activity relationship (QSAR) for prediction of the fraction of a chemical unbound to plasma protein (Fub) in environmentally relevant compounds. Independent model...

  1. ESTIMATION OF MICROBIAL REDUCTIVE TRANSFORMATION RATES FOR CHLORINATED BENZENES AND PHENOLS USING A QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP APPROACH

    EPA Science Inventory

    A set of literature data was used to derive several quantitative structure-activity relationships (QSARs) to predict the rate constants for the microbial reductive dehalogenation of chlorinated aromatics. Dechlorination rate constants for 25 chloroaromatics were corrected for th...

  2. Quantitative structure-activity relationships of antimicrobial fatty acids and derivatives against Staphylococcus aureus *

    PubMed Central

    Zhang, Hui; Zhang, Lu; Peng, Li-juan; Dong, Xiao-wu; Wu, Di; Wu, Vivian Chi-Hua; Feng, Feng-qin

    2012-01-01

    Fatty acids and derivatives (FADs) are resources for natural antimicrobials. In order to screen for additional potent antimicrobial agents, the antimicrobial activities of FADs against Staphylococcus aureus were examined using a microplate assay. Monoglycerides of fatty acids were the most potent class of fatty acids, among which monotridecanoin possessed the most potent antimicrobial activity. The conventional quantitative structure-activity relationship (QSAR) and comparative molecular field analysis (CoMFA) were performed to establish two statistically reliable models (conventional QSAR: R 2=0.942, Q 2 LOO=0.910; CoMFA: R 2=0.979, Q 2=0.588, respectively). Improved forecasting can be achieved by the combination of these two models that provide a good insight into the structure-activity relationships of the FADs and that may be useful to design new FADs as antimicrobial agents. PMID:22302421

  3. Studying the relationship between redox and cell growth using quantitative phase imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Sridharan, Shamira; Leslie, Matthew T.; Bapst, Natalya; Smith, John; Gaskins, H. Rex; Popescu, Gabriel

    2016-03-01

    Quantitative phase imaging has been used in the past to study the dry mass of cells and study cell growth under various treatment conditions. However, the relationship between cellular redox and growth rates has not yet been studied in this context. This study employed the recombinant Glrx-roGFP2 redox biosensor targeted to the mitochondrial matrix or cytosolic compartments of A549 lung epithelial carcinoma cells. The Glrx-roGFP2s biosensor consists of a modified GFP protein containing internal cysteine residues sensitive to the local redox environment. The formation/dissolution of sulfide bridges contorts the internal chromophore, dictating corresponding changes in florescence emission that provide direct measures of the local redox potential. Combining 2-channel florescent imaging of the redox sensor with quantitative phase imaging allowed observation of redox homeostasis alongside measurements of cellular mass during full cycles of cellular division. The results indicate that mitochondrial redox showed a stronger inverse correlation with cell growth than cytoplasmic redox states; although redox changes are restricted to a 5% range. We are now studying the relationship between mitochondrial redox and cell growth in an isogenic series of breast cell lines built upon the MCF-10A genetic background that vary both in malignancy and metastatic potential.

  4. Development and validation of quantitative structure-activity relationship models for compounds acting on serotoninergic receptors.

    PubMed

    Zydek, Grażyna; Brzezińska, Elżbieta

    2012-01-01

    A quantitative structure-activity relationship (QSAR) study has been made on 20 compounds with serotonin (5-HT) receptor affinity. Thin-layer chromatographic (TLC) data and physicochemical parameters were applied in this study. RP2 TLC 60F(254) plates (silanized) impregnated with solutions of propionic acid, ethylbenzene, 4-ethylphenol, and propionamide (used as analogues of the key receptor amino acids) and their mixtures (denoted as S1-S7 biochromatographic models) were used in two developing phases as a model of drug-5-HT receptor interaction. The semiempirical method AM1 (HyperChem v. 7.0 program) and ACD/Labs v. 8.0 program were employed to calculate a set of physicochemical parameters for the investigated compounds. Correlation and multiple linear regression analysis were used to search for the best QSAR equations. The correlations obtained for the compounds studied represent their interactions with the proposed biochromatographic models. The good multivariate relationships (R(2) = 0.78-0.84) obtained by means of regression analysis can be used for predicting the quantitative effect of biological activity of different compounds with 5-HT receptor affinity. "Leave-one-out" (LOO) and "leave-N-out" (LNO) cross-validation methods were used to judge the predictive power of final regression equations.

  5. Extraction, separation and quantitative structure-retention relationship modeling of essential oils in three herbs.

    PubMed

    Wei, Yuhui; Xi, Lili; Chen, Dongxia; Wu, Xin'an; Liu, Huanxiang; Yao, Xiaojun

    2010-07-01

    The essential oils extracted from three kinds of herbs were separated by a 5% phenylmethyl silicone (DB-5MS) bonded phase fused-silica capillary column and identified by MS. Seventy-four of the compounds identified were selected as origin data, and their chemical structure and gas chromatographic retention times (RT) were performed to build a quantitative structure-retention relationship model by genetic algorithm and multiple linear regressions analysis. The predictive ability of the model was verified by internal validation (leave-one-out, fivefold, cross-validation and Y-scrambling). As for external validation, the model was also applied to predict the gas chromatographic RT of the 14 volatile compounds not used for model development from essential oil of Radix angelicae sinensis. The applicability domain was checked by the leverage approach to verify prediction reliability. The results obtained using several validations indicated that the best quantitative structure-retention relationship model was robust and satisfactory, could provide a feasible and effective tool for predicting the gas chromatographic RT of volatile compounds and could be also applied to help in identifying the compound with the same gas chromatographic RT.

  6. Parametric modeling for quantitative analysis of pulmonary structure to function relationships

    NASA Astrophysics Data System (ADS)

    Haider, Clifton R.; Bartholmai, Brian J.; Holmes, David R., III; Camp, Jon J.; Robb, Richard A.

    2005-04-01

    While lung anatomy is well understood, pulmonary structure-to-function relationships such as the complex elastic deformation of the lung during respiration are less well documented. Current methods for studying lung anatomy include conventional chest radiography, high-resolution computed tomography (CT scan) and magnetic resonance imaging with polarized gases (MRI scan). Pulmonary physiology can be studied using spirometry or V/Q nuclear medicine tests (V/Q scan). V/Q scanning and MRI scans may demonstrate global and regional function. However, each of these individual imaging methods lacks the ability to provide high-resolution anatomic detail, associated pulmonary mechanics and functional variability of the entire respiratory cycle. Specifically, spirometry provides only a one-dimensional gross estimate of pulmonary function, and V/Q scans have poor spatial resolution, reducing its potential for regional assessment of structure-to-function relationships. We have developed a method which utilizes standard clinical CT scanning to provide data for computation of dynamic anatomic parametric models of the lung during respiration which correlates high-resolution anatomy to underlying physiology. The lungs are segmented from both inspiration and expiration three-dimensional (3D) data sets and transformed into a geometric description of the surface of the lung. Parametric mapping of lung surface deformation then provides a visual and quantitative description of the mechanical properties of the lung. Any alteration in lung mechanics is manifest by alterations in normal deformation of the lung wall. The method produces a high-resolution anatomic and functional composite picture from sparse temporal-spatial methods which quantitatively illustrates detailed anatomic structure to pulmonary function relationships impossible for translational methods to provide.

  7. Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis

    PubMed Central

    2012-01-01

    Background Public resources of chemical compound are in a rapid growth both in quantity and the types of data-representation. To comprehensively understand the relationship between the intrinsic features of chemical compounds and protein targets is an essential task to evaluate potential protein-binding function for virtual drug screening. In previous studies, correlations were proposed between bioactivity profiles and target networks, especially when chemical structures were similar. With the lack of effective quantitative methods to uncover such correlation, it is demanding and necessary for us to integrate the information from multiple data sources to produce an comprehensive assessment of the similarity between small molecules, as well as quantitatively uncover the relationship between compounds and their targets by such integrated schema. Results In this study a multi-view based clustering algorithm was introduced to quantitatively integrate compound similarity from both bioactivity profiles and structural fingerprints. Firstly, a hierarchy clustering was performed with the fused similarity on 37 compounds curated from PubChem. Compared to clustering in a single view, the overall common target number within fused classes has been improved by using the integrated similarity, which indicated that the present multi-view based clustering is more efficient by successfully identifying clusters with its members sharing more number of common targets. Analysis in certain classes reveals that mutual complement of the two views for compound description helps to discover missing similar compound when only single view was applied. Then, a large-scale drug virtual screen was performed on 1267 compounds curated from Connectivity Map (CMap) dataset based on the fused similarity, which obtained a better ranking result compared to that of single-view. These comprehensive tests indicated that by combining different data representations; an improved assessment of target

  8. Comparison of quantitative structure-activity relationship model performances on carboquinone derivatives.

    PubMed

    Bolboacă, Sorana-Daniela; Jäntschi, Lorentz

    2009-10-14

    Quantitative structure-activity relationship (qSAR) models are used to understand how the structure and activity of chemical compounds relate. In the present study, 37 carboquinone derivatives were evaluated and two different qSAR models were developed using members of the Molecular Descriptors Family (MDF) and the Molecular Descriptors Family on Vertices (MDFV). The usual parameters of regression models and the following estimators were defined and calculated in order to analyze the validity and to compare the models: Akaike's information criteria (three parameters), Schwarz (or Bayesian) information criterion, Amemiya prediction criterion, Hannan-Quinn criterion, Kubinyi function, Steiger's Z test, and Akaike's weights. The MDF and MDFV models proved to have the same estimation ability of the goodness-of-fit according to Steiger's Z test. The MDFV model proved to be the best model for the considered carboquinone derivatives according to the defined information and prediction criteria, Kubinyi function, and Akaike's weights.

  9. Quantitative structure-activity relationships of selective antagonists of glucagon receptor using QuaSAR descriptors.

    PubMed

    Manoj Kumar, Palanivelu; Karthikeyan, Chandrabose; Hari Narayana Moorthy, Narayana Subbiah; Trivedi, Piyush

    2006-11-01

    In the present paper, quantitative structure activity relationship (QSAR) approach was applied to understand the affinity and selectivity of a novel series of triaryl imidazole derivatives towards glucagon receptor. Statistically significant and highly predictive QSARs were derived for glucagon receptor inhibition by triaryl imidazoles using QuaSAR descriptors of molecular operating environment (MOE) employing computer-assisted multiple regression procedure. The generated QSAR models revealed that factors related to hydrophobicity, molecular shape and geometry predominantly influences glucagon receptor binding affinity of the triaryl imidazoles indicating the relevance of shape specific steric interactions between the molecule and the receptor. Further, QSAR models formulated for selective inhibition of glucagon receptor over p38 mitogen activated protein (MAP) kinase of the compounds in the series highlights that the same structural features, which influence the glucagon receptor affinity, also contribute to their selective inhibition.

  10. Quantitative Structure‐activity Relationship (QSAR) Models for Docking Score Correction

    PubMed Central

    Yamasaki, Satoshi; Yasumatsu, Isao; Takeuchi, Koh; Kurosawa, Takashi; Nakamura, Haruki

    2016-01-01

    Abstract In order to improve docking score correction, we developed several structure‐based quantitative structure activity relationship (QSAR) models by protein‐drug docking simulations and applied these models to public affinity data. The prediction models used descriptor‐based regression, and the compound descriptor was a set of docking scores against multiple (∼600) proteins including nontargets. The binding free energy that corresponded to the docking score was approximated by a weighted average of docking scores for multiple proteins, and we tried linear, weighted linear and polynomial regression models considering the compound similarities. In addition, we tried a combination of these regression models for individual data sets such as IC50, Ki, and %inhibition values. The cross‐validation results showed that the weighted linear model was more accurate than the simple linear regression model. Thus, the QSAR approaches based on the affinity data of public databases should improve docking scores. PMID:28001004

  11. A descriptor of amino acids: SVRG and its application to peptide quantitative structure-activity relationship.

    PubMed

    Tong, J; Che, T; Li, Y; Wang, P; Xu, X; Chen, Y

    2011-01-01

    In this work, a descriptor, SVRG (principal component scores vector of radial distribution function descriptors and geometrical descriptors), was derived from principal component analysis (PCA) of a matrix of two structural variables of coded amino acids, including radial distribution function index (RDF) and geometrical index. SVRG scales were then applied in three panels of peptide quantitative structure-activity relationships (QSARs) which were modelled by partial least squares regression (PLS). The obtained models with the correlation coefficient (R²(cum)), cross-validation correlation coefficient (Q²(LOO)) were 0.910 and 0.863 for 48 bitter-tasting dipeptides; 0.968 and 0.931 for 21 oxytocin analogues; and 0.992 and 0.954 for 20 thromboplastin inhibitors. Satisfactory results showed that SVRG contained much chemical information relating to bioactivities. The approach may be a useful structural expression methodology for studies on peptide QSAR.

  12. In vivo toxicity of nitroaromatics: A comprehensive quantitative structure-activity relationship study.

    PubMed

    Gooch, Aminah; Sizochenko, Natalia; Rasulev, Bakhtiyor; Gorb, Leonid; Leszczynski, Jerzy

    2017-02-07

    The toxicity data of 90 nitroaromatic compounds related to their 50% lethal dose concentration for rats (LD50) were analyzed to develop quantitative structure-activity relationship (QSAR) models. Quantum-chemically calculated descriptors together with molecular descriptors generated by DRAGON, PaDEL, and HiT-QSAR software were utilized to build QSAR models. Quality and validity of the models were determined by internal and external validation techniques. The results show that the toxicity of nitroaromatic compounds depends on various factors, such as the number of nitro-groups, the topological state, and the presence of certain structural fragments. The developed models based on the largest (to date) dataset of nitroaromatics in vivo toxicity showed a good predictive ability. The results provide important input that could be applied in a preliminary assessment of nitroaromatic compounds' toxicity to mammals. Environ Toxicol Chem 2017;9999:1-7. © 2017 SETAC.

  13. Quantitative relationships between the parameters of thermal degradation of polyvinyl chloride and the loss of properties

    NASA Astrophysics Data System (ADS)

    Deshmukh, Susheel Ramesh

    Thermal degradation of polyvinyl chloride (PVC) has been extensively studied by a host of eminent researchers, both in terms of its mechanism, and effects. Arrhenius-type relationships have been proposed to correlate the loss of hydrogen chloride (HCl) with temperature and duration of thermal degradation. However, the rate of dehydrochlorination, does not always correlate with the loss of polymer properties. The purpose of this research was to obtain quantitative relationships between the parameters of thermal degradation of PVC, and the loss of mechanical, thermal, and optical properties of the polymer. The parameters of thermal degradation considered in this study were temperature, and heating time. The affected properties considered in this study were color, tensile strength, Izod impact strength, flexural modulus, and heat deflection temperature at 264 psi. Test specimens of PVC containing 1, 3, and 5 phr of dibutyltin bis (isooctyl thioglycolate) and barium-cadmium stearate were prepared. The rigid specimens for mechanical, and thermal testing were prepared by dry blending, extrusion and injection molding, whereas the specimens for optical testing were formulated as plastisols. These test specimens were subjected to five gradually increasing temperatures; 350, 360, 370, 375, and 380sp°F for five different heating times; 30, 60, 120, 240, and 480 minutes. The selected test properties were determined in appropriate tests before and after degradation. 'Percentage property retention' was defined as the ratio of the value of the test property after a given heating time (post-degradation) to the original value of the test property (pre-degradation). The lowest percentage retention value of the test property acceptable for service purposes was assumed as 66% for mechanical properties. The lowest heat deflection temperature acceptable for service purposes was assumed to be 120sp°F. The highest Gardner color number acceptable for service purposes was assumed to be 12

  14. Quantitative Relationships between Photosynthetic, Nitrogen Fixing, and Fermentative H2 Metabolism in a Photosynthetic Microbial Mat

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; Albert, Daniel B.; Bebout, Brad M.; Turk, Kendra A.; DesMarais, David J.

    2004-01-01

    The ultimate potential of any microbial ecosystem to contribute chemically to its environment - and therefore, to impact planetary biogeochemistry or to generate recognizable biosignatures - depends not only on the individual metabolic capabilities of constituent organisms, but also on how those capabilities are expressed through interactions with neighboring organisms. This is particularly important for microbial mats, which compress an extremely broad range of metabolic potential into a small and dynamic system. H2 participates in many of these metabolic processes, including the major elemental cycling processes of photosynthesis, nitrogen fixation, sulfate reduction, and fermentation, and may therefore serve as a mediator of microbial interactions within the mat system. Collectively, the requirements of energy, electron transfer, and biomass element stoichiometry suggest quantitative relationships among the major element cycling processes, as regards H2 metabolism We determined experimentally the major contributions to 32 cycling in hypersaline microbial mats from Baja California, Mexico, and compared them to predicted relationships. Fermentation under dark, anoxic conditions is quantitatively the most important mechanism of H2 production, consistent with expectations for non-heterocystous mats such as those under study. Up to 16% of reducing equivalents fixed by photosynthesis during the day may be released by this mechanism. The direct contribution of nitrogen fixation to H2 production is small in comparison, but this process may indirectly stimulate substantial H2 generation, by requiring higher rates of fermentation. Sulfate reduction, aerobic consumption, diffusive and ebulitive loss, and possibly H2-based photoreduction of CO2 serve as the principal H2 sinks. Collectively, these processes interact to create an orders-of-magnitude daily variation in H2 concentrations and fluxes, and thereby in the oxidation-reduction potential that is imposed on microbial

  15. Quantitative Structure-Cytotoxic Activity Relationship 1-(Benzoyloxy)urea and Its Derivative

    PubMed Central

    Hardjono, Suko; Siswodihardjo, Siswandono; Pramono, Purwanto; Darmanto, Win

    2016-01-01

    Drug development is originally carried out on a trial and error basis and it is cost-prohibitive. To minimize the trial and error risks, drug design is needed. One of the compound development processes to get a new drug is by designing a structure modification of the mother compound whose activities are recognized. A substitution of the mother compounds alters the physicochemical properties: lipophilic, electronic and steric properties. In Indonesia, one of medical treatments to cure cancer is through chemotherapy and hydroxyurea. Some derivatives, phenylthiourea, phenylurea, benzoylurea, thiourea and benzoylphenylurea, have been found to be anticancer drug candidates. To predict the activity of the drug compound before it is synthesized, the in-silico test is required. From the test, Rerank Score which is the energy of interaction between the receptor and the ligand molecule is then obtained. Hydroxyurea derivatives were synthesized by modifying Schotten-Baumann’s method by the addition of benzoyl group and its homologs resulted in the increase of lipophilic, electronic and steric properties, and cytotoxic activity. Synthesized compounds were 1-(benzoyloxy)urea and its derivatives. Structure characterization was obtained by the spectrum of UV, IR, H NMR, C NMR and Mass Spectrometer. Anticancer activity was carried out using MTT method on HeLa cells. The Quantitative Structure-Cytotoxic Activity Relationships of 1-(benzoyloxy)urea compound and its derivatives was calculated using SPSS. The chemical structure was described, namely: ClogP, π, σ, RS, CMR and Es; while, the cytotoxic activity was indicated by log (1 / IC50). The results show that the best equation of Quantitative Structure-Cytotoxic Activity Relationships (QSAR) of 1- (benzoyloxy)urea compound and its derivatives is Log 1/IC50 = - 0.205 (+ 0.068) σ – 0.051 (+ 0.022) Es – 1.911 (+ 0.020) PMID:27222144

  16. Potential antitumor agents. 29. Quantitative structure-activity relationships for the antileukemic bisquaternary ammonium heterocycles.

    PubMed

    Denny, W A; Atwell, G J; Baguley, B C; Cain, B F

    1979-02-01

    Quantitative relationships between physicochemical drug properties and antileukemic (L1210) efficacy have been examined for a series of bisquaternary ammonium heterocycles employing multiple variable regression analysis. Three measures of biologic response were examined: ILSmax, the percentage increase in mean life span of leukemic animals at the LD10 dose; D40, the drug dose necessary to provide 40% increase in life span; and CI (=LD 10/D40), the chemotherapeutic index. A cross correlation matrix between these three measures and the LD10 values demonstrates ILSmax and CI to be independent of toxicity. D40 is highly inversely correlated with LD10 and positively correlated with ILSmax, suggesting that this parameter measures a composite of both drug selectivity and toxicity. Superior regression equations resulted at all stages employing ILSmax as a measure of antitumor selectivity. Acceptable equations modeling LD10 could not be obtained. There was a parabolic relationship between agent lipophilic-hydrophilic balance, measured as chromatographic Rm values, and ILSmax. To reduce residual variance in the L1210 screening data, not accepted by this parabolic equation, measures of agent-DNA interaction were investigated as possible indices of site fit. Relative levels of drug-DNA interaction were obtained by spectrofluorimetric quantitation of drug displacement of DNA-bound ethidium. Addition to regression equations of agent C50 values for calf thymus DNA, those micromolar drug concentrations necessary to displace 50% of the ethidium bound to that DNA, provided a significant reduction in the screening data variance. C50 values for drug interactions with poly[d(A-T)] and poly[d(G-C)] were also investigated as possible indicators of drug selectivity towards different DNA sites. Marked differences were observed in the C50 values for the two synthetic nucleic acids, with those for calf thymus DNA and poly[d(G-C)] proving highly covariant. A regression equation containing a

  17. Quantitative structure-activity relationship and molecular docking studies of a series of quinazolinonyl analogues as inhibitors of gamma amino butyric acid aminotransferase.

    PubMed

    Abdulfatai, Usman; Uzairu, Adamu; Uba, Sani

    2017-01-01

    Quantitative structure-activity relationship and molecular docking studies were carried out on a series of quinazolinonyl analogues as anticonvulsant inhibitors. Density Functional Theory (DFT) quantum chemical calculation method was used to find the optimized geometry of the anticonvulsants inhibitors. Four types of molecular descriptors were used to derive a quantitative relation between anticonvulsant activity and structural properties. The relevant molecular descriptors were selected by Genetic Function Algorithm (GFA). The best model was validated and found to be statistically significant with squared correlation coefficient (R(2)) of 0.934, adjusted squared correlation coefficient (R(2)adj) value of 0.912, Leave one out (LOO) cross validation coefficient (Q(2)) value of 0.8695 and the external validation (R(2)pred) of 0.72. Docking analysis revealed that the best compound with the docking scores of -9.5 kcal/mol formed hydrophobic interaction and H-bonding with amino acid residues of gamma aminobutyric acid aminotransferase (GABAAT). This research has shown that the binding affinity generated was found to be better than the commercially sold anti-epilepsy drug, vigabatrin. Also, it was found to be better than the one reported by other researcher. Our QSAR model and molecular docking results corroborate with each other and propose the directions for the design of new inhibitors with better activity against GABAAT. The present study will help in rational drug design and synthesis of new selective GABAAT inhibitors with predetermined affinity and activity and provides valuable information for the understanding of interactions between GABAAT and the anticonvulsants inhibitors.

  18. Quantitative structure-biodegradability relationships for biokinetic parameter of polycyclic aromatic hydrocarbons.

    PubMed

    Xu, Peng; Ma, Wencheng; Han, Hongjun; Jia, Shengyong; Hou, Baolin

    2015-04-01

    Prediction of the biodegradability of organic pollutants is an ecologically desirable and economically feasible tool for estimating the environmental fate of chemicals. In this paper, stepwise multiple linear regression analysis method was applied to establish quantitative structure biodegradability relationship (QSBR) between the chemical structure and a novel biodegradation activity index (qmax) of 20 polycyclic aromatic hydrocarbons (PAHs). The frequency B3LYP/6-311+G(2df,p) calculations showed no imaginary values, implying that all the structures are minima on the potential energy surface. After eliminating the parameters which had low related coefficient with qmax, the major descriptors influencing the biodegradation activity were screened to be Freq, D, MR, EHOMO and ToIE. The evaluation of the developed QSBR mode, using a leave-one-out cross-validation procedure, showed that the relationships are significant and the model had good robustness and predictive ability. The results would be helpful for understanding the mechanisms governing biodegradation at the molecular level.

  19. The Relationship Between Online Social Networking and Depression: A Systematic Review of Quantitative Studies.

    PubMed

    Baker, David A; Algorta, Guillermo Perez

    2016-11-01

    Online social networking sites (SNSs) such as Facebook, Twitter, and MySpace are used by billions of people every day to communicate and interact with others. There has been increasing interest in the potential impact of online social networking on wellbeing, with a broadening body of new research into factors associated with both positive and negative mental health outcomes such as depression. This systematic review of empirical studies (n = 30) adds to existing research in this field by examining current quantitative studies focused on the relationship between online social networking and symptoms of depression. The academic databases PsycINFO, Web of Science, CINAHL, MEDLINE, and EMBASE were searched systematically using terms related to online social networking and depression. Reporting quality was critically appraised and the findings discussed with reference to their wider implications. The findings suggest that the relationship between online social networking and symptoms of depression may be complex and associated with multiple psychological, social, behavioral, and individual factors. Furthermore, the impact of online social networking on wellbeing may be both positive and negative, highlighting the need for future research to determine the impact of candidate mediators and moderators underlying these heterogeneous outcomes across evolving networks.

  20. Quantitative assessment of the relationship between RASSF1A gene promoter methylation and bladder cancer (PRISMA)

    PubMed Central

    Zhan, Leyun; Zhang, Bingyi; Tan, Yaojun; Yang, Chengliang; Huang, Chenhong; Wu, Qiongya; Zhang, Yulin; Chen, Xiaobo; Zhou, Mi; Shu, Aihua

    2017-01-01

    Abstract Background: Methylation of the Ras-association domain family 1 isoform A (RASSF1A) gene promoter region is thought to participate in the initiation and development of many different cancers. However, in bladder cancer the role of RASSF1A methylation was unclear. To evaluate the relationship between RASSF1A methylation and bladder cancer, a quantitative assessment of an independent meta-analysis was performed. In addition, a DNA methylation microarray database from the cancer genome atlas (TCGA) project was used to validate the results of the meta-analysis. Methods: We searched published articles from computerized databases, and DNA methylation data were extracted from TCGA project. All data were analyzed by R software. Results: The results of the meta-analysis indicated that the frequency of RASSF1A gene methylation in bladder cancer patients is significantly higher than in healthy controls. The hazard ratio (HR) was 2.24 (95% CI = [1.45; 3.48], P = 0.0003) for overall survival (OS), and the RASSF1A gene promoter methylation status was strongly associated with the TNM stage and differentiation grade of the tumor. The similar results were also found by the data from TCGA project. Conclusion: There was a significant relationship between the methylation of the RASSF1A gene promoter and bladder cancer. Therefore, RASSF1A gene promoter methylation will be a potential biomarker for the clinical diagnosis of bladder cancer. PMID:28207521

  1. Quantitative analysis of anatomical relationship between cavernous segment internal carotid artery and pituitary macroadenoma.

    PubMed

    Lin, Bon-Jour; Chung, Tzu-Tsao; Lin, Meng-Chi; Lin, Chin; Hueng, Dueng-Yuan; Chen, Yuan-Hao; Hsia, Chung-Ching; Ju, Da-Tong; Ma, Hsin-I; Liu, Ming-Ying; Tang, Chi-Tun

    2016-10-01

    Cavernous segment internal carotid artery (CSICA) injury during endoscopic transsphenoidal surgery for pituitary tumor is rare but fatal. The aim of this study is to investigate anatomical relationship between pituitary macroadenoma and corresponding CSICA using quantitative means with a sense to improve safety of surgery.In this retrospective study, a total of 98 patients with nonfunctioning pituitary macroadenomas undergoing endoscopic transsphenoidal surgeries were enrolled from 2005 to 2014. Intercarotid distances between bilateral CSICAs were measured in the 4 coronal levels, namely optic strut, convexity of carotid prominence, median sella turcica, and dorsum sellae. Parasellar extension was graded and recorded by Knosp-Steiner classification.Our findings indicated a linear relationship between size of pituitary macroadenoma and intercarotid distance over CSICA. The correlation was absent in pituitary macroadenoma with Knosp-Steiner grade 4 parasellar extension.Bigger pituitary macroadenoma makes more lateral deviation of CSICA. While facing larger tumor, sufficient bony graft is indicated for increasing surgical field, working area and operative safety.

  2. Quantitative causal-comparative relationship between interactive whiteboard instruction and student science proficiency

    NASA Astrophysics Data System (ADS)

    Danelczyk, Ewa Krystyna

    The purpose of this quantitative causal-comparative study was to investigate the relationship between the instructional effects of the interactive whiteboard and students' proficiency levels in eighth-grade science as evidenced by the state FCAT scores. A total of 46 eighth-grade science teachers in a South Florida public school district completed a survey via the Internet. Data were analyzed using descriptive statistics, t tests, Pearson's product moment correlation, and Spearman's rank order correlation. Results revealed a significant difference in mean between eighth-grade students' proficiency percentages reported by participating teachers and the statewide results for the years 2008-2012 (p < .0005), with the exception of results reported in the year 2010 (p > .05). The significant results were not found between use of the interactive whiteboard for science instruction and students' science proficiency levels as evidenced by FCAT (p > .05), and teachers' professional experience and students' proficiency levels (p > .05). The recommendation from the current study is to continue research pertaining to instructional effectiveness of the interactive whiteboard in relationship to standardized tests because existing findings on similar topics are contradictory. There is a need for more empirical evidence on the long-term impact of the interactive whiteboard on students' achievement in science.

  3. Quantitative analysis of anatomical relationship between cavernous segment internal carotid artery and pituitary macroadenoma

    PubMed Central

    Lin, Bon-Jour; Chung, Tzu-Tsao; Lin, Meng-Chi; Lin, Chin; Hueng, Dueng-Yuan; Chen, Yuan-Hao; Hsia, Chung-Ching; Ju, Da-Tong; Ma, Hsin-I; Liu, Ming-Ying; Tang, Chi-Tun

    2016-01-01

    Abstract Cavernous segment internal carotid artery (CSICA) injury during endoscopic transsphenoidal surgery for pituitary tumor is rare but fatal. The aim of this study is to investigate anatomical relationship between pituitary macroadenoma and corresponding CSICA using quantitative means with a sense to improve safety of surgery. In this retrospective study, a total of 98 patients with nonfunctioning pituitary macroadenomas undergoing endoscopic transsphenoidal surgeries were enrolled from 2005 to 2014. Intercarotid distances between bilateral CSICAs were measured in the 4 coronal levels, namely optic strut, convexity of carotid prominence, median sella turcica, and dorsum sellae. Parasellar extension was graded and recorded by Knosp–Steiner classification. Our findings indicated a linear relationship between size of pituitary macroadenoma and intercarotid distance over CSICA. The correlation was absent in pituitary macroadenoma with Knosp–Steiner grade 4 parasellar extension. Bigger pituitary macroadenoma makes more lateral deviation of CSICA. While facing larger tumor, sufficient bony graft is indicated for increasing surgical field, working area and operative safety. PMID:27741111

  4. Genetic programming based quantitative structure-retention relationships for the prediction of Kovats retention indices.

    PubMed

    Goel, Purva; Bapat, Sanket; Vyas, Renu; Tambe, Amruta; Tambe, Sanjeev S

    2015-11-13

    The development of quantitative structure-retention relationships (QSRR) aims at constructing an appropriate linear/nonlinear model for the prediction of the retention behavior (such as Kovats retention index) of a solute on a chromatographic column. Commonly, multi-linear regression and artificial neural networks are used in the QSRR development in the gas chromatography (GC). In this study, an artificial intelligence based data-driven modeling formalism, namely genetic programming (GP), has been introduced for the development of quantitative structure based models predicting Kovats retention indices (KRI). The novelty of the GP formalism is that given an example dataset, it searches and optimizes both the form (structure) and the parameters of an appropriate linear/nonlinear data-fitting model. Thus, it is not necessary to pre-specify the form of the data-fitting model in the GP-based modeling. These models are also less complex, simple to understand, and easy to deploy. The effectiveness of GP in constructing QSRRs has been demonstrated by developing models predicting KRIs of light hydrocarbons (case study-I) and adamantane derivatives (case study-II). In each case study, two-, three- and four-descriptor models have been developed using the KRI data available in the literature. The results of these studies clearly indicate that the GP-based models possess an excellent KRI prediction accuracy and generalization capability. Specifically, the best performing four-descriptor models in both the case studies have yielded high (>0.9) values of the coefficient of determination (R(2)) and low values of root mean squared error (RMSE) and mean absolute percent error (MAPE) for training, test and validation set data. The characteristic feature of this study is that it introduces a practical and an effective GP-based method for developing QSRRs in gas chromatography that can be gainfully utilized for developing other types of data-driven models in chromatography science.

  5. Quantitative Structure Activity Relationship for Inhibition of Human Organic Cation/Carnitine Transporter (OCTN2)

    PubMed Central

    Diao, Lei; Ekins, Sean; Polli, James E.

    2010-01-01

    Organic cation/carnitine transporter (OCTN2; SLC22A5) is an important transporter for L-carnitine homeostasis, but can be inhibited by drugs, which may cause L-carnitine deficiency and possibly other OCTN2-mediated drug-drug interactions. One objective was to develop a quantitative structure–activity relationship (QSAR) of OCTN2 inhibitors, in order to predict and identify other potential OCTN2 inhibitors and infer potential clinical interactions. A second objective was to assess two high renal clearance drugs that interact with OCTN2 in vitro (cetirizine and cephaloridine) for possible OCTN2-mediated drug-drug interactions. Using previously generated in vitro data of 22 drugs, a 3D quantitative pharmacophore model and a Bayesian machine learning model were developed. The four pharmacophore features include two hydrophobic groups, one hydrogen-bond acceptor, and one positive ionizable center. The Bayesian machine learning model was developed using simple interpretable descriptors and function class fingerprints of maximum diameter 6 (FCFP_6). An external test set of 27 molecules, including 15 newly identified OCTN2 inhibitors, and a literature test set of 22 molecules were used to validate both models. The computational models afforded good capability to identify structurally diverse OCTN2 inhibitors, providing a valuable tool to predict new inhibitors efficiently. Inhibition results confirmed our previously observed association between rhabdomyolysis and Cmax/Ki ratio. The two high renal clearance drugs cetirizine and cephaloridine were found not to be OCTN2 substrates and their diminished elimination by other drugs is concluded not to be mediated by OCTN2. PMID:20831193

  6. Quantitative structure-retention relationships of polycyclic aromatic hydrocarbons gas-chromatographic retention indices.

    PubMed

    Drosos, Juan Carlos; Viola-Rhenals, Maricela; Vivas-Reyes, Ricardo

    2010-06-25

    Polycyclic aromatic compounds (PAHs) are of concern in environmental chemistry and toxicology. In the present work, a QSRR study was performed for 209 previously reported PAHs using quantum mechanics and other sources descriptors estimated by different approaches. The B3LYP/6-31G* level of theory was used for geometrical optimization and quantum mechanics related variables. A good linear relationship between gas-chromatographic retention index and electronic or topologic descriptors was found by stepwise linear regression analysis. The molecular polarizability (alpha) and the second order molecular connectivity Kier and Hall index ((2)chi) showed evidence of significant correlation with retention index by means of important squared coefficient of determination, (R(2)), values (R(2)=0.950 and 0.962, respectively). A one variable QSRR model is presented for each descriptor and both models demonstrates a significant predictive capacity established using the leave-many-out LMO (excluding 25% of rows) cross validation method's q(2) cross-validation coefficients q(2)(CV-LMO25%), (obtained q(2)(CV-LMO25%) 0.947 and 0.960, respectively). Furthermore, the physicochemical interpretation of selected descriptors allowed detailed explanation of the source of the observed statistical correlation. The model analysis suggests that only one descriptor is sufficient to establish a consistent retention index-structure relationship. Moderate or non-significant improve was observed for quantitative results or statistical validation parameters when introducing more terms in predictive equation. The one parameter QSRR proposed model offers a consistent scheme to predict chromatographic properties of PAHs compounds.

  7. Quantitative structure-retention relationships of flavonoids unraveled by immobilized artificial membrane chromatography.

    PubMed

    Santoro, Adriana Leandra; Carrilho, Emanuel; Lanças, Fernando Mauro; Montanari, Carlos Alberto

    2016-06-10

    The pharmacokinetic properties of flavonoids with differing degrees of lipophilicity were investigated using immobilized artificial membranes (IAMs) as the stationary phase in high performance liquid chromatography (HPLC). For each flavonoid compound, we investigated whether the type of column used affected the correlation between the retention factors and the calculated octanol/water partition (log Poct). Three-dimensional (3D) molecular descriptors were calculated from the molecular structure of each compound using i) VolSurf software, ii) the GRID method (computational procedure for determining energetically favorable binding sites in molecules of known structure using a probe for calculating the 3D molecular interaction fields, between the probe and the molecule), and iii) the relationship between partition and molecular structure, analyzed in terms of physicochemical descriptors. The VolSurf built-in Caco-2 model was used to estimate compound permeability. The extent to which the datasets obtained from different columns differ both from each other and from both the calculated log Poct and the predicted permeability in Caco-2 cells was examined by principal component analysis (PCA). The immobilized membrane partition coefficients (kIAM) were analyzed using molecular descriptors in partial least square regression (PLS) and a quantitative structure-retention relationship was generated for the chromatographic retention in the cholesterol column. The cholesterol column provided the best correlation with the permeability predicted by the Caco-2 cell model and a good fit model with great prediction power was obtained for its retention data (R(2)=0.96 and Q(2)=0.85 with four latent variables).

  8. Assessing the toxic effects of ethylene glycol ethers using Quantitative Structure Toxicity Relationship models

    SciTech Connect

    Ruiz, Patricia; Mumtaz, Moiz; Gombar, Vijay

    2011-07-15

    Experimental determination of toxicity profiles consumes a great deal of time, money, and other resources. Consequently, businesses, societies, and regulators strive for reliable alternatives such as Quantitative Structure Toxicity Relationship (QSTR) models to fill gaps in toxicity profiles of compounds of concern to human health. The use of glycol ethers and their health effects have recently attracted the attention of international organizations such as the World Health Organization (WHO). The board members of Concise International Chemical Assessment Documents (CICAD) recently identified inadequate testing as well as gaps in toxicity profiles of ethylene glycol mono-n-alkyl ethers (EGEs). The CICAD board requested the ATSDR Computational Toxicology and Methods Development Laboratory to conduct QSTR assessments of certain specific toxicity endpoints for these chemicals. In order to evaluate the potential health effects of EGEs, CICAD proposed a critical QSTR analysis of the mutagenicity, carcinogenicity, and developmental effects of EGEs and other selected chemicals. We report here results of the application of QSTRs to assess rodent carcinogenicity, mutagenicity, and developmental toxicity of four EGEs: 2-methoxyethanol, 2-ethoxyethanol, 2-propoxyethanol, and 2-butoxyethanol and their metabolites. Neither mutagenicity nor carcinogenicity is indicated for the parent compounds, but these compounds are predicted to be developmental toxicants. The predicted toxicity effects were subjected to reverse QSTR (rQSTR) analysis to identify structural attributes that may be the main drivers of the developmental toxicity potential of these compounds.

  9. Quantitative structure-retention relationships of pesticides in reversed-phase high-performance liquid chromatography.

    PubMed

    Aschi, Massimiliano; D'Archivio, Angelo Antonio; Maggi, Maria Anna; Mazzeo, Pietro; Ruggieri, Fabrizio

    2007-01-23

    In this paper, a quantitative structure-retention relationships (QSRR) method is employed to predict the retention behaviour of pesticides in reversed-phase high-performance liquid chromatography (HPLC). A six-parameter nonlinear model is developed by means of a feed-forward artificial neural network (ANN) with back-propagation learning rule. Accurate description of the retention factors of 26 compounds including commonly used insecticides, herbicides and fungicides and some metabolites is successfully achieved. In addition to the acetonitrile content, included to describe composition of the water-acetonitrile mobile phase, the octanol-water partition coefficient (from literature) and four quantum chemical descriptors are considered to account for the effect of solute structure on the retention. These are: the total dipole moment, the mean polarizability, the anisotropy of polarizability and a descriptor of hydrogen bonding ability based on the atomic charges on hydrogen bond donor and acceptor chemical functionalities. The proposed nonlinear QSRR model exhibits a high degree of correlation between observed and computed retention factors and a good predictive performance in wide range of mobile phase composition (40-65%, v/v acetonitrile) that supports its application for the prediction of the chromatographic behaviour of unknown pesticides. A multilinear regression model based on the same six descriptors shows a significantly worse predictive capability.

  10. Utilization of quantitative structure-activity relationships (QSARs) in risk assessment: Alkylphenols

    SciTech Connect

    Beck, B.D.; Toole, A.P.; Callahan, B.G.; Siddhanti, S.K. )

    1991-12-01

    Alkylphenols are a class of environmentally pervasive compounds, found both in natural (e.g., crude oils) and in anthropogenic (e.g., wood tar, coal gasification waste) materials. Despite the frequent environmental occurrence of these chemicals, there is a limited toxicity database on alkylphenols. The authors have therefore developed a 'toxicity equivalence approach' for alkylphenols which is based on their ability to inhibit, in a specific manner, the enzyme cyclooxygenase. Enzyme-inhibiting ability for individual alkylphenols can be estimated based on the quantitative structure-activity relationship developed by Dewhirst (1980) and is a function of the free hydroxyl group, electron-donating ring substituents, and hydrophobic aromatic ring substituents. The authors evaluated the toxicological significance of cyclooxygenase inhibition by comparison of the inhibitory capacity of alkylphenols with the inhibitory capacity of acetylsalicylic acid, or aspirin, a compound whose low-level effects are due to cyclooxygenase inhibition. Since nearly complete absorption for alkylphenols and aspirin is predicted, based on estimates of hydrophobicity and fraction of charged molecules at gastrointestinal pHs, risks from alkylphenols can be expressed directly in terms of 'milligram aspirin equivalence,' without correction for absorption differences. They recommend this method for assessing risks of mixtures of alkylphenols, especially for those compounds with no chronic toxicity data.38 references.

  11. Antimicrobial Photodynamic Therapy with Functionalized Fullerenes: Quantitative Structure-activity Relationships

    PubMed Central

    Mizuno, Kazue; Zhiyentayev, Timur; Huang, Liyi; Khalil, Sarwat; Nasim, Faria; Tegos, George P; Gali, Hariprasad; Jahnke, Ashlee; Wharton, Tim; Hamblin, Michael R

    2011-01-01

    Photosensitive dyes or photo sensitizers (PS) in combination with visible light and oxygen produce reactive oxygen species that kill cells in the process known as photodynamic therapy (PDT). Antimicrobial PDT employs PS that is selective for microbial cells and is a new treatment for infections. Most antimicrobial PS is based on tetrapyrrole or phenothiazinium structures that have been synthesized to carry quaternary cationic charges or basic amino groups. However we recently showed that cationic-substituted fullerene derivative were highly effective in killing a broad spectrum of microbial cells after illumination with white light. In the present report we compared a new group of synthetic fullerene derivatives that possessed either basic or quaternary amino groups as antimicrobial PS against Gram-positive (Staphylococcus aureus), Gram-negative bacteria (Escherichia coli) and fungi (Candida albicans). Quantitative structure-function relationships were derived with LogP and hydrophilic lipophilic balance parameters. Compounds with non-quaternary amino groups tended to form nanoaggregates in water and were only effective against S. aureus. The most important determinant of effectiveness was an increased number of quaternary cationic groups that were widely dispersed around the fullerene cage to minimize aggregation. S. aureus was most susceptible; E. coli was intermediate, while C. albicans was the most resistant species tested. The high effectiveness of antimicrobial PDT with quaternized fullerenes suggest they may have applications in treatment of superficial infections (for instance in wounds and burns) where light penetration into tissue is not problematic. PMID:21743839

  12. Synthesis, photodynamic activity, and quantitative structure-activity relationship modelling of a series of BODIPYs.

    PubMed

    Caruso, Enrico; Gariboldi, Marzia; Sangion, Alessandro; Gramatica, Paola; Banfi, Stefano

    2017-02-01

    Here we report the synthesis of eleven new BODIPYs (14-24) characterized by the presence of an aromatic ring on the 8 (meso) position and of iodine atoms on the pyrrolic 2,6 positions. These molecules, together with twelve BODIPYs already reported by us (1-12), represent a large panel of BODIPYs showing different atoms or groups as substituent of the aromatic moiety. Two physico-chemical features ((1)O2 generation rate and lipophilicity), which can play a fundamental role in the outcome as photosensitizers, have been studied. The in vitro photo-induced cell-killing efficacy of 23 PSs was studied on the SKOV3 cell line treating the cells for 24h in the dark then irradiating for 2h with a green LED device (fluence 25.2J/cm(2)). The cell-killing efficacy was assessed with the MTT test and compared with that one of meso un-substituted compound (13). In order to understand the possible effect of the substituents, a predictive quantitative structure-activity relationship (QSAR) regression model, based on theoretical holistic molecular descriptors, was developed. The results clearly indicate that the presence of an aromatic ring is fundamental for an excellent photodynamic response, whereas the electronic effects and the position of the substituents on the aromatic ring do not influence the photodynamic efficacy.

  13. Antiproliferative Pt(IV) complexes: synthesis, biological activity, and quantitative structure-activity relationship modeling.

    PubMed

    Gramatica, Paola; Papa, Ester; Luini, Mara; Monti, Elena; Gariboldi, Marzia B; Ravera, Mauro; Gabano, Elisabetta; Gaviglio, Luca; Osella, Domenico

    2010-09-01

    Several Pt(IV) complexes of the general formula [Pt(L)2(L')2(L'')2] [axial ligands L are Cl-, RCOO-, or OH-; equatorial ligands L' are two am(m)ine or one diamine; and equatorial ligands L'' are Cl- or glycolato] were rationally designed and synthesized in the attempt to develop a predictive quantitative structure-activity relationship (QSAR) model. Numerous theoretical molecular descriptors were used alongside physicochemical data (i.e., reduction peak potential, Ep, and partition coefficient, log Po/w) to obtain a validated QSAR between in vitro cytotoxicity (half maximal inhibitory concentrations, IC50, on A2780 ovarian and HCT116 colon carcinoma cell lines) and some features of Pt(IV) complexes. In the resulting best models, a lipophilic descriptor (log Po/w or the number of secondary sp3 carbon atoms) plus an electronic descriptor (Ep, the number of oxygen atoms, or the topological polar surface area expressed as the N,O polar contribution) is necessary for modeling, supporting the general finding that the biological behavior of Pt(IV) complexes can be rationalized on the basis of their cellular uptake, the Pt(IV)-->Pt(II) reduction, and the structure of the corresponding Pt(II) metabolites. Novel compounds were synthesized on the basis of their predicted cytotoxicity in the preliminary QSAR model, and were experimentally tested. A final QSAR model, based solely on theoretical molecular descriptors to ensure its general applicability, is proposed.

  14. Antitumor activity of 3,4-ethylenedioxythiophene derivatives and quantitative structure-activity relationship analysis

    NASA Astrophysics Data System (ADS)

    Jukić, Marijana; Rastija, Vesna; Opačak-Bernardi, Teuta; Stolić, Ivana; Krstulović, Luka; Bajić, Miroslav; Glavaš-Obrovac, Ljubica

    2017-04-01

    The aim of this study was to evaluate nine newly synthesized amidine derivatives of 3,4- ethylenedioxythiophene (3,4-EDOT) for their cytotoxic activity against a panel of human cancer cell lines and to perform a quantitative structure-activity relationship (QSAR) analysis for the antitumor activity of a total of 27 3,4-ethylenedioxythiophene derivatives. Induction of apoptosis was investigated on the selected compounds, along with delivery options for the optimization of activity. The best obtained QSAR models include the following group of descriptors: BCUT, WHIM, 2D autocorrelations, 3D-MoRSE, GETAWAY descriptors, 2D frequency fingerprint and information indices. Obtained QSAR models should be relieved in elucidation of important physicochemical and structural requirements for this biological activity. Highly potent molecules have a symmetrical arrangement of substituents along the x axis, high frequency of distance between N and O atoms at topological distance 9, as well as between C and N atoms at topological distance 10, and more C atoms located at topological distances 6 and 3. Based on the conclusion given in the QSAR analysis, a new compound with possible great activity was proposed.

  15. Development of validated quantitative structure-retention relationship models for retention indices of plant essential oils.

    PubMed

    Qin, Li-Tang; Liu, Shu-Shen; Chen, Fu; Wu, Qing-Sheng

    2013-05-01

    Quantitative structure-retention relationship (QSRR) models were developed for the retention indices of 505 frequently reported components of plant essential oils. Multiple linear regression was used to build QSRR models for the dimethyl silicone, dimethyl silicone with 5% phenyl groups, and polyethylene glycol stationary phases. We tried to improve the variable selection and modeling method based on prediction method for selecting the optimum descriptors from the molecular weight, 75 topological indices, and 170 atom-type E-state indices. The three-variable QSRR models perform high correlation coefficients of 0.937 for dimethyl silicone and 0.933 for dimethyl silicone with 5% phenyl groups stationary phase. Four variables were selected to developed QSRR model for the polyethylene glycol stationary phase. The leave-one-out and leave-many-out cross-validations, bootstrapping, and y-randomization test showed the three models are robust and have no chance correlation. The external validation with the test set showed the three models present high externally predictive power. The three models presented high-quality fit, internally, and externally predictive power. It is expected that the models can effectively predict retention indices of essential oils components without experimental value.

  16. Quantitative structure-retention relationship modeling of gas chromatographic retention times based on thermodynamic data.

    PubMed

    Ebrahimi-Najafabadi, Heshmatollah; McGinitie, Teague M; Harynuk, James J

    2014-09-05

    Thermodynamic parameters of ΔH(T0), ΔS(T0), and ΔCP for 156 compounds comprising alkanes, alkyl halides and alcohols were determined for a 5% phenyl 95% methyl stationary phase. The determination of thermodynamic parameters relies on a Nelder-Mead simplex optimization to rapidly obtain the parameters. Two methodologies of external and leave one out cross validations were applied to assess the robustness of the estimations of thermodynamic parameters. The largest absolute errors in predicted retention time across all temperature ramps and all compounds were 1.5 and 0.3s for external and internal sets, respectively. The possibility of an in silico extension of the thermodynamic library was tested using a quantitative structure-retention relationship (QSRR) methodology. The estimated thermodynamic parameters were utilized to develop QSRR models. Individual partial least squares (PLS) models were developed for each of the three classes of the molecules. R(2) values for the test sets of all models across all temperature ramps were larger than 0.99 and the average of relative errors in retention time predictions of the test sets for alkanes, alcohols, and alkyl halides were 1.8%, 2.4%, and 2.5%, respectively.

  17. Quantitative structure-activity relationship of organophosphate compounds based on molecular interaction fields descriptors.

    PubMed

    Zhao, Jinsong; Yu, Shuxia

    2013-03-01

    By using multi-block partial least-squares (MBPLS) method, quantitative structure-activity relationship (QSAR) between 35 organophosphate compounds (OP) and their 24h acute toxicities towards the housefly (Musca nebulo L.) was built on the molecular interaction fields (MIF) descriptors, which were obtained with O, N and DRY as probes, and then normalised with block unscaled weights (BUW) technique. The best QSAR model had 8 principal components, with the coefficient of determination R(2)=0.995 and that of leave-one-out cross-validation Q(2)=0.865, and the corresponding standard deviation of error 0.076 and 0.361, respectively. Block importance in the prediction (BIP) for O, N and DRY probe were 1.030, 0.962 and 1.007, respectively. Contour map of variable coefficients showed that hydrogen bonding between the O atom in PO and the NH groups in acetylcholinesterase (AChE) played an important role in the interaction between OP and AChE. Meanwhile, the hydrophobicity of OP also had significant contribution. QSAR based on the MIF descriptors could be a potential means to interpret the mechanisms of ligand-receptor interaction when the receptor was well known.

  18. Blood-brain barrier permeability mechanisms in view of quantitative structure-activity relationships (QSAR).

    PubMed

    Bujak, Renata; Struck-Lewicka, Wiktoria; Kaliszan, Michał; Kaliszan, Roman; Markuszewski, Michał J

    2015-04-10

    The goal of the present paper was to develop a quantitative structure-activity relationship (QSAR) method using a simple statistical approach, such as multiple linear regression (MLR) for predicting the blood-brain barrier (BBB) permeability of chemical compounds. The "best" MLR models, comprised logP and either molecular mass (M) or isolated atomic energy (E(isol)), tested on a structurally diverse set of 66 compounds, is characterized the by correlation coefficients (R) around 0.8. The obtained models were validated using leave-one-out (LOO) cross-validation technique and the correlation coefficient of leave-one-out- R(LOO)(2) (Q(2)) was at least 0.6. Analysis of a case from legal medicine demonstrated informative value of our QSAR model. To best authors' knowledge the present study is a first application of the developed QSAR models of BBB permeability to case from the legal medicine. Our data indicate that molecular energy-related descriptors, in combination with the well-known descriptors of lipophilicity may have a supportive value in predicting blood-brain distribution, which is of utmost importance in drug development and toxicological studies.

  19. Quantitative structure-activity relationships of imidazole-containing farnesyltransferase inhibitors using different chemometric methods.

    PubMed

    Shayanfar, Ali; Ghasemi, Saeed; Soltani, Somaieh; Asadpour-Zeynali, Karim; Doerksen, Robert J; Jouyban, Abolghasem

    2013-05-01

    Farnesyltranseferase inhibitors (FTIs) are one of the most promising classes of anticancer agents, but though some compounds in this category are in clinical trials there are no marketed drugs in this class yet. Quantitative structure activity relationship (QSAR) models can be used for predicting the activity of FTI candidates in early stages of drug discovery. In this study 192 imidazole-containing FTIs were obtained from the literature, structures of the molecules were optimized using Hyperchem software, and molecular descriptors were calculated using Dragon software. The most suitable descriptors were selected using genetic algorithms-partial least squares (GA-PLS) and stepwise regression, and indicated that the volume, shape and polarity of the FTIs are important for their activities. 2D-QSAR models were prepared using both linear methods, i.e., multiple linear regression (MLR), and non-linear methods, i.e., artificial neural networks (ANN) and support vector machines (SVM). The proposed QSAR models were validated using internal and external validation methods. The results show that the proposed 2D-QSAR models are valid and that they can be applied to predict the activities of imidazole-containing FTIs. The prediction capability of the 2D-QSAR (linear and non-linear) models is comparable to and somewhat better than that of previous 3D-QSAR models and the non-linear models are more accurate than the linear models.

  20. Positive Quantitative Relationship between EMT and Contact-Initiated Sliding on Fiber-like Tracks.

    PubMed

    Milano, Daniel F; Natividad, Robert J; Saito, Yasuhiro; Luo, Catherine Y; Muthuswamy, Senthil K; Asthagiri, Anand R

    2016-10-04

    Epithelial-mesenchymal transition (EMT) is a complex process by which cells acquire invasive properties that enable escape from the primary tumor. Complete EMT, however, is not required for metastasis: circulating tumor cells exhibit hybrid epithelial-mesenchymal states, and genetic perturbations promoting partial EMT induce metastasis in vivo. An open question is whether and to what extent intermediate stages of EMT promote invasiveness. Here, we investigate this question, building on recent observation of a new invasive property. Migrating cancer cell lines and cells transduced with prometastatic genes slide around other cells on spatially confined, fiberlike micropatterns. We show here that low-dosage/short-duration exposure to transforming growth factor beta (TGFβ) induces partial EMT and enables sliding on narrower (26 μm) micropatterns than untreated counterparts (41 μm). High-dosage/long-duration exposure induces more complete EMT, including disrupted cell-cell contacts and reduced E-cadherin expression, and promotes sliding on the narrowest (15 μm) micropatterns. These results identify a direct and quantitative relationship between EMT and cell sliding and show that EMT-associated invasive sliding is progressive, with cells that undergo partial EMT exhibiting intermediate sliding behavior and cells that transition more completely through EMT displaying maximal sliding. Our findings suggest a model in which fiber maturation and EMT work synergistically to promote invasiveness during cancer progression.

  1. Quantitative structure-activity relationship analysis of β-amyloid aggregation inhibitors

    NASA Astrophysics Data System (ADS)

    Stempler, Shiri; Levy-Sakin, Michal; Frydman-Marom, Anat; Amir, Yaniv; Scherzer-Attali, Roni; Buzhansky, Ludmila; Gazit, Ehud; Senderowitz, Hanoch

    2011-02-01

    Inhibiting the aggregation process of the β-amyloid peptide is a promising strategy in treating Alzheimer's disease. In this work, we have collected a dataset of 80 small molecules with known inhibition levels and utilized them to develop two comprehensive quantitative structure-activity relationship models: a Bayesian model and a decision tree model. These models have exhibited high predictive accuracy: 87% of the training and test sets using the Bayesian model and 89 and 93% of the training and test sets, respectively, by the decision tree model. Subsequently these models were used to predict the activities of several new potential β-amyloid aggregation inhibitors and these predictions were indeed validated by in vitro experiments. Key chemical features correlated with the inhibition ability were identified. These include the electro-topological state of carbonyl groups, AlogP and the number of hydrogen bond donor groups. The results demonstrate the feasibility of the developed models as tools for rapid screening, which could help in the design of novel potential drug candidates for Alzheimer's disease.

  2. Quantitative structure-activity relationship models of chemical transformations from matched pairs analyses.

    PubMed

    Beck, Jeremy M; Springer, Clayton

    2014-04-28

    The concepts of activity cliffs and matched molecular pairs (MMP) are recent paradigms for analysis of data sets to identify structural changes that may be used to modify the potency of lead molecules in drug discovery projects. Analysis of MMPs was recently demonstrated as a feasible technique for quantitative structure-activity relationship (QSAR) modeling of prospective compounds. Although within a small data set, the lack of matched pairs, and the lack of knowledge about specific chemical transformations limit prospective applications. Here we present an alternative technique that determines pairwise descriptors for each matched pair and then uses a QSAR model to estimate the activity change associated with a chemical transformation. The descriptors effectively group similar transformations and incorporate information about the transformation and its local environment. Use of a transformation QSAR model allows one to estimate the activity change for novel transformations and therefore returns predictions for a larger fraction of test set compounds. Application of the proposed methodology to four public data sets results in increased model performance over a benchmark random forest and direct application of chemical transformations using QSAR-by-matched molecular pairs analysis (QSAR-by-MMPA).

  3. Quantitative structure-pharmacokinetic relationships (QSPR) of beta blockers derived using neural networks.

    PubMed

    Gobburu, J V; Shelver, W H

    1995-07-01

    This study demonstrates the application of neural networks to predict the pharmacokinetic properties of beta-adrenoreceptor antagonists in humans. A congeneric series of 10 beta-blockers, whose critical pharmacokinetic parameters are well established, was selected for the study. An appropriate neural network system was constructed and tested for its ability to predict the pharmacokinetic parameters from the octanol/water partition coefficient (shake flask method), the pKa, or the fraction bound to plasma proteins. Neural networks successfully trained and the predicted pharmacokinetic values agreed well with the experimental values (average difference = 8%). The neural network-predicted values showed better agreement with the experimental values than those predicted by multiple regression techniques (average difference = 47%). Because the neural networks had a large number of connections, two tests were conducted to determine if the networks were memorizing rather than generalizing. The "leave-one-out" method verified the generalization of the networks by demonstrating that any of the compounds could be deleted from the training set and its value correctly predicted by the new network (average error = 19%). The second test involved the prediction of pharmacokinetic properties of compounds never seen by the network, and reasonable results were obtained for three out of four compounds tested. The results indicate neural networks can be a powerful tool in exploration of quantitative structure-pharmacokinetic relationships.

  4. Quantitative structure-activity relationships for nasal pungency thresholds of volatile organic compounds.

    PubMed

    Hau, K M; Connell, D W; Richardson, B J

    1999-01-01

    A model was developed for describing the triggering of nasal pungency in humans, based on the partition of volatile organic compounds (VOCs) between the air phase and the biophase. Two partition parameters are used in the model: the water-air partition coefficient and the octanol-water partition coefficient. The model was validated using data from the literature, principally on alcohols, acetates and ketones. The model suggests that all test compounds, regardless of their chemical functional groups, bind to a common receptor site within the hydrophobic interior of the bilayer membrane of the trigeminal nerve endings. There is probably only a slight, non-specific interaction between the VOC molecule and the receptor molecule, whereas this type of non-specific interaction for the detection of odor is much stronger. In practical terms, the suggestion that all VOCs share a common irritation receptor site implies that nasal-pungency thresholds of individual VOCs may be additive. Quantitative structure-activity relationships (QSARs) for nasal-pungency thresholds were also developed from the model, which can be used to predict nasal-pungency thresholds of common VOCs. Although the present model does not offer additional precision over that of M.H. Abraham et al., 1996, Fundam. Appl. Toxicol. 31, 71-76, it requires fewer descriptors and offers a physiological basis to the QSAR. Another advantage of the present model is that it also provides a basis for comparison between the olfactory process and nasal pungency.

  5. Quantitative structure-activity relationship study using refractotopological state atom index on some neonicotinoid insecticides.

    PubMed

    Debnath, Bikash; Gayen, Shovanlal; Basu, Anindya; Ghosh, Balaram; Srikanth, Kolluru; Jha, Tarun

    2004-12-01

    Importance of atom-level topological descriptors like electrotopological state atom (E-state) index in QSAR study is increasing. These descriptors help to relate structure and activity at atomic/fragmental level. In view of the earlier success of E-state index on some azidopyridinyl neonicotinoid insecticides, a relatively new atom-level topological descriptor; refractotopological state atom (R-state) index was used in this work. This was used to identify the important atoms/fragments related to dispersive/van der Waals interactions of neonicotinoids with the nicotinic acetylcholine receptor (nAChR). This study showed the structural requirements for the mammal alpha(4)beta(2) and Drosophila nAChR agonistic activity. It also revealed that substituted imine, nitromethylene at X-position were selective to the insecticidal activity. Azido substitution at pyridine ring of neonicotinoids disfavored the binding with the receptors. This study confirmed the validity of the R-state index as a new tool for quantitative structure-activity relationships. It has the ability to find out the required structural features as well as to predict the activity of the neonicotinoids.

  6. Quantitative structure carcinogenicity relationship for detecting structural alerts in nitroso-compounds

    SciTech Connect

    Helguera, Aliuska Morales; Gonzalez, Maykel Perez . E-mail: mpgonzalez76@yahoo.es; Cordeiro, Maria Natalia D.S.; Perez, Miguel Angel Cabrera

    2007-06-01

    Prevention of environmentally induced cancers is a major health problem of which solutions depend on the rapid and accurate screening of potential chemical hazards. Lately, theoretical approaches such as the one proposed here - Quantitative Structure-Activity Relationship (QSAR) - are increasingly used for assessing the risks of environmental chemicals, since they can markedly reduce costs, avoid animal testing, and speed up policy decisions. This paper reports a QSAR study based on the Topological Substructural Molecular Design (TOPS-MODE) approach, aiming at predicting the rodent carcinogenicity of a set of nitroso-compounds selected from the Carcinogenic Potency Data Base (CPDB). The set comprises nitrosoureas (14 chemicals), N-nitrosamines (18 chemicals) C-nitroso-compounds (1 chemical), nitrosourethane (1 chemical) and nitrosoguanidine (1 chemical), which have been bioassayed in male rat using gavage as the route of administration. Here we are especially concerned in gathering the role of both parameters on the carcinogenic activity of this family of compounds. First, the regression model was derived, upon removal of one identified nitrosamine outlier, and was able to account for more than 84% of the variance in the experimental activity. Second, the TOPS-MODE approach afforded the bond contributions - expressed as fragment contributions to the carcinogenic activity - that can be interpreted and provide tools for better understanding the mechanisms of carcinogenesis. Finally, and most importantly, we demonstrate the potentialities of this approach towards the recognition of structural alerts for carcinogenicity predictions.

  7. Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout

    NASA Astrophysics Data System (ADS)

    Mendenhall, Jeffrey; Meiler, Jens

    2016-02-01

    Dropout is an Artificial Neural Network (ANN) training technique that has been shown to improve ANN performance across canonical machine learning (ML) datasets. Quantitative Structure Activity Relationship (QSAR) datasets used to relate chemical structure to biological activity in Ligand-Based Computer-Aided Drug Discovery pose unique challenges for ML techniques, such as heavily biased dataset composition, and relatively large number of descriptors relative to the number of actives. To test the hypothesis that dropout also improves QSAR ANNs, we conduct a benchmark on nine large QSAR datasets. Use of dropout improved both enrichment false positive rate and log-scaled area under the receiver-operating characteristic curve (logAUC) by 22-46 % over conventional ANN implementations. Optimal dropout rates are found to be a function of the signal-to-noise ratio of the descriptor set, and relatively independent of the dataset. Dropout ANNs with 2D and 3D autocorrelation descriptors outperform conventional ANNs as well as optimized fingerprint similarity search methods.

  8. Application of quantitative structure activity relationship (QSAR) models to predict ozone toxicity in the lung.

    PubMed

    Kafoury, Ramzi M; Huang, Ming-Ju

    2005-08-01

    The sequence of events leading to ozone-induced airway inflammation is not well known. To elucidate the molecular and cellular events underlying ozone toxicity in the lung, we hypothesized that lipid ozonation products (LOPs) generated by the reaction of ozone with unsaturated fatty acids in the epithelial lining fluid and cell membranes play a key role in mediating ozone-induced airway inflammation. To test our hypothesis, we ozonized 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) and generated LOPs. Confluent human bronchial epithelial cells were exposed to the derivatives of ozonized POPC-9-oxononanoyl, 9-hydroxy-9-hydroperoxynonanoyl, and 8-(5-octyl-1,2,4-trioxolan-3-yl-)octanoyl-at a concentration of 10 muM, and the activity of phospholipases A2 (PLA2), C (PLC), and D (PLD) was measured (1, 0.5, and 1 h, respectively). Quantitative structure-activity relationship (QSAR) models were utilized to predict the biological activity of LOPs in airway epithelial cells. The QSAR results showed a strong correlation between experimental and computed activity (r = 0.97, 0.98, 0.99, for PLA2, PLC, and PLD, respectively). The results indicate that QSAR models can be utilized to predict the biological activity of the various ozone-derived LOP species in the lung.

  9. Quantitative Structure-Activity Relationships for the Nucleophilicity of Trivalent Boron Compounds.

    PubMed

    García-López, Diego; Cid, Jessica; Marqués, Ruben; Fernández, Elena; Carbó, Jorge J

    2017-04-11

    We describe herein the development of quantitative structure-activity relationships (QSAR) for the nucleophilicity of trivalent boron compounds covering boryl fragments bonded to alkali and alkaline-earth metals, to transition metals, and to sp(3) boron units in diboron reagents. We used the charge of the boryl fragment (q[B]) and the boron p/s population ratio (p/s) to describe the electronic structures of boryl moieties, whereas the distance-weighted volume (Vw ) descriptor was used to evaluate the steric effects. The three-term easy-to-interpret QSAR model showed statistical significance and predictive ability (r(2) =0.88, q(2) =0.83). The use of chemically meaningful descriptors has allowed identification of the factors governing the boron nucleophilicity and indicates that the most efficient nucleophiles are those with enhanced the polarization of the B-X bond towards the boron atom and reduced steric bulk. A detailed analysis of the potential energy surfaces of different types of boron substituents has provided insight into the mechanism and established an order of nucleophilicity for boron in B-X: X=Li>Cu>B(sp(3) )>Pd. Finally, we used the QSAR model to make a priori predictions of experimentally untested compounds.

  10. Docking and quantitative structure-activity relationship of oxadiazole derivates as inhibitors of GSK3β.

    PubMed

    Quesada-Romero, Luisa; Caballero, Julio

    2014-02-01

    The binding modes of 42 oxadiazole derivates inside glycogen synthase kinase 3 beta (GSK3β were determined using docking experiments; thus, the preferred active conformations of these inhibitors are proposed. We found that these compounds adopt a scorpion-shaped conformation and they accept a hydrogen bond (HB) from the residue Val135 of the GSK3β ATP-binding site hinge region. In addition, quantitative structure-activity relationship (QSAR) models were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. In a first approach, three-dimensional (3D) vectors were calculated using docking conformations and, by using multiple-linear regression, we assessed that GETAWAY vectors were able to describe the reported biological activities. In other QSAR approach, SMILES-based optimal descriptors were calculated. The best model included three-SMILES elements SSSβ leading to the identification of key molecular features that contribute to a high GSK3β inhibitory activity.

  11. The Relationship between Shyness and Internet Addiction: A Quantitative Study on Middle and Post Secondary School Students

    ERIC Educational Resources Information Center

    Hollingsworth, W. Craig

    2005-01-01

    This small scale quantitative study looks into the relationship between shyness and internet addiction in middle school students. This study has been conducted on the belief that shyness is a possible predictor of Internet Addiction. To prove this hypothesis a questionnaire was created and distributed to 53 middle school students and 159 post…

  12. Annealing and structural properties of composite films

    NASA Astrophysics Data System (ADS)

    Kotov, L. N.; Ustyugov, V. A.; Vlasov, V. S.; Turkov, V. K.; Dianov, M. Yu; Antonets, I. V.; Kalinin, Yu E.; Sitnikov, A. V.; Golubev, E. A.

    2017-02-01

    The composite films were investigated by AFM methods before and after annealing. Topographic and phase-contrast AFM images of the composite films at different annealing temperature were obtained. The separate metal granules and larger-scale labyrinth-like formations were described. These formations appear by the process of the film growth, also by film annealing. Strong changes of the structural properties of the films are observed after the percolation transition. The significant changes of the structural properties are connected with nanostructural transformations in the metal granules topology and presence of metal crystal phase.

  13. Quantitative Structure Activity Relationship Models for the Antioxidant Activity of Polysaccharides

    PubMed Central

    Nie, Kaiying; Wang, Zhaojing

    2016-01-01

    In this study, quantitative structure activity relationship (QSAR) models for the antioxidant activity of polysaccharides were developed with 50% effective concentration (EC50) as the dependent variable. To establish optimum QSAR models, multiple linear regressions (MLR), support vector machines (SVM) and artificial neural networks (ANN) were used, and 11 molecular descriptors were selected. The optimum QSAR model for predicting EC50 of DPPH-scavenging activity consisted of four major descriptors. MLR model gave EC50 = 0.033Ara-0.041GalA-0.03GlcA-0.025PC+0.484, and MLR fitted the training set with R = 0.807. ANN model gave the improvement of training set (R = 0.96, RMSE = 0.018) and test set (R = 0.933, RMSE = 0.055) which indicated that it was more accurately than SVM and MLR models for predicting the DPPH-scavenging activity of polysaccharides. 67 compounds were used for predicting EC50 of the hydroxyl radicals scavenging activity of polysaccharides. MLR model gave EC50 = 0.12PC+0.083Fuc+0.013Rha-0.02UA+0.372. A comparison of results from models indicated that ANN model (R = 0.944, RMSE = 0.119) was also the best one for predicting the hydroxyl radicals scavenging activity of polysaccharides. MLR and ANN models showed that Ara and GalA appeared critical in determining EC50 of DPPH-scavenging activity, and Fuc, Rha, uronic acid and protein content had a great effect on the hydroxyl radicals scavenging activity of polysaccharides. The antioxidant activity of polysaccharide usually was high in MW range of 4000–100000, and the antioxidant activity could be affected simultaneously by other polysaccharide properties, such as uronic acid and Ara. PMID:27685320

  14. Quantitative structure–activity relationship analysis of the pharmacology of para-substituted methcathinone analogues

    PubMed Central

    Bonano, J S; Banks, M L; Kolanos, R; Sakloth, F; Barnier, M L; Glennon, R A; Cozzi, N V; Partilla, J S; Baumann, M H; Negus, S S

    2015-01-01

    Background and Purpose Methcathinone (MCAT) is a potent monoamine releaser and parent compound to emerging drugs of abuse including mephedrone (4-CH3 MCAT), the para-methyl analogue of MCAT. This study examined quantitative structure–activity relationships (QSAR) for MCAT and six para-substituted MCAT analogues on (a) in vitro potency to promote monoamine release via dopamine and serotonin transporters (DAT and SERT, respectively), and (b) in vivo modulation of intracranial self-stimulation (ICSS), a behavioural procedure used to evaluate abuse potential. Neurochemical and behavioural effects were correlated with steric (Es), electronic (σp) and lipophilic (πp) parameters of the para substituents. Experimental Approach For neurochemical studies, drug effects on monoamine release through DAT and SERT were evaluated in rat brain synaptosomes. For behavioural studies, drug effects were tested in male Sprague-Dawley rats implanted with electrodes targeting the medial forebrain bundle and trained to lever-press for electrical brain stimulation. Key Results MCAT and all six para-substituted analogues increased monoamine release via DAT and SERT and dose- and time-dependently modulated ICSS. In vitro selectivity for DAT versus SERT correlated with in vivo efficacy to produce abuse-related ICSS facilitation. In addition, the Es values of the para substituents correlated with both selectivity for DAT versus SERT and magnitude of ICSS facilitation. Conclusions and Implications Selectivity for DAT versus SERT in vitro is a key determinant of abuse-related ICSS facilitation by these MCAT analogues, and steric aspects of the para substituent of the MCAT scaffold (indicated by Es) are key determinants of this selectivity. PMID:25438806

  15. Quantitative structure-activity relationships (QSARs) for estrogen binding to the estrogen receptor: predictions across species.

    PubMed Central

    Tong, W; Perkins, R; Strelitz, R; Collantes, E R; Keenan, S; Welsh, W J; Branham, W S; Sheehan, D M

    1997-01-01

    The recognition of adverse effects due to environmental endocrine disruptors in humans and wildlife has focused attention on the need for predictive tools to select the most likely estrogenic chemicals from a very large number of chemicals for subsequent screening and/or testing for potential environmental toxicity. A three-dimensional quantitative structure-activity relationship (QSAR) model using comparative molecular field analysis (CoMFA) was constructed based on relative binding affinity (RBA) data from an estrogen receptor (ER) binding assay using calf uterine cytosol. The model demonstrated significant correlation of the calculated steric and electrostatic fields with RBA and yielded predictions that agreed well with experimental values over the entire range of RBA values. Analysis of the CoMFA three-dimensional contour plots revealed a consistent picture of the structural features that are largely responsible for the observed variations in RBA. Importantly, we established a correlation between the predicted RBA values for calf ER and their actual RBA values for human ER. These findings suggest a means to begin to construct a more comprehensive estrogen knowledge base by combining RBA assay data from multiple species in 3D-QSAR based predictive models, which could then be used to screen untested chemicals for their potential to bind to the ER. Another QSAR model was developed based on classical physicochemical descriptors generated using the CODESSA (Comprehensive Descriptors for Structural and Statistical Analysis) program. The predictive ability of the CoMFA model was superior to the corresponding CODESSA model. Images Figure 2. Figure 3. Figure 4. Figure 5. PMID:9353176

  16. Construction of a quantitative structure-permeability relationship (QSPR) for the transdermal delivery of NSAIDs.

    PubMed

    Liou, Yi-Bo; Ho, Hsiu-O; Yang, Chun-Jen; Lin, Ying-Ku; Sheu, Ming-Thau

    2009-09-15

    In this study, an empirical model of the quantitative structure-permeability relationship (QSPR) of the transdermal delivery of non-steroidal anti-inflammatory drugs (NSAIDs) was constructed in an attempt to predict the permeability coefficients (k(P)). Thirteen model NSAIDs were selected, and their in vitro permeation through the full skin of nude mice was examined. The biological parameters of transepidermal water loss (TEWL), hydration content (HD), lipid content (SB), resonance running time (RVM), and elasticity (EL) were measured. The permeability coefficients so obtained were grouped into three datasets of all model drugs and those drugs with clogP or logK(o/w) values of >2 and <2; these datasets were regressed with respect to the physical characters of molecular weight (MW) and polarity factor (clogP or logK(o/w)) or the solubility parameter (delta) of the model drugs rationally chosen to replace the polarity factor with or without taking into consideration the biological parameters of the skin. Results demonstrated that delta could be greatly improved compared to clogP and logK(o/w) in the regression with an adjusted R(2) of >0.90 using the dataset of those drugs with clogP or logK(o/w) values of <2, regardless of whether or not biological parameters were taken into consideration. This indicates that delta might rationally be a more-appropriate drug parameter for predicting the skin permeability of NSAIDs for transdermal delivery. A plot of observed k(P) versus predicted k(P) values by this simple empirical model of QSPR was validated to demonstrate the predictive capability of k(P) for transdermal delivery. In conclusion, an empirical model of QSPR to predict k(P) based on the hydrophilicity of the model drugs was statistically improved with delta and by taking the biological parameters of the skin into consideration.

  17. Validation of Quantitative Structure-Activity Relationship (QSAR) Model for Photosensitizer Activity Prediction

    PubMed Central

    Frimayanti, Neni; Yam, Mun Li; Lee, Hong Boon; Othman, Rozana; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.

    2011-01-01

    Photodynamic therapy is a relatively new treatment method for cancer which utilizes a combination of oxygen, a photosensitizer and light to generate reactive singlet oxygen that eradicates tumors via direct cell-killing, vasculature damage and engagement of the immune system. Most of photosensitizers that are in clinical and pre-clinical assessments, or those that are already approved for clinical use, are mainly based on cyclic tetrapyrroles. In an attempt to discover new effective photosensitizers, we report the use of the quantitative structure-activity relationship (QSAR) method to develop a model that could correlate the structural features of cyclic tetrapyrrole-based compounds with their photodynamic therapy (PDT) activity. In this study, a set of 36 porphyrin derivatives was used in the model development where 24 of these compounds were in the training set and the remaining 12 compounds were in the test set. The development of the QSAR model involved the use of the multiple linear regression analysis (MLRA) method. Based on the method, r2 value, r2 (CV) value and r2 prediction value of 0.87, 0.71 and 0.70 were obtained. The QSAR model was also employed to predict the experimental compounds in an external test set. This external test set comprises 20 porphyrin-based compounds with experimental IC50 values ranging from 0.39 μM to 7.04 μM. Thus the model showed good correlative and predictive ability, with a predictive correlation coefficient (r2 prediction for external test set) of 0.52. The developed QSAR model was used to discover some compounds as new lead photosensitizers from this external test set. PMID:22272096

  18. Quantitative structure-activity relationship of the curcumin-related compounds using various regression methods

    NASA Astrophysics Data System (ADS)

    Khazaei, Ardeshir; Sarmasti, Negin; Seyf, Jaber Yousefi

    2016-03-01

    Quantitative structure activity relationship were used to study a series of curcumin-related compounds with inhibitory effect on prostate cancer PC-3 cells, pancreas cancer Panc-1 cells, and colon cancer HT-29 cells. Sphere exclusion method was used to split data set in two categories of train and test set. Multiple linear regression, principal component regression and partial least squares were used as the regression methods. In other hand, to investigate the effect of feature selection methods, stepwise, Genetic algorithm, and simulated annealing were used. In two cases (PC-3 cells and Panc-1 cells), the best models were generated by a combination of multiple linear regression and stepwise (PC-3 cells: r2 = 0.86, q2 = 0.82, pred_r2 = 0.93, and r2m (test) = 0.43, Panc-1 cells: r2 = 0.85, q2 = 0.80, pred_r2 = 0.71, and r2m (test) = 0.68). For the HT-29 cells, principal component regression with stepwise (r2 = 0.69, q2 = 0.62, pred_r2 = 0.54, and r2m (test) = 0.41) is the best method. The QSAR study reveals descriptors which have crucial role in the inhibitory property of curcumin-like compounds. 6ChainCount, T_C_C_1, and T_O_O_7 are the most important descriptors that have the greatest effect. With a specific end goal to design and optimization of novel efficient curcumin-related compounds it is useful to introduce heteroatoms such as nitrogen, oxygen, and sulfur atoms in the chemical structure (reduce the contribution of T_C_C_1 descriptor) and increase the contribution of 6ChainCount and T_O_O_7 descriptors. Models can be useful in the better design of some novel curcumin-related compounds that can be used in the treatment of prostate, pancreas, and colon cancers.

  19. Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors

    NASA Astrophysics Data System (ADS)

    Oprea, Tudor I.; García, Angel E.

    1996-06-01

    Inhibition of aromatase, a cytochrome P450 that converts androgens to estrogens, is relevant in the therapeutic control of breast cancer. We investigate this inhibition using a three-dimensional quantitative structure-activity relationship (3D QSAR) method known as Comparative Molecular Field Analysis, CoMFA [Cramer III, R.D. et al., J. Am. Chem. Soc., 110 (1988) 5959]. We analyzed the data for 50 steroid inhibitors [Numazawa, M. et al., J. Med. Chem., 37 (1994) 2198, and references cited therein] assayed against androstenedione on human placental microsomes. An initial CoMFA resulted in a three-component model for log(1/Ki), with an explained variance r2 of 0.885, and a cross-validated q2 of 0.673. Chemometric studies were performed using GOLPE [Baroni, M. et al., Quant. Struct.-Act. Relatsh., 12 (1993) 9]. The CoMFA/GOLPE model is discussed in terms of robustness, predictivity, explanatory power and simplicity. After randomized exclusion of 25 or 10 compounds (repeated 25 times), the q2 for one component was 0.62 and 0.61, respectively, while r2 was 0.674. We demonstrate that the predictive r2 based on the mean activity (Ym) of the training set is misleading, while the test set Ym-based predictive r2 index gives a more accurate estimate of external predictivity. Using CoMFA, the observed differences in aromatase inhibition among C6-substituted steroids are rationalized at the atomic level. The CoMFA fields are consistent with known, potent inhibitors of aromatase, not included in the model. When positioned in the same alignment, these compounds have distinct features that overlap with the steric and electrostatic fields obtained in the CoMFA model. The presence of two hydrophobic binding pockets near the aromatase active site is discussed: a steric bulk tolerant one, common for C4, C6-alpha and C7-alpha substitutents, and a smaller one at the C6-beta region.

  20. Ranking of hair dye substances according to predicted sensitization potency: quantitative structure-activity relationships.

    PubMed

    Søsted, H; Basketter, D A; Estrada, E; Johansen, J D; Patlewicz, G Y

    2004-01-01

    Allergic contact dermatitis following the use of hair dyes is well known. Many chemicals are used in hair dyes and it is unlikely that all cases of hair dye allergy can be diagnosed by means of patch testing with p-phenylenediamine (PPD). The objectives of this study are to identify all hair dye substances registered in Europe and to provide their tonnage data. The sensitization potential of each substance was then estimated by using a quantitative structure-activity relationship (QSAR) model and the substances were ranked according to their predicted potency. A cluster analysis was performed in order to help select a number of chemically diverse hair dye substances that could be used in subsequent clinical work. Various information sources, including the Inventory of Cosmetics Ingredients, new regulations on cosmetics, data on total use and ChemId (the Chemical Search Input website provided by the National Library of Medicine), were used in order to identify the names and structures of the hair dyes. A QSAR model, developed with the help of experimental local lymph node assay data and topological sub-structural molecular descriptors (TOPS-MODE), was used in order to predict the likely sensitization potential. Predictions for sensitization potential were made for the 229 substances that could be identified by means of a chemical structure, the majority of these hair dyes (75%) being predicted to be strong/moderate sensitizers. Only 22% were predicted to be weak sensitizers and 3% were predicted to be extremely weak or non-sensitizing. Eight of the most widely used hair dye substances were predicted to be strong/moderate sensitizers, including PPD - which is the most commonly used hair dye allergy marker in patch testing. A cluster analysis by using TOPS-MODE descriptors as inputs helped us group the hair dye substances according to their chemical similarity. This would facilitate the selection of potential substances for clinical patch testing. A patch-test series

  1. The relationship between international trade and non-nutritional health outcomes: A systematic review of quantitative studies.

    PubMed

    Burns, Darren K; Jones, Andrew P; Suhrcke, Marc

    2016-03-01

    Markets throughout the world have been reducing barriers to international trade and investment in recent years. The resulting increases in levels of international trade and investment have subsequently generated research interest into the potential population health impact. We present a systematic review of quantitative studies investigating the relationship between international trade, foreign direct investment and non-nutritional health outcomes. Articles were systematically collected from the SCOPUS, PubMed, EconLit and Web of Science databases. Due to the heterogeneous nature of the evidence considered, the 16 included articles were subdivided into individual level data analyses, selected country analyses and international panel analyses. Articles were then quality assessed using a tool developed as part of the project. Nine of the studies were assessed to be high quality, six as medium quality, and one as low quality. The evidence from the quantitative literature suggests that overall, there appears to be a beneficial association between international trade and population health. There was also evidence of the importance of foreign direct investment, yet a lack of research considering the direction of causality. Taken together, quantitative research into the relationship between trade and non-nutritional health indicates trade to be beneficial, yet this body of research is still in its infancy. Future quantitative studies based on this foundation will provide a stronger basis on which to inform relevant national and international institutions about the health consequences of trade policies.

  2. Finite Element Estimation of Meteorite Structural Properties

    NASA Technical Reports Server (NTRS)

    Hart, Kenneth Arthur

    2015-01-01

    The goal of the project titled Asteroid Threat Assessment at NASA Ames Research Center is to develop risk assessment tools. The expertise in atmospheric entry in the Entry Systems and Technology Division is being used to describe the complex physics of meteor breakup in the atmosphere. The breakup of a meteor is dependent on its structural properties, including homogeneity of the material. The present work describes an 11-week effort in which a literature survey was carried for structural properties of meteoritic material. In addition, the effect of scale on homogeneity isotropy was studied using a Monte Carlo approach in Nastran. The properties were then in a static structural response simulation of an irregularly-shape meteor (138-scale version of Asteroid Itokawa). Finally, an early plan was developed for doctoral research work at Georgia Tech. in the structural failure fragmentation of meteors.

  3. Determinants of Long Bone Structural Properties

    NASA Technical Reports Server (NTRS)

    Cleek, T. M.; Katz, B.; Whalen, R. T.; Wade, Charles E. (Technical Monitor)

    1994-01-01

    The objective of our research is to determine whether a non-invasive determination of long bone cross-sectional areal properties using only the mineral component of bone accurately predicts the true structural properties. In this study section properties of a whole long bone were compared using two methods: (1) special analysis of bone densitometry data, and (2) experimental determination of flexural rigidities from bone surface strain measurements during controlled loading.

  4. Quantitative structure-activity relationship (QSAR) study of a series of benzimidazole derivatives as inhibitors of Saccharomyces cerevisiae.

    PubMed

    Podunavac-Kuzmanović, Sonja O; Cvetković, Dragoljub D; Jevrić, Lidija R; Uzelac, Natasa J

    2013-01-01

    A quantitative structure activity relationship (QSAR) has been carried out on a series of benzimidazole derivatives to identify the structural requirements for their inhibitory activity against yeast Saccharomyces cerevisiae. A multiple linear regression (MLR) procedure was used to model the relationships between various physicochemical, steric, electronic, and structural molecular descriptors and antifungal activity of benzimidazole derivatives. The QSAR expressions were generated using a training set of 16 compounds and the predictive ability of the resulting models was evaluated against a test set of 8 compounds. The best QSAR models were further validated by leave one out technique as well as by the calculation of statistical parameters for the established theoretical models. Therefore, satisfactory relationships between antifungal activity and molecular descriptors were found. QSAR analysis reveals that lipophilicity descriptor (logP), dipole moment (DM) and surface area grid (SAG) govern the inhibitory activity of compounds studied against Saccharomyces cerevisiae.

  5. The determination of toxicities of sulphonylurea and phenylurea herbicides with quantitative structure-toxicity relationship (QSTR) studies.

    PubMed

    Can, Alper; Yildiz, Ilkay; Guvendik, Gulin

    2013-05-01

    Sulphonylurea and phenylurea herbicides are two groups of herbicides that are most commonly used worldwide. Quantitative structure-toxicity relationship models were derived for estimating the acute oral toxicity of these herbicides to male rats. The 20 chemicals of the training set and the seven compounds of external testing set were described by means of using descriptors for lipophilicity, polarity and molecular geometry, as well as the calculation of quantum chemical descriptors for energy. Model development to predict the toxicity of sulphonylurea and phenylurea herbicides in different matrices was carried out using multiple-linear regression. The model was validated internally and externally. In the present study, QSTR model was used for the first time to understand the inherent relationships between the sulphonyl and phenylurea-type herbicide molecules and their toxic behaviour. Such studies provide mechanistic insight about structure-toxicity relationships and assist in the design of less toxic herbicides.

  6. Parent-Caregiver Relationships among Beginning Caregivers in Canada: A Quantitative Study

    ERIC Educational Resources Information Center

    Cantin, Gilles; Plante, Isabelle; Coutu, Sylvain; Brunson, Liesette

    2012-01-01

    Despite the importance of establishing meaningful parent-caregiver relationships, little is known about these dyadic relationships among beginning caregivers, who often feel insufficiently prepared to build successful alliances with parents. The present study examined the congruence between parents' and beginning caregivers' perceptions of their…

  7. Quantitative Evaluation of a First Year Seminar Program: Relationships to Persistence and Academic Success

    ERIC Educational Resources Information Center

    Jenkins-Guarnieri, Michael A.; Horne, Melissa M.; Wallis, Aaron L.; Rings, Jeffrey A.; Vaughan, Angela L.

    2015-01-01

    In the present study, we conducted a quantitative evaluation of a novel First Year Seminar (FYS) program with a coordinated curriculum implemented at a public, four-year university to assess its potential role in undergraduate student persistence decisions and academic success. Participants were 2,188 first-year students, 342 of whom completed the…

  8. Quantitative relationship between sputter-deposited-MoS2 properties and underlying-SiO2 surface roughness

    NASA Astrophysics Data System (ADS)

    Ohashi, Takumi; Muneta, Iriya; Matsuura, Kentaro; Ishihara, Seiya; Hibino, Yusuke; Sawamoto, Naomi; Kakushima, Kuniyuki; Tsutsui, Kazuo; Ogura, Atsushi; Wakabayashi, Hitoshi

    2017-04-01

    Substrate roughness affects the physical and electrical properties of deposited layered materials. However, the quantitative relationship is unknown. In this work, a quantitative analysis of sputter-deposited MoS2 films on an SiO2 substrate was conducted. Flattening the substrate helped realize an MoS2 structure closer to the ideal honeycomb structure and a Hall mobility of ∼26 cm2/(V·s) and a carrier density of ∼1016 cm‑3 (less than that of exfoliated MoS2 by 104). These results stress the necessity of considering even roughness of the order of angstroms to improve the physical and electrical properties of atomically layered functional devices.

  9. Synthesis and Structure - Property Relationships for Regular Multigraft Copolymers

    SciTech Connect

    Mays, Jimmy; Uhrig, David; Gido, Samuel; Zhu, Yuqing; Weidisch, Roland; Iatrou, Hermis; Hadjichristidis, Nikos; Hong, Kunlun; Beyer, Frederick; Lach, Ralph

    2004-01-01

    Multigraft copolymers with polyisoprene backbones and polystyrene branches, having multiple regularly spaced branch points, were synthesized by anionic polymerization high vacuum techniques and controlled chlorosilane linking chemistry. The functionality of the branch points (1, 2 and 4) can be controlled, through the choice of chlorosilane linking agent. The morphologies of the various graft copolymers were investigated by transmission electron microscopy and X-ray scattering. It was concluded that the morphology of these complex architectures is governed by the behavior of the corresponding miktoarm star copolymer associated with each branch point (constituting block copolymer), which follows Milner's theoretical treatment for miktoarm stars. By comparing samples having the same molecular weight backbone and branches but different number of branches it was found that the extent of long range order decreases with increasing number of branch points. The stress-strain properties in tension were investigated for some of these multigraft copolymers. For certain compositions thermoplastic elastomer (TPE) behavior was observed, and in many instances the elongation at break was much higher (2-3X) than that of conventional triblock TPEs.

  10. Structure-Property Relationships in Polycyanurate / Graphene Networks

    DTIC Science & Technology

    2015-12-12

    Motivation • Sequentially Prepared Graphene Types • Polycyanurate / GO Composite Preparation • Composite Morphology • Composite Mechanical and Physical...improved performance in the example applications shown above. 5Distribution A – Approved for public release; distribution is unlimited. GO and TRGO...distribution is unlimited. Sequential Preparation of GO and TRGO • Graphene oxide ( GO ) prepared by Hummers method of oxidation of XG Sciences® xGNP-M-25

  11. Miscibility and structure-property relationships in some novel polyolefins

    NASA Astrophysics Data System (ADS)

    Kamdar, Akshay Rajprakash

    In the first chapter, miscibility of homogeneous propylene/ethylene (P/E) copolymers of relatively narrow molecular weight distribution was studied as a function of constituent comonomer content. Polymers with up to 31 mol% ethylene were blended in pairs in order to vary the comonomer content difference. Copolymers of molecular weight about 200 kg mol-1 were miscible if the difference in ethylene content was less than about 18 mol%, and immiscible if the ethylene content difference was greater than about 20 mol%. Blends with constituent composition difference in the range of 18-20 mol% exhibited partial miscibility in the melt. In the second chapter, the effect of chain microstructure on the miscibility and phase behavior of ethylene-octene (EO) copolymer blends was studied. Binary blends of two statistical copolymers (EO/EO blends) that differed in comonomer content were compared with blends of an EO with an olefinic blocky ethylene-octene copolymer, OBC (EO/OBC blends). Two EOs of molecular weight about 100 kg/mol were miscible if the difference in octene content was less than about 10 mol% and immiscible if the octene content difference was greater than about 13 mol%. The blocky nature of the OBCs reduced the miscibility and broadened the partial miscibility window of EO/OBC blends compared to EO/EO blends. The EO/OBC blends were miscible if the octene content difference was less than 7 mol% and immiscible above 13 mol% octene content difference. In the third chapter, the adhesion of some ethylene-octene copolymers to polypropylene (PP) and high density polyethylene (HDPE) was studied in order to evaluate their suitability as compatibilizers for PP/HDPE blends. A one-dimensional model of the compatibilized blend was fabricated by layer-multiplying coextrusion. The microlayered tapes consisted of many alternating layers of PP and HDPE with a thin tie-layer inserted at each interface. The thickness of the tie-layer varied from 0.1 to 14 mum, which included thicknesses comparable to those of the interfacial layer in a compatibilized blend. A blocky copolymer (OBC) consistently exhibited better adhesion to PP than statistical copolymers (EO). Inspection of the crack-tip damage zone revealed a change from a continuous plastic damage zone in tie-layers 2 mum or thicker to a highly fibrillated damage zone in thinner tie-layers.

  12. Cement-aggregate compatibility and structure property relationships including modelling

    SciTech Connect

    Jennings, H.M.; Xi, Y.

    1993-07-15

    The role of aggregate, and its interface with cement paste, is discussed with a view toward establishing models that relate structure to properties. Both short (nm) and long (mm) range structure must be considered. The short range structure of the interface depends not only on the physical distribution of the various phases, but also on moisture content and reactivity of aggregate. Changes that occur on drying, i.e. shrinkage, may alter the structure which, in turn, feeds back to alter further drying and shrinkage. The interaction is dynamic, even without further hydration of cement paste, and the dynamic characteristic must be considered in order to fully understand and model its contribution to properties. Microstructure and properties are two subjects which have been pursued somewhat separately. This review discusses both disciplines with a view toward finding common research goals in the future. Finally, comment is made on possible chemical reactions which may occur between aggregate and cement paste.

  13. Structure-Property Relationship in Metal Carbides and Bimetallic Alloys

    SciTech Connect

    Chen, Jingguan

    2014-03-04

    The primary objective of our DOE/BES sponsored research is to use carbide and bimetallic catalysts as model systems to demonstrate the feasibility of tuning the catalytic activity, selectivity and stability. Our efforts involve three parallel approaches, with the aim at studying single crystal model surfaces and bridging the “materials gap” and “pressure gap” between fundamental surface science studies and real world catalysis. The utilization of the three parallel approaches has led to the discovery of many intriguing catalytic properties of carbide and bimetallic surfaces and catalysts. During the past funding period we have utilized these combined research approaches to explore the possibility of predicting and verifying bimetallic and carbide combinations with enhanced catalytic activity, selectivity and stability.

  14. Structure-Property Relationships in Oxides Containing Tellurium

    NASA Astrophysics Data System (ADS)

    Siritanon, Theeranun

    Oxides of post-transition metals often show unique structures and properties due to the presence of lone pair electrons and the diffused s orbitals. The present work focuses on synthesis and characterizations of oxides containing Te, a heavy post transition metal. New series of pyrochlore oxides of the formula Cs(M,Te)2O 6 (M = Al, Ga, Cr, Fe, Co, In, Ho, Lu, Yb, Er, Ge, Rh, Ti, Zn, Ni, and Mg) have been prepared. The samples were highly colored (ranging from black to dark green) indicating a possible mixed valency for Te with appreciable charge transfer between them in the octahedral sites. Electronic conductivity was observed in some phases and could be as high as 2S/cm (M=Ge). Seebeck coefficients of conducting samples show negative values which suggest that electrons are the major charge carriers. Temperature dependence of conductivity indicates that the samples are semiconductors with, in some cases, degenerate semiconducting behavior. Detailed studies on the conduction mechanism indicate the mixed valency of tellurium which leads to semiconducting behavior and the color of the compounds. Systematic studies of cesium tellurate with CsTe2O6-x where x = 0, 0.15, 0.25, 1.5 have been investigated. On heating at slightly above 600ºC, CsTe2O6 loses oxygen resulting in cubic structure with disordered Te4+/Te6+ and oxygen vacancies. Two novel phases of CsTe2O6-x were prepared with orthorhombic structure. The first phase with x value of about 0.2-0.3 crystallizes in Pnma symmetry. At higher values of x, a new compound was discovered with a structure related to Rb4Te 8O23. Optical properties of the compounds are consistent with their colors. CsTe2O6 belongs to class II mixed valency according to Robin and Day classification. However, structures and properties of CsTe 2O6-x phases indicate that they are class I mixed valence compounds. Series of compounds with formula CsTe2-xWxO 6 with x=0.2-0.5 have been made which can be considered as solid solution of CsTe2O6 and CsTe0.5W1.5O 6. Although the two end members adopt rhombohedral and trigonal structure, these solid solution phases crystallize in cubic defect pyrochlore structure with W6+, Te6+, and Te4+ randomly occupying 16c octahedral site. The compounds show no electronic conductivity at room temperature. Novel cubic pyrochlore with the formula (CdBi)(MTe)O7, M= Al, Cr, Ga, In, Fe, Mn, and Sc were synthesized by solid state reaction using oxides of the constituent elements. Magnetic properties analyses show paramagnetism in M=Cr and Mn but antiferromagnetism with short-range correlation in M= Fe phase. All compositions are insulating. Dielectric measurements show relatively low dielectric constants which are independent of temperature and frequency. Metallic Tl2TeO6 and insulating In2TeO 6 are both known to crystallize in the Na2SiF6-type structure. We have now prepared a complete Tl2-xInxTeO6 series in a search for a compositionally controlled metal-insulator transition that might be expected if a complete solid solution can be obtained. Unit cell edges and volume vary monotonically with no indication of miscibility gap. The metal-insulator transition occurs at an x value of about 1.4, which can be rationalized on a percolation model. No superconductivity could be detected down to 5K. Rh2MO6, M = Mo, W, and Te were synthesized by solid state reaction. Electronic properties as well as thermoelectric properties were investigated and discussed. The compounds crystallize in rutile-related structure and all show relatively high electronic conductivities with Rh 2TeO6 showing the highest electronic conductivity (˜500 S/cm at room temperature) despite localized electrons in Rh3+ and Te6+. Measurable magnetic moments also indicate valence degeneracy between Rh and the M cation. The measured Seebeck coefficients are relatively low and positive indicating hole-type conduction.

  15. Structure-Property Relationships for Branched Worm-Like Micelles

    NASA Astrophysics Data System (ADS)

    Beaucage, Gregory; Rai, Durgesh

    2013-03-01

    Micellar solutions can display a wide range of phase structure as a function of counter ion content, surfactant concentration, and the presence of ternary components. Under some conditions, common to consumer products, extended cylindrical structures that display persistence and other chain features of polymers are produced. These worm-like micelles (WLMs) can form branched structures that dynamically change under shear and even in quiescent conditions. The rheology of these branched WLMs is strongly dependent on migration of the branch points, and the dynamics of branch formation and removal. Persistence and other polymer-based descriptions are also of importance. We have recently developed a scattering model for branched polyolefins and other topologically complex materials that can quantify the branching density, branch length, branch functionality and the hyperbranch (branch-on-branch) content of polymers. This work is being extended to study branching in WLMs in work coupled with Ron Larson at UMich to predict rheological properties.

  16. Uncovering structure-property relationships of materials by subgroup discovery

    NASA Astrophysics Data System (ADS)

    Goldsmith, Bryan R.; Boley, Mario; Vreeken, Jilles; Scheffler, Matthias; Ghiringhelli, Luca M.

    2017-01-01

    Subgroup discovery (SGD) is presented here as a data-mining approach to help find interpretable local patterns, correlations, and descriptors of a target property in materials-science data. Specifically, we will be concerned with data generated by density-functional theory calculations. At first, we demonstrate that SGD can identify physically meaningful models that classify the crystal structures of 82 octet binary (OB) semiconductors as either rocksalt or zincblende. SGD identifies an interpretable two-dimensional model derived from only the atomic radii of valence s and p orbitals that properly classifies the crystal structures for 79 of the 82 OB semiconductors. The SGD framework is subsequently applied to 24 400 configurations of neutral gas-phase gold clusters with 5–14 atoms to discern general patterns between geometrical and physicochemical properties. For example, SGD helps find that van der Waals interactions within gold clusters are linearly correlated with their radius of gyration and are weaker for planar clusters than for nonplanar clusters. Also, a descriptor that predicts a local linear correlation between the chemical hardness and the cluster isomer stability is found for the even-sized gold clusters.

  17. Structure-Property Relationships of Steel Cylindrical Shells

    DTIC Science & Technology

    2012-03-01

    hoop tensile specimens in the pipe’s transverse orienta- tion. The ERDC machine shop prepared the test specimens using a water - jet cutting system...polishing procedure. Abrasive Lubricant Time (min) Step 1 60-grit silicon carbide distilled water until plane Step 2 120-grit silicon carbide...using the procedure outlined in Table 1. Between each polishing step, sonication using distilled water cleaned the specimens. Table 1. Details of

  18. Structure-Property Relationships in Polyolefin Block Copolymers

    NASA Astrophysics Data System (ADS)

    Mansour, Ameara Salah

    Poly(cyclohexylethylene) (PCHE for a homopolymer or C in a block copolymer) is created by hydrogenating polystyrene, and this polymer exhibits interesting properties, such as a high glass transition temperature (147 °C), high flexural modulus (2.8 GPa), low stress optical coefficient (-0.2 * 10-9 Pa-1), and low cost. However, the inherently brittle nature of PCHE prevents it from being used in applications that simultaneously require high modulus, ductility, thermal stability, and optical clarity. Previous research has shown that incorporating PCHE into a block copolymer with rubbery poly(ethylene-alt-propylene) (P) or poly(ethylethylene) (EE) or semicrystalline polyethylene (E) results in a tough material. In some cases, applications also require specific mechanical or optical properties. In order to tune these properties, this research examined tuning crystallinity using two methods: (1) by controlling the microstructure of the soft block by synthesizing a random copolymer of E and EE, and (2) by blending high C content pentablock copolymers with semicrystalline and rubbery minority components. In the first study, diblock copolymers of C(EcoEE) also were used to understand how the microstructure of the random copolymer affects the thermodynamics of the system. In the second study, CECEC and CPCPC, designed to form the same morphology (hexagonally packed cylinders with glassy C matrices), and have similar order-to-disorder transition temperatures and domain spacings, were blended together. Isothermal crystallization experiments were used to determine how the confining E and P in one domain affects the crystallization process. The effect of architecture, the state of the minority component, and the percent crystallinity on the mechanical properties of high glass content materials was also examined. These results were compared to the mechanical properties of homopolymer PCHE, polystyrene, and polycarbonate. The processing conditions needed to create smooth films of CECEC with a high fraction of C, which could be used in optical experiments, were determined.

  19. Structure Property Relationships in Imidazole-based Deep Eutectic Mixtures

    NASA Astrophysics Data System (ADS)

    Terheggen, Logan; Cosby, Tyler; Sangoro, Joshua

    2015-03-01

    Deep eutectic mixtures of levulinic acid with a systematic series of imidazoles are measured by broadband dielectric spectroscopy, differential scanning calorimetry, and Fourier transform infrared spectroscopy to investigate the impact of steric interactions on charge transport and structural dynamics. An enhancement of dc conductivity is found in each of the imidazoles upon the addition of levulinic acid. However, the extent of increase is dependent upon the alkyl substitution on the imidazole ring. These results highlight the importance of molecular structure on hydrogen bonding and charge transport in deep eutectic mixtures.

  20. Processing-structure-properties relationships in PLA nanocomposite films

    NASA Astrophysics Data System (ADS)

    Di Maio, L.; Scarfato, P.; Garofalo, E.; Galdi, M. R.; D'Arienzo, L.; Incarnato, L.

    2014-05-01

    This work deals on the possibility to improve performances of PLA-based nanocomposite films, for packaging applications, through conveniently tuning materials and processing conditions in melt compounding technology. In particular, two types of polylactic acid and different types of filler selected from montmorillonites and bentonites families were used to prepare the hybrid systems by using a twin-screw extruder. The effect of biaxial drawing on morphology and properties of the nanocomposites, produced by film blowing, was investigated.

  1. Structure-property relationships and biocompatibility of carbohydrate crosslinked polyurethanes.

    PubMed

    Solanki, Archana; Mehta, Jayen; Thakore, Sonal

    2014-09-22

    Biocompatible and biodegradable polyurethanes (PUs) based on castor oil and polypropylene glycols (PPGs) were prepared using various carbohydrate crosslinkers: monosaccharide (glucose), disaccharide (sucrose) and polysaccharides (starch and cellulose). The mechanical and thermal properties were investigated and interpreted on the basis of SEM study. The advantage of incorporating various carbohydrates is to have tunable mechanical properties and biodegradability due to variety in their structure. The glass transition temperature and sorption behavior were dominated by the type of polyol than by the type of crosslinker. All the PUs were observed to be biodegradable as well as non-cytotoxic as revealed by MTT assay in normal lung cell line L132. The study supports the suitability of carbohydrates as important components of biocompatible PUs for development of biomedical devices.

  2. Structure-property-processing relationships in Kevlar fibers

    SciTech Connect

    Lacks, D.J.

    1996-12-31

    Molecular simulations are carried out to elucidate the differences in the properties of the commercial fibers Kevlar 29, Kevlar 49 and Kevlar 149, which are manufactured under different processing conditions, and are composed of poly(p-phenylene teraphthalamide) (PPTA). In going from Kevlar 29 to Kevlar 49 to Kevlar 149, the axial Young`s modulus increases significantly and the torsion modulus decreases significantly, while the compressive strength stays roughly the same. Previous investigators have shown that the increase in the Young`s modulus arises from increased axial orientation. The present paper addresses the torsion modulus and compressive strength of the fibers.

  3. Structure-Property Relationships of Architectural Coatings by Neutron Methods

    NASA Astrophysics Data System (ADS)

    Nakatani, Alan

    2015-03-01

    Architectural coatings formulations are multi-component mixtures containing latex polymer binder, pigment, rheology modifiers, surfactants, and colorants. In order to achieve the desired flow properties for these formulations, measures of the underlying structure of the components as a function of shear rate and the impact of formulation variables on the structure is necessary. We have conducted detailed measurements to understand the evolution under shear of local microstructure and larger scale mesostructure in model architectural coatings formulations by small angle neutron scattering (SANS) and ultra small angle neutron scattering (USANS), respectively. The SANS results show an adsorbed layer of rheology modifier molecules exist on the surface of the latex particles. However, the additional hydrodynamic volume occupied by the adsorbed surface layer is insufficient to account for the observed viscosity by standard hard sphere suspension models (Krieger-Dougherty). The USANS results show the presence of latex aggregates, which are fractal in nature. These fractal aggregates are the primary structures responsible for coatings formulation viscosity. Based on these results, a new model for the viscosity of coatings formulations has been developed, which is capable of reproducing the observed viscosity behavior.

  4. THREE-DIMENSIONAL QUANTITATIVE STRUCTURE-PROPERTY RELATIONSHIP (3D-QSPR) MODELS FOR PREDICTION OF THERMODYNAMIC PROPERTIES OF POLYCHLORINATED BIPHENYLS (PCBS): ENTHALPIES OF FUSION AND THEIR APPLICATION TO ESTIMATES OF ENTHALPIES OF SUBLIMATION AND AQUEOUS SOLUBILITIES. (R826133)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  5. NASA Intellectual Property Negotiation Practices and their Relationship to Quantitative Measures of Technology Transfer

    NASA Technical Reports Server (NTRS)

    Bush, Lance B.

    1997-01-01

    In the current political climate NASA must be able to show reliable measures demonstrating successful technology transfer. The currently available quantitative data of intellectual property technology transfer efforts portray a less than successful performance. In this paper, the use of only quantitative values for measurement of technology transfer is shown to undervalue the effort. In addition, NASA's current policy in negotiating intellectual property rights results in undervalued royalty rates. NASA has maintained that it's position of providing public good precludes it from negotiating fair market value for its technology and instead has negotiated for reasonable cost in order to recover processing fees. This measurement issue is examined and recommendations made which include a new policy regarding the intellectual property rights negotiation, and two measures to supplement the intellectual property measures.

  6. Quantitative structure-activity relationship modeling of polycyclic aromatic hydrocarbon mutagenicity by classification methods based on holistic theoretical molecular descriptors.

    PubMed

    Gramatica, Paola; Papa, Ester; Marrocchi, Assunta; Minuti, Lucio; Taticchi, Aldo

    2007-03-01

    Various polycyclic aromatic hydrocarbons (PAHs), ubiquitous environmental pollutants, are recognized mutagens and carcinogens. A homogeneous set of mutagenicity data (TA98 and TA100,+S9) for 32 benzocyclopentaphenanthrenes/chrysenes was modeled by the quantitative structure-activity relationship classification methods k-nearest neighbor and classification and regression tree, using theoretical holistic molecular descriptors. Genetic algorithm provided the selection of the best subset of variables for modeling mutagenicity. The models were validated by leave-one-out and leave-50%-out approaches and have good performance, with sensitivity and specificity ranges of 90-100%. Mutagenicity assessment for these PAHs requires only a few theoretical descriptors of their molecular structure.

  7. Adiposity is associated with structural properties of the adolescent brain.

    PubMed

    Schwartz, Deborah H; Dickie, Erin; Pangelinan, Melissa M; Leonard, Gabriel; Perron, Michel; Pike, G Bruce; Richer, Louis; Veillette, Suzanne; Pausova, Zdenka; Paus, Tomáš

    2014-12-01

    Obesity, a major risk factor for cardiometabolic disease, is associated with variations in a number of structural properties in the adult brain, as assessed with magnetic resonance imaging (MRI). In this study, we investigated the cross-sectional relationship between visceral fat (VF), total body fat (TBF) and three MRI parameters in the brains of typically developing adolescents: (i) T1-weighted (T1W) signal intensity; (ii) T1W signal contrast between white matter (WM) and gray matter (GM); and (iii) magnetization transfer ratio (MTR). In a community-based sample of 970 adolescents (12-18 years old, 466 males), VF was quantified using MRI, and total body fat was measured using a multifrequency bioimpedance. T1W images of the brain were used to determine signal intensity in lobar GM and WM, as well as WM:GM signal contrast. A magnetization transfer (MT) sequence of MT(ON) and MT(OFF) was used to obtain MTR in GM and WM. We found that both larger volumes of VF and more TBF were independently associated with higher signal intensity in WM and higher WM:GM signal contrast, as well as higher MTR in both GM and WM. These relationships were independent of a number of potential confounders, including age, sex, puberty stage, household income and height. Our results suggest that both visceral fat and fat deposited elsewhere in the body are associated independently with structural properties of the adolescent brain. We speculate that these relationships suggest the presence of adiposity-related variations in phospholipid composition of brain lipids.

  8. Structural properties of small rhodium clusters

    SciTech Connect

    Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    We report a systematic study of the structural properties of rhodium clusters at the atomistic level. A novel global-minimum search algorithm, known as parallel tempering multicanonical basin hopping plus genetic algorithm (PTMBHGA), is used to obtain the geometrical structures with lowest minima at the semi-empirical level where Gupta potential is used to describe the atomic interaction among the rhodium atoms. These structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA). The structures are optimized for different spin multiplicities. The ones with lowest energies will be taken as ground-state structures. In most cases, we observe only minor changes in the geometry and bond length of the clusters as a result of DFT-level re-optimization. Only in some limited cases, the initial geometries obtained from the PTMBHGA are modified by the re-optimization. The variation of structural properties, such as ground-state geometry, symmetry and binding energy, with respect to the cluster size is studied and agreed well with other results available in the literature.

  9. Structural properties of autoclaved aerated concrete masonry

    SciTech Connect

    Matthys, J.H.; Nelson, R.L.

    1999-07-01

    Autoclaved aerated concrete masonry units are manufactured from portland cement, quartz sand, water, lime, gypsum and a gas forming agent. The units are steam cured under pressure in an autoclave transforming the material into a hard calcium silicate. The autoclaved aerated concrete masonry units are large-size solid rectangular prisms which are laid using thin-bed mortar layers into masonry assemblages. The system and product are not new--patented in 1924 by Swedish architect Johan Eriksson. Over a period of 60 years this product has been used in all areas of residential and industrial construction and in virtually all climates. However, the principal locations of application have been generally outside the US Little information in the US is available on the structural properties of this product. Due to the interest in use of this product in the construction industry and the construction of production plants in the US, the Construction Research Center at the University of Texas at Arlington and Robert L. Nelson & Associates conducted a series of tests to determine some of the basic structural properties of this product. This paper presents the findings of those investigations.

  10. Love 2.0: a quantitative exploration of sex and relationships in the virtual world Second Life.

    PubMed

    Craft, Ashley John

    2012-08-01

    This study presents the quantitative results of a web-based survey exploring the experiences of those who seek sex and relationships in the virtual world of Second Life. The survey gathered data on demographics, relationships, and sexual behaviors from 235 Second Life residents to compare with U.S. General Social Survey data on Internet users and the general population. The Second Life survey also gathered data on interests in and experiences with a number of sexual practices in both offline and online environments. Comparative analysis found that survey participants were significantly older, more educated, and less religious than a wider group of Internet users, and in certain age groups were far less likely to be married or have children. Motivations for engaging in cybersex were presented. Analysis of interest and experience of different sexual practices supported findings by other researchers that online environments facilitated access, but also indicated that interest in certain sexual practices could differ between offline and online environments.

  11. Structure-guided unravelling: Phenolic hydroxyls contribute to reduction of acrylamide using multiplex quantitative structure-activity relationship modelling.

    PubMed

    Zhang, Yu; Huang, Mengmeng; Wang, Qiao; Cheng, Jun

    2016-05-15

    We reported a structure-activity relationship study on unravelling phenolic hydroxyls instead of alcoholic hydroxyls contribute to the reduction of acrylamide formation by flavonoids. The dose-dependent study shows a close correlation between the number of phenolic hydroxyls of flavonoids and their reduction effects. In view of positions of hydroxyls, the 3',4'(ortho)-dihydroxyls in B cycle, 3-hydroxyl or hydroxyls of 3-gallate in C cycle, and 5,7(meta)-dihydroxyls in A cycle of flavonoid structures play an important role in the reduction of acrylamide. Flavone C-glycosides are more effective at reducing the formation of acrylamide than flavone O-glycosides when sharing the same aglycone. The current multiplex quantitative structure-activity relationship (QSAR) equations effectively predict the inhibitory rates of acrylamide using selected chemometric parameters (R(2): 0.835-0.938). This pioneer study opens a broad understanding on the chemoprevention of acrylamide contaminants on a structural basis.

  12. Benzimidazole-Based Quinazolines: In Vitro Evaluation, Quantitative Structure-Activity Relationship, and Molecular Modeling as Aurora Kinase Inhibitors.

    PubMed

    Sharma, Alka; Luxami, Vijay; Saxena, Sanjai; Paul, Kamaldeep

    2016-03-01

    A series of benzimidazole-based quinazoline derivatives with different substitutions of primary and secondary amines at the C2 position (1-12) were evaluated for their Aurora kinase inhibitory activities. All compounds except for 3 and 6 showed good activity against Aurora kinase inhibitors, with IC50 values in the range of 0.035-0.532 μM. The ligand efficiency (LE) of the compounds with Aurora A kinase was also determined. The structure-activity relationship and the quantitative structure-activity relationship revealed that the Aurora inhibitory activities of these derivatives primarily depend on the different substitutions of the amine present at the C2 position of the quinazoline core. Molecular docking studies in the active binding site also provided theoretical support for the experimental biological data acquired. The current study identifies a novel class of Aurora kinase inhibitors, which can further be used for the treatment of cancer.

  13. A Quantitative Review of the Relationship between Person-Organization Fit and Behavioral Outcomes

    ERIC Educational Resources Information Center

    Hoffman, Brian J.; Woehr, David J.

    2006-01-01

    This paper extends the meta-analysis of Verquer, Beehr, and Wagner by providing a meta-analytic review of the relationship between person-organization fit (PO fit) and behavioral criteria (job performance, organizational citizenship behaviors, and turnover). Results indicate that PO fit is weakly to moderately related to each of these outcome…

  14. The Relationship of Employee Status to Organizational Culture and Organizational Effectiveness: A Quantitative Analysis

    ERIC Educational Resources Information Center

    Deem, Jackie W.; DeLotell, Pam J.; Kelly, Kathryn

    2015-01-01

    Purpose: This study investigates the relationship between employment status (full time (FT)/part time (PT)), organizational culture and institutional effectiveness in higher education. The purpose of this paper is to answer the question, "Does the growing population of PT faculty preclude effective cultures from developing and, accordingly,…

  15. Uncertainties have a Meaning: Quantitative Interpretation of the Relationship between Subsurface Flow and Geological Data Quality

    NASA Astrophysics Data System (ADS)

    Wellmann, J.; Regenauer-Lieb, K.; Western Australian Geothermal Centre of Excellence

    2011-12-01

    We present a new method to assess system-based measures to classify uncertainties in geological models and in subsurface flow fields. Information entropy is proposed to evaluate uncertainties in geological models, and thermal entropy production is proposed to analyze uncertainties related to hydrothermal flow. As these measures have a fundamental theoretical basis and are related to the internal state of the system, they can be interpreted quantitatively and, consequently, give uncertainties a meaning. Information entropy values are directly related to the state of uncertainty of a geological model. For a point within the model, information entropy is a measure of the minimum number of geological units that could occur at its location. If the information entropy is zero, only one unit is possible and no uncertainty exists. If the value is greater than zero, at least two units are probable. If it increases above 1, three units can occur. In general the measure provides a weight of probabiliy for different states. A strong point of the method is that it gives an entropy measure for the state of the entire model and therefore lends itself as a robust measure to quantitatively compare uncertainties in difference models. In a similar sense, the thermal entropy production provides a quantitative measure of the thermodynamic state of a hydrothermal system. When the entropy production is zero, the system must be in a conductive steady state for a closed system. If the entropy production is larger than zero, the system can be in a convective or transient conductive state. For higher values of entropy production, the convective units show higher complexities and, hence, uncertainty of the hydrothermal field increases. Moreover, the average model entropy production gives a measure of the convective vigour that can be expected in the system. This is directly related to the efficiency of heat transfer over the system. The measure is therefore not only useful for a

  16. Qualitative and quantitative structure-activity relationship modelling for predicting blood-brain barrier permeability of structurally diverse chemicals.

    PubMed

    Gupta, S; Basant, N; Singh, K P

    2015-01-01

    In this study, structure-activity relationship (SAR) models have been established for qualitative and quantitative prediction of the blood-brain barrier (BBB) permeability of chemicals. The structural diversity of the chemicals and nonlinear structure in the data were tested. The predictive and generalization ability of the developed SAR models were tested through internal and external validation procedures. In complete data, the QSAR models rendered ternary classification accuracy of >98.15%, while the quantitative SAR models yielded correlation (r(2)) of >0.926 between the measured and the predicted BBB permeability values with the mean squared error (MSE) <0.045. The proposed models were also applied to an external new in vitro data and yielded classification accuracy of >82.7% and r(2) > 0.905 (MSE < 0.019). The sensitivity analysis revealed that topological polar surface area (TPSA) has the highest effect in qualitative and quantitative models for predicting the BBB permeability of chemicals. Moreover, these models showed predictive performance superior to those reported earlier in the literature. This demonstrates the appropriateness of the developed SAR models to reliably predict the BBB permeability of new chemicals, which can be used for initial screening of the molecules in the drug development process.

  17. Quantitative structure-activity relationship modeling of antioxidant activities of hydroxybenzalacetones using quantum chemical, physicochemical and spatial descriptors.

    PubMed

    Mitra, Indrani; Saha, Achintya; Roy, Kunal

    2009-05-01

    We have modeled antioxidant activities of hydroxybenzalacetones against lipid peroxidation induced by t-butyl hydroperoxide (pC1), gamma-irradiation (pC2) and also their 1,1-diphenyl-2-picryl hydrazyl (DPPH) free radical scavenging activity (pC3) using quantitative structure-activity relationship technique. The quantitative structure-activity relationship models were developed using different statistical methods like stepwise multiple linear regression, genetic function approximation and genetic partial least squares with descriptors of different categories (quantum chemical, physicochemical, spatial and substituent constants). The models were validated by internal validation and randomization techniques. The model predictivity was judged on the basis of their cross-validated squared correlation coefficient (Q2) and modified r2 (r m 2) values. The best models for the two responses, pC1 and pC2, were obtained by genetic partial least squares technique while the best model for the third response, pC3, was obtained by genetic function approximation technique. The developed models suggest that the distribution of charges on the phenolic nucleus and the phenolic oxygen as well as the charged surface areas of the molecules together with the geometry and orientation of the substituents significantly influence all the three types of responses (pC1, pC2 and pC3). The developed models may be used to design hydroxybenzalacetones with better antioxidant activities.

  18. Quantitative structure-activity relationship analysis of acute toxicity of diverse chemicals to Daphnia magna with whole molecule descriptors.

    PubMed

    Moosus, M; Maran, U

    2011-10-01

    Quantitative structure-activity relationship analysis and estimation of toxicological effects at lower-mid trophic levels provide first aid means to understand the toxicity of chemicals. Daphnia magna serves as a good starting point for such toxicity studies and is also recognized for regulatory use in estimating the risk of chemicals. The ECOTOX database was queried and analysed for available data and a homogenous subset of 253 compounds for the endpoint LC50 48 h was established. A four-parameter quantitative structure-activity relationship was derived (coefficient of determination, r (2) = 0.740) for half of the compounds and internally validated (leave-one-out cross-validated coefficient of determination, [Formula: see text] = 0.714; leave-many-out coefficient of determination, [Formula: see text] = 0.738). External validation was carried out with the remaining half of the compounds (coefficient of determination for external validation, [Formula: see text] = 0.634). Two of the descriptors in the model (log P, average bonding information content) capture the structural characteristics describing penetration through bio-membranes. Another two descriptors (energy of highest occupied molecular orbital, weighted partial negative surface area) capture the electronic structural characteristics describing the interaction between the chemical and its hypothetic target in the cell. The applicability domain was subsequently analysed and discussed.

  19. Research of dose-effect relationship parameters of percutaneous microwave ablation for uterine leiomyomas - a quantitative study

    PubMed Central

    Xia, Ma; Jing, Zhang; Zhi-yu, Han; Yu, Yang; Yan-li, Hao; Chang-tao, Xu; Rui-fang, Xu; Bing-song, Zhang; Bao-wei, Dong

    2014-01-01

    Eighty eight patients with 91 uterine leiomyomas who underwent ultrasound-guided percutaneous microwave ablation (PMWA) treatment were prospectively included in the study in order to study the dose-effect relationship parameters (DERP) of PMWA for uterine leiomyomas and its relationship with T2-weighted MR imaging (T2WI). Based on the signal intensity of T2WI, uterine leiomyomas were classified as hypointense, isointense, and hyperintense. During ablation, leiomyomas were treated with quantitative microwave ablation (QMWA) energy of 50 w × 300 s or 60 w × 300 s. After QMWA, contrast-enhanced ultrasound (CEUS) was performed to evaluate DERP. No matter under 50 w × 300 s or 60 w × 300 s, quantitative microwave ablation volume (QMAV) of hyperintense leiomyoma was smaller than that of hypointense and isointense leiomyoma (P<0.016). For hypointense and isointense leiomyoma, QMAV of 60 w × 300 s was larger than that of 50 w × 300 s (P<0.05). DERPs obtained by T2WI can be used to guide the treatment of uterine leiomyoma by PMWA. PMID:25267154

  20. The emotional coaching model: quantitative and qualitative research into relationships, communication and decisions in physical and sports rehabilitation.

    PubMed

    Respizzi, Stefano; Covelli, Elisabetta

    2015-01-01

    The emotional coaching model uses quantitative and qualitative elements to demonstrate some assumptions relevant to new methods of treatment in physical rehabilitation, considering emotional, cognitive and behavioral aspects in patients, whether or not they are sportsmen. Through quantitative tools (Tampa Kinesiophobia Scale, Emotional Interview Test, Previous Re-Injury Test, and reports on test scores) and qualitative tools (training contracts and relationships of emotional alliance or "contagion"), we investigate initial assumptions regarding: the presence of a cognitive and emotional mental state of impasse in patients at the beginning of the rehabilitation pathway; the curative value of the emotional alliance or "emotional contagion" relationship between healthcare provider and patient; the link between the patient's pathology and type of contact with his own body and emotions; analysis of the psychosocial variables for the prediction of possible cases of re-injury for patients who have undergone or are afraid to undergo reconstruction of the anterior cruciate ligament (ACL). Although this approach is still in the experimental stage, the scores of the administered tests show the possibility of integrating quantitative and qualitative tools to investigate and develop a patient's physical, mental and emotional resources during the course of his rehabilitation. Furthermore, it seems possible to identify many elements characterizing patients likely to undergo episodes of re-injury or to withdraw totally from sporting activity. In particular, such patients are competitive athletes, who fear or have previously undergone ACL reconstruction. The theories referred to (the transactional analysis theory, self-determination theory) and the tools used demonstrate the usefulness of continuing this research in order to build a shared coaching model treatment aimed at all patients, sportspeople or otherwise, which is not only physical but also emotional, cognitive and

  1. The emotional coaching model: quantitative and qualitative research into relationships, communication and decisions in physical and sports rehabilitation

    PubMed Central

    RESPIZZI, STEFANO; COVELLI, ELISABETTA

    2015-01-01

    The emotional coaching model uses quantitative and qualitative elements to demonstrate some assumptions relevant to new methods of treatment in physical rehabilitation, considering emotional, cognitive and behavioral aspects in patients, whether or not they are sportsmen. Through quantitative tools (Tampa Kinesiophobia Scale, Emotional Interview Test, Previous Re-Injury Test, and reports on test scores) and qualitative tools (training contracts and relationships of emotional alliance or “contagion”), we investigate initial assumptions regarding: the presence of a cognitive and emotional mental state of impasse in patients at the beginning of the rehabilitation pathway; the curative value of the emotional alliance or “emotional contagion” relationship between healthcare provider and patient; the link between the patient’s pathology and type of contact with his own body and emotions; analysis of the psychosocial variables for the prediction of possible cases of re-injury for patients who have undergone or are afraid to undergo reconstruction of the anterior cruciate ligament (ACL). Although this approach is still in the experimental stage, the scores of the administered tests show the possibility of integrating quantitative and qualitative tools to investigate and develop a patient’s physical, mental and emotional resources during the course of his rehabilitation. Furthermore, it seems possible to identify many elements characterizing patients likely to undergo episodes of re-injury or to withdraw totally from sporting activity. In particular, such patients are competitive athletes, who fear or have previously undergone ACL reconstruction. The theories referred to (the transactional analysis theory, self-determination theory) and the tools used demonstrate the usefulness of continuing this research in order to build a shared coaching model treatment aimed at all patients, sportspeople or otherwise, which is not only physical but also emotional, cognitive

  2. A NON-LINEAR STRUCTURE-PROPERTY MODEL FOR OCTANOL-WATER PARTITION COEFFICIENT.

    PubMed

    Yerramsetty, Krishna M; Neely, Brian J; Gasem, Khaled A M

    2012-10-25

    Octanol-water partition coefficient (K(ow)) is an important thermodynamic property used to characterize the partitioning of solutes between an aqueous and organic phase and has importance in such areas as pharmacology, pharmacokinetics, pharmacodynamics, chemical production and environmental toxicology. We present a non-linear quantitative structure-property relationship model for determining K(ow) values of new molecules in silico. A total of 823 descriptors were generated for 11,308 molecules whose K(ow) values are reported in the PhysProp dataset by Syracuse Research. Optimum network architecture and its associated inputs were identified using a wrapper-based feature selection algorithm that combines differential evolution and artificial neural networks. A network architecture of 50-33-35-1 resulted in the least root-mean squared error (RMSE) in the training set. Further, to improve on single-network predictions, a neural network ensemble was developed by combining five networks that have the same architecture and inputs but differ in layer weights. The ensemble predicted the K(ow) values with RMSE of 0.28 and 0.38 for the training set and internal validation set, respectively. The ensemble performed reasonably well on an external dataset when compared with other popular K(ow) models in the literature.

  3. Dynamically hot galaxies. I - Structural properties

    NASA Technical Reports Server (NTRS)

    Bender, Ralf; Burstein, David; Faber, S. M.

    1992-01-01

    Results are reported from an analysis of the structural properties of dynamically hot galaxies which combines central velocity dispersion, effective surface brightness, and effective radius into a new 3-space (k), in which the axes are parameters that are physically meaningful. Hot galaxies are found to divide into groups in k-space that closely parallel conventional morphological classifications, namely, luminous ellipticals, compacts, bulges, bright dwarfs, and dwarf spheroidals. A major sequence is defined by luminous ellipticals, bulges, and most compacts, which together constitute a smooth continuum in k-space. Several properties vary smoothly with mass along this continuum, including bulge-to-disk ratio, radio properties, rotation, degree of velocity anisotropy, and 'unrelaxed'. A second major sequence is comprised of dwarf ellipticals and dwarf spheroidals. It is suggested that mass loss is a major factor in hot dwarf galaxies, but the dwarf sequence cannot be simply a mass-loss sequence, as it has the wrong direction in k-space.

  4. A Quantitative Relationship between Signal Detection in Attention and Approach/Avoidance Behavior.

    PubMed

    Viswanathan, Vijay; Sheppard, John P; Kim, Byoung W; Plantz, Christopher L; Ying, Hao; Lee, Myung J; Raman, Kalyan; Mulhern, Frank J; Block, Martin P; Calder, Bobby; Lee, Sang; Mortensen, Dale T; Blood, Anne J; Breiter, Hans C

    2017-01-01

    This study examines how the domains of reward and attention, which are often studied as independent processes, in fact interact at a systems level. We operationalize divided attention with a continuous performance task and variables from signal detection theory (SDT), and reward/aversion with a keypress task measuring approach/avoidance in the framework of relative preference theory (RPT). Independent experiments with the same subjects showed a significant association between one SDT and two RPT variables, visualized as a three-dimensional structure. Holding one of these three variables constant, further showed a significant relationship between a loss aversion-like metric from the approach/avoidance task, and the response bias observed during the divided attention task. These results indicate that a more liberal response bias under signal detection (i.e., a higher tolerance for noise, resulting in a greater proportion of false alarms) is associated with higher "loss aversion." Furthermore, our functional model suggests a mechanism for processing constraints with divided attention and reward/aversion. Together, our results argue for a systematic relationship between divided attention and reward/aversion processing in humans.

  5. A Quantitative Relationship between Signal Detection in Attention and Approach/Avoidance Behavior

    PubMed Central

    Viswanathan, Vijay; Sheppard, John P.; Kim, Byoung W.; Plantz, Christopher L.; Ying, Hao; Lee, Myung J.; Raman, Kalyan; Mulhern, Frank J.; Block, Martin P.; Calder, Bobby; Lee, Sang; Mortensen, Dale T.; Blood, Anne J.; Breiter, Hans C.

    2017-01-01

    This study examines how the domains of reward and attention, which are often studied as independent processes, in fact interact at a systems level. We operationalize divided attention with a continuous performance task and variables from signal detection theory (SDT), and reward/aversion with a keypress task measuring approach/avoidance in the framework of relative preference theory (RPT). Independent experiments with the same subjects showed a significant association between one SDT and two RPT variables, visualized as a three-dimensional structure. Holding one of these three variables constant, further showed a significant relationship between a loss aversion-like metric from the approach/avoidance task, and the response bias observed during the divided attention task. These results indicate that a more liberal response bias under signal detection (i.e., a higher tolerance for noise, resulting in a greater proportion of false alarms) is associated with higher “loss aversion.” Furthermore, our functional model suggests a mechanism for processing constraints with divided attention and reward/aversion. Together, our results argue for a systematic relationship between divided attention and reward/aversion processing in humans. PMID:28270776

  6. A quantitative study of subsurface cisterns and their relationships in normal and axotomized hypoglossal neurones.

    PubMed

    Sumner, B E

    1975-01-01

    A quantitative ultrastructural survey was made of subsurface cisterns and their association with overlying structures in the left hypoglossal nucleus of normal rats, and rats which had received left hypoglossal axotomies 7-84 days previously. Subsurface cisterns in normal rats occurred in some hypoglossal neurones, and, sporadically, in proximal dendrites. They were mostly subsynaptic, and often associated with Nissl substance; From 7-14 days postoperatively, when many somatic boutons temporarily lost contact with the perikaryal surface, and were replaced by a microglial sheath, the percentage of perikaryon with underlying cistern was significantly reduced. The Nissl substance was also dispersed at this stage, and not restored until 28 days postoperatively. At 21 days normal percentages of subsurface cistern were restored, but the cisterns were now mostly subastrocytic, an astrocytic sheath having replaced the microglial sheath. From 63 days onwards the cisterns were mostly subsynaptic again as boutons returned to the regenerating perikarya and the temporary astrocytic sheath disappeared. It is suggested that subsurface cisterns might alter the overlying perikaryal surface in some way during neuronal regeneration, causing certain boutons to adhere there.

  7. Relationship between Quantitative CT Metrics and Health Status and Bode in COPD

    PubMed Central

    Martinez, Carlos H.; Chen, Ya-Hong; Westgate, Phillip M.; Liu, Lyrica X.; Murray, Susan; Curtis, Jeffrey L.; Make, Barry J.; Kazerooni, Ella A.; Lynch, David A.; Marchetti, Nathaniel; Washko, George R.; Martinez, Fernando J.; Han, MeiLan K.

    2013-01-01

    Background The value of quantitative computed tomography (QCT) to identify chronic obstructive pulmonary disease (COPD) phenotypes is increasingly appreciated. We hypothesized that QCT-defined emphysema and airway abnormalities relate to St. George's Respiratory Questionnaire (SGRQ) and BODE. Methods 1,200 COPDGene subjects meeting GOLD criteria for COPD with QCT analysis were included. Total lung emphysema was measured using density mask technique with a -950 HU threshold. An automated program measured mean wall thickness (WT), wall area percent (WA%) and pi10 in six segmental bronchi. Separate multivariate analyses examined the relative influence of airway measures and emphysema on SGRQ and BODE. Results In separate models predicting SGRQ score, a one unit standard deviation (SD) increase in each airway measure predicted higher SGRQ scores (for WT, 1.90 points higher, p=0.002; for WA%, 1.52 points higher, p=0.02; for pi10, 2.83 points higher p<0.001). The comparable increase in SGRQ for a one unit SD increase in percent emphysema in these models was relatively weaker, significant only in the pi10 model (for percent emphysema, 1.45 points higher, p=0.01). In separate models predicting BODE, a one unit SD increase in each airway measure predicted higher BODE scores (for WT, 1.07 fold increase, p<0.001; for WA%, 1.20 fold increase, p<0.001; for pi10, 1.16 fold increase, p<0.001). In these models, emphysema more strongly influenced BODE (range 1.24-1.26 fold increase, p<0.001). Conclusion Emphysema and airway disease both relate to clinically important parameters. The relative influence of airway disease is greater for SGRQ; the relative influence of emphysema is greater for BODE. PMID:22514236

  8. Structural properties of Alumnum nitride compound

    NASA Astrophysics Data System (ADS)

    Mohammad, R.; Katırcıoğlu, Ş.

    2014-10-01

    Structural properties of Alumnum nitride in wurtzite, zinc-blende and rock-salt phases have been investigated by Full Potential-Linearized Augmented Plane Waves method based on Density Functional Theory within Local Density Approximation and seven Generalized Gradient schemes. It is found that, Alumnum nitride in wurtzite phase is the stable ground state structure and makes a transition to rock-salt phase at a low transition pressure (11.54 GPa). According to present total energy calculations, zinc-blende phase of Alumnum nitride also makes a transition to rock-salt phase, at a low transition pressure (10.17 GPa). Generalized Gradient functionals of Perdew-Wang-Engel-Vosko and Perdew-Burke-Ernzerhof are found to be more successful than other approximations considered in this work for providing the closest values of the structural features, such as, lattice constants, bulk moduli, first order pressure derivatives of bulk moduli and cohesive energies of Alumnum nitride three phases to available experimental ones. Although Generalized Gradient approaches of Perdew-Wang-Engel-Vosko, Perdew-Burke-Ernzerhof, Becke-Perdew-Wang and Perdew-Burke-Ernzerhof (revised) are found to be accurate schemes for elastic constants of rock-salt AlN, only Perdew-Wang-Engel-Vosko and Perdew-Burke-Ernzerhof functionals are observed to be more successful than the other schemes for supplying accurately both C_{11} and C_{12} of zinc-blende Alumnum nitride structure. Perdew-Wang-Engel-Vosko functional is observed to be superior to Perdew-Burke-Ernzerhof for elastic constants of wurtzite Alumnum nitride structure. Elastic constants of wurtzite Alumnum nitride obtained by self Perdew-Wang-Engel-Vosko approach and Martin's transformation calculations in which elastic constants of zinc-blende Alumnum nitride are calculated with Perdew-Wang-Engel-Vosko scheme, are very close to the experimental ones. Hence, functional of Perdew-Wang-Engel-Vosko is decided to be the most accurate approximation

  9. Semisynthesis and quantitative structure-activity relationship (QSAR) study of some cholesterol-based hydrazone derivatives as insecticidal agents.

    PubMed

    Yang, Chun; Shao, Yonghua; Zhi, Xiaoyan; Huan, Qu; Yu, Xiang; Yao, Xiaojun; Xu, Hui

    2013-09-01

    In continuation of our program aimed at the discovery and development of natural-product-based insecticidal agents, four series of novel cholesterol-based hydrazone derivatives were synthesized, and their insecticidal activity was tested against the pre-third-instar larvae of oriental armyworm, Mythimna separata (Walker) in vivo at 1mg/mL. All the derivatives showed the better insecticidal activity than their precursor cholesterol. Quantitative structure-activity relationship (QSAR) model demonstrated that six descriptors such as RDF085v, Mor06u, Mor11u, Dv, HATS0v and H-046, are likely to influence the insecticidal activity of these compounds. Among them, two important ones are the Mor06u and RDF085v.

  10. In Vitro Photodynamic Therapy and Quantitative Structure–Activity Relationship Studies with Stable Synthetic Near-Infrared-Absorbing Bacteriochlorin Photosensitizers

    PubMed Central

    Huang, Ying-Ying; Mroz, Pawel; Zhiyentayev, Timur; Sharma, Sulbha K.; Balasubramanian, Thiagarajan; Ruzié, Christian; Krayer, Michael; Fan, Dazhong; Borbas, K. Eszter; Yang, Eunkyung; Kee, Hooi Ling; Kirmaier, Christine; Diers, James R.; Bocian, David F.; Holten, Dewey; Lindsey, Jonathan S.; Hamblin, Michael R.

    2010-01-01

    Photodynamic therapy (PDT) is a rapidly developing approach to treating cancer that combines harmless visible and near-infrared light with a nontoxic photoactivatable dye, which upon encounter with molecular oxygen generates the reactive oxygen species that are toxic to cancer cells. Bacteriochlorins are tetrapyrrole compounds with two reduced pyrrole rings in the macrocycle. These molecules are characterized by strong absorption features from 700 to >800 nm, which enable deep penetration into tissue. This report describes testing of 12 new stable synthetic bacteriochlorins for PDT activity. The 12 compounds possess a variety of peripheral substituents and are very potent in killing cancer cells in vitro after illumination. Quantitative structure–activity relationships were derived, and subcellular localization was determined. The most active compounds have both low dark toxicity and high phototoxicity. This combination together with near-infrared absorption gives these bacteriochlorins great potential as photosensitizers for treatment of cancer. PMID:20441223

  11. Quantitative structure-activity relationship studies of a series of sulfa drugs as inhibitors of Pneumocystis carinii dihydropteroate synthetase.

    PubMed

    Johnson, T; Khan, I A; Avery, M A; Grant, J; Meshnick, S R

    1998-06-01

    Sulfone and sulfanilamide sulfa drugs have been shown to inhibit dihydropteroate synthetase (DHPS) isolated from Pneumocystis carinii. In order to develop a pharmacophoric model for this inhibition, quantitative structure-activity relationships (QSAR) for sulfa drugs active against DHPS have been studied. Accurate 50% inhibitory concentrations were collected for 44 analogs, and other parameters, such as partition coefficients and molar refractivity, were calculated. Conventional multiple regression analysis of these data did not provide acceptable QSAR. However, three-dimensional QSAR provided by comparative molecular field analysis did give excellent results. Upon removal of poorly correlated analogs, a data set of 36 analogs, all having a common NHSO2 group, provided a cross-validated r2 value of 0.699 and conventional r2 value of 0.964. The resulting pharmacophore model should be useful for understanding and predicting the binding of DHPS by new sulfa drugs.

  12. Quantitative morphology of the placenta. III. The growth of the placenta and its relationship to birth weight.

    PubMed

    Bouw, G M; Stolte, L A; Baak, J P; Oort, J

    1978-04-01

    The relationship of placental components to birth weight was investigated by stereology. 37 placentas from nonpathological pregnancies delivered after a period of 224-303 days of amenorrhea were examined. The umbilical cord was clamped immediately after birth. The ratios of the volume, the surface, the length of the villous vessels and the surface of the villi with birth weight showed a decrease after 277 days of amenorrhea. In contrast to this decrease, the ratio of the volume of the trophoblast with birth weight seems to increase. No difference could be found for the ratios of the placental volume (placental index), the volume of the villous tissue, the volume of the intervillous space and the volume of the nonfunctional tissue with birth weight. These ratios reveal a quantitative morphological base for the clinical experience that postmature fetuses are at a higher risk through deterioration of the placenta.

  13. [A new SVRDF 3D-descriptor of amino acids and its application to peptide quantitative structure activity relationship].

    PubMed

    Tong, Jian-Bo; Zhang, Sheng-Wan; Cheng, Su-Li; Li, Gai-Xian

    2007-01-01

    To establish a new amino acid structure descriptor that can be applied to polypeptide quantitative structure activity relationship (QSAR) studies, a new descriptor, SVRDF, was derived from a principal components analysis of a matrix of 150 radial distribution function index of amino acids. The scale was then applied in three panels of peptide QSAR that were molded by partial least squares regression. The obtained models with the correlation coefficients (R2(cum)), cross-validation correlation coefficients (Q2(cum)) were 0.766 and 0.724 for 48 bitter tasting dipeptides; 0.941 and 0.811 for 21 oxytocin analogues; 0.996 and 0.919 for 20 thromboplastin inhibitors. Satisfactory results showed that information related to biological activity can be systemically expressed by SVRDF scales, which may be an useful structural expression methodology for the study of peptides QSAR.

  14. Non-linear quantitative structure-activity relationship for adenine derivatives as competitive inhibitors of adenosine deaminase

    SciTech Connect

    Sadat Hayatshahi, Sayyed Hamed; Khajeh, Khosro

    2005-12-16

    Logistic regression and artificial neural networks have been developed as two non-linear models to establish quantitative structure-activity relationships between structural descriptors and biochemical activity of adenosine based competitive inhibitors, toward adenosine deaminase. The training set included 24 compounds with known k {sub i} values. The models were trained to solve two-class problems. Unlike the previous work in which multiple linear regression was used, the highest of positive charge on the molecules was recognized to be in close relation with their inhibition activity, while the electric charge on atom N1 of adenosine was found to be a poor descriptor. Consequently, the previously developed equation was improved and the newly formed one could predict the class of 91.66% of compounds correctly. Also optimized 2-3-1 and 3-4-1 neural networks could increase this rate to 95.83%.

  15. A quantitative structure-activity relationship study on a few series of anti-hepatitis C virus agents.

    PubMed

    Varshney, Jonish; Sharma, Anjana; Gupta, Satya P

    2012-05-01

    A 2-Dimensional Quantitative Structure-Activity Relationship study has been performed on 2 series of hepatitis C virus (HCV) inhibitors, i.e., Isothiazoles and Thiazolones. In each case significant correlations are found between the anti-HCV potencies and some physicochemical, electronic and steric properties of the compounds, indicating that for the first series the activity is controlled by density and two indicator parameters (one for halogen and other for methyl), while for the second series density, Hammett constant and Kier's first order valence molecular connectivity index are important for anti-HCV activity. The validity of the correlation has been judged by leave-one-out jackknife procedure and predicting the activity of some test compounds. Using the correlations obtained, some new compounds of high potency have been predicted in each series.

  16. Chromanyl-isoxazolidines as Antibacterial agents: Synthesis, Biological Evaluation, Quantitative Structure Activity Relationship, and Molecular Docking Studies.

    PubMed

    Singh, Gagandeep; Sharma, Anuradha; Kaur, Harpreet; Ishar, Mohan Paul S

    2016-02-01

    Regio- and stereoselective 1,3-dipolar cycloadditions of C-(chrom-4-one-3-yl)-N-phenylnitrones (N) with different mono-substituted, disubstituted, and cyclic dipolarophiles were carried out to obtain substituted N-phenyl-3'-(chrom-4-one-3-yl)-isoxazolidines (1-40). All the synthesized compounds were assayed for their in vitro antibacterial activity and display significant inhibitory potential; in particular, compound 32 exhibited good inhibitory activity against Salmonella typhymurium-1 & Salmonella typhymurium-2 with minimum inhibitory concentration value of 1.56 μg/mL and also showed good potential against methicillin-resistant Staphylococcus aureus with minimum inhibitory concentration 3.12 μg/mL. Quantitative structure activity relationship investigations with stepwise multiple linear regression analysis and docking simulation studies have been performed for validation of the observed antibacterial potential of the investigated compounds for determination of the most important parameters regulating antibacterial activities.

  17. A quantitative structure-activity relationship (QSAR) study of some diaryl urea derivatives of B-RAF inhibitors

    PubMed Central

    Sadeghian-Rizi, Sedighe; Sakhteman, Amirhossein; Hassanzadeh, Farshid

    2016-01-01

    In the current study, both ligand-based molecular docking and receptor-based quantitative structure activity relationships (QSAR) modeling were performed on 35 diaryl urea derivative inhibitors of V600EB-RAF. In this QSAR study, a linear (multiple linear regressions) and a nonlinear (partial least squares least squares support vector machine (PLS-LS-SVM)) were used and compared. The predictive quality of the QSAR models was tested for an external set of 31 compounds, randomly chosen out of 35 compounds. The results revealed the more predictive ability of PLS-LS-SVM in analysis of compounds with urea structure. The selected descriptors indicated that size, degree of branching, aromaticity, and polarizability affected the inhibition activity of these inhibitors. Furthermore, molecular docking was carried out to study the binding mode of the compounds. Docking analysis indicated some essential H-bonding and orientations of the molecules in the active site. PMID:28003837

  18. Relationship between quantitative measurement of Porphyromonas gingivalis on dental plaque with periodontal status of patients with coronary heart disease

    NASA Astrophysics Data System (ADS)

    Dwiyanti, Stephani; Soeroso, Yuniarti; Sunarto, Hari; Radi, Basuni

    2017-02-01

    Coronary heart disease is a narrowing of coronary artery due to plaque build-up. [1] Chronic periodontitis increases risk of cardiovascular disease. P.gingivalis is linked to both diseases. Objective: to analyse quantitative difference of P.gingivalis on dental plaque and its relationship with periodontal status of CHD patient and control. Methods: Periodontal status of 66 CHD patient and 40 control was checked. Subgingival plaque was isolated and P.gingivalis was measured using real-time PCR. Result: P.gingivalis of CHD patient differs from control. P.gingivalis is linked to pocket depth of CHD patient. Conclusion: P.gingivalis count of CHD patient is higher than control. P.gingivalis count is not linked to any periodontal status, except for pocket depth of CHD patient.

  19. Estimating the persistence of organic contaminants in indirect potable reuse systems using quantitative structure activity relationship (QSAR).

    PubMed

    Lim, Seung Joo; Fox, Peter

    2012-09-01

    Predictions from the quantitative structure activity relationship (QSAR) model EPI Suite were modified to estimate the persistence of organic contaminants in indirect potable reuse systems. The modified prediction included the effects of sorption, biodegradation, and oxidation that may occur during sub-surface transport. A retardation factor was used to simulate the mobility of adsorbed compounds during sub-surface transport to a recovery well. A set of compounds with measured persistent properties during sub-surface transport was used to validate the results of the modifications to the predictions of EPI Suite. A comparison of the predicted values and measured values was done and the residual sum of the squares showed the importance of including oxidation and sorption. Sorption was the most important factor to include in predicting the fates of organic chemicals in the sub-surface environment.

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

    PubMed Central

    2013-01-01

    Background In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Results Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. Conclusions A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation. PMID:24171724

  1. Quantitative radiation dose-response relationships for normal tissues in man - I. Gustatory tissues response during photon and neutron radiotherapy

    SciTech Connect

    Mossman, K.L.

    1982-08-01

    Quantitative radiation dose-response curves for normal gustatory tissue in man were studied. Taste function, expressed as taste loss, was evaluated in 84 patients who were given either photon or neutron radiotherapy for tumors in the head and neck region. Patients were treated to average tumor doses of 6600 cGy (photon) or 2200 cGy intervals for photon patients and 320-cGy intervals for neutron patients during radiotherapy. The dose-response curves for photons and neutrons were analyzed by fitting a four-parameter logistic equation to the data. Photon and neutron curves differed principally in their relative position along the dose axis. Comparison of the dose-response curves were made by determination of RBE. At 320 cGy, the lowest neutron dose at which taste measurements were made, RBE = 5.7. If this RBE is correct, then the therapeutic gain factor may be equal to or less than 1, indicating no biological advantage in using neutrons over photons for this normal tissue. These studies suggest measurements of taste function and evaluation of dose-response relationships may also be useful in quantitatively evaluating the efficacy of chemical modifiers of radiation response such as hypoxic cell radiosensitizers and radioprotectors.

  2. [Quantitative analysis on the relationships between cotton fiber quality and meteorological factors].

    PubMed

    Ma, Fuyu; Cao, Weixing; Li, Shaokun; Zhu, Yan; Zhou, Zhiguo; Zheng, Zhong; Yang, Jianrong

    2005-11-01

    With the method of planting cotton by stages at the sites from Yangtze valley to north Xinjiang, this paper studied the effects of air temperature and sunlight on cotton fiber quality in 2002 approximately 2003. The results showed that with increasing latitude, fiber length increased, while micronaire value and soluble sugar content (SSC) decreased. An ecological model describing the relationships of fiber strength, micronaire value and SSC with air temperature and sunlight was built to determine the optimal range and critical value of air temperature during boll development period. If a high quality fiber (length > or = 27 mm) was targeted, the daily mean temperature (DMT) and minimum temperature (Tmin) during this period should be 21.3 approximately 29.7 and 10.7 approximately 21.3 degrees C, respectively, and the daily temperature difference (DTD) should not be > 15.2 degrees C. Fiber length was the longest when the DMT was 25.4 degrees C. If the lowest fiber length was > or = 25 mm, DMT and Tmin should not be lower than 15.5 and 10.7 degrees C, respectively, and DTD should not be over 17.9 degrees C during boll development period.

  3. Hologram quantitative structure activity relationship, docking, and molecular dynamics studies of inhibitors for CXCR4.

    PubMed

    Zhang, Chongqian; Du, Chunmiao; Feng, Zhiwei; Zhu, Jingyu; Li, Youyong

    2015-02-01

    CXCR4 plays a crucial role as a co-receptor with CCR5 for HIV-1 anchoring to mammalian cell membrane and is implicated in cancer metastasis and inflammation. In the current work, we study the relationship of structure and activity of AMD11070 derivatives and other inhibitors of CXCR4 using HQSAR, docking and molecular dynamics (MD) simulations. We obtain an HQSAR model (q(2) = 0.779), and the HQSAR result illustrates that AMD11070 shows a high antiretroviral activity. As HQSAR only provides 2D information, we perform docking and MD to study the interaction of It1t, AMD3100, and AMD3465 with CXCR4. Our results illustrate that the binding are affected by two crucial residues Asp97 and Glu288. The butyl amine moiety of AMD11070 contributes to its high antiretroviral activity. Without a butyl amine moiety, (2,7a-Dihydro-1H-benzoimidazol-2-ylmethyl)-methyl-(5,6,7,8-tetrahydro-quinolin-8-yl)-amine (compound 5a) shows low antiretroviral activity. Our results provide structural details about the interactions between the inhibitors and CXCR4, which are useful for rational drug design of CXCR4.

  4. A Combined Quantitative Structure-Activity Relationship Research of Quinolinone Derivatives as Androgen Receptor Antagonists.

    PubMed

    Wang, Yuwei; Bai, Fang; Cao, Hong; Li, Jiazhong; Liu, Huanxiang; Gramatica, Paola

    2015-01-01

    Antiandrogens bicalutamide, flutamide and enzalutamide etc. have been used in clinical trials to treat prostate cancer by binding to and antagonizing androgen receptor (AR). Although initially effective, the drug resistance problem will emerge eventually, which results in a high medical need for novel AR antagonist exploitation. Here in this work, to facilitate the rational design of novel AR antagonists, we studied the structure-activity relationships of a series of 2-quinolinone derivatives and investigated the structural requirements for their antiandrogenic activities. Different modeling methods, including 2D MLR, 3D CoMFA and CoMSIA, were implemented to evolve QSAR models. All these models, thoroughly validated, demonstrated satisfactory results especially for the good predictive abilities. The contour maps from 3D CoMFA and CoMSIA models provide visualized explanation of key structural characteristics relevant to the antiandrogenic activities, which is summarized to a position-specific conclusion at the end. The obtained results from this research are practically useful for rational design and screening of promising chemicals with high antiandrogenic activities.

  5. Solvent Effects on Oxygen-17 Chemical Shifts in Amides. Quantitative Linear Solvation Shift Relationships

    NASA Astrophysics Data System (ADS)

    Díez, Ernesto; Fabián, Jesús San; Gerothanassis, Ioannis P.; Esteban, Angel L.; Abboud, José-Luis M.; Contreras, Ruben H.; de Kowalewski, Dora G.

    1997-01-01

    A multiple-linear-regression analysis (MLRA) has been carried out using the Kamlet-Abboud-Taft (KAT) solvatochromic parameters in order to elucidate and quantify the solvent effects on the17O chemical shifts ofN-methylformamide (NMF),N,N-dimethylformamide (DMF),N-methylacetamide (NMA), andN,N-dimethylacetamide (DMA). The chemical shifts of the four molecules show the same dependence (in ppm) on the solvent polarity-polarizability, i.e., -22π*. The influence of the solvent hydrogen-bond-donor (HBD) acidities is slightly larger for the acetamides NMA and DMA, i.e., -48α, than for the formamides NMF and DMF, i.e., -42α. The influence of the solvent hydrogen-bond-acceptor (HBA) basicities is negligible for the nonprotic molecules DMF and DMA but significant for the protic molecules NMF and NMA, i.e., -9β. The effect of substituting the N-H hydrogen by a methyl group amounts to -5.9 ppm in NMF and 5.4 ppm in NMA. The effect of substituting the O=C-H hydrogen amounts to 5.5 ppm in NMF and 16.8 ppm in DMF. The model of specific hydration sites of amides by I. P. Gerothanassis and C. Vakka [J. Org. Chem.59,2341 (1994)] is settled in a more quantitative basis and the model by M. I. Burgar, T. E. St. Amour, and D. Fiat [J. Phys. Chem.85,502 (1981)] is critically evaluated.17O hydration shifts have been calculated for formamide (FOR) by the ab initio LORG method at the 6-31G* level. For a formamide surrounded by the four in-plane molecules of water in the first hydration shell, the calculated17O shift change due to the four hydrogen bonds, -83.2 ppm, is smaller than the empirical hydration shift, -100 ppm. The17O shift change from each out-of-plane water molecule hydrogen-bonded to the amide oxygen is -18.0 ppm. These LORG results support the conclusion that no more than four water molecules are hydrogen-bonded to the amide oxygen in formamide.

  6. Structural Properties of Green Tea Catechins.

    PubMed

    Botten, Dominic; Fugallo, Giorgia; Fraternali, Franca; Molteni, Carla

    2015-10-08

    Green tea catechins are polyphenols which are believed to provide health benefits; they are marketed as health supplements and are studied for their potential effects on a variety of medical conditions. However, their mechanisms of action and interaction with the environment at the molecular level are still not well-understood. Here, by means of atomistic simulations, we explore the structural properties of four green tea catechins, in the gas phase and water solution: specifically, (-)-epigallocatechin-3-gallate, which is the most abundant, (-)-epicatechin-3-gallate, (-)-epigallocatechin-3-O-(3-O-methyl)-gallate, and (-)-epigallocatechin. We characterize the free energy conformational landscapes of these catechins at ambient conditions, as a function of the torsional degrees of freedom of the pholyphenolic rings, determining the stable conformers and their connections. We show that these free energy landscapes are only subtly influenced by the interactions with the solvent and by the structural details of the polyphenolic rings. However, the number and position of the hydroxyl groups (or their sustituents) and the presence/absence of the galloyl moiety have significant impact on the selected catechin solvation shells and hydrogen bond capabilities, which are ultimately linked to their ability to interact with and affect the biological environment.

  7. Electronic and structural properties of functional nanostructures

    NASA Astrophysics Data System (ADS)

    Yang, Teng

    In this Thesis, I present a study of electronic and structural properties of functional nanostructures such as MoSxIy nanowires, self-assembled monolayer on top of metallic surfaces and structural changes induced in graphite by photo excitations. MoSxI y nanowires, which can be easily synthesized in one step, show many advantages over conventional carbon nanotubes in molecular electronics and many other applications. But how to self-assemble them into desired pattern for practical electronic network? Self-assembled monolayers of polymers on metallic surfaces may help to guide pattern formation of some nanomaterials such as MoSxIy nanowires. I have investigated the physical properties of these nanoscale wires and microscopic self-assembly mechanisms of patterns by total energy calculations combined with molecular dynamics simulations and structure optimization. First, I studied the stability of novel Molybdenum chaicohalide nanowires, a candidate for molecular electronics applications. Next, I investigated the self-assembly of nanoparticles into ordered arrays with the aid of a template. Such templates, I showed, can be formed by polymer adsorption on surfaces such as highly ordered pyrolytic graphite and Ag(111). Finally, I studied the physical origin of of structural changes induced in graphite by light in form of a femtosecond laser pulse.

  8. Inverse relationship between photon flux densities and nanotesla magnetic fields over cell aggregates: Quantitative evidence for energetic conservation

    PubMed Central

    Persinger, Michael A.; Dotta, Blake T.; Karbowski, Lukasz M.; Murugan, Nirosha J.

    2015-01-01

    The quantitative relationship between local changes in magnetic fields and photon emissions within ∼2 mm of aggregates of 105–106 cells was explored experimentally. The vertical component of the earth’s magnetic field as measured by different magnetometers was ∼15 nT higher when plates of cells removed from incubation were measured compared to plates containing only medium. Additional experiments indicated an inverse relationship over the first ∼45 min between changes in photon counts (∼10−12 W·m−2) following removal from incubation and similar changes in magnetic field intensity. Calculations indicated that the energy within the aqueous volume containing the cells was equivalent for that associated with the flux densities of the magnetic fields and the photon emissions. For every approximately 1 nT increase in magnetic field intensity value there was a decrease of ∼2 photons (equivalent of 10−18 J). These results complement correlation studies and suggest there may be a conservation of energy between expression as magnetic fields that are subtracted or added to the adjacent geomagnetic field and reciprocal changes in photon emissions when aggregates of cells within a specific volume of medium (water) adapt to new environments. PMID:26005634

  9. Quantitative Trait Loci Affecting Phenotypic Plasticity and the Allometric Relationship of Ovariole Number and Thorax Length in Drosophila melanogaster

    PubMed Central

    Bergland, Alan O.; Genissel, Anne; Nuzhdin, Sergey V.; Tatar, Marc

    2008-01-01

    Environmental factors during juvenile growth such as temperature and nutrition have major effects on adult morphology and life-history traits. In Drosophila melanogaster, ovary size, measured as ovariole number, and body size, measured as thorax length, are developmentally plastic traits with respect to larval nutrition. Herein we investigated the genetic basis for plasticity of ovariole number and body size, as well the genetic basis for their allometric relationship using recombinant inbred lines (RILs) derived from a natural population in Winters, California. We reared 196 RILs in four yeast concentrations and measured ovariole number and body size. The genetic correlation between ovariole number and thorax length was positive, but the strength of this correlation decreased with increasing yeast concentration. Genetic variation and genotype-by-environment (G × E) interactions were observed for both traits. We identified quantitative trait loci (QTL), epistatic, QTL-by-environment, and epistatic-by-environment interactions for both traits and their scaling relationships. The results are discussed in the context of multivariate trait evolution. PMID:18716336

  10. Quantitative structure-activity relationship study on BTK inhibitors by modified multivariate adaptive regression spline and CoMSIA methods.

    PubMed

    Xu, A; Zhang, Y; Ran, T; Liu, H; Lu, S; Xu, J; Xiong, X; Jiang, Y; Lu, T; Chen, Y

    2015-01-01

    Bruton's tyrosine kinase (BTK) plays a crucial role in B-cell activation and development, and has emerged as a new molecular target for the treatment of autoimmune diseases and B-cell malignancies. In this study, two- and three-dimensional quantitative structure-activity relationship (2D and 3D-QSAR) analyses were performed on a series of pyridine and pyrimidine-based BTK inhibitors by means of genetic algorithm optimized multivariate adaptive regression spline (GA-MARS) and comparative molecular similarity index analysis (CoMSIA) methods. Here, we propose a modified MARS algorithm to develop 2D-QSAR models. The top ranked models showed satisfactory statistical results (2D-QSAR: Q(2) = 0.884, r(2) = 0.929, r(2)pred = 0.878; 3D-QSAR: q(2) = 0.616, r(2) = 0.987, r(2)pred = 0.905). Key descriptors selected by 2D-QSAR were in good agreement with the conclusions of 3D-QSAR, and the 3D-CoMSIA contour maps facilitated interpretation of the structure-activity relationship. A new molecular database was generated by molecular fragment replacement (MFR) and further evaluated with GA-MARS and CoMSIA prediction. Twenty-five pyridine and pyrimidine derivatives as novel potential BTK inhibitors were finally selected for further study. These results also demonstrated that our method can be a very efficient tool for the discovery of novel potent BTK inhibitors.

  11. Quantitative structure-activity relationships and mixture toxicity of organic chemicals in Photobacterium phosphoreum: the Microtox test

    SciTech Connect

    Hermens, J.; Busser, F.; Leeuwangh, P.; Musch, A.

    1985-02-01

    Quantitative structure-activity relationships were calculated for the inhibition of bioluminescence of Photobacterium phosphoreum by 22 nonreactive organic chemicals. The inhibition was measured using the Microtox test and correlated with the partition coefficient between n-octanol and water (Poct), molar refractivity (MR), and molar volume (MW/d). At log Poct less than 1 and greater than 3, deviations from linearity were observed. Introduction of MR and MW/d improved the quality of the relationships. The influences of MR or MW/d may be related with an interaction of the tested chemicals to the enzyme system which produces the light emission. The sensitivity of the Microtox test to the 22 tested compounds is comparable to a 14-day acute mortality test with guppies for chemicals with log Poct less than 4. The inhibition of bioluminescence by a mixture of the tested compounds was slightly less than was expected in case of concentration addition. The Microtox test can give a good estimate of the total aspecific minimum toxicity of polluted waters. When rather lipophilic compounds or pollutants with more specific modes of action are present, this test will underestimate the toxicity to other aquatic life.

  12. A Systematic Investigation of Quaternary Ammonium Ions as Asymmetric Phase Transfer Catalysts. Application of Quantitative Structure Activity/Selectivity Relationships

    PubMed Central

    Denmark, Scott E.; Gould, Nathan D.; Wolf, Larry M.

    2011-01-01

    While the synthetic utility of asymmetric phase transfer catalysis continues to expand, the number of proven catalyst types and design criteria remains limited. At the origin of this scarcity is a lack in understanding of how catalyst structural features affect the rate and enantioselectivity of phase transfer catalyzed reactions. Described in this paper is the development of quantitative structure-activity relationships (QSAR) and -selectivity relationships (QSSR) for the alkylation of a protected glycine imine with libraries of quaternary ammonium ion catalysts. Catalyst descriptors including ammonium ion accessibility, interfacial adsorption affinity, and partition coefficient were found to correlate meaningfully with catalyst activity. The physical nature of the descriptors was rationalized through differing contributions of the interfacial and extraction mechanisms to the reaction under study. The variation in the observed enantioselectivity was rationalized employing a comparative molecular field analysis (CoMFA) using both the steric and electrostatic fields of the catalysts. A qualitative analysis of the developed model reveals preferred regions for catalyst binding to afford both configurations of the alkylated product. PMID:21446723

  13. Genetic relationship between lodging and lodging components in barley (Hordeum vulgare) based on unconditional and conditional quantitative trait locus analyses.

    PubMed

    Chen, W Y; Liu, Z M; Deng, G B; Pan, Z F; Liang, J J; Zeng, X Q; Tashi, N M; Long, H; Yu, M Q

    2014-03-17

    Lodging (LD) is a major constraint limiting the yield and forage quality of barley. Detailed analyses of LD component (LDC) traits were conducted using 246 F2 plants generated from a cross between cultivars ZQ320 and 1277. Genetic relationships between LD and LDC were evaluated by unconditional and conditional quantitative trait locus (QTL) mapping with 117 simple sequence repeat markers. Ultimately, 53 unconditional QTL related to LD were identified on seven barley chromosomes. Up to 15 QTL accounted for over 10% of the phenotypic variation, and up to 20 QTL for culm strength were detected. Six QTL with pleiotropic effects showing significant negative correlations with LD were found between markers Bmag353 and GBM1482 on chromosome 4H. These alleles and alleles of QTL for wall thickness, culm strength, plant height, and plant weight originated from ZQ320. Conditional mapping identified 96 additional QTL for LD. Conditional QTL analysis demonstrated that plant height, plant height center of gravity, and length of the sixth internode had the greatest contribution to LD, whereas culm strength and length of the fourth internode, and culm strength of the second internode were the key factors for LD-resistant. Therefore, lodging resistance in barley can be improved based on selection of alleles affecting culm strength, wall thickness, plant height, and plant weight. The conditional QTL mapping method can be used to evaluate possible genetic relationships between LD and LDC while efficiently and precisely determining counteracting QTL, which will help in understanding the genetic basis of LD in barley.

  14. Quantitative structure-toxicity relationships of organophosphorous pesticides to fish (Cyprinus carpio).

    PubMed

    Yan, Dongyun; Jiang, Xin; Yu, Guifen; Zhao, Zhenhua; Bian, Yongrong; Wang, Fang

    2006-05-01

    This study was conducted to determine the relationships between 1381 chemical and structural parameters of 43 organophosphorus pesticides (OPs) and their toxicity to fish, Cyprinus carpio, using ChemOffice 8.03 and Dragon 2.1. By multivariate linear regression and intervariable regression analyses, various equations have been derived to calculate the lethal toxicity value, LC(50), for 43 OPs found in fish with different levels of toxicity. Results show that for all selected OPs, especially those of low toxic OPs (LC(50)< 2.5 mM), the equation, LC(50) = 56.259 - 13.071 lg K(ow)+17.510 MATS8P-17.455 Mor24u - 0.085 MW + 1.706 (lg K(ow))(2) + 2.306 (Mor14e)(2) + 6.849 Mor20 m (n = 43, F = 36.815, r = 0.942, r(adj)(2) = 0.862, SE = 2.899, p < 10(-6)), could account for 86.2% of the variability of the toxic effect. The steric and electronic characteristics and the hydrophobicity of OPs, in particular, are among the most important parameters determining the toxicity of OPs to fish. For the OPs with high toxicity, different structural parameters were introduced into the following two equations: LC(50)=3.795-1.195 (H1p)(2)-0.037 U-2.225 MATS3v-19.593 Tcon (n = 16, F = 56.820, r = 0.977, r(adj)(2) = 0.937, SE = 0.143, p < 10(-6)), where LC(50) is less than 2.5 mM, and LC(50) = 0.341-0.561 (HOMA)(2) + 0.231 HOMA (n = 3,r(adj)(2) = 1), where LC(50) is less than 0.3 mM. These results suggest that chemical and structural parameters could be useful in modeling chemical reactivity within homologous series of OP compounds and elucidating possible mechanisms associated with different levels of toxicity to fish.

  15. A Quantitative Test for the Spatial Relationship Between Aftershock Distributions and Mainshock Rupture Properties

    NASA Astrophysics Data System (ADS)

    Woessner, J.; Ripperger, J.; Mai, M. P.; Wiemer, S.

    2004-12-01

    Correlating the properties of the mainshock rupture with the location of corresponding aftershocks may provide insight into the relationship between mainshock-induced static stress changes and aftershock occurrence. In this study, we develop a rigorous statistical test to quantify the spatial pattern of aftershock locations with the corresponding distributions of coseismic slip and stress-drop. Well-located aftershock hypocenters are projected onto the mainshock fault plane and coseismic slip and stress drop values are interpolated to their respective location. The null hypothesis H0 for the applied test statistic is: Aftershock hypocenters are randomly distributed on the mainshock fault plane and are not correlated with mainshock properties. Because we want to maintain spatial earthquake clustering as one of the important observed features of seismicity, we synthesize slip distributions using a random spatial field model from which we then compute the respective stress-drop distributions. For each simulation of earthquake slip, we compute the test statistic for the slip and stress-drop distribution, testing whether or not an apparent correlation between mainshock properties and aftershock locations exists. Uncertainties in the aftershock locations are accounted for by simulating a thousand catalogues for which we randomize the location of the aftershocks within their given location error bounds. We then determine the number of aftershocks in low-slip or negative stress-drop regions for simulated slip distributions, and compare those to the measurements obtained for finite-source slip inversions. We apply the test to crustal earthquakes in California and Japan. If possible, we use different source models and earthquake catalogues with varying accuracy to investigate the dependence of the test results on, for example, the location uncertainties of aftershocks. Contrary to the visual impression, we find that for some strike-slip earthquakes or segments of the

  16. Toxicity of substituted anilines to Pseudokirchneriella subcapitata and quantitative structure-activity relationship analysis for polar narcotics.

    PubMed

    Chen, Chung-Yuan; Ko, Chia-Wen; Lee, Po-I

    2007-06-01

    This study evaluated the toxic effects of substituted anilines on Pseudokirchneriella subcapitata with the use of a closed algal toxicity testing technique with no headspace. Two response endpoints (i.e., dissolved oxygen production [DO] and algal growth rate) were used to evaluate the toxicity of anilines. Both DO and growth rate endpoints revealed similar sensitivity to the effects of anilines. However, trichloroanilines showed stronger inhibitory effects on microalgal photosynthetic reactions than that on algal growth. For various aquatic organisms, the relative sensitivity relationship for anilines is Daphnia magna > luminescent bacteria (Microtox) > or = Pocelia reticulata > or = Pseudokirchneriella subcapitata > or = fathead minnow > Tetrahymena pyriformis. The susceptibility of P. subcapitata to anilines is similar to fish, but P. subcapitata is apparently less sensitive than the water flea. The lack of correlation between the toxicity revealed by different aquatic organisms (microalgae, D. magna, luminescent bacteria, and P. reticulata) suggests that anilines might have different metabolic routes in these organisms. Both hydrogen bonding donor capacity (the lowest unoccupied molecular orbital energy, Elumo) and hydrophobicity (1-octanol:water partition coefficient, Kow) were found to provide satisfactory descriptions for the toxicity of polar narcotics (substituted anilines and chlorophenols). Quantitative structure-activity relationships (QSARs) based on Elumo, log Kow, or both values were established with r2 values varying from 0.75 to 0.92. The predictive power for the QSAR models were found to be satisfactory through leave-one-out cross-validation. Such relationships could provide useful information for the estimation of toxicity for other polar narcotic compounds.

  17. WE-G-207-05: Relationship Between CT Image Quality, Segmentation Performance, and Quantitative Image Feature Analysis

    SciTech Connect

    Lee, J; Nishikawa, R; Reiser, I; Boone, J

    2015-06-15

    Purpose: Segmentation quality can affect quantitative image feature analysis. The objective of this study is to examine the relationship between computed tomography (CT) image quality, segmentation performance, and quantitative image feature analysis. Methods: A total of 90 pathology proven breast lesions in 87 dedicated breast CT images were considered. An iterative image reconstruction (IIR) algorithm was used to obtain CT images with different quality. With different combinations of 4 variables in the algorithm, this study obtained a total of 28 different qualities of CT images. Two imaging tasks/objectives were considered: 1) segmentation and 2) classification of the lesion as benign or malignant. Twenty-three image features were extracted after segmentation using a semi-automated algorithm and 5 of them were selected via a feature selection technique. Logistic regression was trained and tested using leave-one-out-cross-validation and its area under the ROC curve (AUC) was recorded. The standard deviation of a homogeneous portion and the gradient of a parenchymal portion of an example breast were used as an estimate of image noise and sharpness. The DICE coefficient was computed using a radiologist’s drawing on the lesion. Mean DICE and AUC were used as performance metrics for each of the 28 reconstructions. The relationship between segmentation and classification performance under different reconstructions were compared. Distributions (median, 95% confidence interval) of DICE and AUC for each reconstruction were also compared. Results: Moderate correlation (Pearson’s rho = 0.43, p-value = 0.02) between DICE and AUC values was found. However, the variation between DICE and AUC values for each reconstruction increased as the image sharpness increased. There was a combination of IIR parameters that resulted in the best segmentation with the worst classification performance. Conclusion: There are certain images that yield better segmentation or classification

  18. Modeling the reactivities of hydroxyl radical and ozone towards atmospheric organic chemicals using quantitative structure-reactivity relationship approaches.

    PubMed

    Gupta, Shikha; Basant, Nikita; Mohan, Dinesh; Singh, Kunwar P

    2016-07-01

    The persistence and the removal of organic chemicals from the atmosphere are largely determined by their reactions with the OH radical and O3. Experimental determinations of the kinetic rate constants of OH and O3 with a large number of chemicals are tedious and resource intensive and development of computational approaches has widely been advocated. Recently, ensemble machine learning (EML) methods have emerged as unbiased tools to establish relationship between independent and dependent variables having a nonlinear dependence. In this study, EML-based, temperature-dependent quantitative structure-reactivity relationship (QSRR) models have been developed for predicting the kinetic rate constants for OH (kOH) and O3 (kO3) reactions with diverse chemicals. Structural diversity of chemicals was evaluated using a Tanimoto similarity index. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation performed employing statistical checks. In test data, the EML QSRR models yielded correlation (R (2)) of ≥0.91 between the measured and the predicted reactivities. The applicability domains of the constructed models were determined using methods based on descriptors range, Euclidean distance, leverage, and standardization approaches. The prediction accuracies for the higher reactivity compounds were relatively better than those of the low reactivity compounds. Proposed EML QSRR models performed well and outperformed the previous reports. The proposed QSRR models can make predictions of rate constants at different temperatures. The proposed models can be useful tools in predicting the reactivities of chemicals towards OH radical and O3 in the atmosphere.

  19. Relationships between regional economic sectors and water use in a water-scarce area in China: A quantitative analysis

    NASA Astrophysics Data System (ADS)

    Wang, Weiping; Gao, Lei; Liu, Pin; Hailu, Atakelty

    2014-07-01

    Northern China has been facing severe water scarcity as a result of vigorous economic growth, population expansion and changing lifestyles. A typical case is Shandong province whose water resources per capita is approximately only a sixth of the national average and a twentieth of the global average. It is useful to assess the implications of the province’s growth and trade patterns for water use and water conservation strategies. This study quantitatively analyses relationships between regional economic sectors and water use in Shandong using an input-output model for virtual water resources. The changes in key indicators for 1997-2007 are tracked and the effects of water-saving policies on these changes are examined. The results highlight the benefits of applying a virtual water trade analysis on a water-scarce region where water resources exhibit highly heterogeneous temporal and geographical distributions. The net export of virtual water in Shandong was initially large, but this declined over the years and the province has recently become a net importer. Between 1997 and 2002, water use in most sectors increased due to rapid urbanisation and industrialisation. Since then, water use in all Shandong economic sectors exhibit a downward trend despite continued increases in goods and services net exports, a trend which can be attributed to the vigorous implementation of water-saving policies and measures, especially water use quotas. Economic sectors consume water directly and indirectly and understanding the pattern of virtual water trade implied by sectoral relationships is important for managing water scarcity problems. This study fills the knowledge gap in the existing literature created by the lack of case studies that dynamically assess virtual water trade and analyse the effects of water-saving policies and measures. The study draws policy recommendations that are relevant for future water planning in Shandong and other regions in northern China.

  20. Prediction of Radix Astragali Immunomodulatory Effect of CD80 Expression from Chromatograms by Quantitative Pattern-Activity Relationship

    PubMed Central

    Ng, Michelle Chun-har; Lau, Tsui-yan; Fan, Kei; Xu, Qing-song; Lam, Mary K.

    2017-01-01

    The current use of a single chemical component as the representative quality control marker of herbal food supplement is inadequate. In this CD80-Quantitative-Pattern-Activity-Relationship (QPAR) study, we built a bioactivity predictive model that can be applicable for complex mixtures. Through integrating the chemical fingerprinting profiles of the immunomodulating herb Radix Astragali (RA) extracts, and their related biological data of immunological marker CD80 expression on dendritic cells, a chemometric model using the Elastic Net Partial Least Square (EN-PLS) algorithm was established. The EN-PLS algorithm increased the biological predictive capability with lower value of RMSEP (11.66) and higher values of Rp2 (0.55) when compared to the standard PLS model. This CD80-QPAR platform provides a useful predictive model for unknown RA extract's bioactivities using the chemical fingerprint inputs. Furthermore, this bioactivity prediction platform facilitates identification of key bioactivity-related chemical components within complex mixtures for future drug discovery and understanding of the batch-to-batch consistency for quality clinical trials. PMID:28337449

  1. Kinetics and Quantitative Structure—Activity Relationship Study on the Degradation Reaction from Perfluorooctanoic Acid to Trifluoroacetic Acid

    PubMed Central

    Gong, Chen; Sun, Xiaomin; Zhang, Chenxi; Zhang, Xue; Niu, Junfeng

    2014-01-01

    Investigation of the degradation kinetics of perfluorooctanoic acid (PFOA) has been carried out to calculate rate constants of the main elementary reactions using the multichannel Rice-Ramsperger-Kassel-Marcus theory and canonical variational transition state theory with small-curvature tunneling correction over a temperature range of 200~500 K. The Arrhenius equations of rate constants of elementary reactions are fitted. The decarboxylation is role step in the degradation mechanism of PFOA. For the perfluorinated carboxylic acids from perfluorooctanoic acid to trifluoroacetic acid, the quantitative structure–activity relationship of the decarboxylation was analyzed with the genetic function approximation method and the structure–activity model was constructed. The main parameters governing rate constants of the decarboxylation reaction from the eight-carbon chain to the two-carbon chain were obtained. As the structure–activity model shows, the bond length and energy of C1–C2 (RC1–C2 and EC1–C2) are positively correlated to rate constants, while the volume (V), the energy difference between EHOMO and ELUMO (ΔE), and the net atomic charges on atom C2 (QC2) are negatively correlated. PMID:25196516

  2. A quantitative structure-activity relationship to predict efficacy of granular activated carbon adsorption to control emerging contaminants.

    PubMed

    Kennicutt, A R; Morkowchuk, L; Krein, M; Breneman, C M; Kilduff, J E

    2016-08-01

    A quantitative structure-activity relationship was developed to predict the efficacy of carbon adsorption as a control technology for endocrine-disrupting compounds, pharmaceuticals, and components of personal care products, as a tool for water quality professionals to protect public health. Here, we expand previous work to investigate a broad spectrum of molecular descriptors including subdivided surface areas, adjacency and distance matrix descriptors, electrostatic partial charges, potential energy descriptors, conformation-dependent charge descriptors, and Transferable Atom Equivalent (TAE) descriptors that characterize the regional electronic properties of molecules. We compare the efficacy of linear (Partial Least Squares) and non-linear (Support Vector Machine) machine learning methods to describe a broad chemical space and produce a user-friendly model. We employ cross-validation, y-scrambling, and external validation for quality control. The recommended Support Vector Machine model trained on 95 compounds having 23 descriptors offered a good balance between good performance statistics, low error, and low probability of over-fitting while describing a wide range of chemical features. The cross-validated model using a log-uptake (qe) response calculated at an aqueous equilibrium concentration (Ce) of 1 μM described the training dataset with an r(2) of 0.932, had a cross-validated r(2) of 0.833, and an average residual of 0.14 log units.

  3. A Quantitative Structure Activity Relationship for acute oral toxicity of pesticides on rats: Validation, domain of application and prediction.

    PubMed

    Hamadache, Mabrouk; Benkortbi, Othmane; Hanini, Salah; Amrane, Abdeltif; Khaouane, Latifa; Si Moussa, Cherif

    2016-02-13

    Quantitative Structure Activity Relationship (QSAR) models are expected to play an important role in the risk assessment of chemicals on humans and the environment. In this study, we developed a validated QSAR model to predict acute oral toxicity of 329 pesticides to rats because a few QSAR models have been devoted to predict the Lethal Dose 50 (LD50) of pesticides on rats. This QSAR model is based on 17 molecular descriptors, and is robust, externally predictive and characterized by a good applicability domain. The best results were obtained with a 17/9/1 Artificial Neural Network model trained with the Quasi Newton back propagation (BFGS) algorithm. The prediction accuracy for the external validation set was estimated by the Q(2)ext and the root mean square error (RMS) which are equal to 0.948 and 0.201, respectively. 98.6% of external validation set is correctly predicted and the present model proved to be superior to models previously published. Accordingly, the model developed in this study provides excellent predictions and can be used to predict the acute oral toxicity of pesticides, particularly for those that have not been tested as well as new pesticides.

  4. Quantitative structure-activity relationship modelling of oral acute toxicity and cytotoxic activity of fragrance materials in rodents.

    PubMed

    Papa, E; Luini, M; Gramatica, P

    2009-10-01

    Fragrance materials are used as ingredients in many consumer and personal care products. The wide and daily use of these substances, as well as their mainly uncontrolled discharge through domestic sewage, make fragrance materials both potential indoor and outdoor air pollutants which are also connected to possible toxic effects on humans (asthma, allergies, headaches). Unfortunately, little is known about the environmental fate and toxicity of these substances. However, the use of alternative, predictive approaches, such as quantitative structure-activity relationships (QSARs), can help in filling the data gap and in the characterization of the environmental and toxicological profile of these substances. In the proposed study, ordinary least squares regression-based QSAR models were developed for three toxicological endpoints: mouse oral LD(50), inhibition of NADH-oxidase (EC(50) NADH-Ox) and the effect on mitochondrial membrane potential (EC(50) DeltaPsim). Theoretical molecular descriptors were calculated by using DRAGON software, and the best QSAR models were developed according to the principles defined by the Organization for Economic Co-operation and Development.

  5. Dose-survival relationship for epithelial cells of human skin after multifraction irradiation: evaluation by a quantitative method in vivo

    SciTech Connect

    Arcangeli, G.; Mauro, F.; Nervi, C.; Withers, H.R.

    1980-07-01

    The dose-survival relationship for normal epithelial cells after single and fractionated radiation exposures has been established by Withers for the mouse, but it is not available for humans according to a strict criterion for survival of single cell reproductive integrity. In an attempt to obtain such a quantitative estimation, 2 patients requiring radical radiation therapy to the chest wall were treated according to particular Multiple Daily Fractionation (MDF) protocols: i) 250 + 150 + 150 rad/day, 4 hr interval, 5 days/week; and ii) 150 + 150 + 150 + 150 rad/day, 3.5 hr interval, 5 days/week. In both cases, different strips of skin received different total doses: 6300, 6850, and 7150 rad, and 6300, 6750, and 7200 rad, respectively. In case (i), moist desquamation appeared and thereafter repopulating colonies of epithelium could be recognized and counted. Using these counts a survival curve having a D/sub o/ value of 490 +- 150 rad was estimated according to the formula proposed by Withers. In case (ii), no moist desquamation was reached at the doses delivered. The difference observed may imply that the initial region of the survival curve deviates appreciably from exponential between doses of 150 and 250 rad. If such is the case, a /sub 1/D/sub o/ value of 490 rad may represent an underestimate. These results are discussed from the point of view of both the shape of the survival curve and the effectiveness of nonconventional fractionation courses.

  6. Monte Carlo-based quantitative structure-activity relationship models for toxicity of organic chemicals to Daphnia magna.

    PubMed

    Toropova, Alla P; Toropov, Andrey A; Veselinović, Aleksandar M; Veselinović, Jovana B; Leszczynska, Danuta; Leszczynski, Jerzy

    2016-11-01

    Quantitative structure-activity relationships (QSARs) for toxicity of a large set of 758 organic compounds to Daphnia magna were built up. The simplified molecular input-line entry system (SMILES) was used to represent the molecular structure. The Correlation and Logic (CORAL) software was utilized as a tool to develop the QSAR models. These models are built up using the Monte Carlo method and according to the principle "QSAR is a random event" if one checks a group of random distributions in the visible training set and the invisible validation set. Three distributions of the data into the visible training, calibration, and invisible validation sets are examined. The predictive potentials (i.e., statistical characteristics for the invisible validation set of the best model) are as follows: n = 87, r(2)  = 0.8377, root mean square error = 0.564. The mechanistic interpretations and the domain of applicability of built models are suggested and discussed. Environ Toxicol Chem 2016;35:2691-2697. © 2016 SETAC.

  7. Modeling the Dispersibility of Single Walled Carbon Nanotubes in Organic Solvents by Quantitative Structure-Activity Relationship Approach

    PubMed Central

    Yilmaz, Hayriye; Rasulev, Bakhtiyor; Leszczynski, Jerzy

    2015-01-01

    The knowledge of physico-chemical properties of carbon nanotubes, including behavior in organic solvents is very important for design, manufacturing and utilizing of their counterparts with improved properties. In the present study a quantitative structure-activity/property relationship (QSAR/QSPR) approach was applied to predict the dispersibility of single walled carbon nanotubes (SWNTs) in various organic solvents. A number of additive descriptors and quantum-chemical descriptors were calculated and utilized to build QSAR models. The best predictability is shown by a 4-variable model. The model showed statistically good results (R2training = 0.797, Q2 = 0.665, R2test = 0.807), with high internal and external correlation coefficients. Presence of the X0Av descriptor and its negative term suggest that small size solvents have better SWCNTs solubility. Mass weighted descriptor ATS6m also indicates that heavier solvents (and small in size) most probably are better solvents for SWCNTs. The presence of the Dipole Z descriptor indicates that higher polarizability of the solvent molecule increases the solubility. The developed model and contributed descriptors can help to understand the mechanism of the dispersion process and predictorganic solvents that improve the dispersibility of SWNTs.

  8. Approach on quantitative structure-activity relationship for design of a pH neutral carrier containing tertiary amino group.

    PubMed

    Cao, Zhong; Gong, Fu-Chun; Li, He-Ping; Xiao, Zhong-Liang; Long, Shu; Zhang, Ling; Peng, San-Jun

    2007-01-02

    The quantitative structure-activity relationship (QSAR) for neutral carriers used to prepare hydrogen ion sensors has been studied. A series of synthesized carrier compounds were taken as the training set. Five molecular structure parameters of the compounds were calculated by using CNDO/2 algorithm and used as feature variables in constructing QSAR model. The lower and upper limits of the linear pH response range were taken as the activity measure. The corresponding model equations were derived from the stepwise regression procedure. With the established QSAR model, a new pH carrier, (4-hydroxybenzyl) didodecylamine (XIII) was proposed and synthesized. The PVC membrane pH electrode based on carrier XIII with a wide pH linear response range of 2.0-12.5 was prepared. Having a theoretical Nernstian response slope of 57.2+/-0.3 mV/pH (n=5 at 25 degrees C) without a super-Nernstian phenomenon, the sensor had low resistance, short response time, high selectivity and good reproducibility. Moreover, the sensor was successfully applied to detecting the pH value of serum samples.

  9. Predictive three-dimensional quantitative structure-activity relationship of cytochrome P450 1A2 inhibitors.

    PubMed

    Korhonen, Laura E; Rahnasto, Minna; Mähönen, Niina J; Wittekindt, Carsten; Poso, Antti; Juvonen, Risto O; Raunio, Hannu

    2005-06-02

    The purpose of this study was to determine the cytochrome P450 1A2 (CYP1A2) inhibition potencies of structurally diverse compounds to create a comprehensive three-dimensional quantitative structure-activity relationship (3D-QSAR) model of CYP1A2 inhibitors and to use this model to predict the inhibition potencies of an external set of compounds. Fifty-two compounds including naphthalene, lactone and quinoline derivatives were assayed in a 96-well plate format for CYP1A2 inhibition activity using 7-ethoxyresorufin O-dealkylation as the probe reaction. The IC50 values of the tested compounds varied from 2.3 microM to over 40,000 microM. On the basis of this data set, a comparative molecular field analysis (CoMFA) and GRID/GOLPE models were created that yielded novel structural information about the interaction between inhibitory molecules and the CYP1A2 active site. The created CoMFA model was able to accurately predict inhibitory potencies of several structurally unrelated compounds, including selective inhibitors of other cytochrome P450 forms.

  10. Quantitative studies on structure-ORAC relationships of anthocyanins from eggplant and radish using 3D-QSAR.

    PubMed

    Jing, Pu; Zhao, Shujuan; Ruan, Siyu; Sui, Zhongquan; Chen, Lihong; Jiang, Linlei; Qian, Bingjun

    2014-02-15

    The 3-dimensional quantitative structure activity relationship (3D-QSAR) models were established from 21 anthocyanins based on their oxygen radical absorbing capacity (ORAC) and were applied to predict anthocyanins in eggplant and radish for their ORAC values. The cross-validated q(2)=0.857/0.729, non-cross-validated r(2) = 0.958/0.856, standard error of estimate = 0.153/0.134, and F = 73.267/19.247 were for the best QSAR (CoMFA/CoMSIA) models, where the correlation coefficient r(2)pred = 0.998/0.997 (>0.6) indicated a high predictive ability for each. Additionally, the contour map results suggested that structural characteristics of anthocyanins favourable for the high ORAC. Four anthocyanins from eggplant and radish have been screened based on the QSAR models. Pelargonidin-3-[(6''-p-coumaroyl)-glucosyl(2 → 1)glucoside]-5-(6''-malonyl)-glucoside, delphinidin-3-rutinoside-5-glucoside, and delphinidin-3-[(4''-p-coumaroyl)-rhamnosyl(1 → 6)glucoside]-5-glucoside potential with high ORAC based the QSAR models were isolated and also confirmed for their relative high antioxidant ability, which might attribute to the bulky and/or electron-donating substituent at the 3-position in the C ring or/and hydrogen bond donor group/electron donating group on the R1 position in the B ring.

  11. Prediction of anticancer property of bowsellic acid derivatives by quantitative structure activity relationship analysis and molecular docking study

    PubMed Central

    Satpathy, Raghunath; Guru, R. K.; Behera, R.; Nayak, B.

    2015-01-01

    Context: Boswellic acid consists of a series of pentacyclic triterpene molecules that are produced by the plant Boswellia serrata. The potential applications of Bowsellic acid for treatment of cancer have been focused here. Aims: To predict the property of the bowsellic acid derivatives as anticancer compounds by various computational approaches. Materials and Methods: In this work, all total 65 derivatives of bowsellic acids from the PubChem database were considered for the study. After energy minimization of the ligands various types of molecular descriptors were computed and corresponding two-dimensional quantitative structure activity relationship (QSAR) models were obtained by taking Andrews coefficient as the dependent variable. Statistical Analysis Used: Different types of comparative analysis were used for QSAR study are multiple linear regression, partial least squares, support vector machines and artificial neural network. Results: From the study geometrical descriptors shows the highest correlation coefficient, which indicates the binding factor of the compound. To evaluate the anticancer property molecular docking study of six selected ligands based on Andrews affinity were performed with nuclear factor-kappa protein kinase (Protein Data Bank ID 4G3D), which is an established therapeutic target for cancers. Along with QSAR study and docking result, it was predicted that bowsellic acid can also be treated as a potential anticancer compound. Conclusions: Along with QSAR study and docking result, it was predicted that bowsellic acid can also be treated as a potential anticancer compound. PMID:25709332

  12. Relationship between volcanic ash fallouts and seismic tremor: quantitative assessment of the 2015 eruptive period at Cotopaxi volcano, Ecuador

    NASA Astrophysics Data System (ADS)

    Bernard, Benjamin; Battaglia, Jean; Proaño, Antonio; Hidalgo, Silvana; Vásconez, Francisco; Hernandez, Stephen; Ruiz, Mario

    2016-11-01

    Understanding the relationships between geophysical signals and volcanic products is critical to improving real-time volcanic hazard assessment. Thanks to high-frequency sampling campaigns of ash fallouts (15 campaigns, 461 samples), the 2015 Cotopaxi eruption is an outstanding candidate for quantitatively comparing the amplitude of seismic tremor with the amount of ash emitted. This eruption emitted a total of 1.2E + 9 kg of ash ( 8.6E + 5 m3) during four distinct phases, with masses ranging from 3.5E + 7 to 7.7E + 8 kg of ash. We compare the ash fallout mass and the corresponding cumulative quadratic median amplitude of the seismic tremor and find excellent correlations when the dataset is divided by eruptive phase. We use scaling factors based on the individual correlations to reconstruct the eruptive process and to extract synthetic Eruption Source Parameters (daily mass of ash, mass eruption rate, and column height) from the seismic records. We hypothesize that the change in scaling factor through time, associated with a decrease in seismic amplitudes compared to ash emissions, is the result of a more efficient fragmentation and transport process. These results open the possibility of feeding numerical models with continuous geophysical data, after adequate calibration, in order to better characterize volcanic hazards during explosive eruptions.

  13. Synthetic cannabinoids: In silico prediction of the cannabinoid receptor 1 affinity by a quantitative structure-activity relationship model.

    PubMed

    Paulke, Alexander; Proschak, Ewgenij; Sommer, Kai; Achenbach, Janosch; Wunder, Cora; Toennes, Stefan W

    2016-03-14

    The number of new synthetic psychoactive compounds increase steadily. Among the group of these psychoactive compounds, the synthetic cannabinoids (SCBs) are most popular and serve as a substitute of herbal cannabis. More than 600 of these substances already exist. For some SCBs the in vitro cannabinoid receptor 1 (CB1) affinity is known, but for the majority it is unknown. A quantitative structure-activity relationship (QSAR) model was developed, which allows the determination of the SCBs affinity to CB1 (expressed as binding constant (Ki)) without reference substances. The chemically advance template search descriptor was used for vector representation of the compound structures. The similarity between two molecules was calculated using the Feature-Pair Distribution Similarity. The Ki values were calculated using the Inverse Distance Weighting method. The prediction model was validated using a cross validation procedure. The predicted Ki values of some new SCBs were in a range between 20 (considerably higher affinity to CB1 than THC) to 468 (considerably lower affinity to CB1 than THC). The present QSAR model can serve as a simple, fast and cheap tool to get a first hint of the biological activity of new synthetic cannabinoids or of other new psychoactive compounds.

  14. Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure-Activity Relationship Modeling.

    PubMed

    Yost, Erin E; Stanek, John; DeWoskin, Robert S; Burgoon, Lyle D

    2016-07-19

    The United States Environmental Protection Agency (EPA) identified 1173 chemicals associated with hydraulic fracturing fluids, flowback, or produced water, of which 1026 (87%) lack chronic oral toxicity values for human health assessments. To facilitate the ranking and prioritization of chemicals that lack toxicity values, it may be useful to employ toxicity estimates from quantitative structure-activity relationship (QSAR) models. Here we describe an approach for applying the results of a QSAR model from the TOPKAT program suite, which provides estimates of the rat chronic oral lowest-observed-adverse-effect level (LOAEL). Of the 1173 chemicals, TOPKAT was able to generate LOAEL estimates for 515 (44%). To address the uncertainty associated with these estimates, we assigned qualitative confidence scores (high, medium, or low) to each TOPKAT LOAEL estimate, and found 481 to be high-confidence. For 48 chemicals that had both a high-confidence TOPKAT LOAEL estimate and a chronic oral reference dose from EPA's Integrated Risk Information System (IRIS) database, Spearman rank correlation identified 68% agreement between the two values (permutation p-value =1 × 10(-11)). These results provide support for the use of TOPKAT LOAEL estimates in identifying and prioritizing potentially hazardous chemicals. High-confidence TOPKAT LOAEL estimates were available for 389 of 1026 hydraulic fracturing-related chemicals that lack chronic oral RfVs and OSFs from EPA-identified sources, including a subset of chemicals that are frequently used in hydraulic fracturing fluids.

  15. Interspecies quantitative structure-activity-activity relationships (QSAARs) for prediction of acute aquatic toxicity of aromatic amines and phenols.

    PubMed

    Furuhama, A; Hasunuma, K; Aoki, Y

    2015-01-01

    We propose interspecies quantitative structure-activity-activity relationships (QSAARs), that is, QSARs with descriptors, to estimate species-specific acute aquatic toxicity. Using training datasets consisting of more than 100 aromatic amines and phenols, we found that the descriptors that predicted acute toxicities to fish (Oryzias latipes) and algae were daphnia toxicity, molecular weight (an indicator of molecular size and uptake) and selected indicator variables that discriminated between the absence or presence of various substructures. Molecular weight and the selected indicator variables improved the goodness-of-fit of the fish and algae toxicity prediction models. External validations of the QSAARs proved that algae toxicity could be predicted within 1.0 log unit and revealed structural profiles of outlier chemicals with respect to fish toxicity. In addition, applicability domains based on leverage values provided structural alerts for the predicted fish toxicity of chemicals with more than one hydroxyl or amino group attached to an aromatic ring, but not for fluoroanilines, which were not included in the training dataset. Although these simple QSAARs have limitations, their applicability is defined so clearly that they may be practical for screening chemicals with molecular weights of ≤364.9.

  16. Two- and Three-Dimensional Quantitative Structure-Activity Relationships Studies on a Series of Liver X Receptor Ligands

    PubMed Central

    Honório, Káthia M; Salum, Lívia B; Garratt, Richard C; Polikarpov, Igor; Andricopulo, Adriano D

    2008-01-01

    Liver X receptor (LXR) is an attractive drug target for the development of novel therapeutic agents for the treatment of dyslipidaemia and cholestasis. In the present work, comparative molecular field analysis (CoMFA) and hologram quantitative structure-activity relationship (HQSAR) studies were conducted on a series of potent LXR ligands. Significant correlation coefficients (CoMFA, r2 = 0.98 and q2 = 0.69; HQSAR, r2 = 0.99 and q2 = 0.85) were obtained, indicating the potential of the models for untested compounds. The models were then used to predict the potency of an external test set, and the predicted values obtained from the 2D and 3D models were in good agreement with the experimental results. The final QSAR models, along with the information obtained from 3D steric and electrostatic contour maps and 2D contribution maps should be useful for the design of novel LXR ligands having improved potency. PMID:19696872

  17. Quantitative structure-activity relationship of hydroxyl-substituent Schiff bases in radical-induced hemolysis of human erythrocytes.

    PubMed

    Tang, You-Zhi; Liu, Zai-Qun

    2008-01-01

    The major objective of this work was to explore the quantitative structure-activity relationship (QSAR) of hydroxyl-substituent Schiff bases in protecting human erythrocytes against 2,2'-azobis(2-amidinopropane hydrochloride) (AAPH)- induced hemolysis, in which 10 Schiff bases including 4-phenyliminomethylphenol (PIH); 4-((4-hydroxybenzylidene) amino)phenol (PAH); 2-methoxy-4-((4-hydroxyphenylimino)methyl)phenol (PMH); 4-((furan-2-ylmethylene)amino) phenol (FAH); 4-((4-N,N-dimethylaminobenzylidene)amino)phenol (PDH); 2-((4-N,N-dimethylaminobenzylidene)amino) phenol (ODH); 2-(naphthalene-1-yliminomethyl)phenol (NAH); 2-(benzyliminomethyl)phenol (BPH); 1,4-di((2-hydroxyphenylimino) methyl)benzene (DOH); 1,4-di((4-hydroxyphenylimino)methyl)benzene DPH, were available for this in vitro experimental system. The results revealed that the radical-scavenging activity of the --OH attached to the para position of methylene in Schiff base was much lower than that attached to the ortho position of the N atom. The large conjugate system and low steric hindrance in the framework of Schiff base benefit the Schiff base to trap radicals. Meanwhile, since a Schiff base, even without any substituent, can also play an antioxidative role in this experimental system, the QSAR results suggest that hydroxyl-substituent Schiff bases are potential drugs in the treatment of radical-related diseases, and provide more information for designing novel drugs.

  18. Analysis of positions and substituents on genotoxicity of fluoroquinolones with quantitative structure-activity relationship and 3D Pharmacophore model.

    PubMed

    Fengxian, Chen; Reti, Hai

    2017-02-01

    The genotoxicity values of 21 quinolones were studied to establish a quantitative structure-activity relationship model and 3D Pharmacophore model separately for screening essential positions and substituents that contribute to genotoxicity of fluoroquinolones (FQs). A full factor experimental design was performed to analyze the specific main effect and second-order interaction effect of different positions and substituents on genotoxicity, forming a reasonable modification scheme which was validated on typical FQ with genotoxicity and efficacy data. Four positions (1, 5, 7, 8) were screened finally to form the full factorial experimental design which contained 72 congeners in total, illustrating that: the dominant effect of 5 and 7-positions on genotoxicity of FQs is main effect; meanwhile the effect of 1 and 8-positions is a second-order interaction effect; two adjacent positions always have stronger second-order interaction effect and lower genotoxicity; the obtained modification scheme had been validated on typical FQ congeners with the modified compound has a lower genotoxicity, higher synthesis feasibilities and efficacy.

  19. Comparative analysis of local and consensus quantitative structure-activity relationship approaches for the prediction of bioconcentration factor.

    PubMed

    Piir, G; Sild, S; Maran, U

    2013-01-01

    Quantitative structure-activity relationships (QSARs) are broadly classified as global or local, depending on their molecular constitution. Global models use large and diverse training sets covering a wide range of chemical space. Local models focus on smaller structurally or chemically similar subsets that are conventionally selected by human experts or alternatively using clustering analysis. The current study focuses on the comparative analysis of different clustering algorithms (expectation-maximization, K-means and hierarchical) for seven different descriptor sets as structural characteristics and two rule-based approaches to select subsets for designing local QSAR models. A total of 111 local QSAR models are developed for predicting bioconcentration factor. Predictions from local models were compared with corresponding predictions from the global model. The comparison of coefficients of determination (r(2)) and standard deviations for local models with similar subsets from the global model show improved prediction quality in 97% of cases. The descriptor content of derived QSARs is discussed and analyzed. Local QSAR models were further consolidated within the framework of consensus approach. All different consensus approaches increased performance over the global and local models. The consensus approach reduced the number of strongly deviating predictions by evening out prediction errors, which were produced by some local QSARs.

  20. Dechlorination of chlorinated compounds by Trametes versicolor ATCC 200801 crude laccase and quantitative structure-activity relationship of toxicity.

    PubMed

    Çabuk, Ahmet; Sidir, Yadigar G; Aytar, Pinar; Gedikli, Serap; Sidir, İsa

    2012-01-01

    Chlorinated compounds constitute an important class of xenobiotics. Crude laccase was produced using Trametes versicolor ATCC (200801) in potato dextrose broth, with wheat bran as an inducing medium, and its ability to dechlorinate eight compounds was determined. The compounds were 2-chlorophenol, 4-chlorophenol, 2,4-dichlorophenol, 2,6-dichlorophenol, 2,4,5-trichlorophenol, 2,4,6-trichlorophenol, heptachlor and pentachlorophenol. A range of parameters for the dechlorination of some compounds was tested, including incubation period, pH, initial substrate concentration, temperature, and enzyme quantity. The oxygen consumption was determined during each dechlorination process, under pre-determined optimum conditions. The changes in chemical structure of the compounds were also determined, by using FTIR analysis, following dechlorination of test chlorophenolics. Strong interactions were found to lead to the reactivity of hydroxyl groups in some cases and chlorine atoms were released from the benzene ring. The changes in compound toxicity were monitored before and after enzymatic treatment, using Microtox. Quantitative structure-activity relationships for the toxicity of the chlorinated compounds were developed. Consequently, the toxic activity of the test compounds was controlled by electrophilic index and electronic properties.

  1. Parental Involvement and Student Motivation: A Quantitative Study of the Relationship between Student Goal Orientation and Student Perceptions of Parental Involvement among 5th Grade Students

    ERIC Educational Resources Information Center

    Mendoza, Christine Daryabigi

    2012-01-01

    The purpose of this study was to examine a possible relationship between student perceptions of parental involvement and student goal orientation for an ethnically diverse fifth grade elementary population from high-poverty schools. This study was quantitative in nature and employed the Patterns of Adaptive Learning Scales (PALS) to assess the…

  2. Structure-property study of keto-ether polyimides

    NASA Technical Reports Server (NTRS)

    Dezern, James F.; Croall, Catharine I.

    1991-01-01

    As part of an on-going effort to develop an understanding of how changes in the chemical structure affect polymer properties, an empirical study was performed on polyimides containing only ether and/or carbonyl connecting groups in the polymer backbone. During the past two decades the structure-property relationships in linear aromatic polyimides have been extensively investigated. More recently, work has been performed to study the effect of isomeric attachment of keto-ether polyimides on properties such as glass transition temperature and solubility. However, little work has been reported on the relation of polyimide structure to mechanical properties. The purpose of this study was to determine the effect of structural changes in the backbone of keto-ether polyimides on their mechanical properties, specifically, unoriented thin film tensile properties. This study was conducted in two stages. The purpose of the initial stage was to examine the physical and mechanical properties of a representative group (four) of polyimide systems to determine the optimum solvent and cure cycle requirements. These optimum conditions were then utilized in the second stage to prepare films of keto-ether polyimides which were evaluated for mechanical and physical properties. All of the polyimides were prepared using isomers of oxydianiline (ODA) and diaminobenzophenone (DABP) in combination with 3,3',4,4'-benzophenonetetracarboxylic dianhydride (BTDA) and 4,4'-oxydiphthalic anhydride (ODPA).

  3. Novel aliphatic lipid-based diesters for use in lubricant formulations: Structure property investigations

    NASA Astrophysics Data System (ADS)

    Raghunanan, Latchmi Cindy

    Structure-property relationships are increasingly valued for the identification of specifically engineered materials with properties optimized for targeted application(s). In this work, linear and branched diesters for use in lubricant formulations are prepared from lipid-based oleochemicals and their structure-property relationships reported. It is shown that the branched diesters possess exceptional physical property profiles, including suppression of crystallization, and are superior alternatives for use in lubricant formulations. For the linear aliphatic diesters, both high and low temperature properties were predictable functions of total chain length, and both were differently influenced by the fatty acid versus diol chain length. Symmetry did not influence either, although thermal stability decreased and thermal transition temperatures increased with increasing saturation. All of the linear diesters demonstrated Newtonian flow behaviour. Viscosity was also predictable as a function of total chain length; any microstructural features due to structural effects were superseded by mass effects.

  4. Assessment of quantitative structure-activity relationship of toxicity prediction models for Korean chemical substance control legislation

    PubMed Central

    Kim, Kwang-Yon; Shin, Seong Eun; No, Kyoung Tai

    2015-01-01

    Objectives For successful adoption of legislation controlling registration and assessment of chemical substances, it is important to obtain sufficient toxicological experimental evidence and other related information. It is also essential to obtain a sufficient number of predicted risk and toxicity results. Particularly, methods used in predicting toxicities of chemical substances during acquisition of required data, ultimately become an economic method for future dealings with new substances. Although the need for such methods is gradually increasing, the-required information about reliability and applicability range has not been systematically provided. Methods There are various representative environmental and human toxicity models based on quantitative structure-activity relationships (QSAR). Here, we secured the 10 representative QSAR-based prediction models and its information that can make predictions about substances that are expected to be regulated. We used models that predict and confirm usability of the information expected to be collected and submitted according to the legislation. After collecting and evaluating each predictive model and relevant data, we prepared methods quantifying the scientific validity and reliability, which are essential conditions for using predictive models. Results We calculated predicted values for the models. Furthermore, we deduced and compared adequacies of the models using the Alternative non-testing method assessed for Registration, Evaluation, Authorization, and Restriction of Chemicals Substances scoring system, and deduced the applicability domains for each model. Additionally, we calculated and compared inclusion rates of substances expected to be regulated, to confirm the applicability. Conclusions We evaluated and compared the data, adequacy, and applicability of our selected QSAR-based toxicity prediction models, and included them in a database. Based on this data, we aimed to construct a system that can be used

  5. Quantitative structure-activity relationship modeling of the toxicity of organothiophosphate pesticides to Daphnia magna and Cyprinus carpio.

    PubMed

    Zvinavashe, Elton; Du, Tingting; Griff, Tamas; van den Berg, Hans H J; Soffers, Ans E M F; Vervoort, Jacques; Murk, Albertinka J; Rietjens, Ivonne M C M

    2009-06-01

    Within the REACH regulatory framework in the EU, quantitative structure-activity relationships (QSAR) models are expected to help reduce the number of animals used for experimental testing. The objective of this study was to develop QSAR models to describe the acute toxicity of organothiophosphate pesticides to aquatic organisms. Literature data sets for acute toxicity data of organothiophosphates to fish and one data set from experiments with 15 organothiophosphates on Daphniamagna performed in the present study were used to establish QSARs based on quantum mechanically derived molecular descriptors. The logarithm of the octanol/water partition coefficient, logK(ow,) the energy of the lowest unoccupied molecular orbital, E(lumo), and the energy of the highest occupied molecular orbital, E(homo) were used as descriptors. Additionally, it was investigated if toxicity data for the invertebrate D. magna could be used to build a QSAR model to predict toxicity to fish. Suitable QSAR models (0.80

  6. Acaricidal and quantitative structure activity relationship of monoterpenes against the two-spotted spider mite, Tetranychus urticae.

    PubMed

    Badawy, Mohamed E I; El-Arami, Sailan A A; Abdelgaleil, Samir A M

    2010-11-01

    The acaricidal activity of 12 monoterpenes against the two-spotted spider mite, Tetranychus urticae Koch, was examined using fumigation and direct contact application methods. Cuminaldehyde and (-)-linalool showed the highest fumigant toxicity with LC(50) = 0.31 and 0.56 mg/l, respectively. The other monoterpenes exhibited a strong fumigant toxicity, the LC(50) values ranging from 1.28 to 8.09 mg/l, except camphene, which was the least effective (LC(50) = 61.45 mg/l). Based on contact activity, the results were rather different: menthol displayed the highest acaricidal activity (LC(50) = 128.53 mg/l) followed by thymol (172.0 mg/l), geraniol (219.69 mg/l) and (-)-limonene (255.44 mg/l); 1-8-cineole, cuminaldehyde and (-)-linalool showed moderate toxicity. At 125 mg/l, (-)-Limonene and (-)-carvone caused the highest egg mortality among the tested compounds (70.6 and 66.9% mortality, respectively). In addition, the effect of molecular descriptors was also analyzed using the quantitative structure activity relationship (QSAR) procedure. The QSAR model showed excellent agreement between the estimated and experimentally measured toxicity parameter (LC(50)) for the tested monoterpenes and the fumigant activity increased significantly with the vapor pressure. Comparing the results of the fumigant and contact toxicity assays of monoterpenes against T. urticae with the results of acetylcholinesterase (AChE) inhibitory effect revealed that some of the tested compounds showed a strong acaricidal activity and a potent AChE inhibitory activity, such as cuminaldehyde, (-)-linalool, (-)-limonene and menthol. However, other compounds such as (-)-carvone revealed a strong fumigant activity but a weak AChE inhibitory activity.

  7. Synthesis and quantitative structure-activity relationship (QSAR) study of novel isoxazoline and oxime derivatives of podophyllotoxin as insecticidal agents.

    PubMed

    Wang, Yi; Shao, Yonghua; Wang, Yangyang; Fan, Lingling; Yu, Xiang; Zhi, Xiaoyan; Yang, Chun; Qu, Huan; Yao, Xiaojun; Xu, Hui

    2012-08-29

    In continuation of our program aimed at the discovery and development of natural-product-based insecticidal agents, 33 isoxazoline and oxime derivatives of podophyllotoxin modified in the C and D rings were synthesized and their structures were characterized by Proton nuclear magnetic resonance ((1)H NMR), high-resolution mass spectrometry (HRMS), electrospray ionization-mass spectrometry (ESI-MS), optical rotation, melting point (mp), and infrared (IR) spectroscopy. The stereochemical configurations of compounds 5e, 5f, and 9f were unambiguously determined by X-ray crystallography. Their insecticidal activity was evaluated against the pre-third-instar larvae of northern armyworm, Mythimna separata (Walker), in vivo. Compounds 5e, 9c, 11g, and 11h especially exhibited more promising insecticidal activity than toosendanin, a commercial botanical insecticide extracted from Melia azedarach . A genetic algorithm combined with multiple linear regression (GA-MLR) calculation is performed by the MOBY DIGS package. Five selected descriptors are as follows: one two-dimensional (2D) autocorrelation descriptor (GATS4e), one edge adjacency indice (EEig06x), one RDF descriptor (RDF080v), one three-dimensional (3D) MoRSE descriptor (Mor09v), and one atom-centered fragment (H-052) descriptor. Quantitative structure-activity relationship studies demonstrated that the insecticidal activity of these compounds was mainly influenced by many factors, such as electronic distribution, steric factors, etc. For this model, the standard deviation error in prediction (SDEP) is 0.0592, the correlation coefficient (R(2)) is 0.861, and the leave-one-out cross-validation correlation coefficient (Q(2)loo) is 0.797.

  8. Three dimensional quantitative structure-toxicity relationship modeling and prediction of acute toxicity for organic contaminants to algae.

    PubMed

    Jin, Xiangqin; Jin, Minghao; Sheng, Lianxi

    2014-08-01

    Although numerous chemicals have been identified to have significant toxicological effect on aquatic organisms, there is still lack of a reliable, high-throughput approach to evaluate, screen and monitor the presence of organic contaminants in aquatic system. In the current study, we proposed a synthetic pipeline to automatically model and predict the acute toxicity of chemicals to algae. In the procedure, a new alignment-free three dimensional (3D) structure characterization method was described and, with this method, several 3D-quantitative structure-toxicity relationship (3D-QSTR) models were developed, from which two were found to exhibit strong internal fitting ability and high external predictive power. The best model was established by Gaussian process (GP), which was further employed to perform extrapolation on a random compound library consisting of 1014 virtually generated substituted benzenes. It was found that (i) substitution number can only exert slight influence on chemical׳s toxicity, but low-substituted benzenes seem to have higher toxicity than those of high-substituted entities, and (ii) benzenes substituted by nitro group and halogens exhibit high acute toxicity as compared to other substituents such as methyl and carboxyl groups. Subsequently, several promising candidates suggested by computational prediction were assayed by using a standard algal growth inhibition test. Consequently, four substituted benzenes, namely 2,3-dinitrophenol, 2-chloro-4-nitroaniline, 1,2,3-trinitrobenzene and 3-bromophenol, were determined to have high acute toxicity to Scenedesmus obliquus, with their EC50 values of 2.5±0.8, 10.5±2.1, 1.4±0.2 and 42.7±5.4μmol/L, respectively.

  9. Synthesis and quantitative structure activity relationship (QSAR) of arylidene (benzimidazol-1-yl)acetohydrazones as potential antibacterial agents.

    PubMed

    El-Kilany, Yeldez; Nahas, Nariman M; Al-Ghamdi, Mariam A; Badawy, Mohamed E I; El Ashry, El Sayed H

    2015-01-01

    Ethyl (benzimidazol-1-yl)acetate was subjected to hydrazinolysis with hydrazine hydrate to give (benzimidazol-1-yl)acetohydrazide. The latter was reacted with various aromatic aldehydes to give the respective arylidene (1H-benzimidazol-1-yl)acetohydrazones. Solutions of the prepared hydrazones were found to contain two geometric isomers. Similarly (2-methyl-benzimidazol-1-yl)acetohydrazide was reacted with various aldehydes to give the corresponding hydrazones. The antibacterial activity was evaluated in vitro by minimum inhibitory concentration (MIC) against Agrobacterium tumefaciens (A. tumefaciens), Erwinia carotovora (E. carotovora), Corynebacterium fascians (C. fascians) and Pseudomonas solanacearum (P. solanacearum). MIC result demonstrated that salicylaldehyde(1H-benzimidazol-1-yl)acetohydrazone (4) was the most active compound (MIC = 20, 35, 25 and 30 mg/L against A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively). Quantitative structure activity relationship (QSAR) investigation using Hansch analysis was applied to find out the correlation between antibacterial activity and physicochemical properties. Various physicochemical descriptors and experimentally determined MIC values for different microorganisms were used as independent and dependent variables, respectively. pMICs of the compounds exhibited good correlation (r = 0.983, 0.914, 0.960 and 0.958 for A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively) with the prediction made by the model. QSAR study revealed that the hydrophobic parameter (ClogP), the aqueous solubility (LogS), calculated molar refractivity, topological polar surface area and hydrogen bond acceptor were found to have overall significant correlation with antibacterial activity. The statistical results of training set, correlation coefficient (r and r (2)), the ratio between regression and residual variances (f, Fisher's statistic), the standard error of estimates and

  10. Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium Falciparum cysteine proteases inhibitors

    NASA Astrophysics Data System (ADS)

    Teixeira, Cátia; Gomes, José R. B.; Couesnon, Thierry; Gomes, Paula

    2011-08-01

    Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were conducted on a series (39 molecules) of peptidyl vinyl sulfone derivatives as potential Plasmodium Falciparum cysteine proteases inhibitors. Two different methods of alignment were employed: (i) a receptor-docked alignment derived from the structure-based docking algorithm GOLD and (ii) a ligand-based alignment using the structure of one of the ligands derived from a crystal structure from the PDB databank. The best predictions were obtained for the receptor-docked alignment with a CoMFA standard model ( q 2 = 0.696 and r 2 = 0.980) and with CoMSIA combined electrostatic, and hydrophobic fields ( q 2 = 0.711 and r 2 = 0.992). Both models were validated by a test set of nine compounds and gave satisfactory predictive r 2 pred values of 0.76 and 0.74, respectively. CoMFA and CoMSIA contour maps were used to identify critical regions where any change in the steric, electrostatic, and hydrophobic fields may affect the inhibitory activity, and to highlight the key structural features required for biological activity. Moreover, the results obtained from 3D-QSAR analyses were superimposed on the Plasmodium Falciparum cysteine proteases active site and the main interactions were studied. The present work provides extremely useful guidelines for future structural modifications of this class of compounds towards the development of superior antimalarials.

  11. Development of acute toxicity quantitative structure activity relationships (QSAR) and their use in linear alkylbenzene sulfonate species sensitivity distributions.

    PubMed

    Belanger, Scott E; Brill, Jessica L; Rawlings, Jane M; Price, Brad B

    2016-07-01

    Linear Alkylbenzene Sulfonate (LAS) is high tonnage and widely dispersed anionic surfactant used by the consumer products sector. A range of homologous structures are used in laundry applications that differ primarily on the length of the hydrophobic alkyl chain. This research summarizes the development of a set of acute toxicity QSARs (Quantitative Structure Activity Relationships) for fathead minnows (Pimephales promelas) and daphnids (Daphnia magna, Ceriodaphnia dubia) using accepted test guideline approaches. A series of studies on pure chain length LAS from C10 to C14 were used to develop the QSARs and the robustness of the QSARs was tested by evaluation of two technical mixtures of differing compositions. All QSARs were high quality (R(2) were 0.965-0.997, p < 0.0001). Toxicity normalization employing QSARs is used to interpret a broader array of tests on LAS chain length materials to a diverse group of test organisms with the objective of developing Species Sensitivity Distributions (SSDs) for various chain lengths of interest. Mixtures include environmental distributions measured from exposure monitoring surveys of wastewater effluents, various commercial mixtures, or specific chain lengths. SSD 5th percentile hazardous concentrations (HC5s) ranged from 0.129 to 0.254 mg/L for wastewater effluents containing an average of 11.26-12 alkyl carbons. The SSDs are considered highly robust given the breadth of species (n = 19), use of most sensitive endpoints from true chronic studies and the quality of the underlying statistical properties of the SSD itself. The data continue to indicate a low hazard to the environment relative to expected environmental concentrations.

  12. Quantitative structure-interaction relationship analysis of 1,4-dihydropyridine drugs in concomitant administration with grapefruit juice.

    PubMed

    Uesawa, Y; Mohri, K

    2012-03-01

    Quantitative structure-interaction relationship (QSIR) analyses of 1,4-dihydropyridine drugs were performed on grapefruit juice interaction potentials to characterize the interaction and evaluate drugs not yet tested in clinical research. AUC ratios of drugs with and without grapefruit juice ingestion were estimated as grapefruit juice interaction potentials from clinical studies on dihydropyridine drugs such as amlodipine, azelnidipine, benidipine, cilnidipine, felodipine, manidipine, nicardipine, nifedipine, nimodipine, nisoldipine, and pranidipine. The minimal energy conformation in each dihydropyridine drug was searched for using Merck Molecular Force Field (MMFFaq), and then geometry optimization was performed by density-functional-theory (DFT) calculation (B3LYP/6-31G**). The geometric, electronic, and physicochemical features including molecular size, dipole moment, total energy, HOMO/LUMO energies, and logP values were then obtained. Dragon descriptors were also calculated by optimized 3D-structures. The relation between the potentials and over 1000 of the molecular properties was investigated using statistical techniques including partial least squares analysis with genetic algorithm (GA-PLS) to a variable subset selection. Some PLS regression equations including logP values and dragon descriptors as explanatory variables were constructed in which the maximal contribution coefficient was 94%. These models could be applied to estimate the interaction potentials of other dihydropyridine drugs that have gone unreported in interactions with drugs such as aranidipine, barnidipine, clevidipine, lemildipine, lercanidipine, niguldipine, niludipine, and nilvadipine. In the assessment of major dihydropyridines, amlodipine was found to be the safest drug to avoid interactions among the drugs investigated in the present study.

  13. Investigation on quantitative structure activity relationships and pharmacophore modeling of a series of mGluR2 antagonists.

    PubMed

    Zhang, Meng-Qi; Zhang, Xiao-Le; Li, Yan; Fan, Wen-Jia; Wang, Yong-Hua; Hao, Ming; Zhang, Shu-Wei; Ai, Chun-Zhi

    2011-01-01

    MGluR2 is G protein-coupled receptor that is targeted for diseases like anxiety, depression, Parkinson's disease and schizophrenia. Herein, we report the three-dimensional quantitative structure-activity relationship (3D-QSAR) studies of a series of 1,3-dihydrobenzo[ b][1,4]diazepin-2-one derivatives as mGluR2 antagonists. Two series of models using two different activities of the antagonists against rat mGluR2, which has been shown to be very similar to the human mGluR2, (activity I: inhibition of [(3)H]-LY354740; activity II: mGluR2 (1S,3R)-ACPD inhibition of forskolin stimulated cAMP.) were derived from datasets composed of 137 and 69 molecules respectively. For activity I study, the best predictive model obtained from CoMFA analysis yielded a Q(2) of 0.513, R(2) (ncv) of 0.868, R(2) (pred) = 0.876, while the CoMSIA model yielded a Q(2) of 0.450, R(2) (ncv) = 0.899, R(2) (pred) = 0.735. For activity II study, CoMFA model yielded statistics of Q(2) = 0.5, R(2) (ncv) = 0.715, R(2) (pred) = 0.723. These results prove the high predictability of the models. Furthermore, a combined analysis between the CoMFA, CoMSIA contour maps shows that: (1) Bulky substituents in R(7), R(3) and position A benefit activity I of the antagonists, but decrease it when projected in R(8) and position B; (2) Hydrophilic groups at position A and B increase both antagonistic activity I and II; (3) Electrostatic field plays an essential rule in the variance of activity II. In search for more potent mGluR2 antagonists, two pharmacophore models were developed separately for the two activities. The first model reveals six pharmacophoric features, namely an aromatic center, two hydrophobic centers, an H-donor atom, an H-acceptor atom and an H-donor site. The second model shares all features of the first one and has an additional acceptor site, a positive N and an aromatic center. These models can be used as guidance for the development of new mGluR2 antagonists of high activity and selectivity

  14. Water solubility of selected C9-C18 alkanes using a slow-stir technique: Comparison to structure - property models.

    PubMed

    Letinski, Daniel J; Parkerton, Thomas F; Redman, Aaron D; Connelly, Martin J; Peterson, Brian

    2016-05-01

    Aqueous solubility is a fundamental physical-chemical substance property that strongly influences the distribution, fate and effects of chemicals upon release into the environment. Experimental water solubility was determined for 18 selected C9-C18 normal, branched and cyclic alkanes. A slow-stir technique was applied to obviate emulsion formation, which historically has resulted in significant overestimation of the aqueous solubility of such hydrophobic liquid compounds. Sensitive GC-MS based methods coupled with contemporary sample extraction techniques were employed to enable reproducible analysis of low parts-per billion aqueous concentrations. Water solubility measurements for most of the compounds investigated, are reported for the first time expanding available data for branched and cyclic alkanes. Measured water solubilities spanned four orders of magnitude ranging from 0.3 μg/L to 250 μg/L. Good agreement was observed for selected alkanes tested in this work and reported in earlier literature demonstrating the robustness of the slow-stir water solubility technique. Comparisons of measured alkane water solubilities were also made with those predicted by commonly used quantitative structure-property relationship models (e.g. SPARC, EPIWIN, ACD/Labs). Correlations are also presented between alkane measured water solubilities and molecular size parameters (e.g. molar volume, solvent accessible molar volume) affirming a mechanistic description of empirical aqueous solubility results and prediction previously reported for a more limited set of alkanes.

  15. Reduced short term memory in congenital adrenal hyperplasia (CAH) and its relationship to spatial and quantitative performance.

    PubMed

    Collaer, Marcia L; Hindmarsh, Peter C; Pasterski, Vickie; Fane, Briony A; Hines, Melissa

    2016-02-01

    Girls and women with classical congenital adrenal hyperplasia (CAH) experience elevated androgens prenatally and show increased male-typical development for certain behaviors. Further, individuals with CAH receive glucocorticoid (GC) treatment postnatally, and this GC treatment could have negative cognitive consequences. We investigated two alternative hypotheses, that: (a) early androgen exposure in females with CAH masculinizes (improves) spatial perception and quantitative abilities at which males typically outperform females, or (b) CAH is associated with performance decrements in these domains, perhaps due to reduced short-term-memory (STM). Adolescent and adult individuals with CAH (40 female and 29 male) were compared with relative controls (29 female and 30 male) on spatial perception and quantitative abilities as well as on Digit Span (DS) to assess STM and on Vocabulary to assess general intelligence. Females with CAH did not perform better (more male-typical) on spatial perception or quantitative abilities than control females, failing to support the hypothesis of cognitive masculinization. Rather, in the sample as a whole individuals with CAH scored lower on spatial perception (p ≤ .009), a quantitative composite (p ≤ .036), and DS (p ≤ .001), despite no differences in general intelligence. Separate analyses of adolescent and adult participants suggested the spatial and quantitative effects might be present only in adult patients with CAH; however, reduced DS performance was found in patients with CAH regardless of age group. Separate regression analyses showed that DS predicted both spatial perception and quantitative performance (both p ≤ .001), when age, sex, and diagnosis status were controlled. Thus, reduced STM in CAH patients versus controls may have more general cognitive consequences, potentially reducing spatial perception and quantitative skills. Although hyponatremia or other aspects of salt-wasting crises or additional hormone

  16. Effect of wet grinding on structural properties of ball clay

    SciTech Connect

    Purohit, A. Chander, S.; Dhaka, M. S.; Hameed, A.; Singh, P.; Nehra, S. P.

    2015-05-15

    In this paper, the effect of wet grinding on structural properties of ball clay is undertaken. The wet grinding treatment was performed employing ball and vibro mills for different time spells of 2, 4, 8 and 16 hours. The structural properties were carried out using X-ray diffraction (XRD). The structure of ground samples is found to be simple cubic. The crystallographic parameters are calculated and slight change in lattice constant, inter planner spacing and particle size is observed with grinding treatment. The results are in agreement with the available literature.

  17. Receptor binding profiles and quantitative structure-affinity relationships of some 5-substituted-N,N-diallyltryptamines.

    PubMed

    Cozzi, Nicholas V; Daley, Paul F

    2016-02-01

    N,N-Diallyltryptamine (DALT) and 5-methoxy-N,N-diallyltryptamine (5-MeO-DALT) are two tryptamines synthesized and tested by Alexander Shulgin. In self-experiments, 5-MeO-DALT was reported to be psychoactive in the 12-20mg range, while the unsubstituted compound DALT had few discernible effects in the 42-80 mg range. Recently, 5-MeO-DALT has been used in nonmedical settings for its psychoactive effects, but these effects have been poorly characterized and little is known of its pharmacological properties. We extended the work of Shulgin by synthesizing additional 5-substituted-DALTs. We then compared them to DALT and 5-MeO-DALT for their binding affinities at 45 cloned receptors and transporter proteins. Based on in vitro binding affinity, we identified 27 potential receptor targets for the 5-substituted-DALT compounds. Five of the DALT compounds had affinity in the 10-80 nM range for serotonin 5-HT1A and 5-HT2B receptors, while the affinity of DALT itself at 5-HT1A receptors was slightly lower at 100 nM. Among the 5-HT2 subtypes, the weakest affinity was at 5-HT2A receptors, spanning 250-730 nM. Five of the DALT compounds had affinity in the 50-400 nM range for serotonin 5-HT1D, 5-HT6, and 5-HT7 receptors; again, it was the unsubstituted DALT that had the weakest affinity at all three subtypes. The test drugs had even weaker affinity for 5-HT1B, 5-HT1E, and 5-HT5A subtypes and little or no affinity for the 5-HT3 subtype. These compounds also had generally nanomolar affinities for adrenergic α2A, α2B, and α2C receptors, sigma receptors σ1 and σ2, histamine H1 receptors, and norepinephrine and serotonin uptake transporters. They also bound to other targets in the nanomolar-to-low micromolar range. Based on these binding results, it is likely that multiple serotonin receptors, as well as several nonserotonergic sites are important for the psychoactive effects of DALT drugs. To learn whether any quantitative structure-affinity relationships existed, we evaluated

  18. Investigation on Quantitative Structure Activity Relationships and Pharmacophore Modeling of a Series of mGluR2 Antagonists

    PubMed Central

    Zhang, Meng-Qi; Zhang, Xiao-Le; Li, Yan; Fan, Wen-Jia; Wang, Yong-Hua; Hao, Ming; Zhang, Shu-Wei; Ai, Chun-Zhi

    2011-01-01

    MGluR2 is G protein-coupled receptor that is targeted for diseases like anxiety, depression, Parkinson’s disease and schizophrenia. Herein, we report the three-dimensional quantitative structure–activity relationship (3D-QSAR) studies of a series of 1,3-dihydrobenzo[ b][1,4]diazepin-2-one derivatives as mGluR2 antagonists. Two series of models using two different activities of the antagonists against rat mGluR2, which has been shown to be very similar to the human mGluR2, (activity I: inhibition of [3H]-LY354740; activity II: mGluR2 (1S,3R)-ACPD inhibition of forskolin stimulated cAMP.) were derived from datasets composed of 137 and 69 molecules respectively. For activity I study, the best predictive model obtained from CoMFA analysis yielded a Q2 of 0.513, R2 ncv of 0.868, R2 pred = 0.876, while the CoMSIA model yielded a Q2 of 0.450, R2 ncv = 0.899, R2 pred = 0.735. For activity II study, CoMFA model yielded statistics of Q2 = 0.5, R2 ncv = 0.715, R2 pred = 0.723. These results prove the high predictability of the models. Furthermore, a combined analysis between the CoMFA, CoMSIA contour maps shows that: (1) Bulky substituents in R7, R3 and position A benefit activity I of the antagonists, but decrease it when projected in R8 and position B; (2) Hydrophilic groups at position A and B increase both antagonistic activity I and II; (3) Electrostatic field plays an essential rule in the variance of activity II. In search for more potent mGluR2 antagonists, two pharmacophore models were developed separately for the two activities. The first model reveals six pharmacophoric features, namely an aromatic center, two hydrophobic centers, an H-donor atom, an H-acceptor atom and an H-donor site. The second model shares all features of the first one and has an additional acceptor site, a positive N and an aromatic center. These models can be used as guidance for the development of new mGluR2 antagonists of high activity and selectivity. This work is the first report on 3

  19. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

    PubMed

    Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-lin; Du, Guan-hua

    2016-05-01

    A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives.

  20. Impact of observational incompleteness on the structural properties of protein interaction networks

    NASA Astrophysics Data System (ADS)

    Kuhnt, Mathias; Glauche, Ingmar; Greiner, Martin

    2007-01-01

    The observed structure of protein interaction networks is corrupted by many false positive/negative links. This observational incompleteness is abstracted as random link removal and a specific, experimentally motivated (spoke) link rearrangement. Their impact on the structural properties of gene-duplication-and-mutation network models is studied. For the degree distribution a curve collapse is found, showing no sensitive dependence on the link removal/rearrangement strengths and disallowing a quantitative extraction of model parameters. The spoke link rearrangement process moves other structural observables, like degree correlations, cluster coefficient and motif frequencies, closer to their counterparts extracted from the yeast data. This underlines the importance to take a precise modeling of the observational incompleteness into account when network structure models are to be quantitatively compared to data.

  1. Reduced short term memory in congenital adrenal hyperplasia (CAH) and its relationship to spatial and quantitative performance

    PubMed Central

    Collaer, Marcia L.; Hindmarsh, Peter C.; Pasterski, Vickie; Fane, Briony A.; Hines, Melissa

    2015-01-01

    Girls and women with classical congenital adrenal hyperplasia (CAH) experience elevated androgens prenatally and show increased male-typical development for certain behaviors. Further, individuals with CAH receive glucocorticoid (GC) treatment postnatally, and this GC treatment could have negative cognitive consequences. We investigated two alternative hypotheses, that: (a) early androgen exposure in females with CAH masculinizes (improves) spatial perception and quantitative abilities at which males typically outperform females, or (b) CAH is associated with performance decrements in these domains, perhaps due to reduced short-term-memory (STM). Adolescent and adult individuals with CAH (40 female and 29 male) were compared with relative controls (29 female and 30 male) on spatial perception and quantitative abilities as well as on Digit Span (DS) to assess STM and on Vocabulary to assess general intelligence. Females with CAH did not perform better (more male-typical) on spatial perception or quantitative abilities than control females, failing to support the hypothesis of cognitive masculinization. Rather, in the sample as a whole individuals with CAH scored lower on spatial perception (p ≤ .009), a quantitative composite (p ≤ .036), and DS (p ≤ .001), despite no differences in general intelligence. Separate analyses of adolescent and adult participants suggested the spatial and quantitative effects might be present only in adult patients with CAH; however, reduced DS performance was found in patients with CAH regardless of age group. Separate regression analyses showed that DS predicted both spatial perception and quantitative performance (both p ≤ .001), when age, sex, and diagnosis status were controlled. Thus, reduced STM in CAH patients versus controls may have more general cognitive consequences, potentially reducing spatial perception and quantitative skills. Although hyponatremia or other aspects of salt-wasting crises, or additional hormone

  2. Perspective: Composition-structure-property mapping in high-throughput experiments: Turning data into knowledge

    NASA Astrophysics Data System (ADS)

    Hattrick-Simpers, Jason R.; Gregoire, John M.; Kusne, A. Gilad

    2016-05-01

    With their ability to rapidly elucidate composition-structure-property relationships, high-throughput experimental studies have revolutionized how materials are discovered, optimized, and commercialized. It is now possible to synthesize and characterize high-throughput libraries that systematically address thousands of individual cuts of fabrication parameter space. An unresolved issue remains transforming structural characterization data into phase mappings. This difficulty is related to the complex information present in diffraction and spectroscopic data and its variation with composition and processing. We review the field of automated phase diagram attribution and discuss the impact that emerging computational approaches will have in the generation of phase diagrams and beyond.

  3. Novel anti-tumour barringenol-like triterpenoids from the husks of Xanthoceras sorbifolia Bunge and their three dimensional quantitative structure activity relationships analysis.

    PubMed

    Wang, Da; Su, Dan; Yu, Bin; Chen, Chuming; Cheng, Li; Li, Xianzhe; Xi, Ronggang; Gao, Huiyuan; Wang, Xiaobo

    2017-01-01

    The high edible oil content of Xanthoceras sorbifolia Bunge seeds contributes to its economic value. In this study, we analysed the barrigenol-like triterpenoids derived from X. sorbifolia husks. We also identified anti-tumour agents that could enhance the health benefits and medicinal value of X. sorbifolia. We isolated 10 barrigenol triterpenoids, including six new compounds (1-6) and four known compounds (7-10). New compounds 3 and 5 showed significant inhibitory activity against the proliferation of three human tumour cell lines, namely, HepG2, HCT-116 and U87-MG. We determined the relationship between the structures and inhibitory activity of 25 barrigenol triterpenoids and 15 penta-cyclic triterpenoids through analysis of three-dimensional quantitative structure activity relationships (3D-QSAR). The isolation of novel barrigenol derivatives with anti-tumour activity from X. sorbifolia implied that husks of this plant may be a good source of anti-tumour agents.

  4. Comparison between 5,10,15,20-tetraaryl- and 5,15-diarylporphyrins as photosensitizers: synthesis, photodynamic activity, and quantitative structure-activity relationship modeling.

    PubMed

    Banfi, Stefano; Caruso, Enrico; Buccafurni, Loredana; Murano, Roberto; Monti, Elena; Gariboldi, Marzia; Papa, Ester; Gramatica, Paola

    2006-06-01

    The synthesis of a panel of seven nonsymmetric 5,10,15,20-tetraarylporphyrins, 13 symmetric and nonsymmetric 5,15-diarylporphyrins, and one 5,15-diarylchlorin is described. In vitro photodynamic activities on HCT116 human colon adenocarcinoma cells were evaluated by standard cytotoxicity assays. A predictive quantitative structure-activity relationship (QSAR) regression model, based on theoretical holistic molecular descriptors, of a series of 34 tetrapyrrolic photosensitizers (PSs), including the 24 compounds synthesized in this work, was developed to describe the relationship between structural features and photodynamic activity. The present study demonstrates that structural features significantly influence the photodynamic activity of tetrapyrrolic derivatives: diaryl compounds were more active with respect to the tetraarylporphyrins, and among the diaryl derivatives, hydroxy-substituted compounds were more effective than the corresponding methoxy-substituted ones. Furthermore, three monoarylporphyrins, isolated as byproducts during diarylporphyrin synthesis, were considered for both photodynamic and QSAR studies; surprisingly they were found to be particularly active photosensitizers.

  5. Augmented multivariate image analysis applied to quantitative structure-activity relationship modeling of the phytotoxicities of benzoxazinone herbicides and related compounds on problematic weeds.

    PubMed

    Freitas, Mirlaine R; Matias, Stella V B G; Macedo, Renato L G; Freitas, Matheus P; Venturin, Nelson

    2013-09-11

    Two of major weeds affecting cereal crops worldwide are Avena fatua L. (wild oat) and Lolium rigidum Gaud. (rigid ryegrass). Thus, development of new herbicides against these weeds is required; in line with this, benzoxazinones, their degradation products, and analogues have been shown to be important allelochemicals and natural herbicides. Despite earlier structure-activity studies demonstrating that hydrophobicity (log P) of aminophenoxazines correlates to phytotoxicity, our findings for a series of benzoxazinone derivatives do not show any relationship between phytotoxicity and log P nor with other two usual molecular descriptors. On the other hand, a quantitative structure-activity relationship (QSAR) analysis based on molecular graphs representing structural shape, atomic sizes, and colors to encode other atomic properties performed very accurately for the prediction of phytotoxicities of these compounds against wild oat and rigid ryegrass. Therefore, these QSAR models can be used to estimate the phytotoxicity of new congeners of benzoxazinone herbicides toward A. fatua L. and L. rigidum Gaud.

  6. Why are there race/ethnic differences in adult body mass index-adiposity relationships? A quantitative critical review.

    PubMed

    Heymsfield, S B; Peterson, C M; Thomas, D M; Heo, M; Schuna, J M

    2016-03-01

    Body mass index (BMI) is now the most widely used measure of adiposity on a global scale. Nevertheless, intense discussion centers on the appropriateness of BMI as a phenotypic marker of adiposity across populations differing in race and ethnicity. BMI-adiposity relations appear to vary significantly across race/ethnic groups, but a collective critical analysis of these effects establishing their magnitude and underlying body shape/composition basis is lacking. Accordingly, we systematically review the magnitude of these race-ethnic differences across non-Hispanic (NH) white, NH black and Mexican American adults, their anatomic body composition basis and potential biologically linked mechanisms, using both earlier publications and new analyses from the US National Health and Nutrition Examination Survey. Our collective observations provide a new framework for critically evaluating the quantitative relations between BMI and adiposity across groups differing in race and ethnicity; reveal new insights into BMI as a measure of adiposity across the adult age-span; identify knowledge gaps that can form the basis of future research and create a quantitative foundation for developing BMI-related public health recommendations.

  7. Using metal-ligand binding characteristics to predict metal toxicity: quantitative ion character-activity relationships (QICARs).

    PubMed Central

    Newman, M C; McCloskey, J T; Tatara, C P

    1998-01-01

    Ecological risk assessment can be enhanced with predictive models for metal toxicity. Modelings of published data were done under the simplifying assumption that intermetal trends in toxicity reflect relative metal-ligand complex stabilities. This idea has been invoked successfully since 1904 but has yet to be applied widely in quantitative ecotoxicology. Intermetal trends in toxicity were successfully modeled with ion characteristics reflecting metal binding to ligands for a wide range of effects. Most models were useful for predictive purposes based on an F-ratio criterion and cross-validation, but anomalous predictions did occur if speciation was ignored. In general, models for metals with the same valence (i.e., divalent metals) were better than those combining mono-, di-, and trivalent metals. The softness parameter (sigma p) and the absolute value of the log of the first hydrolysis constant ([symbol: see text] log KOH [symbol: see text]) were especially useful in model construction. Also, delta E0 contributed substantially to several of the two-variable models. In contrast, quantitative attempts to predict metal interactions in binary mixtures based on metal-ligand complex stabilities were not successful. PMID:9860900

  8. Why are there race/ethnic differences in adult body mass index–adiposity relationships? A quantitative critical review

    PubMed Central

    Heymsfield, S. B.; Peterson, C. M.; Thomas, D. M.; Heo, M.; Schuna, J. M.

    2016-01-01

    Summary Body mass index (BMI) is now the most widely used measure of adiposity on a global scale. Nevertheless, intense discussion centers on the appropriateness of BMI as a phenotypic marker of adiposity across populations differing in race and ethnicity. BMI-adiposity relations appear to vary significantly across race/ethnic groups, but a collective critical analysis of these effects establishing their magnitude and underlying body shape/composition basis is lacking. Accordingly, we systematically review the magnitude of these race-ethnic differences across non-Hispanic (NH) white, NH black and Mexican American adults, their anatomic body composition basis and potential biologically linked mechanisms, using both earlier publications and new analyses from the US National Health and Nutrition Examination Survey. Our collective observations provide a new framework for critically evaluating the quantitative relations between BMI and adiposity across groups differing in race and ethnicity; reveal new insights into BMI as a measure of adiposity across the adult age-span; identify knowledge gaps that can form the basis of future research and create a quantitative foundation for developing BMI-related public health recommendations. PMID:26663309

  9. Quantitative relationships between microstructures and electrochemical properties in Si core-SiOx shell nanoparticles for Li-ion battery anodes

    NASA Astrophysics Data System (ADS)

    Lee, Jeongeun; Koo, Jeongboon; Jang, Boyun; Kim, Sungsoo

    2016-10-01

    Nanoparticles having four different ratios of crystalline silicon (Si) cores and amorphous SiOx shells were synthesized by using a microwave-generated plasma. Their microstructures were analyzed to find quantitative relationships with electrochemical properties. By measuring XRD, SEM, HR-TEM, and Raman spectra of four samples with different core-shell microstructures, the quantitative fractions of crystalline Si core and amorphous SiOx shell in the nanoparticles were calculated. Also, electrochemical properties of the nanoparticles were measured and compared with the calculated fractions. The electrochemical properties such as the initial reversible capacity, the initial coulombic efficiency, and the capacity retention exhibited tendencies remarkably similar to those implied by the calculated fractions. Analysis of each sample's dQ/dV profile also gave us good evidence of understandable relationships between the fractions and electrochemical properties. Details of calculating the fractions from microstructural data are given, with suitable consideration having been given to the fact that several assumptions could lead to errors during the analysis. The approach introduced in this research offers a good means of analysis with which to further the optimal design of nanoparticle microstructure for Li-ion battery anodes.

  10. Quantitative structure-activity relationship of organosulphur compounds as soybean 15-lipoxygenase inhibitors using CoMFA and CoMSIA.

    PubMed

    Caballero, Julio; Fernández, Michael; Coll, Deysma

    2010-12-01

    Three-dimensional quantitative structure-activity relationship studies were carried out on a series of 28 organosulphur compounds as 15-lipoxygenase inhibitors using comparative molecular field analysis and comparative molecular similarity indices analysis. Quantitative information on structure-activity relationships is provided for further rational development and direction of selective synthesis. All models were carried out over a training set including 22 compounds. The best comparative molecular field analysis model only included steric field and had a good Q² = 0.789. Comparative molecular similarity indices analysis overcame the comparative molecular field analysis results: the best comparative molecular similarity indices analysis model also only included steric field and had a Q² = 0.894. In addition, this model predicted adequately the compounds contained in the test set. Furthermore, plots of steric comparative molecular similarity indices analysis field allowed conclusions to be drawn for the choice of suitable inhibitors. In this sense, our model should prove useful in future 15-lipoxygenase inhibitor design studies.

  11. Structural property of regulatory elements in human promoters

    NASA Astrophysics Data System (ADS)

    Cao, Xiao-Qin; Zeng, Jia; Yan, Hong

    2008-04-01

    The capacity of transcription factors to activate gene expression is encoded in the promoter sequences, which are composed of short regulatory motifs that function as transcription factor binding sites (TFBSs) for specific proteins. To the best of our knowledge, the structural property of TFBSs that controls transcription is still poorly understood. Rigidity is one of the important structural properties of DNA, and plays an important role in guiding DNA-binding proteins to the target sites efficiently. After analyzing the rigidity of 2897 TFBSs in 1871 human promoters, we show that TFBSs are generally more flexible than other genomic regions such as exons, introns, 3' untranslated regions, and TFBS-poor promoter regions. Furthermore, we find that the density of TFBSs is consistent with the average rigidity profile of human promoters upstream of the transcription start site, which implies that TFBSs directly influence the promoter structure. We also examine the local rigid regions probably caused by specific TFBSs such as the DNA sequence TATA(A/T)A(A/T) box, which may inhibit nucleosomes and thereby facilitate the access of transcription factors bound nearby. Our results suggest that the structural property of TFBSs accounts for the promoter structure as well as promoter activity.

  12. Relationship between Quantitative Adverse Plaque Features from Coronary CT Angiography and Downstream Impaired Myocardial Flow Reserve by 13N-Ammonia Positron Emission Tomography: A Pilot Study

    PubMed Central

    Dey, Damini; Zamudio, Mariana Diaz; Schuhbaeck, Annika; Orozco, Luis Eduardo Juarez; Otaki, Yuka; Gransar, Heidi; Li, Debiao; Germano, Guido; Achenbach, Stephan; Berman, Daniel S.; Meave, Aloha; Alexanderson, Erick; Slomka, Piotr J.

    2016-01-01

    Background We investigated the relationship of quantitative plaque features from coronary CT Angiography (CTA) and coronary vascular dysfunction by impaired myocardial flow reserve (MFR) by 13N-Ammonia Positron Emission Tomography (PET). Methods and Results Fifty-one patients (32 men, 62.4±9.5 years) underwent combined rest-stress 13N-ammonia PET and CTA scans by hybrid PET/CT. Regional MFR was measured from PET. From CTA, 153 arteries were evaluated by semi-automated software, computing arterial non-calcified plaque (NCP), low-density NCP (NCP<30 HU), calcified and total plaque volumes, and corresponding plaque burden (plaque volumex100%/vessel volume), stenosis, remodeling index, contrast density difference (maximum difference in luminal attenuation per unit area in the lesion), and plaque length. Quantitative stenosis, plaque burden and myocardial mass were combined by boosted ensemble machine-learning algorithm into a composite risk score to predict impaired MFR (MFR≤2.0) by PET, in each artery. Nineteen patients (37%) had impaired regional MFR in at least one territory, (41/153 vessels). Patients with impaired regional MFR had higher arterial NCP (32.4 vs.17.2 %), low-density NCP (7 vs 4 %) and total plaque burden (37 vs 19.3 %, p<0.02). In multivariable analysis with 10-fold cross-validation, NCP burden was the most significant predictor of impaired MFR (Odds Ratio 1.35, p=0.021). For prediction of impaired MFR with 10-fold cross-validation, receiver-operating-characteristics-area-under-the-curve for the composite score was 0.83 (95%CI:0.79–0.91), greater than for quantitative stenosis (0.66, 95%CI:0.57–0.76, p = 0.005). Conclusions Compared to stenosis, arterial NCP burden and a composite score combining quantitative stenosis and plaque burden from CTA significantly improves identification of downstream regional vascular dysfunction. PMID:26467104

  13. A quantitative analysis of the relationship between an online homework system and student achievement in pre-calculus

    NASA Astrophysics Data System (ADS)

    Babaali, Parisa; Gonzalez, Lidia

    2015-07-01

    Supporting student success in entry-level mathematics courses at the undergraduate level has and continues to be a challenge. Recently we have seen an increased reliance on technological supports including software to supplement more traditional in-class instruction. In this paper, we explore the effects on student performance of the use of a computer software program to supplement instruction in an entry-level mathematics course at the undergraduate level, specifically, a pre-calculus course. Relying on data from multiple sections of the course over various semesters, we compare student performance in those classes utilizing the software against those in which it was not used. Quantitative analysis of the data then leads us to conclusions about the effectiveness of the software as well as recommendations for future iterations of the course and others like it.

  14. Quantitative structure-activity relationships of insecticides and plant growth regulators: comparative studies toward understanding the molecular mechanism of action.

    PubMed Central

    Iwamura, H; Nishimura, K; Fujita, T

    1985-01-01

    Emphasis was put on the comparative quantitative structure-activity approaches to the exploration of action mechanisms of structurally different classes of compounds showing the same type of activity as well as those of the same type of compounds having different actions. Examples were selected from studies performed on insecticides and plant growth regulators, i.e., neurotoxic carbamates, phosphates, pyrethroids and DDT analogs, insect juvenile hormone mimics, and cytokinin agonistic and antagonistic compounds. Similarities and dissimilarities in structures required to elicit activity between compounds classes were revealed in terms of physicochemical parameters, provoking further exploration and evoking insights into the molecular mechanisms of action which may lead to the development of new structures having better qualities. PMID:3905379

  15. Study of the micro-structural properties of RISUG--a newly developed male contraceptive.

    PubMed

    Kumar, Sunil; Roy, Sohini; Chaudhury, Koel; Sen, Prasenjit; Guha, Sujoy K

    2008-07-01

    A new male contraceptive given the name RISUG (an acronym for reversible inhibition of sperm under guidance) and presently undergoing advanced clinical trials has been developed. When injected into the lumen of the vas deferens, its polyelectrolytic nature induces a surface charge imbalance on sperm membrane system leading to the leakage of enzymes essential for fertilization. Contact mode atomic force microscopy (AFM) has been used to analyze quantitatively the micro-structural properties of RISUG and its precipitate in various systems. Hydrolysis of the contraceptive gel resulted in the formation of pores of varying dimensions. RISUG being a highly charged molecule, as evident from zeta potential measurements, has a tendency to form a complex with ionic biomolecules present in the seminal plasma. This is supported by the experimental observations using AFM. This RISUG-biomolecule complex possibly acts as an ionic trap for spermatozoa passing through the vas deferens. Micro-structural properties of RISUG including amplitude (root mean square, peak-to-valley distance, skewness and kurtosis) and spatial roughness have been studied to understand its response to various physiological conditions. Significant alterations in the surface charge distribution of the sperm cell is observed on exposure to RISUG.

  16. The Relationship between Small Pulmonary Vascular Alteration and Aortic Atherosclerosis in Chronic Obstructive Pulmonary Disease: Quantitative CT Analysis

    PubMed Central

    Matsuoka, Shin; Yamashiro, Tsuneo; Diaz, Alejandro; Estépar, Raúl San José; Ross, James C.; Silverman, Edwin K.; Kobayashi, Yasuyuki; Dransfield, Mark T.; Bartholmai, Brian J.; Hatabu, Hiroto; Washko, George R.

    2010-01-01

    Rationale and Objectives The relationship between chronic obstructive pulmonary disease (COPD) and atherosclerosis has been suggested; this association may relate to systemic inflammation and endothelial dysfunction, which can lead to alteration of small pulmonary vessels. The relationship between atherosclerosis and small pulmonary vessel alteration, however, has not been assessed in COPD patients. We tested the hypothesis that the severity of thoracic aortic calcification measured by computed tomography (CT) would be associated with the total cross-sectional area of small pulmonary vessels (CSA) on CT images. Materials and Methods The study was approved by the institutional review board and was HIPAA compliant. Informed consent was waived. For 51 COPD patients enrolled in the NHBLI Lung Tissue Research Consortium (LTRC), we calculated the percentage of total CSAs of less than 5 mm2 for the total lung area (%CSA<5). Thoracic aortic calcification, quantified by modified Agatston score, was measured. The correlations between thoracic aortic calcification score and %CSA<5, pulmonary function, and extent of emphysema were evaluated. Multiple linear regression analysis using aortic calcification score as the dependent outcome was also performed. Results The %CSA<5 had a significant negative correlation with the thoracic aortic calcification score (r=−0.566, p<0.0001). Multiple linear regression analysis showed significant correlation between the aortic calcification score and %CSA<5 (p<0.0001) independent of age, pack-years, extent of emphysema, and FEV1%. Conclusions Atherosclerosis, assessed by aortic calcification, is associated with the small pulmonary vascular alteration in COPD. Systemic inflammation and endothelial dysfunction may cause the close relationship between atherosclerosis and small pulmonary vessel alteration. PMID:20947389

  17. Intracellular PK/PD Relationships of Free and Liposomal Doxorubicin: Quantitative Analyses and PK/PD Modeling.

    PubMed

    Soininen, Suvi K; Vellonen, Kati-Sisko; Heikkinen, Aki T; Auriola, Seppo; Ranta, Veli-Pekka; Urtti, Arto; Ruponen, Marika

    2016-04-04

    Nanomedicines are widely studied for intracellular delivery of cancer drugs. However, the relationship between intracellular drug concentrations and drug responses are poorly understood. In this study, cellular and nuclear concentrations of doxorubicin were quantified with LC/MS after cell exposure with free and liposomal doxorubicin (pH-sensitive and pegylated liposomes). Cellular uptake of pegylated liposomes was low (∼3-fold extracellular concentrations) compared with doxorubicin in free form and pH-sensitive liposomes (up to 280-fold extracellular concentrations) in rat glioma (BT4C) and renal clear cell carcinoma (Caki-2) cells. However, after the cell exposure with pegylated liposomes, intracellular doxorubicin was distributed into the nuclear compartment in both cell types. Despite high drug concentrations in the nuclei, Caki-2 cells showed strong resistance toward doxorubicin. A model was successfully built to describe PK/PD relationship between drug concentrations in nucleus and cytotoxic responses in BT4C cells. This model is the first step to link target site concentration of doxorubicin into its effect and can be a useful part of more comprehensive future in vivo PK/PD models.

  18. Relationship between N2O Fluxes from an Almond Soil and Denitrifying Bacterial Populations Estimated by Quantitative PCR

    NASA Astrophysics Data System (ADS)

    Matiasek, M.; Suddick, E. C.; Smart, D. R.; Scow, K. M.

    2008-12-01

    Cultivated soils emit substantial quantities of nitrous oxide (N2O), a greenhouse gas with almost 300 times the radiative forcing potential of CO2. Agriculture-related activities generate from 6 to 35 Tg N2O-N per year, or about 60 to 70% of global production. The microbial processes of nitrification, denitrification and nitrifier denitrification are major biogenic sources of N2O to the atmosphere from soils. Denitrification is considered the major source of N2O especially when soils are wet. The microbial N transformations that produce N2O depend primarily on nitrogen (N) fertilizer, with water content, available carbon and soil temperature being secondary controllers. Despite the fact that microbial processes are responsible for N2O emissions, very little is known about the numbers or types of populations involved. The objective of this study was to relate changes in denitrifying population densities, using quantitative PCR (qPCR) of functional genes, to N2O emissions in a fertilized almond orchard. Quantitative PCR targeted three specific genes involved in denitrification: nirS, nirK and nosZ. Copy numbers of the genes were related back to population densities and the portion of organisms likely to produce nitrous oxide. The study site, a 21.7 acre almond orchard fitted with micro-sprinklers, was fertigated (irrigated and fertilized simultaneously) with 50 lbs/acre sodium nitrate in late March 2008, then irrigated weekly. Immediately after the initial fertigation, fluxes of N2O and CO2, moisture content, inorganic N and denitrification gene copy numbers were measured 6 times over 24 days. Despite the fact that N2O emissions increased following fertigation, there was no consistent increase in any of the targeted genes. The genes nirK and nirS ranged from 0.4-1.4 × 107 and 0.4-1.4 × 108, whereas nosZ ranged from 2-8 × 106 copy numbers per g soil, respectively. Considerable variation, compounded by the small sample sizes used for DNA analysis, made it difficult

  19. Relationship between Peeled Internal Limiting Membrane Area and Anatomic Outcomes following Macular Hole Surgery: A Quantitative Analysis

    PubMed Central

    Goker, Yasin Sakir; Koc, Mustafa; Yuksel, Kemal; Yazici, Ahmet Taylan; Gunes, Hasan; Ozpinar, Yavuz

    2016-01-01

    Purpose. To quantitatively evaluate the effects of peeled internal limiting membrane (ILM) area and anatomic outcomes following macular hole surgery using spectral domain optical coherence tomography (SD-OCT). Methods. Forty-one eyes in 37 consecutive patients with idiopathic, Gass stage 3-4 macular hole (MH) were enrolled in this retrospective comparative study. All patients were divided into 2 groups according to anatomic success or failure. Basal MH diameter, peeled ILM area, and MH height were calculated using SD-OCT. Other prognostic parameters, including age, stage, preoperative BCVA, and symptom duration were also assessed. Results. Thirty-two cases were classified as anatomic success, and 9 cases were classified as anatomic failure. Peeled ILM area was significantly wider and MH basal diameter was significantly less in the anatomic success group (p = 0.024 and 0.032, resp.). Other parameters did not demonstrate statistical significance. Conclusion. The findings of the present study show that the peeled ILM area can affect the anatomic outcomes of MH surgery. PMID:27413544

  20. Graph Theoretic Foundations of Multibody Dynamics Part I: Structural Properties

    PubMed Central

    Jain, Abhinandan

    2011-01-01

    This is the first part of two papers that use concepts from graph theory to obtain a deeper understanding of the mathematical foundations of multibody dynamics. The key contribution is the development of a unifying framework that shows that key analytical results and computational algorithms in multibody dynamics are a direct consequence of structural properties and require minimal assumptions about the specific nature of the underlying multibody system. This first part focuses on identifying the abstract graph theoretic structural properties of spatial operator techniques in multibody dynamics. The second part paper exploits these structural properties to develop a broad spectrum of analytical results and computational algorithms. Towards this, we begin with the notion of graph adjacency matrices and generalize it to define block-weighted adjacency (BWA) matrices and their 1-resolvents. Previously developed spatial operators are shown to be special cases of such BWA matrices and their 1-resolvents. These properties are shown to hold broadly for serial and tree topology multibody systems. Specializations of the BWA and 1-resolvent matrices are referred to as spatial kernel operators (SKO) and spatial propagation operators (SPO). These operators and their special properties provide the foundation for the analytical and algorithmic techniques developed in the companion paper. We also use the graph theory concepts to study the topology induced sparsity structure of these operators and the system mass matrix. Similarity transformations of these operators are also studied. While the detailed development is done for the case of rigid-link multibody systems, the extension of these techniques to a broader class of systems (e.g. deformable links) are illustrated. PMID:22102790

  1. Quantitative estimates of relationships between geomagnetic activity and equatorial spread-F as determined by TID occurrence levels

    NASA Astrophysics Data System (ADS)

    Bowman, G. G.; Mortimer, I. K.

    2000-06-01

    Using a world-wide set of stations for 15 years, quantitative estimates of changes to equatorial spread-F (ESF) occurrence rates obtained from ionogram scalings, have been determined for a range of geomagnetic activity (GA) levels, as well as for four different levels of solar activity. Average occurrence rates were used as a reference. The percentage changes vary significantly depending on these subdivisions. For example for very high GA the inverse association is recorded by a change of -33% for Rz≥ 150, and -10% for Rz< 50. Using data for 9 years for the equatorial station, Huancayo, these measurements of ESF, which indicate the presence of TIDs, have also been investigated by somewhat similar analyses. Additional parameters were used which involved the local times of GA, with the ESF being examined separately for occurrence pre-midnight (PM) and after-midnight (AM). Again the negative changes were most pronounced for high GA in Rz-max years (-21%). This result is for PM ESF for GA at a local time of 1700. There were increased ESF levels (+31%) for AM ESF in Rz-min years for high GA around 2300 LT. This additional knowledge of the influence of GA on ESF occurrence involving not only percentage changes, but these values for a range of parameter levels, may be useful if ever short-term forecasts are needed. There is some discussion on comparisons which can be made between ESF results obtained by coherent scatter from incoherent-scatter equipment and those obtained by ionosondes.

  2. Determination of HART I Blade Structural Properties by Laboratory Testing

    NASA Technical Reports Server (NTRS)

    Jung, Sung N.; Lau, Benton H.

    2012-01-01

    The structural properties of higher harmonic Aeroacoustic Rotor Test (HART I) blades were measured using the original set of blades tested in the German-dutch wind tunnel (DNW) in 1994. the measurements include bending and torsion stiffness, geometric offsets, and mass and inertia properties of the blade. the measured properties were compared to the estimated values obtained initially from the blade manufacturer. The previously estimated blade properties showed consistently higher stiffness, up to 30 percent for the flap bending in the blade inboard root section.

  3. Density Functional Study of the structural properties in Tamoxifen

    NASA Astrophysics Data System (ADS)

    de Coss-Martinez, Romeo; Tapia, Jorge A.; Quijano-Quiñones, Ramiro F.; Canto, Gabriel I.

    2013-03-01

    Using the density functional theory, we have studied the structural properties of Tamoxifen. The calculations were performed with two methodological approaches, which were implemented in SIESTA and Spartan codes. For SIESTA, we considerate a linear combination of atomic orbitals method, using pseudopotentials and the van der Waals approximation for the exchange-correlation potential. Here we analyzed and compared the atomic structure between our results and other theoretical study. We found differences in the bond lengths between the results, that could be attributed to code approaches in each one. This work was supported under Grant FOMIX 2011-09 N: 170297 of Ph.D. A. Tapia.

  4. Structural properties of amorphous silicon produced by electron irradiation

    SciTech Connect

    Yamasaki, J.; Takeda, S.

    1999-07-01

    The structural properties of the amorphous Si (a-Si), which was created from crystalline silicon by 2 MeV electron irradiation at low temperatures about 25 K, are examined in detail by means of transmission electron microscopy and transmission electron diffraction. The peak positions in the radial distribution function (RDF) of the a-Si correspond well to those of a-Si fabricated by other techniques. The electron-irradiation-induced a-Si returns to crystalline Si after annealing at 550 C.

  5. Three-dimensional quantitative structure-activity relationship study on anti-cancer activity of 3,4-dihydroquinazoline derivatives against human lung cancer A549 cells

    NASA Astrophysics Data System (ADS)

    Cho, Sehyeon; Choi, Min Ji; Kim, Minju; Lee, Sunhoe; Lee, Jinsung; Lee, Seok Joon; Cho, Haelim; Lee, Kyung-Tae; Lee, Jae Yeol

    2015-03-01

    A series of 3,4-dihydroquinazoline derivatives with anti-cancer activities against human lung cancer A549 cells were subjected to three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using the comparative molecular similarity indices analysis (CoMSIA) approaches. The most potent compound, 1 was used to align the molecules. As a result, the best prediction was obtained with CoMSIA combined the steric, electrostatic, hydrophobic, hydrogen bond donor, and hydrogen bond acceptor fields (q2 = 0.720, r2 = 0.897). This model was validated by an external test set of 6 compounds giving satisfactory predictive r2 value of 0.923 as well as the scrambling stability test. This model would guide the design of potent 3,4-dihydroquinazoline derivatives as anti-cancer agent for the treatment of human lung cancer.

  6. QSAR for cholinesterase inhibition by organophosphorus esters and CNDO/2 calculations for organophosphorus ester hydrolysis. [quantitative structure-activity relationship, complete neglect of differential overlap

    NASA Technical Reports Server (NTRS)

    Johnson, H.; Kenley, R. A.; Rynard, C.; Golub, M. A.

    1985-01-01

    Quantitative structure-activity relationships were derived for acetyl- and butyrylcholinesterase inhibition by various organophosphorus esters. Bimolecular inhibition rate constants correlate well with hydrophobic substituent constants, and with the presence or absence of cationic groups on the inhibitor, but not with steric substituent constants. CNDO/2 calculations were performed on a separate set of organophosphorus esters, RR-primeP(O)X, where R and R-prime are alkyl and/or alkoxy groups and X is fluorine, chlorine or a phenoxy group. For each subset with the same X, the CNDO-derived net atomic charge at the central phosphorus atom in the ester correlates well with the alkaline hydrolysis rate constant. For the whole set of esters with different X, two equations were derived that relate either charge and leaving group steric bulk, or orbital energy and bond order to the hydrolysis rate constant.

  7. Inhibition of /sup 125/I-labeled ristocetin binding to Micrococcus luteus cells by the peptides related to bacterial cell wall mucopeptide precursors: quantitative structure-activity relationships

    SciTech Connect

    Kim, K.H.; Martin, Y.; Otis, E.; Mao, J.

    1989-01-01

    Quantitative structure-activity relationships (QSAR) of N-Ac amino acids, N-Ac dipeptides, and N-Ac tripeptides in inhibition of /sup 125/I-labeled ristocetin binding to Micrococcus luteus cell wall have been developed to probe the details of the binding between ristocetin and N-acetylated peptides. The correlation equations indicate that (1) the binding is stronger for peptides in which the side chain of the C-terminal amino acid has a large molar refractivity (MR) value, (2) the binding is weaker for peptides with polar than for those with nonpolar C-terminal side chains, (3) the N-terminal amino acid in N-Ac dipeptides contributes 12 times that of the C-terminal amino acid to binding affinity, and (4) the interactions between ristocetin and the N-terminal amino acid of N-acetyl tripeptides appear to be much weaker than those with the first two amino acids.

  8. Using quantitative structure activity relationship models to predict an appropriate solvent system from a common solvent system family for countercurrent chromatography separation.

    PubMed

    Marsden-Jones, Siân; Colclough, Nicola; Garrard, Ian; Sumner, Neil; Ignatova, Svetlana

    2015-06-12

    Countercurrent chromatography (CCC) is a form of liquid-liquid chromatography. It works by running one immiscible solvent (mobile phase) over another solvent (stationary phase) being held in a CCC column using centrifugal force. The concentration of compound in each phase is characterised by the partition coefficient (Kd), which is the concentration in the stationary phase divided by the concentration in the mobile phase. When Kd is between approximately 0.2 and 2, it is most likely that optimal separation will be achieved. Having the Kd in this range allows the compound enough time in the column to be separated without resulting in a broad peak and long run time. In this paper we report the development of quantitative structure activity relationship (QSAR) models to predict logKd. The QSAR models use only the molecule's 2D structure to predict the molecular property logKd.

  9. Synthesis, quantitative structure-activity relationship and biological evaluation of 1,3,4-oxadiazole derivatives possessing diphenylamine moiety as potential anticancer agents.

    PubMed

    Abdel Rahman, Doaa Ezzat

    2013-01-01

    Synthesis of 2,5-disubstituted-1,3,4-oxadiazole (2a-c), 3-substituted aminomethyl-5-substituted-1,3,4-oxadiazole-2(3H)-thione (4a-m) and 2-substituted thio-5-substituted-1,3,4-oxadiazole (5a, b) had been described. All the synthesized derivatives were screened for anticancer activity against HT29 and MCF7 cancer cell lines using Sulfo-Rodamine B (SRB) standard method. Most of the tested compounds exploited potent antiproliferative activity against HT29 cancer cell line rather than MCF7 cancer cell line. Compounds 2a-c, 4f and 5a exhibited potent cytotoxicity (IC(50) 1.3-2.0 µM) and selectivity against HT29 cancer cell line. Quantitative structure-activity relationship (QSAR) study was applied to find a correlation between the experimental antiproliferative activities of the newly synthesized oxadiazole derivatives with their physicochemical parameter and topological index.

  10. Docking and quantitative structure-activity relationship studies for sulfonyl hydrazides as inhibitors of cytosolic human branched-chain amino acid aminotransferase.

    PubMed

    Caballero, Julio; Vergara-Jaque, Ariela; Fernández, Michael; Coll, Deysma

    2009-11-01

    We have performed the docking of sulfonyl hydrazides complexed with cytosolic branched-chain amino acid aminotransferase (BCATc) to study the orientations and preferred active conformations of these inhibitors. The study was conducted on a selected set of 20 compounds with variation in structure and activity. In addition, the predicted inhibitor concentration (IC(50)) of the sulfonyl hydrazides as BCAT inhibitors were obtained by a quantitative structure-activity relationship (QSAR) method using three-dimensional (3D) vectors. We found that three-dimensional molecule representation of structures based on electron diffraction (3D-MoRSE) scheme contains the most relevant information related to the studied activity. The statistical parameters [cross-validate correlation coefficient (Q(2) = 0.796) and fitted correlation coefficient (R(2) = 0.899)] validated the quality of the 3D-MoRSE predictive model for 16 compounds. Additionally, this model adequately predicted four compounds that were not included in the training set.

  11. Quantitative and qualitative aspects of the social network in schizophrenic patients living in the community. Relationship to sociodemographic characteristics and clinical factors and subjective quality of life.

    PubMed

    Bengtsson-Tops, A; Hansson, L

    2001-01-01

    Quantitative and qualitative aspects of the social network were investigated in a sample of 120 schizophrenic out-patients. Sociodemographic and clinical factors as well as subjective quality of life were investigated as to their relationship to the social network. The Interview Schedule for Social Integration (ISSI) was used to assess social network and Lancashire Quality of Life Profile was used to assess subjective quality of life. Psychopathology was measured by BPRS and psychosocial functioning by GAF. The patients reported a significantly worse social network compared to a normal sample both regarding quantitative and qualitative aspects of the network. Almost half of the patients wanted access to more social contacts. Relatives and friends turned out to be the patient's main source of supportive contacts. More severe negative and positive symptoms were related to a worse social network. Support was found for an association between characteristics of the social network, such as satisfaction with social contacts, and quality of life. The results give reason to suggest that the care system should consider the informal caregivers' situation and focus on interventions, which enhance the patient's satisfaction with social contacts.

  12. Quantitative detection of mass concentration of sand-dust storms via wind-profiling radar and analysis of Z-M relationship

    NASA Astrophysics Data System (ADS)

    Wang, Minzhong; Ming, Hu; Ruan, Zheng; Gao, Lianhui; Yang, Di

    2016-12-01

    With the aim to achieve quantitative monitoring of sand-dust storms in real time, wind-profiling radar is applied to monitor and study the process of four sand-dust storms in the Tazhong area of the Taklimakan Desert. Through evaluation and analysis of the spatial-temporal distribution of reflectivity factor, it is found that reflectivity factor ranges from 2 to 18 dBz under sand-dust storm weather. Using echo power spectrum of radar vertical beams, sand-dust particle spectrum and sand-dust mass concentration at the altitude of 600 ˜ 1500 m are retrieved. This study shows that sand-dust mass concentration reaches 700 μg/m3 under blowing sand weather, 2000 μg/m3 under sand-dust storm weather, and 400 μg/m3 under floating dust weather. The following equations are established to represent the relationship between the reflectivity factor and sand-dust mass concentration: Z = 20713.5 M 0.995 under floating dust weather, Z = 22988.3 M 1.006 under blowing sand weather, and Z = 24584.2 M 1.013 under sand-dust storm weather. The retrieval results from this paper are almost consistent with previous monitoring results achieved by former researchers; thus, it is implied that wind-profiling radar can be used as a new reference device to quantitatively monitor sand-dust storms.

  13. First report on development of quantitative interspecies structure-carcinogenicity relationship models and exploring discriminatory features for rodent carcinogenicity of diverse organic chemicals using OECD guidelines.

    PubMed

    Kar, Supratik; Roy, Kunal

    2012-04-01

    Different regulatory agencies in food and drug administration and environmental protection worldwide are employing quantitative structure-activity relationship (QSAR) models to fill the data gaps related with properties of chemicals affecting the environment and human health. Carcinogenicity is a toxicity endpoint of major concern in recent times. Interspecies toxicity correlations may provide a tool for estimating sensitivity towards toxic chemical exposure with known levels of uncertainty for a diversity of wildlife species. In this background, we have developed quantitative interspecies structure-carcinogenicity correlation models for rat and mouse [rodent species according to the Organization for Economic Cooperation and Development (OECD) guidelines] based on the carcinogenic potential of 166 organic chemicals with wide diversity of molecular structures, spanning a large number of chemical classes and biological mechanisms. All the developed models have been assessed according to the OECD principles for the validation of QSAR models. Consensus predictions for carcinogenicity of the individual compounds are presented here for any one species when the data for the other species are available. Informative illustrations of the contributing structural fragments of chemicals which are responsible for specific carcinogenicity endpoints are identified by the developed models. The models have also been used to predict mouse carcinogenicities of 247 organic chemicals (for which rat carcinogenicities are present) and rat carcinogenicities of 150 chemicals (for which mouse carcinogenicities are present). Discriminatory features for rat and mouse carcinogenicity values have also been explored.

  14. Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity

    NASA Astrophysics Data System (ADS)

    Zhou, Peng; Wang, Congcong; Tian, Feifei; Ren, Yanrong; Yang, Chao; Huang, Jian

    2013-01-01

    Quantitative structure-activity relationship (QSAR), a regression modeling methodology that establishes statistical correlation between structure feature and apparent behavior for a series of congeneric molecules quantitatively, has been widely used to evaluate the activity, toxicity and property of various small-molecule compounds such as drugs, toxicants and surfactants. However, it is surprising to see that such useful technique has only very limited applications to biomacromolecules, albeit the solved 3D atom-resolution structures of proteins, nucleic acids and their complexes have accumulated rapidly in past decades. Here, we present a proof-of-concept paradigm for the modeling, prediction and interpretation of the binding affinity of 144 sequence-nonredundant, structure-available and affinity-known protein complexes (Kastritis et al. Protein Sci 20:482-491, 2011) using a biomacromolecular QSAR (BioQSAR) scheme. We demonstrate that the modeling performance and predictive power of BioQSAR are comparable to or even better than that of traditional knowledge-based strategies, mechanism-type methods and empirical scoring algorithms, while BioQSAR possesses certain additional features compared to the traditional methods, such as adaptability, interpretability, deep-validation and high-efficiency. The BioQSAR scheme could be readily modified to infer the biological behavior and functions of other biomacromolecules, if their X-ray crystal structures, NMR conformation assemblies or computationally modeled structures are available.

  15. Quantitative Relationship between Cadmium Uptake and the Kinetics of Phytochelatin Induction by Cadmium in a Marine Diatom

    PubMed Central

    Wu, Yun; Guo, Zhiqiang; Zhang, Wei; Tan, Qiaoguo; Zhang, Li; Ge, Xinlei; Chen, Mindong

    2016-01-01

    Heavy metals activate the synthesis of phytochelatins (PCs), while the induced PCs might affect metal uptake via chelating intracellular free metals. However, the relationship of PCs to metal uptake is poorly understood. In this study, we examined the kinetics of cadmium (Cd) accumulation and the synthesis of PCs in a marine diatom, Thalassiosira weissflogii, under different irradiance levels. Irradiance alone could not change the concentrations of PCs in the Cd-free treatments, while higher irradiance accelerated the induction of intracellular PCs at the same [Cd2+] level. PC-SH (2 × PC2 + 3 × PC3 + 4 × PC4) was bound with Cd at a stoichiometric ratio of 2 to 49 in our short-term uptake experiments, indicating that PC induction is sufficient to serve as the first line of defense against Cd stress. A positive linear correlation between the induction rate of PCs and the Cd uptake rate was observed, while the ratio of the PC content to intracellular Cd varied greatly when the irradiance was increased several fold. Because metal uptake has been successfully used in predicting acute metal toxicity, our findings are helpful for understanding the role of PCs in metal detoxification and developing PCs as biomarkers for metal sensitivity. PMID:27779209

  16. Interspecies quantitative structure-activity relationships (QSARs) for eco-toxicity screening of chemicals: the role of physicochemical properties.

    PubMed

    Furuhama, A; Hasunuma, K; Aoki, Y

    2015-01-01

    In addition to molecular structure profiles, descriptors based on physicochemical properties are useful for explaining the eco-toxicities of chemicals. In a previous study we reported that a criterion based on the difference between the partition coefficient (log POW) and distribution coefficient (log D) values of chemicals enabled us to identify aromatic amines and phenols for which interspecies relationships with strong correlations could be developed for fish-daphnid and algal-daphnid toxicities. The chemicals that met the log D-based criterion were expected to have similar toxicity mechanisms (related to membrane penetration). Here, we investigated the applicability of log D-based criteria to the eco-toxicity of other kinds of chemicals, including aliphatic compounds. At pH 10, use of a log POW - log D > 0 criterion and omission of outliers resulted in the selection of more than 100 chemicals whose acute fish toxicities or algal growth inhibition toxicities were almost equal to their acute daphnid toxicities. The advantage of log D-based criteria is that they allow for simple, rapid screening and prioritizing of chemicals. However, inorganic molecules and chemicals containing certain structural elements cannot be evaluated, because calculated log D values are unavailable.

  17. A pilot study of quantitative assessment of mandible advancement using pressure-flow relationship during midazolam sedation.

    PubMed

    Ayuse, T; Hoshino, Y; Inazawa, T; Oi, K; Schneider, H; Schwartz, A R

    2006-11-01

    It has been proposed that a titration of the mandibular positioner would be a promising method for predicting the outcome of nasal continuous positive airway pressure (CPAP) therapy. This study was carried out to test the hypothesis that mandible advancement could be evaluated by analysis of inspiratory flow limitation using a titration procedure. To explore its effect, we examined upper airway pressure-flow relationships using a titrated mandible positioner during midazolam sedation. Non-flow limited inspiration occurred when the mandible was advanced 7.1 +/- 1.2 mm from centric occlusion position. In the centric occlusion position (0 mm advancement), Pcrit was -1.9 +/- 2.9 cmH2O and Rua was 23.3 +/- 4.5 cmH2O L(-1) s(-1). In the eMAP position, Pcrit was -7.3 +/- 1.9 cmH2O and Rua was 27.8 +/- 3.3 cmH2O L(-1) s(-1). Essentially no CPAP was required to overcome flow limitation in eMAP position, whereas 3.7 +/- 2.2 cmH2O CPAP was required in centric occlusion position. We conclude that assessing inspiratory flow limitation using a titrated mandible positioner was effective for estimating individual-matched mandible positions.

  18. Quantitative Relationship between Cadmium Uptake and the Kinetics of Phytochelatin Induction by Cadmium in a Marine Diatom

    NASA Astrophysics Data System (ADS)

    Wu, Yun; Guo, Zhiqiang; Zhang, Wei; Tan, Qiaoguo; Zhang, Li; Ge, Xinlei; Chen, Mindong

    2016-10-01

    Heavy metals activate the synthesis of phytochelatins (PCs), while the induced PCs might affect metal uptake via chelating intracellular free metals. However, the relationship of PCs to metal uptake is poorly understood. In this study, we examined the kinetics of cadmium (Cd) accumulation and the synthesis of PCs in a marine diatom, Thalassiosira weissflogii, under different irradiance levels. Irradiance alone could not change the concentrations of PCs in the Cd-free treatments, while higher irradiance accelerated the induction of intracellular PCs at the same [Cd2+] level. PC-SH (2 × PC2 + 3 × PC3 + 4 × PC4) was bound with Cd at a stoichiometric ratio of 2 to 49 in our short-term uptake experiments, indicating that PC induction is sufficient to serve as the first line of defense against Cd stress. A positive linear correlation between the induction rate of PCs and the Cd uptake rate was observed, while the ratio of the PC content to intracellular Cd varied greatly when the irradiance was increased several fold. Because metal uptake has been successfully used in predicting acute metal toxicity, our findings are helpful for understanding the role of PCs in metal detoxification and developing PCs as biomarkers for metal sensitivity.

  19. Evaluation of negative fixed-charge density in tissue-engineered cartilage by quantitative MRI and relationship with biomechanical properties.

    PubMed

    Miyata, Shogo; Homma, Kazuhiro; Numano, Tomokazu; Tateishi, Tetsuya; Ushida, Takashi

    2010-07-01

    Applying tissue-engineered cartilage in a clinical setting requires noninvasive evaluation to detect the maturity of the cartilage. Magnetic resonance imaging (MRI) of articular cartilage has been widely accepted and applied clinically in recent years. In this study, we evaluated the negative fixed-charge density (nFCD) of tissue-engineered cartilage using gadolinium-enhanced MRI and determined the relationship between nFCD and biomechanical properties. To reconstruct cartilage tissue, articular chondrocytes from bovine humeral heads were embedded in agarose gel and cultured in vitro for up to 4 weeks. The nFCD of the cartilage was determined using the MRI gadolinium exclusion method. The equilibrium modulus was determined using a compressive stress relaxation test, and the dynamic modulus was determined by a dynamic compression test. The equilibrium compressive modulus and dynamic modulus of the tissue-engineered cartilage increased with an increase in culture time. The nFCD value--as determined with the [Gd-DTPA(2-)] measurement using the MRI technique--increased with culture time. In the regression analysis, nFCD showed significant correlations with equilibrium compressive modulus and dynamic modulus. From these results, gadolinium-enhanced MRI measurements can serve as a useful predictor of the biomechanical properties of tissue-engineered cartilage.

  20. RaptorX-Property: a web server for protein structure property prediction

    PubMed Central

    Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo

    2016-01-01

    RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence–structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-state SS, ∼66% Q3 accuracy for 3-state solvent accessibility, and ∼0.89 area under the ROC curve (AUC) for disorder prediction. PMID:27112573

  1. RaptorX-Property: a web server for protein structure property prediction.

    PubMed

    Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo

    2016-07-08

    RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-state SS, ∼66% Q3 accuracy for 3-state solvent accessibility, and ∼0.89 area under the ROC curve (AUC) for disorder prediction.

  2. PROS1 genotype phenotype relationships in a large cohort of adults with suspicion of inherited quantitative protein S deficiency.

    PubMed

    Alhenc-Gelas, Martine; Plu-Bureau, Genevieve; Horellou, Marie Hélène; Rauch, Antoine; Suchon, Pierre

    2016-03-01

    Inherited protein S deficiency (PSD) is an established risk factor for venous thromboembolism (VTE). However, data are conflicting concerning risk of VTE associated with decreased free PS level (FPS) and information on PROS1 genotype-phenotype relationship is sparse. In a retrospective cohort of 579 patients with inherited type I/III deficiency suspicion, PROS1 genotyping was performed and the effect of genotype on FPS and on VTE risk was investigated. We found 116 (including 65 novel) detrimental mutations (DM) in 222 (type I/III in 194, type II in 28), PS Heerlen in 74, possibly non DM in 38 and no mutation in 245 subjects. Among DMs, type I/IIIDMs only were found in subjects with FPS< 30 %. Prevalence of type I/III DM decreased with increasing FPS level. Risk of VT associated with FPS level and genotype was studied in the 467 subjects with personal or family history of thrombosis. Only type I/IIIDM carriers presented with an increased risk of VTE [1.41 (95 %CI (1.05-1.89)] compared to subjects with no mutation. Among the group of type I/IIIDM heterozygotes and subjects with no mutation, the optimal FPS cut-off point for identifying subjects at increased VTE risk was searched for. We found that only subjects with FPS< 30 % and type I/IIIDM presented with an increased risk [1.48 (95 %CI 1.08-2.04)]. Our findings confirm the value of a cut-off FPS level for identifying subjects at increased VTE risk far below the lower limit of the normal range and suggest a place for PROS1 genotyping in PSD diagnosis strategy.

  3. Predicting criteria continuous concentrations of metals or metalloids for protecting marine life by use of quantitative ion characteristic-activity relationships-species sensitivity distributions (QICAR-SSD).

    PubMed

    Qie, Yu; Chen, Cheng; Guo, Fei; Mu, Yunsong; Sun, Fuhong; Wang, Hao; Wang, Ying; Wang, Huanhua; Wu, Fengchang; Hu, Qing; Dang, Zhi; Giesy, John P

    2017-02-26

    Marine pollution by metals has been a major challenge for ecological systems; however, water quality criteria (WQC) for metals in saltwater is still lacking. Especially from a regulatory perspective, chronic effects of metals on marine organisms should receive more attention. A quantitative ion characteristic-activity relationships-species sensitivity distributions (QICAR-SSD) model, based on chronic toxicities for eight marine organisms, was established to predict the criteria continuous concentrations (CCCs) of 21 metals. The results showed that the chronic toxicities of various metals had good relationships with their physicochemical properties. Predicted CCCs of six metals (Hg(2+), Cu(2+), Pb(2+), Cd(2+), Ni(2+) and Zn(2+)) were in accordance with the values recommended by the U.S. EPA, with prediction errors being less than an order of magnitude. The QICAR-SSD approach provides an alternative tool to empirical methods and can be useful for deriving scientifically defensible WQC for metals for marine organisms and conducting ecological risk assessments.

  4. Quantitative relationships between huntingtin levels, polyglutamine length, inclusion body formation, and neuronal death provide novel insight into Huntington’s disease molecular pathogenesis

    PubMed Central

    Miller, Jason; Arrasate, Montserrat; Shaby, Benjamin A.; Mitra, Siddhartha; Masliah, Eliezer; Finkbeiner, Steven

    2010-01-01

    An expanded polyglutamine (polyQ) stretch in the protein huntingtin (htt) induces self-aggregation into inclusion bodies (IBs) and causes Huntington’s disease (HD). Defining precise relationships between early observable variables and neuronal death at the molecular and cellular levels should improve our understanding of HD pathogenesis. Here, we utilized an automated microscope that can track thousands of neurons individually over their entire lifetime to quantify interconnected relationships between early variables, such as htt levels, polyQ length, and IB formation, and neuronal death in a primary striatal model of HD. The resulting model revealed that: mutant htt increases the risk of death by tonically interfering with homeostatic coping mechanisms rather than producing accumulated damage to the neuron; htt toxicity is saturable; the rate limiting steps for inclusion body formation and death can be traced to different conformational changes in monomeric htt; and IB formation reduces the impact of a neuron’s starting levels of htt on its risk of death. Finally, the model that emerges from our quantitative measurements places critical limits on the potential mechanisms by which mutant htt might induce neurodegeneration, which should help direct future research. PMID:20685997

  5. Quantitative structure-activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods.

    PubMed

    Ahmadi, Mehdi; Shahlaei, Mohsen

    2015-01-01

    P2X7 antagonist activity for a set of 49 molecules of the P2X7 receptor antagonists, derivatives of purine, was modeled with the aid of chemometric and artificial intelligence techniques. The activity of these compounds was estimated by means of combination of principal component analysis (PCA), as a well-known data reduction method, genetic algorithm (GA), as a variable selection technique, and artificial neural network (ANN), as a non-linear modeling method. First, a linear regression, combined with PCA, (principal component regression) was operated to model the structure-activity relationships, and afterwards a combination of PCA and ANN algorithm was employed to accurately predict the biological activity of the P2X7 antagonist. PCA preserves as much of the information as possible contained in the original data set. Seven most important PC's to the studied activity were selected as the inputs of ANN box by an efficient variable selection method, GA. The best computational neural network model was a fully-connected, feed-forward model with 7-7-1 architecture. The developed ANN model was fully evaluated by different validation techniques, including internal and external validation, and chemical applicability domain. All validations showed that the constructed quantitative structure-activity relationship model suggested is robust and satisfactory.

  6. Paclitaxel-loaded polymeric microparticles: Quantitative relationships between in vitro drug release rate and in vivo pharmacodynamics

    PubMed Central

    Tsai, Max; Lu, Ze; Wientjes, M. Guillaume; Au, Jessie L.-S.

    2013-01-01

    Intraperitoneal therapy (IP) has demonstrated survival advantages in patients with peritoneal cancers, but has not become a widely practiced standard-of-care in part due to local toxicity and sub-optimal drug delivery. Paclitaxel-loaded, polymeric microparticles were developed to overcome these limitations. The present study evaluated the effects of microparticle properties on paclitaxel release (extent and rate) and in vivo pharmacodynamics. In vitro paclitaxel release from microparticles with varying physical characteristics (i.e., particle size, copolymer viscosity and composition) was evaluated. A method was developed to simulate the dosing rate and cumulative dose released in the peritoneal cavity based on the in vitro release data. The relationship between the simulated drug delivery and treatment outcomes of seven microparticle compositions was studied in mice bearing IP human pancreatic tumors, and compared to that of the intravenous Cremophor micellar paclitaxel solution used off-label in previous IP studies. Paclitaxel release from polymeric microparticles in vitro was multi-phasic; release was greater and more rapid from microparticles with lower polymer viscosities and smaller diameters (e.g., viscosity of 0.17 vs. 0.67 dl/g and diameter of 5–6 vs. 50–60 μm). The simulated drug release in the peritoneal cavity linearly correlated with treatment efficacy in mice (r2>0.8, p<0.001). The smaller microparticles, which distribute more evenly in the peritoneal cavity compared to the large microparticles, showed greater dose efficiency. For single treatment, the microparticles demonstrated up to 2-times longer survival extension and 4-times higher dose efficiency, relative to the paclitaxel/Cremophor micellar solution. Upon repeated dosing, the paclitaxel/Cremophor micellar solution showed cumulative toxicity whereas the microparticle that yielded 2-times longer survival did not display cumulative toxicity. The efficacy of IP therapy depended on both

  7. Application of a quantitative structure retention relationship approach for the prediction of the two-dimensional gas chromatography retention times of polycyclic aromatic sulfur heterocycle compounds.

    PubMed

    Gieleciak, Rafal; Hager, Darcy; Heshka, Nicole E

    2016-03-11

    Information on the sulfur classes present in petroleum is a key factor in determining the value of refined products and processing behavior in the refinery. A large part of the sulfur present is included in polycyclic aromatic sulfur heterocycles (PASHs), which in turn are difficult to desulfurize. Furthermore, some PASHs are potentially more mutagenic and carcinogenic than polycyclic aromatic hydrocarbons, PAHs. All of this calls for improved methods for the identification and quantification of individual sulfur species. Recent advances in analytical techniques such as comprehensive two-dimensional gas chromatography (GC×GC) have enabled the identification of many individual sulfur species. However, full identification of individual components, particularly in virgin oil fractions, is still out of reach as standards for numerous compounds are unavailable. In this work, a method for accurately predicting retention times in GC×GC using a QSRR (quantitative structure retention relationship) method was very helpful for the identification of individual sulfur compounds. Retention times for 89 saturated, aromatic, and polyaromatic sulfur-containing heterocyclic compounds were determined using two-dimensional gas chromatography. These retention data were correlated with molecular descriptors generated with CODESSA software. Two independent QSRR relationships were derived for the primary as well as the secondary retention characteristics. The predictive ability of the relationships was tested by using both independent sets of compounds and a cross-validation technique. When the corresponding chemical standards are unavailable, the equations developed for predicting retention times can be used to identify unknown chromatographic peaks by matching their retention times with those of sulfur compounds of known molecular structure.

  8. Structural properties of fluorozirconate-based glass ceramics doped with multivalent europium

    SciTech Connect

    PaBlick, C.; Müller, O.; Lützenkirchen-Hecht, D.; Frahm, R.; Johnson, J.A.; Schweizer, S.

    2012-10-10

    The structure/property relationships of fluorochlorozirconate glass ceramics as a function of divalent and trivalent europium (Eu) co-doping and thermal processing have been investigated; the influence of doping ratio on the formation of barium chloride (BaCl2) nanocrystals therein was elucidated. X-ray absorption near-edge structure spectroscopy shows that the post-thermal annealing changes the Eu valence of the as-poured glass slightly, but during the melting process Eu3+ is more strongly reduced to Eu2+, in particular, when doped as a chloride instead of fluoride compound. The Eu2+-to-Eu3+ doping ratio also plays a significant role in chemical equilibrium in the melt. X-ray diffraction measurements indicate that a higher Eu2+ fraction leads to a BaCl2 phase transition from hexagonal to orthorhombic structure at a lower temperature.

  9. Electronic and structural properties of ultrathin tungsten nanowires and nanotubes by density functional theory calculation

    SciTech Connect

    Sun, Shih-Jye; Lin, Ken-Huang; Li, Jia-Yun; Ju, Shin-Pon

    2014-10-07

    The simulated annealing basin-hopping method incorporating the penalty function was used to predict the lowest-energy structures for ultrathin tungsten nanowires and nanotubes of different sizes. These predicted structures indicate that tungsten one-dimensional structures at this small scale do not possess B.C.C. configuration as in bulk tungsten material. In order to analyze the relationship between multi-shell geometries and electronic transfer, the electronic and structural properties of tungsten wires and tubes including partial density of state and band structures which were determined and analyzed by quantum chemistry calculations. In addition, in order to understand the application feasibility of these nanowires and tubes on nano-devices such as field emitters or chemical catalysts, the electronic stability of these ultrathin tungsten nanowires was also investigated by density functional theory calculations.

  10. Structural properties of fluorozirconate-based glass ceramics doped with multivalent europium

    SciTech Connect

    Passlick, C.; Mueller, O.; Luetzenkirchen-Hecht, D.; Frahm, R.; Johnson, J. A.; Schweizer, S.

    2011-12-01

    The structure/property relationships of fluorochlorozirconate glass ceramics as a function of divalent and trivalent europium (Eu) co-doping and thermal processing have been investigated; the influence of doping ratio on the formation of barium chloride (BaCl{sub 2}) nanocrystals therein was elucidated. X-ray absorption near-edge structure spectroscopy shows that the post-thermal annealing changes the Eu valence of the as-poured glass slightly, but during the melting process Eu{sup 3+} is more strongly reduced to Eu{sup 2+}, in particular, when doped as a chloride instead of fluoride compound. The Eu{sup 2+}-to-Eu{sup 3+} doping ratio also plays a significant role in chemical equilibrium in the melt. X-ray diffraction measurements indicate that a higher Eu{sup 2+} fraction leads to a BaCl{sub 2} phase transition from hexagonal to orthorhombic structure at a lower temperature.

  11. Structural properties for determining mechanisms of toxic action

    SciTech Connect

    Bradbury, S.P.; Lipnick, R.L.

    1989-01-01

    The results of a workshop co-sponsored by EPA through the Health and Environmental Review Division, Office of Toxic Substances and the Environmental Research Laboratory-Duluth, of the Office of Research and Development are briefly summarized as an introduction to a series of manuscripts dealing with the structural properties of chemicals that determine their toxic mechanisms. Results of the workshop are intended to be incorporated in an expert system to predict mechanisms from chemical structure and aid in predictive toxicology applications in the Agency. The goal of the workshop was to review current understanding of fundamental mechanisms, and develop an initial knowledge base on chemical features and properties from which toxic mechanisms could be predicted from structure. Areas addressed included general anesthesia, or narcosis, oxidative phosphorylation uncoupling, electrophile and free-radical reactivity, and a variety of pesticide-based mechanisms.

  12. Structural properties of bismuth-bearing semiconductor alloys

    NASA Technical Reports Server (NTRS)

    Berding, M. A.; Sher, A.; Chen, A.-B.; Miller, W. E.

    1988-01-01

    The structural properties of bismuth-bearing III-V semiconductor alloys InPBi, InAsBi, and InSbBi were studied theoretically. Bond energies, bond lengths, and strain coefficients were calculated for pure AlBi, GaBi, and InBi compounds and their alloys, and predictions were made for the mixing enthalpies, miscibility gaps, and critical metastable-to-stable material transition temperatures. Miscibility calculations indicate that InSbBi will be the most miscible, and the InPBi will be the the most difficult to mix. However, calculations of the hardness of the Bi compounds indicate that, once formed, the InPBi alloy will be harder than the other Bi alloys and substantially harder than the currently favored narrow-gap semiconductor HgCdTe.

  13. DNA-linked nanoparticle materials: optical, electrical, and structural properties

    NASA Astrophysics Data System (ADS)

    Lazarides, A.; Park, S.-J.; Mirkin, C.; Storhoff, J.; Schatz, G.; Brazis, P.; Kannewurf, C.

    2001-03-01

    Novel bioinorganic materials composed of Au nanoparticles linked with DNA have been developed as colorimetric DNA sensors. In the presence of complimentary DNA, particles dressed with one of two oligonucleotide sequences are linked to form binary nanoparticle aggregates. Assemblies linked at 298K have plasmon frequency shifts that decrease with increasing linker length; annealing, however, eliminates the length dependence of the shift. Neither sedimentation rate measurements nor theoretical studies of the optical properties provide unambiguous explanation. However, small-angle X-ray scattering (SAXS) measurements indicate that separations between nanoparticles with or without annealing are proportional to the number of base pairs in the oligonucleotide linkers. DNA is thus shown to offer a means for tuning separations in nanoparticle materials. We have also investigated the electrical and structural properties of dry Au nanoparticle films linked by DNA. The assemblies are semiconducting, which suggests that DNA can be used as a chemically specific scaffolding material for assembly of conductive structures.

  14. Vibrational and structural properties of tetramethyltin under pressure

    NASA Astrophysics Data System (ADS)

    Qin, Zhen-Xing; Chen, Xiao-Jia; Zhang, Chao; Tang, Ling-Yun; Zhong, Guo-Hua; Lin, Hai-Qing; Meng, Yue; Mao, Ho-Kwang

    2013-01-01

    The vibrational and structural properties of a hydrogen-rich group IVa hydride, Sn(CH3)4, have been investigated by combining Raman spectroscopy and synchrotron x-ray diffraction measurements at room temperature and at pressures up to 49.9 GPa. Both techniques allow the obtaining of complementary information on the high-pressure behaviors and yield consistent phase transitions at 0.9 GPa for the liquid to solid and 2.8, 10.4, 20.4, and 32.6 GPa for the solid to solid. The foregoing solid phases are identified to have the orthorhombic, tetragonal, monoclinic crystal structures with space groups of Pmmm for phase I, P4/mmm for phase II, P2/m for phase III, respectively. The phases IV and V coexist with phase III, resulting in complex analysis on the possible structures. These transitions suggest the variation in the inter- and intra-molecular bonding of this compound.

  15. Studies on structural properties of clay magnesium ferrite nano composite

    NASA Astrophysics Data System (ADS)

    Kaur, Manpreet; Singh, Mandeep; Jeet, Kiran; Kaur, Rajdeep

    2015-08-01

    Magnesium ferrite-bentonite clay composite was prepared by sol-gel combustion method employing citric acid as complexing agent and fuel. The effect of clay on the structural properties was studied with X-ray diffraction (XRD), Fourier transform infrared (FT-IR) Spectroscopy, Scanning electron microscopy (SEM), SEM- Energy dispersive Spectroscope (EDS) and BET surface area analyzer. Decrease in particle size and density was observed on addition of bentonite clay. The BET surface area of nano composite containing just 5 percent clay was 74.86 m2/g. Whereas porosity increased from 40.5 per cent for the pure magnesium ferrite to 81.0 percent in the composite showing that nano-composite has potential application as an adsorbent.

  16. TECHNIQUES FOR THE STUDY OF THE STRUCTURAL PROPERTIES.

    SciTech Connect

    FERNANDEZ-GARCIA, M.; RODRIGUEZ, J.A.; MARTINEZ-ARIAS, A.; HANSON, J.C.

    2006-06-30

    The evolution of our understanding of the behavior of oxide nanostructures depends heavily on the structural information obtained from a wide range of physical methods traditionally used in solid state physics, surface science and inorganic chemistry. In this chapter, we describe several techniques that are useful for the characterization of the structural properties of oxide nanostructures: X-ray diffraction (XRD) and scattering, X-ray absorption fine structure (XAFS), Raman spectroscopy, transmission electron microscopy (TEM), scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The ultimate goal is to obtain information about the spatial arrangement of atoms in the nanostructures with precise interatomic distances and bond angles. This may not be possible for complex systems and one may get only partial information about the local geometry or morphology.

  17. Studies on structural properties of clay magnesium ferrite nano composite

    SciTech Connect

    Kaur, Manpreet Singh, Mandeep; Jeet, Kiran Kaur, Rajdeep

    2015-08-28

    Magnesium ferrite-bentonite clay composite was prepared by sol-gel combustion method employing citric acid as complexing agent and fuel. The effect of clay on the structural properties was studied with X-ray diffraction (XRD), Fourier transform infrared (FT-IR) Spectroscopy, Scanning electron microscopy (SEM), SEM- Energy dispersive Spectroscope (EDS) and BET surface area analyzer. Decrease in particle size and density was observed on addition of bentonite clay. The BET surface area of nano composite containing just 5 percent clay was 74.86 m{sup 2}/g. Whereas porosity increased from 40.5 per cent for the pure magnesium ferrite to 81.0 percent in the composite showing that nano-composite has potential application as an adsorbent.

  18. Environmental toxicological fate prediction of diverse organic chemicals based on steady-state compartmental chemical mass ratio using quantitative structure-fate relationship (QSFR) models.

    PubMed

    Pramanik, Subrata; Roy, Kunal

    2013-07-01

    Four quantitative prediction models for steady-state compartmental chemical mass concentrations (Wn,g) were obtained from structural information, physiochemical properties, degradation rate and transport coefficients of 455 diverse organic chemicals using chemometric tools in a quantitative structure-fate relationship (QSFR) study. The mass ratio assessment of environmentally prevalent organic chemicals may be helpful to predict their toxicological fate in the ecosystems. Four sets of mass ratios [(1) log(Wair) from water emissions (water to air compartment), (2) log(Wair) from air emissions (within different zones of the air compartment), (3) log(Wwater) from water emissions (within different zones of the water compartment) and (4) log(Wwater) from air emissions (air to water compartment)] have been used. The developed models using genetic function approximation followed by multiple linear regression (GFA-MLR) and subsequent partial least squares (PLS) treatment identify only four descriptors for log(Wair) from water emission, six descriptors for log(Wair) from air emission, five descriptors for log(Wwater) from water emission and seven descriptors for log(Wwater) from air emission for predicting efficiently a large number of test set chemicals (ntest=182). The conclusive models suggest that descriptors such as partition coefficients (Kaw, Kow and Ksw), degradation parameters (Ksoil,Kwater and Kair), vapor pressure (Pv), diffusivity (Dwater), spatial descriptors (Jurs-WNSA-1, Jurs-WNSA-2, Jurs-WPSA-3, Jurs-FNSA-3 and Density), thermodynamic descriptors (MolRef and AlogP98), electrotopological state indices (S_dsN, S_ssNH and S_dsCH) are important for predicting the chemical mass ratios. The developed models may be applicable in toxicological fate prediction of diverse chemicals in the ecosystems.

  19. Relationship between DNA damage response, initiated by camptothecin or oxidative stress, and DNA replication, analyzed by quantitative 3D image analysis.

    PubMed

    Berniak, K; Rybak, P; Bernas, T; Zarębski, M; Biela, E; Zhao, H; Darzynkiewicz, Z; Dobrucki, J W

    2013-10-01

    A method of quantitative analysis of spatial (3D) relationship between discrete nuclear events detected by confocal microscopy is described and applied in analysis of a dependence between sites of DNA damage signaling (γH2AX foci) and DNA replication (EdU incorporation) in cells subjected to treatments with camptothecin (Cpt) or hydrogen peroxide (H2O2). Cpt induces γH2AX foci, likely reporting formation of DNA double-strand breaks (DSBs), almost exclusively at sites of DNA replication. This finding is consistent with the known mechanism of induction of DSBs by DNA topoisomerase I (topo1) inhibitors at the sites of collisions of the moving replication forks with topo1-DNA "cleavable complexes" stabilized by Cpt. Whereas an increased level of H2AX histone phosphorylation is seen in S-phase of cells subjected to H2O2, only a minor proportion of γH2AX foci coincide with DNA replication sites. Thus, the increased level of H2AX phosphorylation induced by H2O2 is not a direct consequence of formation of DNA lesions at the sites of moving DNA replication forks. These data suggest that oxidative stress induced by H2O2 and formation of the primary H2O2-induced lesions (8-oxo-7,8-dihydroguanosine) inhibits replication globally and triggers formation of γH2AX at various distances from replication forks. Quantitative analysis of a frequency of DNA replication sites and γH2AX foci suggests also that stalling of replicating forks by Cpt leads to activation of new DNA replication origins. © 2013 International Society for Advancement of Cytometry.

  20. Rational design of novel anti-microtubule agent (9-azido-noscapine) from quantitative structure activity relationship (QSAR) evaluation of noscapinoids.

    PubMed

    Santoshi, Seneha; Naik, Pradeep K; Joshi, Harish C

    2011-10-01

    An anticough medicine, noscapine [(S)-3-((R)4-methoxy-6-methyl-5,6,7,8-tetrahydro-[1,3]dioxolo[4,5-g]isoquinolin-5-yl)-6,7-dimethoxyiso-benzofuran-1(3H)-one], was discovered in the authors' laboratory as a novel type of tubulin-binding agent that mitigates polymerization dynamics of microtubule polymers without changing overall subunit-polymer equilibrium. To obtain systematic insight into the relationship between the structural framework of noscapine scaffold and its antitumor activity, the authors synthesized strategic derivatives (including two new ones in this article). The IC(50) values of these analogs vary from 1.2 to 56.0 µM in human acute lymphoblastic leukemia cells (CEM). Geometrical optimization was performed using semiempirical quantum chemical calculations at the 3-21G* level. Structures were in agreement with nuclear magnetic resonance analysis of molecular flexibility in solution and crystal structures. A genetic function approximation algorithm of variable selection was used to generate the quantitative structure activity relationship (QSAR) model. The robustness of the QSAR model (R(2) = 0.942) was analyzed by values of the internal cross-validated regression coefficient (R(2) (LOO) = 0.815) for the training set and determination coefficient (R(2) (test) = 0.817) for the test set. Validation was achieved by rational design of further novel and potent antitumor noscapinoid, 9-azido-noscapine, and reduced 9-azido-noscapine. The experimentally determined value of pIC(50) for both the compounds (5.585 M) turned out to be very close to predicted pIC(50) (5.731 and 5.710 M).

  1. Exploring the quantitative relationship between metabolism and enzymatic phenotype by physiological modeling of glucose metabolism and lactate oxidation in solid tumors

    NASA Astrophysics Data System (ADS)

    Wang, Qian; Vaupel, Peter; Ziegler, Sibylle I.; Shi, Kuangyu

    2015-03-01

    Molecular imaging using PET or hyperpolarized MRI can characterize tumor phenotypes by assessing the related metabolism of certain substrates. However, the interpretation of the substrate turnover in terms of a pathophysiological understanding is not straightforward and only semiquantitative. The metabolism of imaging probes is influenced by a number of factors, such as the microvascular structure or the expression of key enzymes. This study aims to use computational simulation to investigate the relationship between the metabolism behind molecular imaging and the underlying tumor phenotype. The study focused on the pathways of glucose metabolism and lactate oxidation in order to establish the quantitative relationship between the expression of several transporters (GLUT, MCT1 and MCT4), expression of the enzyme hexokinase (HK), microvasculature and the metabolism of glucose or lactate and the extracellular pH distribution. A computational model for a 2D tumor tissue phantom was constructed and the spatio-temporal evolution of related species (e.g. oxygen, glucose, lactate, protons, bicarbonate ions) was estimated by solving reaction-diffusion equations. The proposed model was tested by the verification of the simulation results using in vivo and in vitro literature data. The influences of different expression levels of GLUT, MCT1, MCT4, HK and microvessel distribution on substrate concentrations were analyzed. The major results are consistent with experimental data (e.g. GLUT is more influential to glycolytic flux than HK; extracellular pH is not correlated with MCT expressions) and provide theoretical interpretation of the co-influence of multiple factors of the tumor microenvironment. This computational simulation may assist the generation of hypotheses to bridge the discrepancy between tumor metabolism and the functions of transporters and enzymes. It has the potential to accelerate the development of multi-modal imaging strategies for assessment of tumor

  2. Quantitative structure-activity relationships predicting the antioxidant potency of 17β-estradiol-related polycyclic phenols to inhibit lipid peroxidation.

    PubMed

    Prokai, Laszlo; Rivera-Portalatin, Nilka M; Prokai-Tatrai, Katalin

    2013-01-11

    The antioxidant potency of 17β-estradiol and related polycyclic phenols has been well established. This property is an important component of the complex events by which these types of agents are capable to protect neurons against the detrimental consequences of oxidative stress. In order to relate their molecular structure and properties with their capacity to inhibit lipid peroxidation, a marker of oxidative stress, quantitative structure-activity relationship (QSAR) studies were conducted. The inhibition of Fe3+-induced lipid peroxidation in rat brain homogenate, measured through an assay detecting thiobarbituric acid reactive substances for about seventy compounds were correlated with various molecular descriptors. We found that lipophilicity (modeled by the logarithm of the n-octanol/water partition coefficient, logP) was the property that influenced most profoundly the potency of these compounds to inhibit lipid peroxidation in the biological medium studied. Additionally, the important contribution of the bond dissociation enthalpy of the phenolic O-H group, a shape index, the solvent-accessible surface area and the energy required to remove an electron from the highest occupied molecular orbital were also confirmed. Several QSAR equations were validated as potentially useful exploratory tools for identifying or designing novel phenolic antioxidants incorporating the structural backbone of 17β-estradiol to assist therapy development against oxidative stress-associated neurodegeneration.

  3. The Discovery of Geranylgeranyltransferase-I Inhibitors with Novel Scaffolds by the Means of Quantitative Structure-Activity Relationship Modeling, Virtual Screening, and Experimental Validation

    PubMed Central

    Peterson, Yuri K.; Wang, Xiang S.; Casey, Patrick J.; Tropsha, Alexander

    2009-01-01

    Geranylgeranylation is critical to the function of several proteins including Rho, Rap1, Rac, Cdc42, and G-protein gamma subunits. Geranylgeranyltransferase type I (GGTase-I) inhibitors (GGTIs) have therapeutic potential to treat inflammation, multiple sclerosis, atherosclerosis, and many other diseases. Following our standard QSAR modeling workflow, we have developed and rigorously validated Quantitative Structure Activity Relationship (QSAR) models for 48 GGTIs using variable selection k nearest neighbor (kNN), automated lazy learning (ALL), and partial least square (PLS) methods. The QSAR models were employed for virtual screening of 9.5 million commercially available chemicals yielding 47 diverse computational hits. Seven of these compounds with novel scaffolds and high predicted GGTase-I inhibitory activities were tested in vitro, and all were found to be bona fide and selective micromolar inhibitors. Notably, these novel hits could not be identified using traditional similarity search. These data demonstrate that rigorously developed QSAR models can serve as reliable virtual screening tools. PMID:19537691

  4. Synthesis and quantitative structure-activity relationship (QSAR) study of novel 4-acyloxypodophyllotoxin derivatives modified in the A and C rings as insecticidal agents.

    PubMed

    He, Shuzhen; Shao, Yonghua; Fan, Lingling; Che, Zhiping; Xu, Hui; Zhi, Xiaoyan; Wang, Juanjuan; Yao, Xiaojun; Qu, Huan

    2013-01-23

    In continuation of our program aimed at the discovery and development of natural-product-based insecticidal agents, we have synthesized three series of novel 4-acyloxy compounds derived from podophyllotoxin modified in the A and C rings, which is isolated as the main secondary metabolite from the roots and rhizomes of Podophyllum hexandrum . Their insecticidal activity was preliminarily evaluated against the pre-third-instar larvae of Mythimna separata in vivo. Compound 9g displayed the best promising insecticidal activity. It revealed that cleavage of the 6,7-methylenedioxy group of podophyllotoxin will lead to a less active compound and that the C-4 position of podophyllotoxin was the important modification location. A quantitative structure-activity relationship (QSAR) model was developed by genetic algorithm combined with multiple linear regression (GA-MLR). For this model, the squared correlation coefficient (R(2)) is 0.914, the leave-one-out cross-validation correlation coefficient (Q(2)(LOO)) is 0.881, and the root-mean-square error (RMSE) is 0.024. Five descriptors, BEHm2, Mor14v, Wap, G1v, and RDF020e, are likely to influence the biological activity of these compounds. Among them, two important ones are BEHm2 and Mor14v. This study will pave the way for further design, structural modification, and development of podophyllotoxin derivatives as insecticidal agents.

  5. Formulation development of transdermal dosage forms: quantitative structure-activity relationship model for predicting activities of terpenes that enhance drug penetration through human skin.

    PubMed

    Kang, L; Yap, C W; Lim, P F C; Chen, Y Z; Ho, P C; Chan, Y W; Wong, G P; Chan, S Y

    2007-07-31

    Terpenes and terpenoids have been used as enhancers in transdermal formulations for facilitating penetration of drugs into human skin. Knowledge of the correlation between the human skin penetration effect (HSPE) and the physicochemical properties of these enhancers is important for facilitating the discovery and development of more enhancers. In this work, the HSPE of 49 terpenes and terpenoids were compared by the in vitro permeability coefficients of haloperidol (HP) through excised human skin. A first-order multiple linear regression (MLR) model was constructed to link the permeability coefficient of the drug to the lipophilicity, molecular weight, boiling point, the terpene type and the functional group of each enhancer. The Quantitative Structure-Activity Relationship (QSAR) model was derived from our data generated by using standardized experimental protocols, which include: HP in propylene glycol (PG) of 3 mg/ml as the donor solution containing 5% (w/v) of the respective terpene, the same composition and volume of receptor solution, similar human skin samples, in the same set of automated flow-through diffusion cells. The model provided a simple method to predict the enhancing effects of terpenes for drugs with physicochemical properties similar to HP. Our study suggested that an ideal terpene enhancer should possess at least one or combinations of the following properties: hydrophobic, in liquid form at room temperature, with an ester or aldehyde but not acid functional group, and is neither a triterpene nor tetraterpene. Possible mechanisms revealed by the QSAR model were discussed.

  6. Quantitative Structure activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors using the k Nearest Neighbor Method and QSAR-based Database Mining

    NASA Astrophysics Data System (ADS)

    Medina-Franco, Jose Luis; Golbraikh, Alexander; Oloff, Scott; Castillo, Rafael; Tropsha, Alexander

    2005-04-01

    We have developed quantitative structure-activity relationship (QSAR) models for 44 non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs) of the pyridinone derivative type. The k nearest neighbor ( kNN) variable selection approach was used. This method utilizes multiple descriptors such as molecular connectivity indices, which are derived from two-dimensional molecular topology. The modeling process entailed extensive validation including the randomization of the target property (Y-randomization) test and the division of the dataset into multiple training and test sets to establish the external predictive power of the training set models. QSAR models with high internal and external accuracy were generated, with leave-one-out cross-validated R 2 ( q 2) values ranging between 0.5 and 0.8 for the training sets and R 2 values exceeding 0.6 for the test sets. The best models with the highest internal and external predictive power were used to search the National Cancer Institute database. Derivatives of the pyrazolo[3,4- d]pyrimidine and phenothiazine type were identified as promising novel NNRTIs leads. Several candidates were docked into the binding pocket of nevirapine with the AutoDock (version 3.0) software. Docking results suggested that these types of compounds could be binding in the NNRTI binding site in a similar mode to a known non-nucleoside inhibitor nevirapine.

  7. Three-dimensional quantitative structure-activity relationships and docking studies of some structurally diverse flavonoids and design of new aldose reductase inhibitors

    PubMed Central

    Chandra De, Utpal; Debnath, Tanusree; Sen, Debanjan; Debnath, Sudhan

    2015-01-01

    Aldose reductase (AR) plays an important role in the development of several long-term diabetic complications. Inhibition of AR activities is a strategy for controlling complications arising from chronic diabetes. Several AR inhibitors have been reported in the literature. Flavonoid type compounds are shown to have significant AR inhibition. The objective of this study was to perform a computational work to get an idea about structural insight of flavonoid type compounds for developing as well as for searching new flavonoid based AR inhibitors. The data-set comprising 68 flavones along with their pIC50 values ranging from 0.44 to 4.59 have been collected from literature. Structure of all the flavonoids were drawn in Chembiodraw Ultra 11.0, converted into corresponding three-dimensional structure, saved as mole file and then imported to maestro project table. Imported ligands were prepared using LigPrep option of maestro 9.6 version. Three-dimensional quantitative structure-activity relationships and docking studies were performed with appropriate options of maestro 9.6 version installed in HP Z820 workstation with CentOS 6.3 (Linux). A model with partial least squares factor 5, standard deviation 0.2482, R2 = 0.9502 and variance ratio of regression 122 has been found as the best statistical model. PMID:25709964

  8. The Development of Quantitative Structure-Binding Affinity Relationship (QSBR) Models Based on Novel Geometrical Chemical Descriptors of the Protein-Ligand Interfaces

    PubMed Central

    Zhang, Shuxing; Golbraikh, Alexander; Tropsha, Alexander

    2009-01-01

    Novel geometrical chemical descriptors have been derived based on the computational geometry of protein-ligand interfaces and Pauling atomic electronegativities (EN). Delaunay tessellation has been applied to a diverse set of 517 X-ray characterized protein-ligand complexes yielding a unique collection of interfacial nearest neighbor atomic quadruplets for each complex. Each quadruplet composition was characterized by a single descriptor calculated as the sum of the EN values for the four participating atom types. We termed these simple descriptors generated from atomic EN values and derived with the Delaunay Tessellation the ENTess descriptors and used them in the variable selection k-Nearest Neighbor quantitative structure-binding affinity relationship (QSBR) studies of 264 diverse protein-ligand complexes with known binding constants. 24 complexes with chemically dissimilar ligands were set aside as an independent validation set, and the remaining dataset of 240 complexes was divided into multiple training and test sets. The best models were characterized by the leave-one-out cross-validated correlation coefficient q2 as high as 0.66 for the training set and the correlation coefficient R2 as high as 0.83 for the test set. High predictive power of these models was confirmed independently by applying them to the validation set of 24 complexes yielding R2 as high as 0.85. We conclude that QSBR models built with the ENTess descriptors can be instrumental for predicting the binding affinity of receptor-ligand complexes. PMID:16640331

  9. Quantitative Structure-Activity Relationships Predicting the Antioxidant Potency of 17β-Estradiol-Related Polycyclic Phenols to Inhibit Lipid Peroxidation

    PubMed Central

    Prokai, Laszlo; Rivera-Portalatin, Nilka M.; Prokai-Tatrai, Katalin

    2013-01-01

    The antioxidant potency of 17β-estradiol and related polycyclic phenols has been well established. This property is an important component of the complex events by which these types of agents are capable to protect neurons against the detrimental consequences of oxidative stress. In order to relate their molecular structure and properties with their capacity to inhibit lipid peroxidation, a marker of oxidative stress, quantitative structure-activity relationship (QSAR) studies were conducted. The inhibition of Fe3+-induced lipid peroxidation in rat brain homogenate, measured through an assay detecting thiobarbituric acid reactive substances for about seventy compounds were correlated with various molecular descriptors. We found that lipophilicity (modeled by the logarithm of the n-octanol/water partition coefficient, logP) was the property that influenced most profoundly the potency of these compounds to inhibit lipid peroxidation in the biological medium studied. Additionally, the important contribution of the bond dissociation enthalpy of the phenolic O–H group, a shape index, the solvent-accessible surface area and the energy required to remove an electron from the highest occupied molecular orbital were also confirmed. Several QSAR equations were validated as potentially useful exploratory tools for identifying or designing novel phenolic antioxidants incorporating the structural backbone of 17β-estradiol to assist therapy development against oxidative stress-associated neurodegeneration. PMID:23344051

  10. Quantitative assessment of the relationship between radiant heat exposure and protective performance of multilayer thermal protective clothing during dry and wet conditions.

    PubMed

    Fu, M; Weng, W G; Yuan, H Y

    2014-07-15

    The beneficial effect of clothing on a person is important to the criteria for people exposure to radiant heat flux from fires. The thermal protective performance of multilayer thermal protective clothing exposed to low heat fluxes during dry and wet conditions was studied using two designed bench-scale test apparatus. The protective clothing with four fabric layers (outer shell, moisture barrier, thermal linear and inner layer) was exposed to six levels of thermal radiation (1, 2, 3, 5, 7 and 10kW/m(2)). Two kinds of the moisture barrier (PTFE and GoreTex) with different vapor permeability were compared. The outside and inside surface temperatures of each fabric layer were measured. The fitting analysis was used to quantitatively assess the relationship between the temperature of each layer during thermal exposure and the level of external heat flux. It is indicated that there is a linear correlation between the temperature of each layer and the radiant level. Therefore, a predicted equation is developed to calculate the thermal insulation of the multilayer clothing from the external heat flux. It can also provide some useful information on the beneficial effects of clothing for the exposure criteria of radiant heat flux from fire.

  11. Quantitative structure-retention relationships applied to liquid chromatography gradient elution method for the determination of carbonyl-2,4-dinitrophenylhydrazone compounds.

    PubMed

    Cirera-Domènech, Elisenda; Estrada-Tejedor, Roger; Broto-Puig, Francesc; Teixidó, Jordi; Gassiot-Matas, Miquel; Comellas, Lluís; Lliberia, Josep Lluís; Méndez, Alberto; Paz-Estivill, Susanna; Delgado-Ortiz, Maria Rosa

    2013-02-08

    A usual method for the determination of aldehydes and ketones in different matrices consists of a derivatization with 2,4-dinitrophenylhydrazine (DNPH) followed by HPLC-UV analysis. In the present work, a HPLC-UV gradient elution method has been applied to the analysis of 13 aldehydes and ketones-DNPH in automotive emission samples. In addition to these 13 compounds-DNPH, several carbonyl-DNPH compounds (linear, ramified and cyclic, saturated and unsaturated compounds) have been analyzed by HPLC-UV. Quantitative structure-retention relationships (QSRR) methods have been applied to predict the logarithm of capacity factor (logk') of carbonyl-DNPH compounds. According to its physicochemical meaning, combinations of 2 and 3 molecular descriptors have been proposed in order to achieve higher correlation with logk'. Using linear and non-linear QSRR methodologies, the resulting prediction models allowed the screening of the most probable carbonyl-DNPH derivative candidates that correspond to unknown compounds detected in automotive emission samples. This information has been useful for their identification by UPLC(®)-MS/MS. In addition, the chromatographic retention of different carbonyl-DNPH compound families was studied using two HPLC isocratic methods working with two orthogonal stationary phases (octadecylpolyethoxysilane and cyanopropyl). Differences between the retention indexes obtained for each column were used for classifying carbonyl-DNPH into compounds families.

  12. Quantitative structure-activity relationship and molecular docking revealed a potency of anti-hepatitis C virus drugs against human corona viruses.

    PubMed

    Elfiky, Abdo A; Mahdy, Samah M; Elshemey, Wael M

    2016-11-19

    A number of human coronaviruses (HCoVs) were reported in the last and present centuries. Some outbreaks of which (eg, SARS and MERS CoVs) caused the mortality of hundreds of people worldwide. The problem of finding a potent drug against HCoV strains lies in the inability of finding a drug that stops the viral replication through inhibiting its important proteins. In spite of its limited efficacy and potential side effects, Ribavirin is extensively used as a first choice against HCoVs. Therefore, scientists reverted towards the investigation of different drugs that can more specifically target proteins. In this study, four anti-HCV drugs (one approved by FDA and others under clinical trials) are tested against HCoV polymerases. Quantitative Structure-Activity Relationship (QSAR) and molecular docking are both used to compare the performance of the selected nucleotide inhibitors to their parent nucleotides and Ribavirin. Both QSAR and molecular docking showed that IDX-184 is superior compared to Ribavirin against MERS CoV, a result that was also reported for HCV. MK-0608 showed a performance that is comparable to Ribavirin. We strongly suggest an in vitro study on the potency of these two drugs against MERS CoV.

  13. Docking and three-dimensional quantitative structure-activity relationship analyses of imidazole and thiazolidine derivatives as Aurora A kinase inhibitors.

    PubMed

    Im, Chaeuk

    2016-12-01

    Aurora A kinase is involved in the inactivation of apoptosis leading to ovarian, breast, colon, and pancreatic cancers. Inhibitors of Aurora A kinase promote aberrant mitosis resulting in arrest at a pseudo G1 state to induce mitotic catastrophe, ultimately leading to apoptosis. In this study, ligand-based and docking-based three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses of imidazole and thiazolidine derivatives as potential Aurora A kinase inhibitors were performed. The results provided highly reliable and predictive 3D-QSAR comparative molecular similarity index analysis (CoMSIA) models with a cross-validated q(2) value of 0.768, non-cross-validated r(2) value of 0.983, and predictive coefficient [Formula: see text] value of 0.978. CoMSIA contour maps suggested that the NH and benzyl hydroxy groups in R9, and the CO group in the thiazolidine ring and pyridine ring were important components for biological activity. The maps also suggest that the introduction of hydroxy groups at C2 of the imino-phenyl ring, C5 in the pyridine ring, or the substitution of the imino-phenyl ring for the imino-2-pyridine ring could be applied to enhance biological activity.

  14. Substituted phenyl 4-(2-oxoimidazolidin-1-yl)benzenesulfonamides as antimitotics. Antiproliferative, antiangiogenic and antitumoral activity, and quantitative structure-activity relationships.

    PubMed

    Fortin, Sébastien; Wei, Lianhu; Moreau, Emmanuel; Lacroix, Jacques; Côté, Marie-France; Petitclerc, Eric; Kotra, Lakshmi P; Gaudreault, René C

    2011-11-01

    The importance of the bridge linking the two phenyl moieties of substituted phenyl 4-(2-oxoimidazolidin-1-yl)benzenesulfonates (PIB-SOs) was assessed using a sulfonamide group, which is a bioisostere of sulfonate and ethenyl groups. Forty one phenyl 4-(2-oxoimidazolidin-1-yl)benzenesulfonamide (PIB-SA) derivatives were prepared and biologically evaluated. PIB-SAs exhibit antiproliferative activities at the nanomolar level against sixteen cancer cell lines, block the cell cycle progression in G(2)/M phase, leading to cytoskeleton disruption and anoikis. These results were subjected to CoMFA and CoMSIA analyses to establish quantitative structure-activity relationships. These results evidence that the sulfonate and sulfonamide moieties are reciprocal bioisosteres and that phenylimidazolidin-2-one could mimic the trimethoxyphenyl moiety found in the structure of numerous potent antimicrotubule agents. Finally, compounds 16 and 17 exhibited potent antitumor and antiangiogenic activities on HT-1080 fibrosarcoma cells grafted onto chick chorioallantoic membrane similar to CA-4 without significant toxicity for the chick embryos, making this class of compounds a promising class of anticancer agents.

  15. An orientation sensitive approach in biomolecule interaction quantitative structure-activity relationship modeling and its application in ion-exchange chromatography.

    PubMed

    Kittelmann, Jörg; Lang, Katharina M H; Ottens, Marcel; Hubbuch, Jürgen

    2017-01-27

    Quantitative structure-activity relationship (QSAR) modeling for prediction of biomolecule parameters has become an established technique in chromatographic purification process design. Unfortunately available descriptor sets fail to describe the orientation of biomolecules and the effects of ionic strength in the mobile phase on the interaction with the stationary phase. The literature describes several special descriptors used for chromatographic retention modeling, all of these do not describe the screening of electrostatic potential by the mobile phase in use. In this work we introduce two new approaches of descriptor calculations, namely surface patches and plane projection, which capture an oriented binding to charged surfaces and steric hindrance of the interaction with chromatographic ligands with regard to electrostatic potential screening by mobile phase ions. We present the use of the developed descriptor sets for predictive modeling of Langmuir isotherms for proteins at different pH values between pH 5 and 10 and varying ionic strength in the range of 10-100mM. The resulting model has a high correlation of calculated descriptors and experimental results, with a coefficient of determination of 0.82 and a predictive coefficient of determination of 0.92 for unknown molecular structures and conditions. The agreement of calculated molecular interaction orientations with both, experimental results as well as molecular dynamic simulations from literature is shown. The developed descriptors provide the means for improved QSAR models of chromatographic processes, as they reflect the complex interactions of biomolecules with chromatographic phases.

  16. Use of the ciliated protozoan Tetrahymena pyriformis for the assessment of toxicity and quantitative structure--activity relationships of xenobiotics: comparison with the Microtox test.

    PubMed

    Bogaerts, P; Bohatier, J; Bonnemoy, F

    2001-07-01

    Cytotoxicity and quantitative structure-activity relationships of 13 inorganic and 21 organic substances were determined using three bioassays performed on the ciliated protozoan Tetrahymena pyriformis and the luminescent bacterium Vibrio fischeri. The best concordance of toxicity results was observed between the T. pyriformis FDA--esterase activity and population growth inhibition tests for the organic compounds. The sensitivity of these two assays is compared with that of the Microtox test. The T. pyriformis FDA test showed a high sensitivity is most cases. The aim of the current research was to determine whether the relative toxicity of metal ions and organic molecules, with these three bioassays, was predictable using three ion characteristics and hydrophobicity, respectively. For metal ions, the variable that best modeled the toxicity data obtained with the two T. pyriformis tests was the softness index [sigma(p), i.e., (coordinate bond energy of the metal fluoride--coordinate bond energy of the metal iodide)/(coordinate bond energy of the metal fluoride)]. No correlation was found with the Microtox test. For organic compounds, a significant correlation was observed between the hydrophobicity coefficient and the toxicity data. This correlation is closer with the two tests using Tetrahymena.

  17. Towards cheminformatics-based estimation of drug therapeutic index: Predicting the protective index of anticonvulsants using a new quantitative structure-index relationship approach.

    PubMed

    Chen, Shangying; Zhang, Peng; Liu, Xin; Qin, Chu; Tao, Lin; Zhang, Cheng; Yang, Sheng Yong; Chen, Yu Zong; Chui, Wai Keung

    2016-06-01

    The overall efficacy and safety profile of a new drug is partially evaluated by the therapeutic index in clinical studies and by the protective index (PI) in preclinical studies. In-silico predictive methods may facilitate the assessment of these indicators. Although QSAR and QSTR models can be used for predicting PI, their predictive capability has not been evaluated. To test this capability, we developed QSAR and QSTR models for predicting the activity and toxicity of anticonvulsants at accuracy levels above the literature-reported threshold (LT) of good QSAR models as tested by both the internal 5-fold cross validation and external validation method. These models showed significantly compromised PI predictive capability due to the cumulative errors of the QSAR and QSTR models. Therefore, in this investigation a new quantitative structure-index relationship (QSIR) model was devised and it showed improved PI predictive capability that superseded the LT of good QSAR models. The QSAR, QSTR and QSIR models were developed using support vector regression (SVR) method with the parameters optimized by using the greedy search method. The molecular descriptors relevant to the prediction of anticonvulsant activities, toxicities and PIs were analyzed by a recursive feature elimination method. The selected molecular descriptors are primarily associated with the drug-like, pharmacological and toxicological features and those used in the published anticonvulsant QSAR and QSTR models. This study suggested that QSIR is useful for estimating the therapeutic index of drug candidates.

  18. Combined Toxic Effects of Polar and Nonpolar Chemicals on Human Hepatocytes (HepG2) Cells by Quantitative Property-Activity Relationship Modeling

    PubMed Central

    Kim, Ki-Woong; Won, Yong Lim; Park, Dong Jin; Kim, Young Sun; Jin, Eun Sil; Lee, Sung Kwang

    2016-01-01

    We determined the toxicity of mixtures of ethyl acetate (EA), isopropyl alcohol (IPA), methyl ethyl ketone (MEK), toluene (TOL) and xylene (XYL) with half-maximal effective concentration (EC50) values obtained using human hepatocytes cells. According to these data, quantitative property-activity relationships (QPAR) models were successfully proposed to predict the toxicity of mixtures by multiple linear regressions (MLR). The leave-one-out cross validation method was used to find the best subsets of descriptors in the learning methods. Significant differences in physico-chemical properties such as boiling point (BP), specific gravity (SG), Reid vapor pressure (rVP) and flash point (FP) were observed between the single substances and the mixtures. The EC50 of the mixture of EA and IPA was significantly lower than that of contained TOL and XYL. The mixture toxicity was related to the mixing ratio of MEK, TOL and XYL (MLR equation EC50 = 3.3081 − 2.5018 × TOL − 3.2595 × XYL − 12.6596 × MEK × XYL), as well as to BP, SG, VP and FP (MLR equation EC50 = 1.3424 + 6.2250 × FP − 7.1198 × SG × FP − 0.03013 × rVP × FP). These results suggest that QPAR-based models could accurately predict the toxicity of polar and nonpolar mixtures used in rotogravure printing industries. PMID:27818736

  19. Performance comparison of partial least squares-related variable selection methods for quantitative structure retention relationships modelling of retention times in reversed-phase liquid chromatography.

    PubMed

    Talebi, Mohammad; Schuster, Georg; Shellie, Robert A; Szucs, Roman; Haddad, Paul R

    2015-12-11

    The relative performance of six multivariate data analysis methods derived from or combined with partial least squares (PLS) has been compared in the context of quantitative structure-retention relationships (QSRR). These methods include, GA (genetic algorithm)-PLS, Monte Carlo uninformative variable elimination (MC-UVE), competitive adaptive reweighted sampling (CARS), iteratively retaining informative variables (IRIV), variable iterative space shrinkage approach (VISSA) and PLS with automated backward selection of predictors (autoPLS). A set of 825 molecular descriptors was computed for 86 suspected sports doping compounds and used for predicting their gradient retention times in reversed-phase liquid chromatography (RPLC). The correlation between molecular descriptors selected by each technique and the retention time was established using the PLS method. All models derived from a selected subset of descriptors outperformed the reference PLS model derived from all descriptors, with very small demands of computational time and effort. A performance comparison indicated great diversity of these methods in selecting the most relevant molecular descriptors, ranging from 28 for CARS to 263 for MC-UVE. While VISSA provided the lowest degree of over-fitting for the training set, CARS demonstrated the best compromise between the prediction accuracy and the number of selected descriptors, with the prediction error of as low as 46s for the external test set. Only ten descriptors were found to be common for all models, with the characteristics of these descriptors being representative of the retention mechanism in RPLC.

  20. Binding studies and quantitative structure-activity relationship of 3-amino-1H-indazoles as inhibitors of GSK3β.

    PubMed

    Caballero, Julio; Zilocchi, Szymon; Tiznado, William; Collina, Simona; Rossi, Daniela

    2011-10-01

    Docking of 3-amino-1H-indazoles complexed with glycogen synthase kinase 3 beta (GSK3β) was performed to gain insight into the structural requirements and preferred conformations of these inhibitors. The study was conducted on a selected set of 57 compounds with variation in structure and activity. We found that the most active compounds established three hydrogen bonds with the residues of the hinge region of GSK3β, but some of the less active compounds have other binding modes. In addition, models able to predict GSK3β inhibitory activities (IC(50) ) of the studied compounds were obtained by 3D-QSAR methods CoMFA and CoMSIA. Ligand-based and receptor-guided alignment methods were utilized. Adequate R(2) and Q(2) values were obtained by each method, although some striking differences existed between the obtained contour maps. Each of the predictive models exhibited a similar ability to predict the activity of a test set. The application of docking and quantitative structure-activity relationship together allowed conclusions to be drawn for the choice of suitable GSK3β inhibitors.

  1. Application of Quantitative Structure–Activity Relationship Models of 5-HT1A Receptor Binding to Virtual Screening Identifies Novel and Potent 5-HT1A Ligands

    PubMed Central

    2015-01-01

    The 5-hydroxytryptamine 1A (5-HT1A) serotonin receptor has been an attractive target for treating mood and anxiety disorders such as schizophrenia. We have developed binary classification quantitative structure–activity relationship (QSAR) models of 5-HT1A receptor binding activity using data retrieved from the PDSP Ki database. The prediction accuracy of these models was estimated by external 5-fold cross-validation as well as using an additional validation set comprising 66 structurally distinct compounds from the World of Molecular Bioactivity database. These validated models were then used to mine three major types of chemical screening libraries, i.e., drug-like libraries, GPCR targeted libraries, and diversity libraries, to identify novel computational hits. The five best hits from each class of libraries were chosen for further experimental testing in radioligand binding assays, and nine of the 15 hits were confirmed to be active experimentally with binding affinity better than 10 μM. The most active compound, Lysergol, from the diversity library showed very high binding affinity (Ki) of 2.3 nM against 5-HT1A receptor. The novel 5-HT1A actives identified with the QSAR-based virtual screening approach could be potentially developed as novel anxiolytics or potential antischizophrenic drugs. PMID:24410373

  2. The observation of AE events under uniaxial compression and the quantitative relationship between the anisotropy index and the main failure plane

    NASA Astrophysics Data System (ADS)

    Zhang, Zhibo; Wang, Enyuan; Chen, Dong; Li, Xuelong; Li, Nan

    2016-11-01

    In this paper, the P-wave velocities in different directions of sandstone samples under uniaxial compression are measured. The results indicate that the changes in the P-wave velocity in different directions are almost the same. In the initial stage of loading, the P-wave velocity exhibits a rising trend due to compaction and closure of preexisting fissures. As the stress increase, preexisting fissures are closed but induced fractures are not yet generated. The sandstone samples become denser and more uniform. The P-wave velocity remains in a steady state at a high level. In the late stage of loading, the P-wave velocity drops significantly due to the expansion and breakthrough of induced fractures. The P-wave velocity anisotropy index ε is analyzed during the process of loading. It can be observed that the change in the degree of wave velocity anisotropy can be divided into three stages: the AB stage, the BC stage and the CD stage, with a changing trend from decline to incline. In the initial stage of loading, the preexisting fissures have a randomized distribution, and the change is large-scale and uniform. The difference in each spatial point decreases gradually, and synchronization increases gradually. Thus, the P-wave velocity anisotropy declines. As the stress increases gradually, with the expansion and breakthrough of induced fractures, the difference in each spatial point increases. Before failure of rock samples, the violent change region of the rock samples' internal structure is focused on a narrow two-dimensional zone, and the rock samples' structural change is obviously local. Therefore, the degree of velocity anisotropy rises after declining, and it also has good corresponding relation among the AE count, the location of AE events and the degree of wave velocity anisotropy. The projection plane of the main fracture plane on the axis plane is recorded as M plane. Based on the AFF equation, for the CD stage, we analyze the quantitative relationship

  3. Structural properties of bismuth-bearing semiconductor alloys

    NASA Technical Reports Server (NTRS)

    Berding, M. A.; Sher, A.; Chen, A. B.

    1986-01-01

    The structural properties of bismuth-bearing III-V semiconductor alloys are addressed. Because the Bi compounds are not known to form zincblende structures, only the anion-substituted alloys InPBi, InAsBi, and InSbBi are considered candidates as narrow-gap semiconductors. Miscibility calculations indicate that InSbBi will be the most miscible, and InPBi, with the large lattice mismatch of the constituents, will be the most difficult to mix. Calculations of the hardness of the Bi compounds indicate that, once formed, the InPBi alloy will be harder than the other Bi alloys, and substantially harder than the currently favored narrow-gap semiconductor HgCdTe. Thus, although InSbBi may be an easier material to prepare, InPBi promises to be a harder material. Growth of the Bi compounds will require high effective growth temperatures, probably attainable only through the use of nonequilibrium energy-assisted epitaxial growth techniques.

  4. Structure-Property Correlations in Microwave Joining of Inconel 718

    NASA Astrophysics Data System (ADS)

    Bansal, Amit; Sharma, Apurbba Kumar; Kumar, Pradeep; Das, Shantanu

    2015-09-01

    The butt joining of Inconel 718 plates at 981°C solution treated and aged (981STA) condition was carried out using the microwave hybrid heating technique with Inconel 718 powder as a filler material. The developed joints were free from any microfissures (cracks) and were metallurgically bonded through complete melting of the powder particles. The as-welded joints were subjected to postweld heat treatments, including direct-aged, 981STA and 1080STA. The microstructural features of the welded joints were investigated using a field emission-scanning electron microscope equipped with x-ray elemental analysis. Microhardness and room-temperature tensile properties of the welded joints were evaluated. The postweld heat-treated specimens exhibited higher microhardness and tensile strength than the as-welded specimens due to the formation of strengthening precipitates in the microstructure after postweld heat treatments. The microhardness of the fusion zone of the joint in 1080STA condition was higher than all welded conditions due to the complete dissolution of Laves phase after 1080STA treatment. However, the tensile strength of the welded specimen in 981STA condition was higher than all welded conditions. The tensile strength in 1080STA condition was lower than that in 981STA condition because of the grain coarsening that took place after 1080STA condition. The fractography of the fractured surfaces was carried out to determine the structure-property-fracture correlation.

  5. Unusual structural properties of polymers confined in a nanocylinder

    NASA Astrophysics Data System (ADS)

    Jiang, Zhi-Bin; Peng, Meng-Jie; Li, Lin-Ling; Zhou, Dong-Shan; Wang, Rong; Xue, Gi

    2015-07-01

    Structural properties of polymers confined in nanocylinders are investigated by Monte Carlo simulation, which is successfully used to consider the conformational property of constrained polymers. The conformational properties of the polymers close to the walls exhibit different features. The density profiles of polymers are enhanced near the wall of the nanocylinder, which shows that the packing densities differ near the wall and far from the wall. The highest densities near the wall of the nanocylinder decrease with increasing radius of the nanocylinder. Furthermore, the density excess is not only near the wall of the nanocylinder, but also shifts to the center of the nanocylinder at lower temperatures. The radius of gyration and the bond length of polymers in the nanocylinder show that the polymer chains tend to extend along the axis of the nanocylinder in highly confined nanocylinder and contract at lower temperature. Our results are very helpful in understanding the packing induced physical behaviors of polymers in nanocylinders, such as glass transition, crystallization, etc. Project supported by the National Natural Science Foundation of China (Grant Nos. 21474051, 21074053, and 51133002), the National Basic Research Program of China (Grant No. 2012CB821503), and the Program for Changjiang Scholars and Innovative Research Team in University, China.

  6. Structural properties of amorphous Fe2O3 nanoparticles

    NASA Astrophysics Data System (ADS)

    Khanh, B. T. H. L.; Hoang, V. V.; Zung, H.

    2008-10-01

    We have investigated the microstructure of amorphous Fe2O3 nanoparticles by using molecular dynamics (MD) simulations. Non-periodic boundary conditions with Born-Mayer type pair potentials were used to simulate a spherical model of different diameters of 2, 3, 4 and 5 nm. Structural properties of an amorphous model obtained at 350 K have been analyzed in detail through the partial radial distribution functions (PRPFs), coordination number distributions, bond-angle distributions and interatomic distances. Calculations showed that structural characteristics of the model are in qualitative agreement with the experimental data. The observation of a large amount of structural defects as the particle size is decreased suggested that surface structure strongly depends on the size of nanoparticles. In addition, surface structure of amorphous Fe2O3 nanoparticles have been studied and compared with that observed in the core and in the bulk counterpart. Radial density profiles and stoichiometry in morphous Fe2O3 nanoparticles were also found and discussed.

  7. Dielectric and structural properties of ferroelectric betaine arsenate films

    NASA Astrophysics Data System (ADS)

    Balashova, E. V.; Krichevtsov, B. B.; Zaitseva, N. V.; Yurko, E. I.; Svinarev, F. B.

    2014-12-01

    Ferroelectric films of betaine arsenate and partially deuterated betaine arsenate have been grown by evaporation on LiNbO3, α-Al2O3, and NdGaO3 substrates with a preliminarily deposited structure of interdigitated electrodes, as well as on the Al/glass substrate. This paper presents the results of the examination of the block structure of the films in a polarizing microscope, the X-ray diffraction analysis of their crystal structure, and the investigation of the dielectric properties in a measuring field oriented both parallel and perpendicular to the plane of the film. The transition of the films to the ferroelectric state at T = T c is accompanied by anomalies of the capacitance of the structure, an increase in the dielectric loss, and the appearance of dielectric hysteresis loops. The growth of the films from a solution of betaine arsenate in a heavy water leads to an increase in the ferroelectric transition temperature from T c = 119 K in the films without deuterium to T c = 149 K, which corresponds to the degree of deuteration of approximately 60-70%. The dielectric and structural properties of the films are compared with those of the betaine arsenate single crystals and the previously studied films of betaine phosphite and glycine phosphite.

  8. Energetics and structural properties of twist grain boundaries in Cu

    NASA Technical Reports Server (NTRS)

    Karimi, Majid

    1992-01-01

    Structural and energetics properties of atoms near a grain boundary are of great importance from theoretical and experimental standpoints. From various experimental work it is concluded that diffusion at low temperatures at polycrystalline materials take place near grain boundary. Experimental and theoretical results also indicate changes of up to 70 percent in physical properties near a grain boundary. The Embedded Atom Method (EAM) calculations on structural properties of Au twist grain boundaries are in quite good agreement with their experimental counterparts. The EAM is believed to predict reliable values for the single vacancy formation energy as well as migration energy. However, it is not clear whether the EAM functions which are fitted to the bulk properties of a perfect crystalline solid can produce reliable results on grain boundaries. One of the objectives of this work is to construct the EAM functions for Cu and use them in conjunction with the molecular static simulation to study structures and energetics of atoms near twist grain boundaries in Cu. This provides tests of the EAM functions near a grain boundary. In particular, we determine structure, single vacancy formation energy, migration energy, single vacancy activation energy, and interlayer spacing as a function of distance from grain boundary. Our results are compared with the available experimental and theoretical results from grain boundaries and bulk.

  9. Optical and structural properties of zinc iodine thin films

    NASA Astrophysics Data System (ADS)

    Kariper, İ. A.

    2015-06-01

    Zinc iodide (ZnI2) crystalline thin film is produced with chemical bath deposition on substrates (commercial glass). The pH of chemical bath is scanned with controlled potassium hydroxide. Some properties of films changed with pH and changes of pH were analyzed. The pH values are scanned at 6.01-6.29. Transmittance, absorption, optical band gap and refractive index are investigated by UV/Vis. spectrum. The hexagonal and tetragonal form in structural properties in XRD at pH: 6.01 were seen. The pH of bath was up to 6.01, KZnI3ṡ2H2O (orthorhombic), KZnI3ṡ(H2O)2 (orthorhombic), ZnI2 (tetragonal) and ZnI2 (hexagonal) forms were observed in XRD patterns. The structural and optical properties of ZnI2 thin films analyzed at different pH. SEM analysis studied for surface analysis in films. The SEM analyses were agreed with XRD patterns. The optical band gap increased with pH between 3.4 and 3.6 eV. The film thickness changed with pH at 108-345 nm. Also refractive index and transmission generally increased with pH.

  10. Sexual Dimorphism and Population Differences in Structural Properties of Barn Swallow (Hirundo rustica) Wing and Tail Feathers.

    PubMed

    Pap, Péter L; Osváth, Gergely; Aparicio, José Miguel; Bărbos, Lőrinc; Matyjasiak, Piotr; Rubolini, Diego; Saino, Nicola; Vágási, Csongor I; Vincze, Orsolya; Møller, Anders Pape

    2015-01-01

    Sexual selection and aerodynamic forces affecting structural properties of the flight feathers of birds are poorly understood. Here, we compared the structural features of the innermost primary wing feather (P1) and the sexually dimorphic outermost (Ta6) and monomorphic second outermost (Ta5) tail feathers of barn swallows (Hirundo rustica) from a Romanian population to investigate how sexual selection and resistance to aerodynamic forces affect structural differences among these feathers. Furthermore, we compared structural properties of Ta6 of barn swallows from six European populations. Finally, we determined the relationship between feather growth bars width (GBW) and the structural properties of tail feathers. The structure of P1 indicates strong resistance against aerodynamic forces, while the narrow rachis, low vane density and low bending stiffness of tail feathers suggest reduced resistance against airflow. The highly elongated Ta6 is characterized by structural modifications such as large rachis width and increased barbule density in relation to the less elongated Ta5, which can be explained by increased length and/or high aerodynamic forces acting at the leading tail edge. However, these changes in Ta6 structure do not allow for full compensation of elongation, as reflected by the reduced bending stiffness of Ta6. Ta6 elongation in males resulted in feathers with reduced resistance, as shown by the low barb density and reduced bending stiffness compared to females. The inconsistency in sexual dimorphism and in change in quality traits of Ta6 among six European populations shows that multiple factors may contribute to shaping population differences. In general, the difference in quality traits between tail feathers cannot be explained by the GBW of feathers. Our results show that the material and structural properties of wing and tail feathers of barn swallows change as a result of aerodynamic forces and sexual selection, although the result of these

  11. Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array*

    PubMed Central

    Shinkai-Ouchi, Fumiko; Koyama, Suguru; Ono, Yasuko; Hata, Shoji; Ojima, Koichi; Shindo, Mayumi; duVerle, David; Ueno, Mika; Kitamura, Fujiko; Doi, Naoko; Takigawa, Ichigaku; Mamitsuka, Hiroshi; Sorimachi, Hiroyuki

    2016-01-01

    Calpains are intracellular Ca2+-regulated cysteine proteases that are essential for various cellular functions. Mammalian conventional calpains (calpain-1 and calpain-2) modulate the structure and function of their substrates by limited proteolysis. Thus, it is critically important to determine the site(s) in proteins at which calpains cleave. However, the calpains' substrate specificity remains unclear, because the amino acid (aa) sequences around their cleavage sites are very diverse. To clarify calpains' substrate specificities, 84 20-mer oligopeptides, corresponding to P10-P10′ of reported cleavage site sequences, were proteolyzed by calpains, and the catalytic efficiencies (kcat/Km) were globally determined by LC/MS. This analysis revealed 483 cleavage site sequences, including 360 novel ones. The kcat/Kms for 119 sites ranged from 12.5–1,710 M−1s−1. Although most sites were cleaved by both calpain-1 and −2 with a similar kcat/Km, sequence comparisons revealed distinct aa preferences at P9-P7/P2/P5′. The aa compositions of the novel sites were not statistically different from those of previously reported sites as a whole, suggesting calpains have a strict implicit rule for sequence specificity, and that the limited proteolysis of intact substrates is because of substrates' higher-order structures. Cleavage position frequencies indicated that longer sequences N-terminal to the cleavage site (P-sites) were preferred for proteolysis over C-terminal (P′-sites). Quantitative structure-activity relationship (QSAR) analyses using partial least-squares regression and >1,300 aa descriptors achieved kcat/Km prediction with r = 0.834, and binary-QSAR modeling attained an 87.5% positive prediction value for 132 reported calpain cleavage sites independent of our model construction. These results outperformed previous calpain cleavage predictors, and revealed the importance of the P2, P3′, and P4′ sites, and P1-P2 cooperativity. Furthermore, using our

  12. Structure-property optimizations in donor polymers via electronics, substituents, and side chains toward high efficiency solar cells.

    PubMed

    Uy, Rycel L; Price, Samuel C; You, Wei

    2012-07-26

    Many advances in organic photovoltaic efficiency are not yet fully understood and new insight into structure-property relationships is required to push this technology into broad commercial use. The aim of this article is not to comprehensively review recent work, but to provide commentary on recent successes and forecast where researchers should look to enhance the efficiency of photovoltaics. By lowering the LUMO level, utilizing electron-withdrawing substituents advantageously, and employing appropriate side chains on donor polymers, researchers can elucidate further aspects of polymer-PCBM interactions while ultimately developing materials that will push past 10% efficiency.

  13. Investigating the quantitative structure-activity relationships for antibody recognition of two immunoassays for polycyclic aromatic hydrocarbons by multiple regression methods.

    PubMed

    Zhang, Yan-Feng; Zhang, Li; Gao, Zhi-Xian; Dai, Shu-Gui

    2012-01-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous contaminants found in the environment. Immunoassays represent useful analytical methods to complement traditional analytical procedures for PAHs. Cross-reactivity (CR) is a very useful character to evaluate the extent of cross-reaction of a cross-reactant in immunoreactions and immunoassays. The quantitative relationships between the molecular properties and the CR of PAHs were established by stepwise multiple linear regression, principal component regression and partial least square regression, using the data of two commercial enzyme-linked immunosorbent assay (ELISA) kits. The objective is to find the most important molecular properties that affect the CR, and predict the CR by multiple regression methods. The results show that the physicochemical, electronic and topological properties of the PAH molecules have an integrated effect on the CR properties for the two ELISAs, among which molar solubility (S(m)) and valence molecular connectivity index ((3)χ(v)) are the most important factors. The obtained regression equations for Ris(C) kit are all statistically significant (p < 0.005) and show satisfactory ability for predicting CR values, while equations for RaPID kit are all not significant (p > 0.05) and not suitable for predicting. It is probably because that the Ris(C) immunoassay employs a monoclonal antibody, while the RaPID kit is based on polyclonal antibody. Considering the important effect of solubility on the CR values, cross-reaction potential (CRP) is calculated and used as a complement of CR for evaluation of cross-reactions in immunoassays. Only the compounds with both high CR and high CRP can cause intense cross-reactions in immunoassays.

  14. Synthesis and quantitative structure-activity relationship (QSAR) study of novel N-arylsulfonyl-3-acylindole arylcarbonyl hydrazone derivatives as nematicidal agents.

    PubMed

    Che, Zhiping; Zhang, Shaoyong; Shao, Yonghua; Fan, Lingling; Xu, Hui; Yu, Xiang; Zhi, Xiaoyan; Yao, Xiaojun; Zhang, Rui

    2013-06-19

    In continuation of our program aimed at the discovery and development of natural-product-based pesticidal agents, 54 novel N-arylsulfonyl-3-acylindole arylcarbonyl hydrazone derivatives were prepared, and their structures were well characterized by ¹H NMR, ¹³C NMR, HRMS, ESI-MS, and mp. Their nematicidal activity was evaluated against that of the pine wood nematode, Bursaphelenchus xylophilus in vivo. Among all of the derivatives, especially V-12 and V-39 displayed the best promising nematicidal activity with LC₅₀ values of 1.0969 and 1.2632 mg/L, respectively. This suggested that introduction of R¹ and R² together as the electron-withdrawing substituents, R³ as the methyl group, and R⁴ as the phenyl with the electron-donating substituents could be taken into account for further preparation of these kinds of compounds as nematicidal agents. Six selected descriptors are a WHIM descriptor (E1m), two GETAWAY descriptors (R1m+ and R3m+), a Burden eigenvalues descriptor (BEHm8), and two edge-adjacency index descriptors (EEig05x and EEig13d). Quantitative structure-activity relationship (QSAR) studies demonstrated that the structural factors, such as molecular mass (a negative correlation with the bioactivity) and molecular polarity (a positive correlation with bioactivity), are likely to govern the nematicidal activities of these compounds. For this model, the correlation coefficient (R²(training set)), the leave-one-out cross-validation correlation coefficient (Q²(LOO)), and the 7-fold cross-validation correlation coefficient (Q²(7-fold)) were 0.791, 0.701, and 0.715, respectively. The external cross-validation correlation coefficient (Q²ext) and the root-mean-square error for the test set (RMSE(test set)) were 0.774 and 3.412, respectively. This study will pave the way for future design, structural modification, and development of indole derivatives as nematicidal agents.

  15. Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors

    NASA Astrophysics Data System (ADS)

    Kharkar, Prashant S.; Reith, Maarten E. A.; Dutta, Aloke K.

    2008-01-01

    Three-dimensional quantitative structure-activity relationship (3D QSAR) using comparative molecular field analysis (CoMFA) was performed on a series of substituted tetrahydropyran (THP) derivatives possessing serotonin (SERT) and norepinephrine (NET) transporter inhibitory activities. The study aimed to rationalize the potency of these inhibitors for SERT and NET as well as the observed selectivity differences for NET over SERT. The dataset consisted of 29 molecules, of which 23 molecules were used as the training set for deriving CoMFA models for SERT and NET uptake inhibitory activities. Superimpositions were performed using atom-based fitting and 3-point pharmacophore-based alignment. Two charge calculation methods, Gasteiger-Hückel and semiempirical PM3, were tried. Both alignment methods were analyzed in terms of their predictive abilities and produced comparable results with high internal and external predictivities. The models obtained using the 3-point pharmacophore-based alignment outperformed the models with atom-based fitting in terms of relevant statistics and interpretability of the generated contour maps. Steric fields dominated electrostatic fields in terms of contribution. The selectivity analysis (NET over SERT), though yielded models with good internal predictivity, showed very poor external test set predictions. The analysis was repeated with 24 molecules after systematically excluding so-called outliers (5 out of 29) from the model derivation process. The resulting CoMFA model using the atom-based fitting exhibited good statistics and was able to explain most of the selectivity (NET over SERT)-discriminating factors. The presence of -OH substituent on the THP ring was found to be one of the most important factors governing the NET selectivity over SERT. Thus, a 4-point NET-selective pharmacophore, after introducing this newly found H-bond donor/acceptor feature in addition to the initial 3-point pharmacophore, was proposed.

  16. Reaction of vascular adhesion protein-1 (VAP-1) with primary amines: mechanistic insights from isotope effects and quantitative structure-activity relationships.

    PubMed

    Heuts, Dominic P H M; Gummadova, Jennet O; Pang, Jiayun; Rigby, Stephen E J; Scrutton, Nigel S

    2011-08-26

    Human vascular adhesion protein-1 (VAP-1) is an endothelial copper-dependent amine oxidase involved in the recruitment and extravasation of leukocytes at sites of inflammation. VAP-1 is an important therapeutic target for several pathological conditions. We expressed soluble VAP-1 in HEK293 EBNA1 cells at levels suitable for detailed mechanistic studies with model substrates. Using the model substrate benzylamine, we analyzed the steady-state kinetic parameters of VAP-1 as a function of solution pH. We found two macroscopic pK(a) values that defined a bell-shaped plot of turnover number k(cat,app) as a function of pH, representing ionizable groups in the enzyme-substrate complex. The dependence of (k(cat)/K(m))(app) on pH revealed a single pK(a) value (∼9) that we assigned to ionization of the amine group in free benzylamine substrate. A kinetic isotope effect (KIE) of 6 to 7.6 on (k(cat)/K(m))(app) over the pH range of 6 to 10 was observed with d(2)-benzylamine. Over the same pH range, the KIE on k(cat) was found to be close to unity. The unusual KIE values on (k(cat)/K(m))(app) were rationalized using a mechanistic scheme that includes the possibility of multiple isotopically sensitive steps. We also report the analysis of quantitative structure-activity relationships (QSAR) using para-substituted protiated and deuterated phenylethylamines. With phenylethylamines we observed a large KIE on k(cat,app) (8.01 ± 0.28 with phenylethylamine), indicating that C-H bond breakage is limiting for 2,4,5-trihydroxyphenylalanine quinone reduction. Poor correlations were observed between steady-state rate constants and QSAR parameters. We show the importance of combining KIE, QSAR, and structural studies to gain insight into the complexity of the VAP-1 steady-state mechanism.

  17. A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis.

    PubMed

    Pastor, M; Cruciani, G; Watson, K A

    1997-12-05

    Water present in a ligand binding site of a protein has been recognized to play a major role in ligand-protein interactions. To date, rational drug design techniques do not usually incorporate the effect of these water molecules into the design strategy. This work represents a new strategy for including water molecules into a three-dimensional quantitative structure-activity relationship analysis using a set of glucose analogue inhibitors of glycogen phosphorylase (GP). In this series, the structures of the ligand-enzyme complexes have been solved by X-ray crystallography, and the positions of the ligands and the water molecules at the ligand binding site are known. For the structure-activity analysis, some water molecules adjacent to the ligands were included into an assembly which encompasses both the inhibitor and the water involved in the ligand-enzyme interaction. The mobility of some water molecules at the ligand binding site of GP gives rise to differences in the ligand-water assembly which have been accounted for using a simulation study involving force-field energy calculations. The assembly of ligand plus water was used in a GRID/GOLPE analysis, and the models obtained compare favorably with equivalent models when water was excluded. Both models were analyzed in detail and compared with the crystallographic structures of the ligand-enzyme complexes in order to evaluate their ability to reproduce the experimental observations. The results demonstrate that incorporation of water molecules into the analysis improves the predictive ability of the models and makes them easier to interpret. The information obtained from interpretation of the models is in good agreement with the conclusions derived from the structural analysis of the complexes and offers valuable insights into new characteristics of the ligands which may be exploited for the design of more potent inhibitors.

  18. Support vector regression-guided unravelling: antioxidant capacity and quantitative structure-activity relationship predict reduction and promotion effects of flavonoids on acrylamide formation

    PubMed Central

    Huang, Mengmeng; Wei, Yan; Wang, Jun; Zhang, Yu

    2016-01-01

    We used the support vector regression (SVR) approach to predict and unravel reduction/promotion effect of characteristic flavonoids on the acrylamide formation under a low-moisture Maillard reaction system. Results demonstrated the reduction/promotion effects by flavonoids at addition levels of 1–10000 μmol/L. The maximal inhibition rates (51.7%, 68.8% and 26.1%) and promote rates (57.7%, 178.8% and 27.5%) caused by flavones, flavonols and isoflavones were observed at addition levels of 100 μmol/L and 10000 μmol/L, respectively. The reduction/promotion effects were closely related to the change of trolox equivalent antioxidant capacity (ΔTEAC) and well predicted by triple ΔTEAC measurements via SVR models (R: 0.633–0.900). Flavonols exhibit stronger effects on the acrylamide formation than flavones and isoflavones as well as their O-glycosides derivatives, which may be attributed to the number and position of phenolic and 3-enolic hydroxyls. The reduction/promotion effects were well predicted by using optimized quantitative structure-activity relationship (QSAR) descriptors and SVR models (R: 0.926–0.994). Compared to artificial neural network and multi-linear regression models, SVR models exhibited better fitting performance for both TEAC-dependent and QSAR descriptor-dependent predicting work. These observations demonstrated that the SVR models are competent for predicting our understanding on the future use of natural antioxidants for decreasing the acrylamide formation. PMID:27586851

  19. Quantitative structure-retention relationships models for prediction of high performance liquid chromatography retention time of small molecules: endogenous metabolites and banned compounds.

    PubMed

    Goryński, Krzysztof; Bojko, Barbara; Nowaczyk, Alicja; Buciński, Adam; Pawliszyn, Janusz; Kaliszan, Roman

    2013-10-03

    Quantitative structure-retention relationship (QSRR) is a technique capable of improving the identification of analytes by predicting their retention time on a liquid chromatography column (LC) and/or their properties. This approach is particularly useful when LC is coupled with a high-resolution mass spectrometry (HRMS) platform. The main aim of the present study was to develop and describe appropriate QSRR models that provide usable predictive capability, allowing false positive identification to be removed during the interpretation of metabolomics data, while additionally increasing confidence of experimental results in doping control area. For this purpose, a dataset consisting of 146 drugs, metabolites and banned compounds from World Anti-Doping Agency (WADA) lists, was used. A QSRR study was carried out separately on high quality retention data determined by reversed-phase (RP-LC-HRMS) and hydrophilic interaction chromatography (HILIC-LC-HRMS) systems, employing a single protocol for each system. Multiple linear regression (MLR) was applied to construct the linear QSRR models based on a variety of theoretical molecular descriptors. The regression equations included a set of three descriptors for each model: ALogP, BELe6, R2p and ALogP(2), FDI, BLTA96, were used in the analysis of reversed-phase and HILIC column models, respectively. Statistically significant QSRR models (squared correlation coefficient for model fitting, R(2)=0.95 for RP and R(2)=0.84 for HILIC) indicate a strong correlation between retention time and the molecular descriptors. An evaluation of the best correlation models, performed by validation of each model using three tests (leave-one-out, leave-many-out, external tests), demonstrated the reliability of the models. This paper provides a practical and effective method for analytical chemists working with LC/HRMS platforms to improve predictive confidence of studies that seek to identify small molecules.

  20. Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function

    SciTech Connect

    Schormann, N.; Senkovich, O.; Walker, K.; Wright, D.L.; Anderson, A.C.; Rosowsky, A.; Ananthan, S.; Shinkre, B.; Velu, S.; Chattopadhyay, D.

    2009-07-10

    We have employed a structure-based three-dimensional quantitative structure-activity relationship (3D-QSAR) approach to predict the biochemical activity for inhibitors of T. cruzi dihydrofolate reductase-thymidylate synthase (DHFR-TS). Crystal structures of complexes of the enzyme with eight different inhibitors of the DHFR activity together with the structure in the substrate-free state (DHFR domain) were used to validate and refine docking poses of ligands that constitute likely active conformations. Structural information from these complexes formed the basis for the structure-based alignment used as input for the QSAR study. Contrary to indirect ligand-based approaches the strategy described here employs a direct receptor-based approach. The goal is to generate a library of selective lead inhibitors for further development as antiparasitic agents. 3D-QSAR models were obtained for T. cruzi DHFR-TS (30 inhibitors in learning set) and human DHFR (36 inhibitors in learning set) that show a very good agreement between experimental and predicted enzyme inhibition data. For crossvalidation of the QSAR model(s), we have used the 10% leave-one-out method. The derived 3D-QSAR models were tested against a few selected compounds (a small test set of six inhibitors for each enzyme) with known activity, which were not part of the learning set, and the quality of prediction of the initial 3D-QSAR models demonstrated that such studies are feasible. Further refinement of the models through integration of additional activity data and optimization of reliable docking poses is expected to lead to an improved predictive ability.

  1. Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function.

    PubMed

    Schormann, N; Senkovich, O; Walker, K; Wright, D L; Anderson, A C; Rosowsky, A; Ananthan, S; Shinkre, B; Velu, S; Chattopadhyay, D

    2008-12-01

    We have employed a structure-based three-dimensional quantitative structure-activity relationship (3D-QSAR) approach to predict the biochemical activity for inhibitors of T. cruzi dihydrofolate reductase-thymidylate synthase (DHFR-TS). Crystal structures of complexes of the enzyme with eight different inhibitors of the DHFR activity together with the structure in the substrate-free state (DHFR domain) were used to validate and refine docking poses of ligands that constitute likely active conformations. Structural information from these complexes formed the basis for the structure-based alignment used as input for the QSAR study. Contrary to indirect ligand-based approaches the strategy described here employs a direct receptor-based approach. The goal is to generate a library of selective lead inhibitors for further development as antiparasitic agents. 3D-QSAR models were obtained for T. cruzi DHFR-TS (30 inhibitors in learning set) and human DHFR (36 inhibitors in learning set) that show a very good agreement between experimental and predicted enzyme inhibition data. For crossvalidation of the QSAR model(s), we have used the 10% leave-one-out method. The derived 3D-QSAR models were tested against a few selected compounds (a small test set of six inhibitors for each enzyme) with known activity, which were not part of the learning set, and the quality of prediction of the initial 3D-QSAR models demonstrated that such studies are feasible. Further refinement of the models through integration of additional activity data and optimization of reliable docking poses is expected to lead to an improved predictive ability.

  2. Prediction of blood-brain barrier permeation of α-adrenergic and imidazoline receptor ligands using PAMPA technique and quantitative-structure permeability relationship analysis.

    PubMed

    Vucicevic, Jelica; Nikolic, Katarina; Dobričić, Vladimir; Agbaba, Danica

    2015-02-20

    Imidazoline receptor ligands are a numerous family of biologically active compounds known to produce central hypotensive effect by interaction with both α2-adrenoreceptors (α2-AR) and imidazoline receptors (IRs). Recent hypotheses connect those ligands with several neurological disorders. Therefore some IRs ligands are examined as novel centrally acting antihypertensives and drug candidates for treatment of various neurological diseases. Effective Blood-Brain Barrier (BBB) permeability (P(e)) of 18 IRs/α-ARs ligands and 22 Central Nervous System (CNS) drugs was experimentally determined using Parallel Artificial Membrane Permeability Assay (PAMPA) and studied by the Quantitative-Structure-Permeability Relationship (QSPR) methodology. The dominant molecules/cations species of compounds have been calculated at pH = 7.4. The analyzed ligands were optimized using Density Functional Theory (B3LYP/6-31G(d,p)) included in ChemBio3D Ultra 13.0 program and molecule descriptors for optimized compounds were calculated using ChemBio3D Ultra 13.0, Dragon 6.0 and ADMET predictor 6.5 software. Effective permeability of compounds was used as dependent variable (Y), while calculated molecular parametres were used as independent variables (X) in the QSPR study. SIMCA P+ 12.0 was used for Partial Least Square (PLS) analysis, while the stepwise Multiple Linear Regression (MLR) and Artificial Neural Networks (ANN) modeling were performed using STASTICA Neural Networks 4.0. Predictive potential of the formed models was confirmed by Leave-One-Out Cross- and external-validation and the most reliable models were selected. The descriptors that are important for model building are identified as well as their influence on BBB permeability. Results of the QSPR studies could be used as time and cost efficient screening tools for evaluation of BBB permeation of novel α-adrenergic/imidazoline receptor ligands, as promising drug candidates for treatment of hypertension or neurological diseases.

  3. Toxicity of aryl- and benzylhalides to Daphnia magna and classification of their mode of action based on quantitative structure-activity relationship

    SciTech Connect

    Marchini, S.; Passerini, L.; Hoglund, M.D.; Pino, A.; Nendza, M.

    1999-12-01

    The acute toxicity of aryl- and benzylhalides to Daphnia magna was investigated to test the validity of existing classification schemes for chemicals by mode of action, mainly based on fish studies, and the applicability of predictive quantitative structure-activity relationship (QSAR) models. Halobenzenes and halotoluenes are generally agreed to be unambiguous baseline toxicants (class 1) with the major exception of the benzylic structures, which are reactive in fish tests (class 3). Eighty-nine percent of the arylhalides tested in this study match a log P{sub ow}-dependent QSAR, including fluorinated, chlorinated, brominated, and iodinated derivatives, thereby confirming the validity of the baseline models also for variously halogenated compounds (other than only-chloro compounds). The toxicities of the benzylhalides relative to baseline QSARs clearly indicate that these compounds belong to two classes of mode of action, i.e., they either act as narcotic toxicants (class 1) or reveal excess toxicity due to unspecific reactivity (class 3). On some occasions, the assignment to the two classes of F. magna deviates from the structural rules derived from fish, i.e., iodinated compounds as well as {alpha},{alpha}-Cl{sub 2}-toluene's lack reactive excess toxicity but behave as nonpolar nonspecific toxicants. The QSARs derived during this study reveal lower slopes and higher intercepts than typical baseline models and, together with the analysis of mixture toxicity studies, behavioral studies, and critical body burden, advocate the hypothesis that there are several different ways to produce baseline toxicity. Most halobenzenes and halotoluenes are actually baseline chemicals with some extra reactivity and as such form a subgroup, whose limits still have to be defined. Different primary sites of action could explain why the chemicals are discriminated by different classification systems, but still they must have some rate-limiting interaction in common as they fit the

  4. Quantitative relationship between anticapsular antibody measured by enzyme-linked immunosorbent assay or radioimmunoassay and protection of mice against challenge with Streptococcus pneumoniae serotype 4.

    PubMed Central

    Musher, D M; Johnson, B; Watson, D A

    1990-01-01

    We have recently shown that a substantial proportion of antibody to pneumococcal polysaccharide as measured by enzyme-linked immunosorbent assay (ELISA) or radioimmunoassay is removed by adsorption with pneumococcal cell wall polysaccharide (CWPS). The present study was undertaken to validate the hypothesis that only serotype-specific antibody that remains after adsorption with CWPS provides protection against pneumococcal infection. Serum samples were obtained from human subjects before and after they had been vaccinated with pneumococcal polysaccharide vaccine. Antibody to Streptococcus pneumoniae serotype 4 was measured by ELISA without adsorption or after adsorption of serum with CWPS. Groups of mice were injected with graded doses of serum and then challenged intraperitoneally with 10, 100, or 1,000 50% lethal doses (LD50) of S. pneumoniae serotype 4. Without adsorption, prevaccination sera from five healthy adults appeared to contain up to 33 micrograms of antibody to S. pneumoniae serotype 4 antigen per ml; adsorption with CWPS removed all detectable antibody, and pretreating mice with up to 0.1 ml of these sera (less than or equal to 3.3 micrograms of antibody) failed to protect them against challenge with 100 LD50. In contrast, postvaccination sera contained 2.9 to 30 micrograms of antibody per ml that was not removed by adsorption. Diluting sera to administer desired amounts of serotype-specific immunoglobulin G showed a significant relationship between protection and antibody remaining after adsorption (P less than 0.05 by linear regression analysis); 150 ng was uni